Using and developing bioinfomatics indeep level phylogenomic
reconstructions and Development
Matthew W. Brown
Donald L. Hall Professor of Biology

Fellow - High Performance Computing Collaboratory (HPC²)

Department of Biological Sciences, Mississippi State University
http://amoeba.msstate.edu

ida

OBA

RPHE

ZOA

A

A
m

oe

bo

zo

a

tea

ona
d

AMO

Bre
via

tista

a

tist

p
Cry

ta

Stramenopileshy

Alveolata

op

Rhizaria

ta

He
l
as
mim
tid
+T
elo astiga
nem op
ho
ia
ra

hy

op

uc

la

SAR

G

C
R
A
Ch
lo
ro
p

od
Rh

E
A
H

Hap

PL

som

AS

Apu

A
D
TI

Opisthokonta

Eukaryotic Tree of Life

s
M

u
R
C

n
o
m

o
r
y
nc

A

a
d
i
ad
a
d
i
ad

n
o
im

w
a
l
Ma

EXCAVATA

Discoba
Metamonada
Burki et al. 2021 TREE | Tice et al. 2021 PLoS Biology | redrawn from Tice & Brown 2022. Current Biology

Amoeboid protists

Amoeba proteus

ida

OBA

RPHE

ZOA

A

A
m

oe

bo

zo

a

tea

ona
d

AMO

Bre
via

tista

a

tist

ta

hy

Stramenopiles

op

Alveolatata

Rhizaria

hy

op

uc

la

He
l
as
mim
tid
+T
elo astiga
nem opArchibald
ho
ia
ra
SAR

p
Cry

G

C
R
A
Ch
lo
ro
p

od
Rh

E
A
H

Hap

PL

som

AS

Apu

A
D
TI

Opisthokonta

Eukaryotic Tree of Life

s
M

u
R
C

n
o
m

o
r
y
nc

A

a
d
i
ad
a
d
i
ad

n
o
im

w
a
l
Ma

EXCAVATA

Discoba
Metamonada

Azuma, Panek, Tice et al. 2022 MBE
Burki et al. 2021 TREE | Tice et al. 2021 PLoS Biology | redrawn from Tice & Brown 2022 Current Biology

AMOEBOZOA

ActinDNA

Community
Composition

Soil Microbiome Seq.
Soil DNA

Zurweller, Ph.D.

Tice, Ph.D.

Quentin Blandenier, Ph.D.

Agri. Soil Protist Culture

Nicholas Gibson

Poor resolution

SSU rDNA (18S) has
long been the solephylogenetic target
for Amoebozoa

Seungho Kang
= >95/>95/1.0

SSU rDNA: GTR + Γ + I: RaxML/GarliML/MrBayes

Brown et al. 2011. Protist

Amoebozoa evolving as long as divergence between Metazoa and Fungi

Canis familiaris~1.1BYAAge Estimates (Myr)Eme et al. 2014. CSHL Persp. Biol.; Sharpe et al. 2015

Phylogenetics of Amoebozoa et al.
• Restricted to SSU rDNA (18S) phylogenetics– Poor resolution• Very limited genomic-level data
• Major goal 1:– Phylogenomics of Amoebozoa• Robust phylogeny• Major goal 2:– Phylogenies to inform evolutionary events• Mapping of morphological characters• Gene distributions and genomic innovations

Methods – Single Cell
Uncultured or Eukaryote predators
Pelomyxa

TriZOL

AmoebaSingle cell isolation(Photo and Video Voucher)
SMARTseq 2 (Picelli et al. 2014
Onsbring et al. 2021)
NexteraXT (Illumina)
QC (1.8x TBE), QPCR (KAPA), and library pooling
Ship

Paired End (125bp)
HiSeqX

Panek et al. 2016: MPE
Tice et al. 2016: Biology Direct
Kang et al. 2017: MBE
Onsbring, Tice et al. 2021: BMC Genomics

Cultured Cell

Single Cell

Methods – Data

de novo Assembly +Trimmomatic quality trimming

TransDecoder

ORF Prediction/translation
PFAM domains

ORFS
translation (Amino Acids)

OrthoLager: A Phylogenomic Pipeline (Brown & Kolisko)
Input

Nucleotides(EST, RNAseq, etc.)
TBlastN

Collect“Orthologs”

Collect top
N hitsProteins(Genomes, etc.)

351
Query Proteins

BlastP
Collect top
N hitsSupermatrix
351 orthologs~100,000AA

Recode to AA

Ortholog
Check

B l a s t P against
OrthoMCL
Check top hit of each putative ortholog against a dictionaryof inspected ortholog’s OrthoMCL numbers

Align

M A F F T- l i n s i

Mask

BMGE

Single Gene Tree
Identify artifacts

RAxML
70% bipartition screen

I Q - Tr e e
Phylobayes

Seed Alignments

Loose
Consensus
Tree

Brown et al. 2012
Current Biology

Multigene Phylogenetics – Phylogenomics• Take multiple genes and infer a phylogeny• Genes A+B+C+D+E• Offers more data
• Can handle missing data from taxa
• Concatenation• implies 1 taxon = 1 orthologous sequence
Taxon 4

Taxon 5

GENE SAMPLING

a

AMO
RPHE
A
ZOA
zo

a

tea

oe

bo

via

Ms

m
A

Bre

omo
n

adid

OBA

Apu
s

ta

ta
ptis

a

StramenopilesytAlveolataaytRhizaria

ph

o
od

h
op

uc

la

SAR

Cry

Rh

E
HA
C
AR
Ch
lo
ro
pl
He
as
m
tid
+ T ima
elo stiga
nem op
h
ia
ora

tis
Hap

PL

CONCATENTATION(Gene Matrix)

A

ID

T
AS

konta

Taxon 3

G

Taxon 1
Taxon 2
Taxon 3
Taxon 4
Taxon 5

Taxon 2

Opistho

Gene A
Gene B
Gene C
Gene D
Gene E

Taxon 1

ida

u
CR

ad
on

om
cyr

An

Ma

ida

nad

mo
lawi

EXCAVATA

Discoba
Metamonada

Poor resolution= >95/>95/1.0

SSU rDNA: GTR + Γ + I: RaxML/GarliML/MrBayes

Brown et al. 2011. Protist

60

98

69

97
*

63

99
71

*

*

60

92

69

*

63

*

92

97

97

Eumycetozoa

Flabellinia

Variosea

Our Data

Centramoebia

Flabellinia= 1.0 Bayesian PP
CAT+GTR= 100% ML Bootstrap
LG+G4+C60+PMSF

0.2

0% 50% 100%
Site Coverage

Centramoebia= 1.0 Bayesian PP
CAT+GTR= 100% ML Bootstrap
LG+G4+C60+PMSF

0.2

Obazoa99

Archamoebae

Obazoa325 Proteins
PhyloBayes CAT-GTR
IQ-Tree ML LG+G4+C60+PSMF*

Cutosea

Discosea

Discosea99

98

Variosea

GenomeAmoebozoa*

99

ElaridaDiscosea
Evosea64

Echinamoebida

Amoebozoa

Tevosa*99

Corycida
Eumycetozoa

EvoseaTubulinea

64

Physarum polycephalum
Trichosphaerium sp.
Echinosteliopsis
oligospora
Diplochlamys
sp.
Echinostelium
minutum sp.
Amphizonella
Echinostelium bisporum
Micriamoeba sp.
Protosporangium articulatum
Echinamoeba exudans
Clastostelium recurvatum
Vermamoeba vermiformis
Ceratiomyxa fruticulosa
Vermamoeba sp. [CCAP1503-5]
Flamella fluviatilis
Rhizamoeba saxonica
Flamella aegyptia
Flabellula citata
Phalansterium solitarium
Cryptodifflugia operculata
Schizoplasmodiopsis vulgaris
Difflugia bryophila
Tychosporium acutostipes Arcella intermedia
Schizoplasmodiopsis pseudoendospora
Nolandella sp.
Cavostelium apophysatum
Copromyxa protea
Protostelium nocturnum
Amoeba proteus
Filamoeba nolandi
Sapocribrum chincoteaguense
Soliformovum irregularis Squamamoeba japonica
Grellamoeba
robustaisolate [ATCC PRA-29]
cutosean
Nematostelium gracile
Rhizomastix elongata
Ceratiomyxella tahitiensis
Pelomyxa sp.
Acramoeba dendroida
Mastigella eilhardi
Stenamoeba stenopodia
Mastigamoeba balamuthi
Stenamoeba limacina
Mastigamoeba abducta
Thecamoeba quadrilineata
Entamoeba histolytica
Thecamoeba pallidum
sp.
Polysphondylium
Sappinia pedata
Dictyostelium
discoideum
Thecamoebida isolate [RHP1-1]
Physarum polycephalum
Mayorella cantabrigiensis
Echinosteliopsis
oligospora
Paradermamoeba
levis
Echinostelium minutum
Dermamoeba algensis
Echinosteliumbisporum
Vermistellaarticulatum
antarctica
Protosporangium
Stygamoeba
Clastostelium recurvatumregulata
Vexillifera minutissima
Ceratiomyxa fruticulosa
Vexillifera bacillipedes
Flamella
fluviatilis
0.85/* 96
Vexillifera sp. [MMETSP0173]
Flamella aegyptia
Paramoeba atlantica
Phalansterium solitarium
Paramoeba aestuarina
Schizoplasmodiopsis vulgaris
Cunea sp. [MMETSP0417]
Tychosporium acutostipes
Cunea sp.
[JDS-Ruffled]
Schizoplasmodiopsis
pseudoendospora
Vannellasp.
[MMETSP0168]
Cavostelium apophysatum
Vannella robusta
Protostelium nocturnum
Vannella schaefferi
Filamoeba nolandi
Vannellafimicola
Soliformovum irregularis
Grellamoeba robustaRipella sp.
Lingulamoeba sp.
Nematostelium gracile
Clydonella sp.
Ceratiomyxella tahitiensis
Ovalopodium desertum
Acramoeba dendroida
Parvamoeba rugata
Stenamoeba stenopodia
Cochliopodium minus
Stenamoeba limacina
Pellita catalonica
Thecamoeba quadrilineata
Goceviafonbrunei
Thecamoeba sp.
Goceviafonbrunei[Tekle et al. 2016]
Sappinia
pedataEndostelium
zonatum [PRA-191]
Thecamoebida
isolate [RHP1-1]
Endostelium
zonatum [LINKS]
Mayorella cantabrigiensis
Dracoamoeba
joomungandrii
Paradermamoeba levis
Protacanthamoeba
bohemica
Dermamoeba algensis
Luapelamoeba
arachisporum
Vermistella antarctica
Luapelamoeba
Stygamoebahula
regulata
Acanthamoeba castellanii
Vexillifera minutissima
Acanthamoeba pyriformis
Vexillifera bacillipedes
0.85/* 96
Pygsuiabiforma
Vexillifera
sp. [MMETSP0173]
Thecamonas
Paramoeba
atlanticatrahens
Paramoeba aestuarinaFonticula alba
Spizellomyces punctatus
Cunea sp. [MMETSP0417]
Coprinus cinereus
Cunea sp. [JDS-Ruffled]
Monosiga
brevicollis
Vannella sp. [MMETSP0168]
Homo sapiens
Vannella robusta
Amphimedon
queenslandica
Vannellaschaefferi
Ministeria
vibrans
Vannella fimicola
Capsaspora owczarzaki
Ripella sp.
Amoebidium parasiticum
Lingulamoeba sp.
Clydonella sp.
Ovalopodium desertum
Parvamoeba rugata
Cochliopodium minus
Pellita catalonica
Gocevia fonbrunei
Gocevia fonbrunei [Tekle et al. 2016]
Endostelium zonatum [PRA-191]
Endostelium zonatum [LINKS]
Dracoamoeba joomungandrii
Protacanthamoeba bohemica
Luapelamoeba arachisporum
Luapelamoeba hula
Acanthamoeba castellanii
Acanthamoeba pyriformis
Pygsuia biforma
Thecamonas trahens
Fonticula alba
Spizellomyces punctatus
Coprinus cinereus
Monosiga brevicollis
Homo sapiens
Amphimedon queenslandica
Ministeria vibrans
Capsaspora owczarzaki
Amoebidium parasiticum

0% 50% 100%
Site Coverage

Kang et al. 2017, MBE

A fully resolved Tree of Amoebozoa• 2 deepest clades Discosea and Tevosa• Fully-supported clades in Maximum Likelihood(IQ-Tree) and Bayesian inferences (PhyloBayes)• All known amoebozoan clades have beensampled• Goal of RNAseq projects from 87 taxa
– Sequenced 61 taxa (shown)– Another 180+ sequenced• Kang et al. 2017 MBE

NEW ORDERNEW FAMILY

10µm

Nick Fry“Janelia velum”

Robert Jones“Ouiwing truum”

Peter Kooienga

NEW ORDERNEW FAMILY

10µm

Nick Fry“Janelia velum”

Robert Jones“Ouiwing truum”

Peter Kooienga

Amoeprot
100
AmprBL5C
Coprprot
MSU12
95
Ptolbull NolaAFSM
Arcearen10Arcegibb
100
0Arcevulg
100 100
Cycllobo
Netzelsp
76
DiffUSP
Diffbryo
1 010010
0 0 Diffcomp
98
Lesqmime
1 0 0LesqspiraCentacul
100
98
CentspS2
Hyaleleg
100
Hyalpapi
100
Nebela42
960
Nebela430
1 0 01 0 01
Nebela4497
1Quadsy41
0Quadsymme0
7 7 Nebetinc
1 0Plancari0
Helespha
97
Helesylv
1 01
0 0 0 Schoensp
100
Micro1A3
100
Microrsp
1
0
0
Micrpate
Spumosp
100 9 2100
Pyxioper
Crypoper8
1
PhryparT
8
1
PhryparTP
81
100
1 0PhryacrA
0Phryacro97
Flabcita
100
Rhizsaxo
Deutalgo
1 01HarnW183
000
Vermverm
100
100
1 0Echiexud
0EcexuMSU
100
MicrA134
Amphiz10100Amphizo2
1Amphizo800
100
Amphizo9100
Diploch3
100
1Tri40319
00
Trichossp
100
TricYANA
Acradend
Ceratahi
100
1 0 0 9 9 Nemagrac
100
Nemaova1
Grelrobu
100
Soliexpu
100
Soliirre
96
BassF20
100
Cavoapop
78
Schivulg
Snowball Tychacut
100 7 3
100
97
Schipseu
Filanola
HarnW1815100
100
Protfung
94
100
Protnoct100
Hodofilo
1
0
0
MSU21
55
Flamaegy100
Flamfluv Belonosp
100 5 854
Schoutsp
MultHAKH
Phalsoli
Acytlept100Acytsubg
100
16020Hetegloe
Hetemult
Hetepall1 0 01 0 0
Rostelli
Synspoly100
1 0 0Cavebifu
Cavefasc
100
Caveparv
1
0
0
Cavedemi
100
Cavemult
Corepoly Dictbref
100
1Dictcapi
0000
Dictdisc
1 0 0 1510Dictinte
2Dictcitr
0100
Dictgarg
1 0 0 19030 1Dictfirm
00
Dictgiga
Dictrosa
100
Dictpurp
Polyviol100
Rapeaust
1 0 0 1 0100 0 Hagirhiz
Rapepota
100
Rapegrac
Tieglact100
1 0 0 Tiegmeno
Spelcave
Arcydenu
Arcyvers
4 97 2 1 0 0
Triccrat
Perivermi2
1 0 0 Tricfavo
1 0 08 9
Dictplum100
Lycoepid2
Lindtubu
Badhaino2
3 7 Fulilevi
100
Badhcaps2
0Badhmel20
2 8 1 8019
Fulicine
0Physcine
22071 0Physpoly
0Badhutri
1106
0Willreti2
1 0 Physrose
0 Cratminu2
Physbite
7 8 5 3 Physmell
45
Kellfimi2 Physviri2
73
100
1 0Dideeffu
0Didehemi
1 0100 0 Dideglob2
Lepitigr2
4 54 9 1 0 0Didefall
LepicareDidydubi
9 5 1 0100 0 Didymela
Myxomysp
93
Didysqua
Diacsilv
4 4 100
UnknownLamparcy
100100
Mericare100
Lampsci2
100 7 1
Elaeomsp
Stemfusc
100
Echibisp
100Echiminu
100
Echiolig
CerafrKM
CspBYNF10
880
CspBYNF2
10
1 0100Cerafrut
CspBYNF3
Clasrecu
100
Protart1
3591
Protart3
100
Protart2
1 0 08 7
Protarti
YetiRNAC
100

100

100

100

88
100

100
100
100

100 9 3
100
100

100
100
100

100
98
100

1 0 0 1 0904
100

100

100

100

100

100
100
100

100

100
100

100
100
100
100
94

100

100

100

100
100

88
100

100

83
100
100

100

100
100

100

100

Mastbala
Masteilh
PelospArmalangSquajapo Rhizelon
100
Sapochin
Idiovort
CuneRUFF
1
00
Cuneruss
Paraaest
1 0 0 Parapema
100
Paraatla
Vexillsp
Veximinu
100
VexispNF
LingRSL
RipDP13
Vannfimi
Vannrobu
Vannscha
1 0907100
VanspBx2100
VanspPSC
1VanspRAM
00100
Vansp225
Vasp0168
RHP11
Stenlima
Stensten
Sapppeda
ThecSK13
100
Thecquad
Vermanta
Dermalge Stygregu
Paralevi
Mayocant
HHMI3
Mycagemm Micropaxi
1 0 0 Mpax1011
Cochminu
Parvmono
100
Parvruga
Ovaldese
Endoamer
Gocefonb
Endostsp
100
Pellcata Endozona
Dracjorm
Luaparac
Luapelsp
1 0100 0
Luaphula
ProtboheBalaman2
1Balamand00
VacuacanAcanroyr0
AcspBR21
1 0 0 1 0Acanculb
Acanpyro
Acanlen1100
670
Acanlen3
10Acanlen2
Acancas1
100 1
1
00
0
Acancast
0
Acancas2
Acancas3
91
Acanpear370
9 9 19002
Acanpol2
Acanquin
10
Acanlugd
8
9
Acanpoly
1019Acanmaur
0800
1Acanrhys
00
AcspBRA3
1 0Acantria
0Acanheal
140
05AcantSUN
AcaBEL03
1 0Acancoma0
Acanastr
1
0
0
Acanast2
Amoepara
Capsowcz
Minivibr
Homosapi Amphquee Monobrev
Coprcine
Spizpunc
Fontalba
Thectrah
Pygsbifo
100

100

100

100

0.3

Phrypara

100

Entadisp
110
Entahist000
Entanutt
Entainva

240 Proteins
IQ-Tree ML LG+G4+C60+PSMF
100 Real Bootstraps

OrthoLager: A Phylogenomic Pipeline (Brown & Kolisko)
Robert JonesDavid Žihala
Input

Nucleotides(EST, RNAseq, etc.)
TBlastN

Collect“Orthologs”

Collect top
N hitsProteins(Genomes, etc.)

351
Query Proteins

BlastP
Collect top
N hitsSupermatrix
351 orthologs~100,000AA

Recode to AA

Ortholog
Check

B l a s t P against
OrthoMCL
Check top hit of each putative ortholog against a dictionaryof inspected ortholog’s OrthoMCL numbers

Align

M A F F T- l i n s i

Mask

BMGE

Single Gene Tree
Identify artifacts
Alexander Tice, Ph.D.

RAxML

I Q - Tr e e
Phylobayes

Seed Alignments

Loose
Consensus
Tree

70% bipartition screen

Tomáš Pánek, Ph.D.

nad
ida

AMO
RPHE
A
ZOA
oe
bo
zo
a

tea

m

via

A

Bre

o mo

OBA

Apu
s

konta
Opistho

ta

SAR

tis
Hap

t
hy
op
uc

ta
ptis
Cry
ta
hy
op
od
a
Rh

EP
HA
C
AR
Ch
lo
ro
pl
He
as
mim
tid
+T
elo astiga
nem op
ho
ia
ra

la
G

PhyloFisher Plug

A

TID

S
LA

s

uM

CR

o
cyr

An

Alveolata

ida

nad

mo
lawi

Ma

Rhizaria

da

adi

n
mo

EXCAVATA

Discoba
Metamonada

Stramenopiles

Tice, Panek, Žihala, Jones,
et al. 2021 PLoS Biology

Phylogenomic
dataset/tree
80
90
99
94
99
96
99
92
95

97
97

98

99

YouTube Seminars on PhyloFisher

97

Chloroplastida
Glaucophyta
Rhodophyta
Rhodelphidia
Picozoa MS584-11
Cryptista
Centroheliozoa
Haptophyta
Ancoracysta twista
Hemimastigophora
Telonemia
Stramenopiles
Alveolata
Rhizaria
Amoebozoa
ObazoaCRuMs
Ancyromonada
Malawimonada
0.3
Discoba
Metamonada

https://www.youtube.com/watch?v=TcKhLiUxBTU&t=11s
https://www.youtube.com/watch?v=MJfb5CalWPA

https://github.com/TheBrownLab/PhyloFisher• Easily installed and simple usage• Ships with our dataset• Includes Paralogs for tree building, more accurate identification• Your own gene sets can be incorporated or used independently

dida

OBA

AMO

RPHE

ZOA

Bre
via
tea
A
m
oe
bo
zo
a

ona
som
Apu

ta

ptis

tista

Cry

ta

Stramenopileshy

Alveolata

op

Rhizaria

od

pl
He
as
mim
tid
+T
elo astiga
nem op
ho
ia
ra

ta
hy

op

uc
la

SAR

G

CH
R
A
Ch
lo
ro

Rh

AE

Hap

A
PL

Opistho

A

ID
ST

konta

• Tools for post-phylogenomic analyses

A

s

C

M
Ru

ida

ad
on

rom

cy
An

aw

Mal

dida

na
imo

EXCAVATA

Discoba
Metamonada

304 Taxa across all
known diversity with
their predicted
proteomes

80
90
99
94
99
96
99
92
95

97
97

98

99
97

Chloroplastida
Glaucophyta
Rhodophyta
Rhodelphidia
Picozoa MS584-11
Cryptista
Centroheliozoa
Haptophyta
Ancoracysta twista
Hemimastigophora
Telonemia
Stramenopiles
Hemimastigophora-TSAR
Alveolata
Rhizaria
Tice, Panek, Žihala, Jones,
Amoebozoa
et al. 2021 PLoS Biology
ObazoaCRuMs
Ancyromonada
Malawimonada
240 orthologs: 305 taxa: 72,632AA sites
0.3
Discoba
IQtree- LG+G+c20 => LG+G+c60(PMSF)
350 Bootstrap Reps
Metamonada

Phylogenomic Tree

Amoebae are much more complicatedn

Sporocarpic
Life Cycle

2nmyxogastrid (myxomycete) amoebae~1200 species

nSporocarpic
Life Cycle

2nmyxogastrid (myxomycete) amoebae~1200 species

Sporocarpic Life Cycle

protosteloid amoebae
32 species (10+ to be described)

Sporocarpic Life Cycle

protosteloid amoebae
32 species (10+ to be described)

Evosea

Polysphondylium pallidum
Trichosphaerium sp.
Dictyostelium discoideum
Corycida
Physarum polycephalum Diplochlamys sp.
Amphizonellasp.
Echinosteliopsis oligospora
Micriamoeba sp.
Eumycetozoa
Echinostelium minutum
Echinamoeba exudans
Echinostelium bisporum
Echinamoebida
Protosporangium articulatum
Vermamoeba vermiformis
Clastostelium recurvatumVermamoeba sp. [CCAP1503-5]
Ceratiomyxa fruticulosa
Rhizamoeba saxonica
Flamella fluviatilis
Flabellula citata
Flamella aegyptia
Cryptodifflugia operculata
Phalansterium solitarium
Difflugia bryophila
Schizoplasmodiopsis vulgaris
Elarida*Tychosporium acutostipes
Arcella intermedia
98
Schizoplasmodiopsis pseudoendospora
Nolandella sp.
69
Cavostelium apophysatum
Copromyxa protea
Variosea
Protostelium nocturnum
Amoebaproteus
Filamoeba nolandi
Sapocribrum chincoteaguense
Soliformovum irregularis
Cutosea
Squamamoeba japonica
Grellamoeba robusta
cutosean isolate [ATCC PRA-29]
Nematostelium gracile
Ceratiomyxella tahitiensis
Rhizomastix elongata
Acramoeba dendroida
Pelomyxa sp.
Stenamoeba stenopodia
Mastigella eilhardi
Archamoebae
Stenamoeba limacina
Mastigamoebabalamuthi
Thecamoeba quadrilineata
Mastigamoeba abducta
Thecamoeba sp.
Entamoeba histolytica
Sappinia pedata
Polysphondylium
pallidum
Thecamoebida
isolate [RHP1-1]
Mayorella cantabrigiensis
Dictyostelium discoideum
Paradermamoeba
levis
Physarum polycephalum
Dermamoebaalgensis
Echinosteliopsis oligospora
Vermistella antarctica
Eumycetozoa
Echinostelium
minutum
Stygamoeba regulata
Echinostelium bisporum
Vexillifera minutissima
Lepidoderma tigrinum
Protosporangium articulatum 46 Myxogastrid Taxa 7 outgroup
Flabellinia
Vexilliferataxa
bacillipedes
88 genes (17,666 aa sites)
0.85/*
96
Diderma globosum
Clastostelium recurvatumVexillifera sp. [MMETSP0173]
Genes
used
are
present
in
at
least
75%
of
includedtaxa
Diderma effusum
Paramoeba
atlantica
Ceratiomyxa fruticulosa
Diderma hemisphaericum
Paramoeba
aestuarina
Flamella fluviatilis
IQ Tree LG+C60+F+G+PMSF
Cunea
sp.
[MMETSP0417]
Lepidoderma
carestianum
Flamella aegyptia
Cunea sp. [JDS-Ruffled]
Supportvaluse
come
from
1000
ultra
fast
bootstrap
replicates
DidermafallaxPhalansteriumVannella
solitarium
sp. [MMETSP0168]
Badhamia capsulifera
Schizoplasmodiopsis
vulgaris
Vannellarobusta*Badhamia melanospora
TychosporiumVannella
acutostipes
schaefferi
98
Fuligo cinerea
Vannellafimicola
Schizoplasmodiopsis pseudoendospora
69
Physarum
cinereum
Ripellasp.
74
Cavostelium apophysatum
Variosea
Lingulamoebasp.
Willkommlangea
reticulata
Protostelium nocturnum
Clydonella sp.
PhysarumroseumFilamoeba nolandi Ovalopodium desertum
40
Craterium minutum
Soliformovum irregularis
Parvamoeba rugata
Fuligoseptica
Grellamoeba robusta
Cochliopodium minus
Fuligo leviderma
Nematostelium
gracilePellitacatalonica
Physarum polycephalum
Gocevia fonbrunei
Ceratiomyxellatahitiensis
Goceviafonbrunei[Tekleetal.
2016]
Badhamiautricularis
Acramoeba dendroida
83
Endostelium
zonatum[PRA-191]
Badhamiopsis
ainoaeStenamoeba stenopodia
Centramoebia
Endostelium zonatum [LINKS]
PhysarumvirideStenamoeba
limacina
63
Dracoamoeba
joomungandrii
Physarum bitectum
Thecamoeba
Protacanthamoeba
bohemica quadrilineata
Physarummelleum
Thecamoeba
sp.
Luapelamoeba arachisporum
Kelleromyxa fimicola
Luapelamoeba hula
Sappinia pedata
Acanthamoeba castellanii
Unknown sp.
Thecamoebida isolate [RHP1-1]
Acanthamoeba
pyriformis
Diachealeucopodia
Mayorella cantabrigiensis
Pygsuiabiforma
DiachearadiataParadermamoeba levis
Thecamonas trahens
Diachea silviaepluviales
Dermamoeba algensis
Fonticula alba
Didymiun
dubiumVermistellaantarctica
Spizellomyces punctatus= 1.0 Bayesian PP Didymiun squamulosum
Stygamoeba regulataCoprinus cinereus
CAT+GTR
Monosiga
brevicollis
Didymium melanospermum
Vexillifera
minutissima
Homo sapiens
Meridermacarestia
Vexillifera bacillipedes= 100% ML Bootstrap Flabellinia
0.85/* 96
Amphimedon queenslandica
Lamproderma
arcyrioides
Vexillifera sp. [MMETSP0173]
LG+G4+C60+PMSF
Ministeria vibrans
Lamproderma scintillans
Paramoeba atlantica
Capsaspora owczarzaki
Elaeomyxa sp.
Paramoeba
aestuarina
Amoebidium parasiticum

64

Tubulinea

71

Sporocarps

Myxogastrids

60

97
*

63

99
71

*

60

*

63

*

Joaquina (Kina) García Martín
97

*

92

Cunea sp. [MMETSP0417]
Cunea sp. [JDS-Ruffled]
Vannella sp. [MMETSP0168]
Vannella robusta
Vannella schaefferi
Vannella fimicola
Ripella sp.
Lingulamoeba sp.
Clydonella sp.
86
Ovalopodium desertum

Cochliopodium minus

Pellita catalonica
Gocevia fonbrunei
Gocevia fonbrunei [Tekle et al. 2016]
Endostelium zonatum [PRA-191]
Endostelium zonatum [LINKS]
Dracoamoeba joomungandrii
Protacanthamoeba bohemica
Luapelamoeba arachisporum
Luapelamoeba hula
Acanthamoeba castellanii
Acanthamoeba pyriformis

0.2

Parvamoeba rugata

0.2

Discosea

Obazoa99

dark-spored clade

Amoebozoa

99
92

Discosea*

Evosea64

Amoebozoa

99

M
y
x
o
m
y
c
e
t
e
s

E
u
m
y
c
e
t
o
z
o
a

100%
Stemonitis
fusca
0% 50%
SiteEchinosteliopsis
Coverageoligosporum

Echinostelium bisporum
Echinosteliales
Echinostelium minumtum
Lindbladia tubulina
Lycogala epidendrum
Licea variabilis
Dictydiaethalium plumbeum
bright-spored clade
Arcyria denudata
Trichia crateriformis
Arcyria versicolor
Trichia favoginea
Perichaena vermicularis
Protosporangium articulatum
Clastostelium recurvatum
Tice et al. 2016: Biology Direct
Ceratiomyxa
fruticulosa
Centramoebia
Polysphondyllium palladium
Kang et al. 2017: MBE
Dictyostelium discoideum
Vannella diva
Out-group Amoebozoans
Acanthamoeba castellanii
Fiore-Donno,
Tice, & Brown. 2019. JEMB

García Martín et al. In Prep

97

Tubulinea
Myxogastrids

99

Amoebozoa

EvoseaDiscosea

60

69

97
*

63

99

*

98

Nick Fry

Microglomus

Parvamoeba rugata

Pellita catalonica
Gocevia fonbrunei
Gocevia fonbrunei [Tekle et al. 2016]
Endostelium zonatum [PRA-191]
Endostelium zonatum [LINKS]
Dracoamoeba joomungandrii
Protacanthamoeba bohemica
Luapelamoeba arachisporum
Luapelamoeba hula
Acanthamoeba castellanii
Acanthamoeba pyriformis
Pygsuia biforma
Thecamonas trahens
Fonticula alba
Spizellomyces punctatus
Coprinus cinereus
Monosiga brevicollis
Homo sapiens
Amphimedon queenslandica
Ministeria vibrans
Capsaspora owczarzaki
Amoebidium parasiticum

Centramoebia= 1.0 Bayesian PP
CAT+GTR= 100% ML Bootstrap
LG+G4+C60+PMSF

0.2

0% 50% 100%
Site Coverage

Discosea

97

Cochliopodium minus

Flabellinia

Vexillifera bacillipedes

Obazoa99

Vexillifera sp. [MMETSP0173]
Paramoeba atlantica
Paramoeba aestuarina
Cunea sp. [MMETSP0417]
Cunea sp. [JDS-Ruffled]
Vannella sp. [MMETSP0168]
Vannella robusta
Vannella schaefferi
Vannella fimicola
Ripella sp.
Lingulamoeba sp.
Clydonella sp.
Ovalopodium desertum

Amoebozoa

92

Ceratiomyxa fruticulosa

Evosea*96

Discosea

0.85/*

Variosea

Amoebozoa*

99

Eumycetozoa

Evosea64

Polysphondylium pallidum
Dictyostelium discoideum
Physarum polycephalum
Echinosteliopsis oligospora
Echinostelium minutum
Echinostelium bisporum
Protosporangium articulatum
Clastostelium recurvatum
Ceratiomyxa fruticulosa
Flamella fluviatilis
Flamella aegyptia
Phalansterium solitarium
Schizoplasmodiopsis vulgaris
Tychosporium acutostipes
Schizoplasmodiopsis pseudoendospora
Cavostelium apophysatum
Protostelium nocturnum
Filamoeba nolandi
Soliformovum irregularis
Grellamoeba robusta
Nematostelium gracile
Ceratiomyxella tahitiensis
Acramoeba dendroida
Stenamoeba stenopodia
Stenamoeba limacina
Thecamoeba quadrilineata
Thecamoeba sp.
Sappinia pedata
Thecamoebida isolate [RHP1-1]
Mayorella cantabrigiensis
Paradermamoeba levis
Dermamoeba algensis
Vermistella antarctica
Stygamoeba regulata
Vexillifera minutissima

Tubulinea

71

97

Tubulinea
Myxogastrids

99

Amoebozoa

EvoseaDiscosea

60

69

97
*

63

99

*

98

Cochliopodium minus

Parvamoeba rugata

Pellita catalonica
Gocevia fonbrunei
Gocevia fonbrunei [Tekle et al. 2016]
Endostelium zonatum [PRA-191]
Endostelium zonatum [LINKS]
Dracoamoeba joomungandrii
Protacanthamoeba bohemica
Luapelamoeba arachisporum
Luapelamoeba hula
Acanthamoeba castellanii
Acanthamoeba pyriformis
Pygsuia biforma
Thecamonas trahens
Fonticula alba
Spizellomyces punctatus
Coprinus cinereus
Monosiga brevicollis
Homo sapiens
Amphimedon queenslandica
Ministeria vibrans
Capsaspora owczarzaki
Amoebidium parasiticum

Centramoebia= 1.0 Bayesian PP
CAT+GTR= 100% ML Bootstrap
LG+G4+C60+PMSF

0.2

0% 50% 100%
Site Coverage

Discosea

97

Flabellinia

Vexillifera bacillipedes

Obazoa99

10µm

Amoebozoa

92

Vexillifera sp. [MMETSP0173]
Paramoeba atlantica
Paramoeba aestuarina
Cunea sp. [MMETSP0417]
Cunea sp. [JDS-Ruffled]
Vannella sp. [MMETSP0168]
Vannella robusta
Vannella schaefferi
Vannella fimicola
Ripella sp.
Lingulamoeba sp.
Clydonella sp.
Ovalopodium desertum

Evosea*96

Variosea

Discosea

0.85/*

Microglomus paxillus
Amoebozoa*

99

Eumycetozoa

Evosea64

Polysphondylium pallidum
Dictyostelium discoideum
Physarum polycephalum
Echinosteliopsis oligospora
Echinostelium minutum
Echinostelium bisporum
Protosporangium articulatum
Clastostelium recurvatum
Ceratiomyxa fruticulosa
Flamella fluviatilis
Flamella aegyptia
Phalansterium solitarium
Schizoplasmodiopsis vulgaris
Tychosporium acutostipes
Schizoplasmodiopsis pseudoendospora
Cavostelium apophysatum
Protostelium nocturnum
Filamoeba nolandi
Soliformovum irregularis
Grellamoeba robusta
Nematostelium gracile
Ceratiomyxella tahitiensis
Acramoeba dendroida
Stenamoeba stenopodia
Stenamoeba limacina
Thecamoeba quadrilineata
Thecamoeba sp.
Sappinia pedata
Thecamoebida isolate [RHP1-1]
Mayorella cantabrigiensis
Paradermamoeba levis
Dermamoeba algensis
Vermistella antarctica
Stygamoeba regulata
Vexillifera minutissima

Tubulinea

71

Tice & Brown. Submitted

60

69

97
*

63

99

*

98

Cochliopodium minus

Pellita catalonica
Gocevia fonbrunei
Gocevia fonbrunei [Tekle et al. 2016]
Endostelium zonatum [PRA-191]
Endostelium zonatum [LINKS]
Dracoamoeba joomungandrii
Protacanthamoeba bohemica
Luapelamoeba arachisporum
Luapelamoeba hula
Acanthamoeba castellanii
Acanthamoeba pyriformis
Pygsuia biforma
Thecamonas trahens
Fonticula alba
Spizellomyces punctatus
Coprinus cinereus
Monosiga brevicollis
Homo sapiens
Amphimedon queenslandica
Ministeria vibrans
Capsaspora owczarzaki
Amoebidium parasiticum

Centramoebia= 1.0 Bayesian PP
CAT+GTR= 100% ML Bootstrap
LG+G4+C60+PMSF

0.2

0% 50% 100%
Site Coverage

Discosea

97

Parvamoeba rugata

Obazoa99

Flabellinia

Vexillifera bacillipedes

Amoebozoa

92

Vexillifera sp. [MMETSP0173]
Paramoeba atlantica
Paramoeba aestuarina
Cunea sp. [MMETSP0417]
Cunea sp. [JDS-Ruffled]
Vannella sp. [MMETSP0168]
Vannella robusta
Vannella schaefferi
Vannella fimicola
Ripella sp.
Lingulamoeba sp.
Clydonella sp.
Ovalopodium desertum

Evosea*96

Discosea

0.85/*

Variosea

Amoebozoa*

99

Eumycetozoa

Evosea64

Polysphondylium pallidum
Dictyostelium discoideum
Physarum polycephalum
Echinosteliopsis oligospora
Echinostelium minutum
Echinostelium bisporum
Protosporangium articulatum
Clastostelium recurvatum
Ceratiomyxa fruticulosa
Flamella fluviatilis
Flamella aegyptia
Phalansterium solitarium
Schizoplasmodiopsis vulgaris
Tychosporium acutostipes
Schizoplasmodiopsis pseudoendospora
Cavostelium apophysatum
Protostelium nocturnum
Filamoeba nolandi
Soliformovum irregularis
Grellamoeba robusta
Nematostelium gracile
Ceratiomyxella tahitiensis
Acramoeba dendroida
Stenamoeba stenopodia
Stenamoeba limacina
Thecamoeba quadrilineata
Thecamoeba sp.
Sappinia pedata
Thecamoebida isolate [RHP1-1]
Mayorella cantabrigiensis
Paradermamoeba levis
Dermamoeba algensis
Vermistella antarctica
Stygamoeba regulata
Vexillifera minutissima

Tubulinea

71

Sporocarpic Hypothesis
97• Single origin of sporocarpy
dida

AMO

OBA

RPHE

A

– Life cycles are complex and varieda– Stalk bearing structures arecomplex, but similar across taxa

zo
oe
bo

s
M
u

A

m

via

tea

ZOA

Bre

ona
Apu
som

Opistho
konta

tista

Hap

a

Stramenopiles

tist

Alveolata

ta

a
yt
ph
co

He
la
mim
st
+T
id
elo astiga
nem ophoiaraRhizaria

hy
op
od

u
la
G

SAR

Rh

HA

p
Cry

L
EP

– Restricted to Amoebozoa

99

I

T
AS

C
R
A
Ch
lo
ro
p

DA

CR

a

o

om
r
y
c

An

id
d
a
n
m

i
w
a
l
Ma

a

did
a
n
o

EXCAVATA

Discoba
Metamonada• Hard to invent?
– Unlike sorocarpy, sporocarpy is
restricted to Amoebozoa• What is more parsimonious?
– single origin, many losses?
– 9 independent origins?

• We can examine this usingdevelopmental transcriptomics!

SMART-Seq2 Picelli et al. 2014, 2015, Onsbring & Tice et al. 2021

Developmental Stages in Sporocarpic Fruiting Amoebae
Platinum wire

trophozoite

pre-sporocarp

rising sporocarp

Tubulinea

97

sporocarp

99

Amoebozoa

EvoseaDiscosea1:30h timelapse

Soliformovum irregularis

Sample Correlation Matrix
Vannellafimicola

Pearson Correlation

10 cells per tube
90 total cells sampled

648 transcripts DE
Pairwise FC = 4
p-value < 0.001

trophozoite

pre-sporocarp

rising sporocarp

sporocarpDifferential Expression: Samples vs Features
Vannellafimicola

Log Fold Change

32
89

527

19916 Transcripts
648 transcripts DE
Pairwise FC = 4
p-value < 0.001

trophozoite

pre-sporocarp

rising sporocarp

sporocarp

92

sporocarp

Color Key
samples vs. features
diffExpr.P0.001_C2.matrix.log2.centeredrising sporocarp−50sporocarp

lcl|MDYQ01000362.1_cds_PRP7
lcl|MDYQ01000121.1_cds_PRP81568.1_3282
lcl|MDYQ01000132.1_cds_PRP81024.1_3973
lcl|MDYQ01000047.1_cds_PRP85333.1_13508
lcl|MDYQ01000007.1_cds_PRP88840.1_16217
lcl|MDYQ01000378.1_cds_PRP75545.1_12276
lcl|MDYQ01000400.1_cds_PRP75269.1_12675
lcl|MDYQ01000030.1_cds_PRP86463.1_9836
lcl|MDYQ01000020.1_cds_PRP87439.1_6553
lcl|MDYQ01000430.1_cds_PRP74913.1_13407
lcl|MDYQ01000115.1_cds_PRP81875.1_3097
lcl|MDYQ01000283.1_cds_PRP77070.1_9996
lcl|MDYQ01000016.1_cds_PRP87942.1_5236
lcl|MDYQ01000077.1_cds_PRP83748.1_425
lcl|MDYQ01000331.1_cds_PRP76380.1_11158
lcl|MDYQ01000048.1_cds_PRP85257.1_13612
lcl|MDYQ01000059.1_cds_PRP84643.1_15180
lcl|MDYQ01000058.1_cds_PRP84705.1_15099
lcl|MDYQ01000238.1_cds_PRP78152.1_8513
lcl|MDYQ01000460.1_cds_PRP74525.1_14118
lcl|MDYQ01000139.1_cds_PRP80736.1_4307
lcl|MDYQ01000599.1_cds_PRP73567.1_16478
lcl|MDYQ01000383.1_cds_PRP75459.1_12349
lcl|MDYQ01000005.1_cds_PRP89082.1_14324
lcl|MDYQ01000128.1_cds_PRP81287.1_3657
lcl|MDYQ01000464.1_cds_PRP74410.1_14291
lcl|MDYQ01000001.1_cds_PRP89735.1_77
lcl|MDYQ01000281.1_cds_PRP77090.1_9954
lcl|MDYQ01000071.1_cds_PRP84019.1_16824
lcl|MDYQ01000056.1_cds_PRP84796.1_14822
lcl|MDYQ01000520.1_cds_PRP73965.1_15249
lcl|MDYQ01000257.1_cds_PRP77569.1_9106
lcl|MDYQ01000064.1_cds_PRP84377.1_15777
lcl|MDYQ01000122.1_cds_PRP81548.1_3464
lcl|MDYQ01000068.1_cds_PRP84177.1_16338
lcl|MDYQ01000101.1_cds_PRP82520.1_2274
lcl|MDYQ01000011.1_cds_PRP88378.1_2423
lcl|MDYQ01000083.1_cds_PRP83396.1_1040
lcl|MDYQ01000033.1_cds_PRP86289.1_10444
lcl|MDYQ01000055.1_cds_PRP84848.1_14700
lcl|MDYQ01000080.1_cds_PRP83555.1_621
lcl|MDYQ01000200.1_cds_PRP79026.1_7088
lcl|MDYQ01000093.1_cds_PRP82948.1_1775
lcl|MDYQ01000105.1_cds_PRP82333.1_2524
lcl|MDYQ01000143.1_cds_PRP80609.1_4526
lcl|MDYQ01000380.1_cds_PRP75502.1_12331
lcl|MDYQ01000199.1_cds_PRP79062.1_7081
lcl|MDYQ01000303.1_cds_PRP76764.1_10523
lcl|MDYQ01000001.1_cds_PRP89776.1_118
lcl|MDYQ01000131.1_cds_PRP81035.1_3910
lcl|MDYQ01000152.1_cds_PRP80362.1_5018
lcl|MDYQ01000395.1_cds_PRP75304.1_12582
lcl|MDYQ01000599.1_cds_PRP73544.1_16455
lcl|MDYQ01000135.1_cds_PRP80906.1_4077
lcl|MDYQ01000151.1_cds_PRP80393.1_4999
lcl|MDYQ01000337.1_cds_PRP76280.1_11271
lcl|MDYQ01000132.1_cds_PRP81018.1_3967
lcl|MDYQ01000139.1_cds_PRP80745.1_4316
lcl|MDYQ01000052.1_cds_PRP84990.1_14132
lcl|MDYQ01000001.1_cds_PRP89772.1_114
lcl|MDYQ01000042.1_cds_PRP85584.1_12502
lcl|MDYQ01000085.1_cds_PRP83297.1_1153
lcl|MDYQ01000031.1_cds_PRP86404.1_10057
lcl|MDYQ01000157.1_cds_PRP80214.1_5146
lcl|MDYQ01000001.1_cds_PRP89739.1_81
lcl|MDYQ01000029.1_cds_PRP86580.1_9671
lcl|MDYQ01000257.1_cds_PRP77605.1_9142
lcl|MDYQ01000056.1_cds_PRP84798.1_14824
lcl|MDYQ01000256.1_cds_PRP77744.1_9088
lcl|MDYQ01000004.1_cds_PRP89295.1_13012
lcl|MDYQ01000175.1_cds_PRP79689.1_6047
lcl|MDYQ01000027.1_cds_PRP86751.1_8966
lcl|MDYQ01000005.1_cds_PRP89164.1_14406
lcl|MDYQ01000111.1_cds_PRP82068.1_2839
lcl|MDYQ01000010.1_cds_PRP88481.1_1958
lcl|MDYQ01000057.1_cds_PRP84732.1_15019
lcl|MDYQ01000264.1_cds_PRP77450.1_9469
lcl|MDYQ01000169.1_cds_PRP79834.1_5786
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lcl|MDYQ01000121.1_cds_PRP81634.1_3348
lcl|MDYQ01000017.1_cds_PRP87828.1_5663
lcl|MDYQ01000002.1_cds_PRP89525.1_4773
lcl|MDYQ01000042.1_cds_PRP85593.1_12511
lcl|MDYQ01000448.1_cds_PRP74634.1_13838
lcl|MDYQ01000188.1_cds_PRP79309.1_6477
lcl|MDYQ01000251.1_cds_PRP77868.1_8833
lcl|MDYQ01000132.1_cds_PRP81009.1_3958
lcl|MDYQ01000090.1_cds_PRP83071.1_1603
lcl|MDYQ01000615.1_cds_PRP73370.1_16688
lcl|MDYQ01000028.1_cds_PRP86668.1_9398
lcl|MDYQ01000056.1_cds_PRP84766.1_14792
lcl|MDYQ01000007.1_cds_PRP88777.1_16154
lcl|MDYQ01000124.1_cds_PRP81470.1_3526
lcl|MDYQ01000051.1_cds_PRP85063.1_14038
lcl|MDYQ01000007.1_cds_PRP88904.1_16281
lcl|MDYQ01000257.1_cds_PRP77650.1_9187
lcl|MDYQ01000207.1_cds_PRP78776.1_7397
lcl|MDYQ01000038.1_cds_PRP85897.1_11800
lcl|MDYQ01000264.1_cds_PRP77447.1_9466
lcl|MDYQ01000122.1_cds_PRP81513.1_3429
lcl|MDYQ01000039.1_cds_PRP85822.1_11972
lcl|MDYQ01000054.1_cds_PRP84932.1_14609
lcl|MDYQ01000186.1_cds_PRP79370.1_6436
lcl|MDYQ01000014.1_cds_PRP88106.1_4474
lcl|MDYQ01000032.1_cds_PRP86361.1_10273
lcl|MDYQ01000099.1_cds_PRP82661.1_2152
lcl|MDYQ01000069.1_cds_PRP84089.1_16562
lcl|MDYQ01000254.1_cds_PRP77772.1_9006
lcl|MDYQ01000244.1_cds_PRP78035.1_8600
lcl|MDYQ01000180.1_cds_PRP79562.1_6269
lcl|MDYQ01000006.1_cds_PRP88970.1_15282
lcl|MDYQ01000150.1_cds_PRP80412.1_4741
lcl|MDYQ01000098.1_cds_PRP82690.1_2111
lcl|MDYQ01000599.1_cds_PRP73490.1_16401
lcl|MDYQ01000020.1_cds_PRP87496.1_6610
lcl|MDYQ01000003.1_cds_PRP89385.1_8003
lcl|MDYQ01000401.1_cds_PRP75260.1_12680
lcl|MDYQ01000074.1_cds_PRP83883.1_248
lcl|MDYQ01000065.1_cds_PRP84350.1_15899
lcl|MDYQ01000441.1_cds_PRP74757.1_13634
lcl|MDYQ01000362.1_cds_PRP75781.1_11869
lcl|MDYQ01000121.1_cds_PRP81630.1_3344
lcl|MDYQ01000539.1_cds_PRP73840.1_15655
lcl|MDYQ01000257.1_cds_PRP77704.1_9241
lcl|MDYQ01000090.1_cds_PRP83073.1_1605
lcl|MDYQ01000312.1_cds_PRP76618.1_10751
lcl|MDYQ01000005.1_cds_PRP89168.1_14410
lcl|MDYQ01000337.1_cds_PRP76261.1_11252
lcl|MDYQ01000028.1_cds_PRP86609.1_9339
lcl|MDYQ01000042.1_cds_PRP85599.1_12517
lcl|MDYQ01000007.1_cds_PRP88763.1_16140
lcl|MDYQ01000049.1_cds_PRP85173.1_13769
lcl|MDYQ01000107.1_cds_PRP82228.1_2604
lcl|MDYQ01000125.1_cds_PRP81427.1_3544
lcl|MDYQ01000352.1_cds_PRP76088.1_11526
lcl|MDYQ01000018.1_cds_PRP87728.1_5935
lcl|MDYQ01000135.1_cds_PRP80901.1_4072
lcl|MDYQ01000128.1_cds_PRP81339.1_3709
lcl|MDYQ01000283.1_cds_PRP77063.1_9989
lcl|MDYQ01000268.1_cds_PRP77370.1_9531
lcl|MDYQ01000132.1_cds_PRP81026.1_3975
lcl|MDYQ01000129.1_cds_PRP81189.1_3806
lcl|MDYQ01000077.1_cds_PRP83724.1_401
lcl|MDYQ01000103.1_cds_PRP82433.1_2363
lcl|MDYQ01000253.1_cds_PRP77837.1_8900
lcl|MDYQ01000362.1_cds_PRP75782.1_11870
lcl|MDYQ01000282.1_cds_PRP77077.1_9971
lcl|MDYQ01000065.1_cds_PRP84303.1_15852
lcl|MDYQ01000099.1_cds_PRP82659.1_2150
lcl|MDYQ01000133.1_cds_PRP80985.1_4007
lcl|MDYQ01000033.1_cds_PRP86257.1_10412
lcl|MDYQ01000257.1_cds_PRP77689.1_9226
lcl|MDYQ01000032.1_cds_PRP86344.1_10256
lcl|MDYQ01000337.1_cds_PRP76272.1_11263
lcl|MDYQ01000280.1_cds_PRP77117.1_9944
lcl|MDYQ01000289.1_cds_PRP76975.1_10137
lcl|MDYQ01000012.1_cds_PRP88269.1_2954
lcl|MDYQ01000517.1_cds_PRP73977.1_15203
lcl|MDYQ01000437.1_cds_PRP74873.1_13444
lcl|MDYQ01000283.1_cds_PRP77065.1_9991
lcl|MDYQ01000658.1_cds_PRP73220.1_16962
lcl|MDYQ01000122.1_cds_PRP81514.1_3430
lcl|MDYQ01000003.1_cds_PRP89461.1_8079
lcl|MDYQ01000168.1_cds_PRP79842.1_5734
lcl|MDYQ01000326.1_cds_PRP76451.1_11034
lcl|MDYQ01000456.1_cds_PRP74553.1_14010
lcl|MDYQ01000162.1_cds_PRP80054.1_5424
lcl|MDYQ01000372.1_cds_PRP75630.1_12118
lcl|MDYQ01000002.1_cds_PRP89534.1_4782
lcl|MDYQ01000090.1_cds_PRP83077.1_1609
lcl|MDYQ01000021.1_cds_PRP87291.1_6890
lcl|MDYQ01000783.1_cds_PRP72865.1_1234
lcl|MDYQ01000231.1_cds_PRP78303.1_8361
lcl|MDYQ01000020.1_cds_PRP87446.1_6560
lcl|MDYQ01000096.1_cds_PRP82751.1_2024
lcl|MDYQ01000001.1_cds_PRP89808.1_150
lcl|MDYQ01000293.1_cds_PRP76895.1_10311
lcl|MDYQ01000021.1_cds_PRP87377.1_6976
lcl|MDYQ01000080.1_cds_PRP83573.1_639
lcl|MDYQ01000387.1_cds_PRP75417.1_12454
lcl|MDYQ01000373.1_cds_PRP75599.1_12149
lcl|MDYQ01000009.1_cds_PRP88616.1_1490
lcl|MDYQ01000247.1_cds_PRP77997.1_8655
lcl|MDYQ01000119.1_cds_PRP81755.1_3228
lcl|MDYQ01000045.1_cds_PRP85405.1_13083
lcl|MDYQ01000421.1_cds_PRP75021.1_13280
lcl|MDYQ01000337.1_cds_PRP76253.1_11244
lcl|MDYQ01000009.1_cds_PRP88529.1_1403
lcl|MDYQ01000289.1_cds_PRP76978.1_10140
lcl|MDYQ01000029.1_cds_PRP86587.1_9678
lcl|MDYQ01000138.1_cds_PRP80777.1_4275
lcl|MDYQ01000027.1_cds_PRP86758.1_8973
lcl|MDYQ01000117.1_cds_PRP81782.1_3159
lcl|MDYQ01000129.1_cds_PRP81206.1_3823
lcl|MDYQ01000067.1_cds_PRP84238.1_16081
lcl|MDYQ01000019.1_cds_PRP87647.1_6243
lcl|MDYQ01000069.1_cds_PRP84134.1_16607
lcl|MDYQ01000249.1_cds_PRP77958.1_8759
lcl|MDYQ01000184.1_cds_PRP79435.1_6376
lcl|MDYQ01000095.1_cds_PRP82802.1_1896
lcl|MDYQ01000151.1_cds_PRP80386.1_4992
lcl|MDYQ01000007.1_cds_PRP88908.1_16285
lcl|MDYQ01000437.1_cds_PRP74874.1_13445
lcl|MDYQ01000162.1_cds_PRP80060.1_5430
lcl|MDYQ01000136.1_cds_PRP80843.1_4187
lcl|MDYQ01000136.1_cds_PRP80867.1_4211
lcl|MDYQ01000129.1_cds_PRP81207.1_3824
lcl|MDYQ01000021.1_cds_PRP87354.1_6953
lcl|MDYQ01000472.1_cds_PRP74331.1_14483
lcl|MDYQ01000018.1_cds_PRP87717.1_5924
lcl|MDYQ01000107.1_cds_PRP82273.1_2649
lcl|MDYQ01000599.1_cds_PRP73539.1_16450
lcl|MDYQ01000020.1_cds_PRP87554.1_6668
lcl|MDYQ01000056.1_cds_PRP84828.1_14854
lcl|MDYQ01000114.1_cds_PRP81917.1_3066
lcl|MDYQ01000262.1_cds_PRP77487.1_9438
lcl|MDYQ01000064.1_cds_PRP84366.1_15766
lcl|MDYQ01000017.1_cds_PRP87851.1_5686
lcl|MDYQ01000027.1_cds_PRP86771.1_8986
lcl|MDYQ01000363.1_cds_PRP75764.1_11989
lcl|MDYQ01000081.1_cds_PRP83488.1_716
lcl|MDYQ01000395.1_cds_PRP75354.1_12632
lcl|MDYQ01000033.1_cds_PRP86267.1_10422
lcl|MDYQ01000117.1_cds_PRP81818.1_3195
lcl|MDYQ01000046.1_cds_PRP85363.1_13323
lcl|MDYQ01000131.1_cds_PRP81047.1_3922
lcl|MDYQ01000066.1_cds_PRP84292.1_16012
lcl|MDYQ01000044.1_cds_PRP85503.1_12917
lcl|MDYQ01000036.1_cds_PRP86008.1_11069
lcl|MDYQ01000026.1_cds_PRP86837.1_8711
lcl|MDYQ01000128.1_cds_PRP81312.1_3682
lcl|MDYQ01000173.1_cds_PRP79739.1_5996
lcl|MDYQ01000048.1_cds_PRP85271.1_13626
lcl|MDYQ01000012.1_cds_PRP88255.1_2940
lcl|MDYQ01000146.1_cds_PRP80515.1_4627
lcl|MDYQ01000020.1_cds_PRP87489.1_6603
lcl|MDYQ01000021.1_cds_PRP87271.1_6870
lcl|MDYQ01000105.1_cds_PRP82345.1_2536
lcl|MDYQ01000112.1_cds_PRP81970.1_2882
lcl|MDYQ01000188.1_cds_PRP79314.1_6482
lcl|MDYQ01000107.1_cds_PRP82221.1_2597
lcl|MDYQ01000004.1_cds_PRP89321.1_13038
lcl|MDYQ01000065.1_cds_PRP84309.1_15858
lcl|MDYQ01000032.1_cds_PRP86371.1_10283
lcl|MDYQ01000796.1_cds_PRP72843.1_1255
lcl|MDYQ01000595.1_cds_PRP73608.1_16113
lcl|MDYQ01000162.1_cds_PRP80061.1_5431
lcl|MDYQ01000162.1_cds_PRP80062.1_5432
lcl|MDYQ01000251.1_cds_PRP77885.1_8850
lcl|MDYQ01000280.1_cds_PRP77107.1_9934
lcl|MDYQ01000082.1_cds_PRP83410.1_922
lcl|MDYQ01000018.1_cds_PRP87732.1_5939
lcl|MDYQ01000125.1_cds_PRP81420.1_3537
lcl|MDYQ01000176.1_cds_PRP79655.1_6070
lcl|MDYQ01000004.1_cds_PRP89293.1_13010
lcl|MDYQ01000104.1_cds_PRP82374.1_2480
lcl|MDYQ01000212.1_cds_PRP78659.1_7690
lcl|MDYQ01000070.1_cds_PRP84043.1_16710
lcl|MDYQ01000008.1_cds_PRP88728.1_904
lcl|MDYQ01000050.1_cds_PRP85118.1_13966
lcl|MDYQ01000067.1_cds_PRP84239.1_16082
lcl|MDYQ01000801.1_cds_PRP72830.1_1313
lcl|MDYQ01000162.1_cds_PRP80066.1_5436
lcl|MDYQ01000021.1_cds_PRP87372.1_6971
lcl|MDYQ01000125.1_cds_PRP81432.1_3549
lcl|MDYQ01000372.1_cds_PRP75613.1_12101

5

Pfun−e3

Pfun−e2Pfun−e1

Pfun−v2

SiDEVa_TRINITY_DN4558_c0_g12_i1.p1
SiDEVa_TRINITY_DN4393_c0_g9_i1.p2
SiDEVa_TRINITY_DN4598_c0_g2_i1.p1
SiDEVa_TRINITY_DN4716_c0_g1_i1.p1
SiDEVa_TRINITY_DN4374_c1_g15_i2.p2
SiDEVa_TRINITY_DN4644_c0_g12_i1.p1
SiDEVa_TRINITY_DN4245_c0_g3_i3.p1
SiDEVa_TRINITY_DN4011_c0_g1_i1.p1
SiDEVa_TRINITY_DN3995_c1_g13_i1.p1
SiDEVa_TRINITY_DN4451_c0_g7_i1.p1
SiDEVa_TRINITY_DN4006_c1_g4_i3.p2
SiDEVa_TRINITY_DN4504_c0_g1_i7.p1
SiDEVa_TRINITY_DN4631_c0_g3_i11.p1
SiDEVa_TRINITY_DN4669_c0_g3_i3.p1
SiDEVa_TRINITY_DN3904_c1_g12_i2.p2
SiDEVa_TRINITY_DN4006_c1_g4_i7.p1
SiDEVa_TRINITY_DN4364_c0_g13_i4.p1
SiDEVa_TRINITY_DN4685_c0_g1_i3.p1
SiDEVa_TRINITY_DN4153_c1_g11_i1.p1
SiDEVa_TRINITY_DN4522_c0_g8_i2.p1
SiDEVa_TRINITY_DN4393_c0_g9_i2.p1
SiDEVa_TRINITY_DN3904_c1_g12_i2.p1
SiDEVa_TRINITY_DN4406_c0_g10_i4.p2
SiDEVa_TRINITY_DN3904_c1_g12_i2.p3
SiDEVa_TRINITY_DN4631_c0_g1_i1.p2
SiDEVa_TRINITY_DN4631_c0_g2_i1.p2
SiDEVa_TRINITY_DN4535_c0_g18_i1.p2
SiDEVa_TRINITY_DN4715_c2_g4_i2.p2
SiDEVa_TRINITY_DN4016_c1_g4_i1.p1
SiDEVa_TRINITY_DN4631_c0_g2_i8.p1
SiDEVa_TRINITY_DN4662_c0_g1_i13.p1
SiDEVa_TRINITY_DN4535_c0_g18_i1.p1
SiDEVa_TRINITY_DN4678_c1_g11_i3.p1
SiDEVa_TRINITY_DN3804_c0_g1_i4.p1
SiDEVa_TRINITY_DN4246_c0_g4_i3.p1
SiDEVa_TRINITY_DN4246_c0_g10_i1.p1
SiDEVa_TRINITY_DN4054_c0_g23_i1.p2
SiDEVa_TRINITY_DN4669_c0_g2_i2.p1
SiDEVa_TRINITY_DN4314_c0_g2_i3.p2
SiDEVa_TRINITY_DN4662_c0_g1_i15.p1
SiDEVa_TRINITY_DN3715_c0_g1_i2.p1
SiDEVa_TRINITY_DN4225_c0_g10_i1.p1
SiDEVa_TRINITY_DN4113_c0_g19_i2.p1
SiDEVa_TRINITY_DN4402_c1_g6_i2.p1
SiDEVa_TRINITY_DN4372_c0_g9_i3.p2
SiDEVa_TRINITY_DN3889_c0_g20_i1.p1
SiDEVa_TRINITY_DN4706_c2_g1_i2.p1
SiDEVa_TRINITY_DN4716_c0_g9_i2.p2
SiDEVa_TRINITY_DN3983_c0_g12_i1.p2
SiDEVa_TRINITY_DN4054_c0_g23_i1.p1
SiDEVa_TRINITY_DN4459_c0_g11_i1.p2
SiDEVa_TRINITY_DN4459_c0_g11_i1.p1
SiDEVa_TRINITY_DN4716_c0_g9_i2.p1
SiDEVa_TRINITY_DN4666_c0_g8_i4.p1
SiDEVa_TRINITY_DN4459_c0_g15_i1.p1
SiDEVa_TRINITY_DN3804_c0_g1_i4.p2
SiDEVa_TRINITY_DN4263_c1_g10_i1.p1
SiDEVa_TRINITY_DN4685_c0_g1_i3.p2
SiDEVa_TRINITY_DN4433_c1_g2_i2.p1
SiDEVa_TRINITY_DN4553_c0_g2_i3.p2
SiDEVa_TRINITY_DN4459_c0_g13_i1.p1
SiDEVa_TRINITY_DN4666_c0_g8_i1.p1
SiDEVa_TRINITY_DN4464_c0_g15_i1.p1
SiDEVa_TRINITY_DN4594_c1_g8_i2.p1
SiDEVa_TRINITY_DN4577_c0_g3_i2.p2
SiDEVa_TRINITY_DN4490_c0_g4_i4.p1
SiDEVa_TRINITY_DN4490_c0_g4_i4.p2
SiDEVa_TRINITY_DN3930_c0_g6_i3.p1
SiDEVa_TRINITY_DN3871_c1_g1_i1.p2
SiDEVa_TRINITY_DN4594_c1_g8_i2.p3
SiDEVa_TRINITY_DN4706_c2_g1_i2.p2
SiDEVa_TRINITY_DN3871_c1_g1_i1.p1
SiDEVa_TRINITY_DN4584_c1_g10_i1.p1
SiDEVa_TRINITY_DN3937_c0_g14_i1.p1
SiDEVa_TRINITY_DN4392_c1_g2_i3.p1
SiDEVa_TRINITY_DN4553_c0_g2_i2.p1
SiDEVa_TRINITY_DN4545_c0_g3_i1.p1
SiDEVa_TRINITY_DN4374_c1_g15_i1.p1
SiDEVa_TRINITY_DN3867_c0_g2_i1.p1
SiDEVa_TRINITY_DN4297_c0_g5_i2.p1
SiDEVa_TRINITY_DN3795_c0_g1_i1.p1
SiDEVa_TRINITY_DN4640_c0_g3_i1.p1
SiDEVa_TRINITY_DN4406_c0_g10_i5.p1
SiDEVa_TRINITY_DN4062_c0_g20_i1.p1
SiDEVa_TRINITY_DN4136_c1_g3_i2.p1
SiDEVa_TRINITY_DN3924_c1_g15_i1.p2
SiDEVa_TRINITY_DN4458_c0_g1_i2.p1
SiDEVa_TRINITY_DN4378_c0_g11_i2.p1
SiDEVa_TRINITY_DN4586_c0_g5_i4.p1
SiDEVa_TRINITY_DN3963_c0_g20_i1.p1
SiDEVa_TRINITY_DN4378_c0_g3_i4.p1
SiDEVa_TRINITY_DN3388_c0_g1_i2.p1
SiDEVa_TRINITY_DN3971_c0_g9_i3.p1
SiDEVa_TRINITY_DN3979_c0_g1_i5.p1
SiDEVa_TRINITY_DN3181_c0_g1_i1.p1
SiDEVa_TRINITY_DN4085_c0_g5_i2.p1
SiDEVa_TRINITY_DN4377_c0_g14_i1.p1
SiDEVa_TRINITY_DN4478_c1_g10_i3.p1
SiDEVa_TRINITY_DN4451_c0_g4_i4.p1
SiDEVa_TRINITY_DN4504_c0_g6_i2.p1
SiDEVa_TRINITY_DN4409_c0_g10_i1.p1
SiDEVa_TRINITY_DN3844_c0_g1_i1.p1
SiDEVa_TRINITY_DN3368_c0_g1_i1.p2
SiDEVa_TRINITY_DN4006_c1_g2_i2.p1
SiDEVa_TRINITY_DN4635_c3_g2_i4.p1
SiDEVa_TRINITY_DN3437_c0_g1_i2.p1
SiDEVa_TRINITY_DN4683_c0_g10_i1.p1
SiDEVa_TRINITY_DN4148_c0_g9_i2.p1
SiDEVa_TRINITY_DN3932_c1_g15_i1.p1
SiDEVa_TRINITY_DN4715_c2_g4_i2.p1
SiDEVa_TRINITY_DN4631_c0_g1_i2.p1
SiDEVa_TRINITY_DN4662_c0_g1_i4.p1
SiDEVa_TRINITY_DN4617_c0_g13_i1.p1
SiDEVa_TRINITY_DN4252_c0_g5_i2.p1
SiDEVa_TRINITY_DN4552_c0_g2_i1.p1
SiDEVa_TRINITY_DN4269_c0_g4_i2.p1
SiDEVa_TRINITY_DN4631_c0_g3_i8.p2
SiDEVa_TRINITY_DN4631_c0_g3_i1.p1
SiDEVa_TRINITY_DN4372_c0_g9_i3.p1
SiDEVa_TRINITY_DN4631_c0_g3_i2.p2
SiDEVa_TRINITY_DN3288_c0_g1_i1.p1
SiDEVa_TRINITY_DN4578_c1_g4_i2.p1
SiDEVa_TRINITY_DN4271_c1_g4_i2.p1
SiDEVa_TRINITY_DN3922_c0_g12_i3.p1
SiDEVa_TRINITY_DN4262_c0_g7_i6.p1
SiDEVa_TRINITY_DN4398_c0_g7_i1.p1
SiDEVa_TRINITY_DN4503_c0_g10_i2.p1
SiDEVa_TRINITY_DN4333_c2_g1_i1.p1
SiDEVa_TRINITY_DN4452_c0_g16_i1.p1
SiDEVa_TRINITY_DN4685_c0_g3_i1.p1
SiDEVa_TRINITY_DN4261_c0_g4_i1.p1
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SiDEVa_TRINITY_DN4229_c1_g3_i3.p1
SiDEVa_TRINITY_DN4463_c0_g9_i2.p1
SiDEVa_TRINITY_DN4342_c1_g13_i2.p1
SiDEVa_TRINITY_DN4330_c0_g14_i2.p1
SiDEVa_TRINITY_DN3861_c1_g20_i1.p1
SiDEVa_TRINITY_DN4000_c1_g1_i1.p1
SiDEVa_TRINITY_DN3699_c0_g1_i1.p1
SiDEVa_TRINITY_DN4169_c0_g18_i1.p1
SiDEVa_TRINITY_DN4309_c1_g3_i2.p1
SiDEVa_TRINITY_DN4172_c2_g4_i2.p1
SiDEVa_TRINITY_DN4672_c0_g11_i1.p1
SiDEVa_TRINITY_DN4598_c0_g3_i1.p1
SiDEVa_TRINITY_DN4336_c1_g13_i1.p1
SiDEVa_TRINITY_DN4301_c1_g2_i4.p1
SiDEVa_TRINITY_DN4599_c0_g3_i3.p1
SiDEVa_TRINITY_DN4394_c0_g24_i1.p1
SiDEVa_TRINITY_DN4421_c0_g5_i2.p1
SiDEVa_TRINITY_DN3976_c1_g2_i3.p1
SiDEVa_TRINITY_DN4174_c0_g7_i4.p1
SiDEVa_TRINITY_DN4620_c0_g10_i1.p1
SiDEVa_TRINITY_DN3951_c0_g1_i1.p1
SiDEVa_TRINITY_DN4403_c0_g1_i3.p1
SiDEVa_TRINITY_DN4164_c0_g14_i1.p1
SiDEVa_TRINITY_DN4723_c1_g1_i3.p2
SiDEVa_TRINITY_DN4539_c0_g5_i1.p1
SiDEVa_TRINITY_DN3377_c0_g1_i3.p1
SiDEVa_TRINITY_DN4308_c0_g1_i2.p3
SiDEVa_TRINITY_DN4723_c1_g1_i3.p1
SiDEVa_TRINITY_DN4304_c0_g19_i2.p1
SiDEVa_TRINITY_DN4089_c0_g2_i2.p1
SiDEVa_TRINITY_DN3135_c0_g1_i1.p1
SiDEVa_TRINITY_DN4234_c0_g2_i1.p1
SiDEVa_TRINITY_DN1739_c0_g1_i1.p1
SiDEVa_TRINITY_DN4270_c0_g7_i2.p1
SiDEVa_TRINITY_DN1587_c0_g1_i1.p1
SiDEVa_TRINITY_DN3910_c0_g1_i1.p1
SiDEVa_TRINITY_DN4391_c1_g11_i1.p1
SiDEVa_TRINITY_DN4243_c0_g8_i6.p1
SiDEVa_TRINITY_DN4280_c1_g14_i1.p1
SiDEVa_TRINITY_DN3876_c3_g1_i3.p1
SiDEVa_TRINITY_DN4459_c0_g1_i2.p1
SiDEVa_TRINITY_DN4735_c2_g26_i1.p1
SiDEVa_TRINITY_DN4100_c0_g18_i1.p1
SiDEVa_TRINITY_DN4111_c0_g13_i1.p1
SiDEVa_TRINITY_DN3370_c0_g1_i1.p1
SiDEVa_TRINITY_DN4340_c1_g6_i1.p1
SiDEVa_TRINITY_DN3868_c1_g9_i1.p1
SiDEVa_TRINITY_DN4340_c1_g9_i2.p1
SiDEVa_TRINITY_DN4735_c2_g30_i1.p1
SiDEVa_TRINITY_DN4538_c0_g6_i1.p1
SiDEVa_TRINITY_DN4442_c1_g9_i4.p1
SiDEVa_TRINITY_DN3732_c0_g1_i2.p1
SiDEVa_TRINITY_DN2652_c0_g1_i1.p1
SiDEVa_TRINITY_DN3965_c1_g8_i1.p1
SiDEVa_TRINITY_DN4384_c1_g4_i4.p1
SiDEVa_TRINITY_DN4524_c0_g3_i3.p1
SiDEVa_TRINITY_DN3879_c0_g2_i1.p1
SiDEVa_TRINITY_DN4656_c1_g21_i1.p1
SiDEVa_TRINITY_DN3986_c0_g14_i1.p1
SiDEVa_TRINITY_DN4699_c1_g13_i3.p1
SiDEVa_TRINITY_DN4270_c0_g4_i2.p1
SiDEVa_TRINITY_DN4587_c0_g3_i2.p1
SiDEVa_TRINITY_DN4273_c2_g3_i2.p1
SiDEVa_TRINITY_DN4688_c1_g8_i1.p1
SiDEVa_TRINITY_DN4236_c0_g6_i1.p1
SiDEVa_TRINITY_DN4463_c0_g12_i1.p1
SiDEVa_TRINITY_DN3926_c2_g13_i2.p1
SiDEVa_TRINITY_DN4388_c0_g7_i1.p1
SiDEVa_TRINITY_DN4258_c0_g4_i4.p1
SiDEVa_TRINITY_DN4178_c0_g3_i3.p1
SiDEVa_TRINITY_DN4339_c0_g5_i4.p1
SiDEVa_TRINITY_DN4151_c0_g2_i4.p1
SiDEVa_TRINITY_DN4254_c0_g4_i2.p1
SiDEVa_TRINITY_DN4615_c1_g4_i1.p1
SiDEVa_TRINITY_DN3933_c1_g2_i4.p1
SiDEVa_TRINITY_DN4452_c0_g17_i2.p1
SiDEVa_TRINITY_DN4412_c0_g10_i2.p1
SiDEVa_TRINITY_DN3996_c1_g11_i2.p1
SiDEVa_TRINITY_DN4015_c0_g13_i1.p1
SiDEVa_TRINITY_DN4683_c0_g6_i7.p1
SiDEVa_TRINITY_DN4397_c0_g11_i2.p1
SiDEVa_TRINITY_DN4552_c0_g7_i1.p1
SiDEVa_TRINITY_DN4077_c1_g5_i4.p1
SiDEVa_TRINITY_DN4360_c0_g1_i1.p1
SiDEVa_TRINITY_DN4134_c0_g9_i1.p1
SiDEVa_TRINITY_DN3958_c0_g8_i3.p1
SiDEVa_TRINITY_DN4568_c0_g4_i1.p2
SiDEVa_TRINITY_DN3966_c1_g16_i1.p1
SiDEVa_TRINITY_DN3865_c0_g1_i1.p1
SiDEVa_TRINITY_DN4424_c1_g10_i2.p1
SiDEVa_TRINITY_DN4404_c0_g5_i2.p1
SiDEVa_TRINITY_DN4351_c1_g18_i1.p1
SiDEVa_TRINITY_DN3276_c0_g1_i1.p1
SiDEVa_TRINITY_DN4568_c0_g4_i1.p1
SiDEVa_TRINITY_DN4361_c0_g6_i6.p2
SiDEVa_TRINITY_DN4291_c0_g33_i1.p1
SiDEVa_TRINITY_DN3945_c0_g6_i1.p1
SiDEVa_TRINITY_DN3923_c0_g14_i2.p1
SiDEVa_TRINITY_DN4712_c0_g1_i15.p1
SiDEVa_TRINITY_DN4332_c0_g12_i1.p1
SiDEVa_TRINITY_DN1675_c0_g1_i2.p1
SiDEVa_TRINITY_DN4375_c2_g3_i3.p1
SiDEVa_TRINITY_DN4252_c0_g3_i1.p1
SiDEVa_TRINITY_DN4376_c0_g14_i2.p1
SiDEVa_TRINITY_DN4274_c0_g3_i2.p1
SiDEVa_TRINITY_DN3864_c0_g11_i2.p1
SiDEVa_TRINITY_DN3484_c0_g1_i2.p1
SiDEVa_TRINITY_DN4559_c0_g7_i2.p1
SiDEVa_TRINITY_DN4189_c0_g15_i1.p1
SiDEVa_TRINITY_DN4650_c0_g4_i1.p1
SiDEVa_TRINITY_DN3981_c0_g10_i3.p1
SiDEVa_TRINITY_DN4085_c0_g8_i1.p1
SiDEVa_TRINITY_DN3970_c1_g1_i1.p1
SiDEVa_TRINITY_DN2680_c0_g1_i1.p1
SiDEVa_TRINITY_DN4151_c0_g3_i1.p1
SiDEVa_TRINITY_DN1236_c0_g1_i1.p1
SiDEVa_TRINITY_DN4185_c0_g3_i1.p2
SiDEVa_TRINITY_DN4115_c0_g13_i1.p1
SiDEVa_TRINITY_DN4345_c0_g6_i1.p1
SiDEVa_TRINITY_DN4101_c0_g16_i1.p1
SiDEVa_TRINITY_DN4082_c0_g12_i1.p1
SiDEVa_TRINITY_DN4363_c1_g1_i1.p1
SiDEVa_TRINITY_DN4234_c0_g1_i1.p1
SiDEVa_TRINITY_DN4542_c1_g18_i2.p2
SiDEVa_TRINITY_DN4290_c0_g1_i2.p1
SiDEVa_TRINITY_DN4529_c1_g3_i6.p1
SiDEVa_TRINITY_DN4105_c0_g20_i1.p1
SiDEVa_TRINITY_DN4447_c0_g12_i1.p1
SiDEVa_TRINITY_DN4552_c0_g6_i1.p1
SiDEVa_TRINITY_DN4229_c1_g3_i21.p1
SiDEVa_TRINITY_DN4056_c1_g5_i4.p1
SiDEVa_TRINITY_DN4014_c0_g13_i1.p1
SiDEVa_TRINITY_DN3940_c0_g10_i1.p1
SiDEVa_TRINITY_DN4654_c0_g5_i6.p1
SiDEVa_TRINITY_DN4688_c1_g4_i1.p1
SiDEVa_TRINITY_DN4603_c0_g12_i1.p1
SiDEVa_TRINITY_DN3814_c0_g2_i2.p1
SiDEVa_TRINITY_DN3836_c0_g1_i2.p1
SiDEVa_TRINITY_DN4070_c1_g15_i1.p1
SiDEVa_TRINITY_DN3396_c0_g1_i1.p1
SiDEVa_TRINITY_DN3917_c0_g15_i1.p1
SiDEVa_TRINITY_DN4451_c0_g2_i2.p1
SiDEVa_TRINITY_DN4620_c0_g2_i3.p1
SiDEVa_TRINITY_DN4671_c0_g1_i1.p1
SiDEVa_TRINITY_DN4594_c1_g10_i2.p1
SiDEVa_TRINITY_DN4699_c1_g12_i1.p1
SiDEVa_TRINITY_DN4285_c0_g5_i1.p1
SiDEVa_TRINITY_DN4306_c0_g5_i2.p1
SiDEVa_TRINITY_DN4419_c0_g7_i5.p1
SiDEVa_TRINITY_DN4162_c0_g2_i2.p1
SiDEVa_TRINITY_DN4057_c0_g1_i2.p1
SiDEVa_TRINITY_DN4709_c0_g16_i1.p1
SiDEVa_TRINITY_DN4048_c0_g2_i4.p2
SiDEVa_TRINITY_DN4048_c0_g2_i4.p1
SiDEVa_TRINITY_DN4683_c0_g5_i2.p5
SiDEVa_TRINITY_DN4406_c0_g21_i1.p1
SiDEVa_TRINITY_DN4020_c1_g14_i2.p1
SiDEVa_TRINITY_DN4387_c0_g1_i2.p1
SiDEVa_TRINITY_DN4205_c0_g1_i1.p1
SiDEVa_TRINITY_DN4284_c0_g13_i1.p1
SiDEVa_TRINITY_DN4217_c0_g1_i1.p1
SiDEVa_TRINITY_DN4284_c0_g7_i2.p1
SiDEVa_TRINITY_DN2967_c0_g1_i1.p1
SiDEVa_TRINITY_DN3912_c0_g4_i5.p2
SiDEVa_TRINITY_DN4049_c0_g19_i1.p3
SiDEVa_TRINITY_DN3820_c0_g1_i1.p1
SiDEVa_TRINITY_DN4359_c0_g7_i1.p1
SiDEVa_TRINITY_DN4351_c1_g17_i1.p1
SiDEVa_TRINITY_DN4667_c0_g5_i1.p1
SiDEVa_TRINITY_DN3968_c0_g6_i3.p1
SiDEVa_TRINITY_DN4240_c0_g15_i2.p1
SiDEVa_TRINITY_DN3898_c0_g14_i2.p1
SiDEVa_TRINITY_DN3881_c0_g9_i2.p1
SiDEVa_TRINITY_DN3792_c0_g1_i1.p1
SiDEVa_TRINITY_DN4248_c0_g1_i7.p2
SiDEVa_TRINITY_DN4171_c0_g11_i3.p1
SiDEVa_TRINITY_DN4596_c0_g15_i1.p1
SiDEVa_TRINITY_DN4172_c2_g10_i3.p1
SiDEVa_TRINITY_DN3850_c0_g3_i2.p1
SiDEVa_TRINITY_DN4518_c1_g4_i1.p1
SiDEVa_TRINITY_DN4285_c0_g4_i1.p1
SiDEVa_TRINITY_DN4661_c2_g3_i2.p1
SiDEVa_TRINITY_DN4112_c0_g4_i4.p1
SiDEVa_TRINITY_DN4372_c0_g10_i1.p1
SiDEVa_TRINITY_DN4134_c0_g4_i1.p1
SiDEVa_TRINITY_DN745_c0_g1_i1.p1
SiDEVa_TRINITY_DN3878_c0_g1_i2.p1
SiDEVa_TRINITY_DN4623_c0_g5_i4.p1
SiDEVa_TRINITY_DN4414_c0_g7_i2.p1
SiDEVa_TRINITY_DN4016_c1_g8_i1.p1
SiDEVa_TRINITY_DN4646_c0_g8_i1.p1
SiDEVa_TRINITY_DN4416_c0_g12_i3.p1
SiDEVa_TRINITY_DN4401_c0_g2_i2.p1
SiDEVa_TRINITY_DN4347_c0_g5_i2.p1
SiDEVa_TRINITY_DN4626_c0_g11_i3.p1
SiDEVa_TRINITY_DN3991_c0_g11_i2.p1
SiDEVa_TRINITY_DN4623_c0_g22_i2.p1
SiDEVa_TRINITY_DN4279_c0_g14_i1.p1
SiDEVa_TRINITY_DN4338_c1_g22_i1.p1
SiDEVa_TRINITY_DN4684_c0_g6_i2.p1
SiDEVa_TRINITY_DN4526_c0_g9_i1.p1
SiDEVa_TRINITY_DN4463_c0_g3_i5.p1
SiDEVa_TRINITY_DN3456_c0_g1_i2.p1
SiDEVa_TRINITY_DN4563_c0_g13_i1.p1
SiDEVa_TRINITY_DN4448_c0_g12_i4.p1
SiDEVa_TRINITY_DN4665_c0_g8_i1.p1
SiDEVa_TRINITY_DN4089_c0_g8_i2.p2
SiDEVa_TRINITY_DN4248_c0_g1_i1.p1
SiDEVa_TRINITY_DN4215_c1_g13_i7.p2
SiDEVa_TRINITY_DN4482_c1_g9_i1.p1
SiDEVa_TRINITY_DN4125_c1_g4_i3.p2
SiDEVa_TRINITY_DN4330_c0_g9_i3.p1
SiDEVa_TRINITY_DN4164_c0_g6_i1.p1
SiDEVa_TRINITY_DN4591_c1_g10_i1.p3
SiDEVa_TRINITY_DN4475_c1_g7_i3.p2
SiDEVa_TRINITY_DN4112_c0_g2_i2.p1
SiDEVa_TRINITY_DN4324_c0_g1_i1.p1
SiDEVa_TRINITY_DN4147_c0_g3_i1.p1
SiDEVa_TRINITY_DN4083_c0_g2_i3.p1
SiDEVa_TRINITY_DN4729_c1_g20_i1.p1
SiDEVa_TRINITY_DN4240_c0_g1_i5.p1
SiDEVa_TRINITY_DN4399_c1_g4_i1.p1
SiDEVa_TRINITY_DN4640_c0_g7_i1.p1
SiDEVa_TRINITY_DN3741_c0_g1_i3.p1
SiDEVa_TRINITY_DN4146_c0_g1_i1.p1
SiDEVa_TRINITY_DN3568_c0_g2_i2.p1
SiDEVa_TRINITY_DN4567_c0_g5_i1.p1
SiDEVa_TRINITY_DN3926_c1_g1_i1.p1
SiDEVa_TRINITY_DN4704_c0_g10_i2.p1
SiDEVa_TRINITY_DN4159_c0_g22_i1.p1
SiDEVa_TRINITY_DN4163_c0_g28_i1.p1
SiDEVa_TRINITY_DN3890_c0_g1_i2.p1
SiDEVa_TRINITY_DN4177_c0_g13_i2.p1
SiDEVa_TRINITY_DN3907_c0_g21_i1.p1
SiDEVa_TRINITY_DN4651_c0_g1_i2.p1
SiDEVa_TRINITY_DN3926_c2_g2_i4.p1
SiDEVa_TRINITY_DN2683_c0_g1_i1.p1
SiDEVa_TRINITY_DN4608_c0_g9_i1.p1
SiDEVa_TRINITY_DN4391_c1_g19_i1.p1
SiDEVa_TRINITY_DN4274_c0_g7_i1.p1
SiDEVa_TRINITY_DN4351_c1_g12_i1.p1
SiDEVa_TRINITY_DN3897_c2_g5_i3.p1
SiDEVa_TRINITY_DN4239_c0_g5_i2.p1
SiDEVa_TRINITY_DN4294_c0_g15_i1.p1
SiDEVa_TRINITY_DN3740_c0_g1_i2.p1
SiDEVa_TRINITY_DN4169_c0_g1_i1.p1
SiDEVa_TRINITY_DN4089_c0_g7_i1.p1
SiDEVa_TRINITY_DN4102_c2_g7_i1.p1
SiDEVa_TRINITY_DN4093_c1_g8_i1.p1
SiDEVa_TRINITY_DN4596_c0_g2_i2.p1
SiDEVa_TRINITY_DN3813_c0_g1_i2.p1
SiDEVa_TRINITY_DN3405_c0_g1_i2.p1
SiDEVa_TRINITY_DN4286_c0_g5_i3.p1
SiDEVa_TRINITY_DN4556_c0_g8_i2.p1
SiDEVa_TRINITY_DN3974_c3_g4_i1.p1
SiDEVa_TRINITY_DN4250_c0_g9_i1.p1
SiDEVa_TRINITY_DN3995_c1_g4_i1.p1
SiDEVa_TRINITY_DN4149_c0_g4_i1.p1
SiDEVa_TRINITY_DN3768_c0_g1_i2.p1
SiDEVa_TRINITY_DN4127_c0_g3_i2.p1
SiDEVa_TRINITY_DN4130_c0_g6_i2.p1
SiDEVa_TRINITY_DN3839_c0_g1_i1.p1
SiDEVa_TRINITY_DN4374_c1_g3_i1.p1
SiDEVa_TRINITY_DN4364_c0_g13_i2.p1
SiDEVa_TRINITY_DN4045_c0_g10_i1.p1
SiDEVa_TRINITY_DN4487_c2_g6_i3.p1
SiDEVa_TRINITY_DN3826_c0_g1_i1.p1
SiDEVa_TRINITY_DN4019_c0_g9_i1.p1
SiDEVa_TRINITY_DN3908_c1_g3_i3.p1
SiDEVa_TRINITY_DN3978_c0_g8_i2.p1
SiDEVa_TRINITY_DN4228_c0_g4_i2.p1
SiDEVa_TRINITY_DN4615_c0_g12_i1.p1
SiDEVa_TRINITY_DN3772_c0_g1_i1.p1
SiDEVa_TRINITY_DN4139_c0_g11_i1.p1
SiDEVa_TRINITY_DN4327_c0_g3_i2.p1
SiDEVa_TRINITY_DN3998_c0_g5_i2.p1
SiDEVa_TRINITY_DN4550_c0_g12_i1.p1
SiDEVa_TRINITY_DN3238_c0_g1_i2.p1
SiDEVa_TRINITY_DN3963_c0_g16_i1.p1
SiDEVa_TRINITY_DN4162_c0_g11_i1.p1
SiDEVa_TRINITY_DN4157_c0_g7_i1.p1
SiDEVa_TRINITY_DN3780_c0_g1_i2.p1
SiDEVa_TRINITY_DN4144_c0_g11_i2.p1
SiDEVa_TRINITY_DN4541_c2_g7_i1.p1
SiDEVa_TRINITY_DN4548_c1_g6_i2.p1
SiDEVa_TRINITY_DN4051_c0_g18_i1.p1
SiDEVa_TRINITY_DN4091_c0_g12_i2.p1
SiDEVa_TRINITY_DN4531_c2_g1_i3.p1
SiDEVa_TRINITY_DN4036_c0_g12_i2.p1
SiDEVa_TRINITY_DN3709_c1_g1_i1.p1
SiDEVa_TRINITY_DN4567_c0_g11_i1.p1
SiDEVa_TRINITY_DN4037_c1_g20_i1.p1
SiDEVa_TRINITY_DN3895_c1_g8_i1.p1
SiDEVa_TRINITY_DN3662_c0_g2_i1.p1
SiDEVa_TRINITY_DN4571_c0_g5_i1.p1
SiDEVa_TRINITY_DN4221_c2_g20_i2.p1
SiDEVa_TRINITY_DN4339_c0_g11_i3.p1
SiDEVa_TRINITY_DN4009_c0_g4_i5.p1
SiDEVa_TRINITY_DN4650_c0_g1_i1.p1
SiDEVa_TRINITY_DN4053_c1_g1_i8.p1
SiDEVa_TRINITY_DN4485_c0_g5_i1.p1
SiDEVa_TRINITY_DN4038_c0_g2_i2.p1
SiDEVa_TRINITY_DN4436_c0_g2_i5.p1
SiDEVa_TRINITY_DN4393_c0_g11_i1.p1
SiDEVa_TRINITY_DN4176_c0_g17_i1.p1
SiDEVa_TRINITY_DN4078_c0_g4_i3.p1
SiDEVa_TRINITY_DN3912_c0_g2_i1.p1
SiDEVa_TRINITY_DN4325_c0_g3_i1.p1
SiDEVa_TRINITY_DN4336_c1_g2_i1.p1
SiDEVa_TRINITY_DN4289_c5_g1_i2.p1
SiDEVa_TRINITY_DN4439_c0_g7_i1.p1
SiDEVa_TRINITY_DN3702_c0_g1_i1.p1

Si9−RS

sporocarp
Si8−RS

rising sporocarp

Si5−PSTC

Pfun−v3

RS
PSC

Pfun−v1

Value
Variosea

Flabellinia

Color Keyrising sporocarp
−5

0

5

Value

RS
PSC
TC

Discosea*

rising sporocarp

Si4−PS*TC

Si6−PS

63

RS

PSC

Pfun−l3*69

Eumycetozoa

Si2−TC

60

98

Va ue

Pfun−l1

99

Co o Key

sporocarp

Centramoebia
rising sporocarp
sporocarp

c12327_g1
c7290_g1c17328_g1
c12108_g1
c14315_g1
c12095_g1
c14874_g1
c14723_g1
c13987_g1
c12032_g1
c14815_g1
c14241_g1
c13259_g1
c13928_g1
c11993_g1
c14629_g1
c14069_g1
c13180_g1
c12639_g1
c14868_g1
c12291_g1
c9443_g1
c11822_g1
c12139_g1
c12762_g1
c10113_g1
c8608_g1
c10644_g1
c8610_g1c11471_g1
c12859_g1
c8347_g1
c12416_g2
c12164_g1
c11440_g1
c11111_g1
c8353_g1c10828_g1
c14750_g1
c11074_g1
c9563_g1
c8081_g1
c14923_g1
c11939_g1
c14728_g1
c14302_g1
c14722_g1
c7982_g1
c14946_g6
c14754_g1
c14780_g5
c141_g1
c6860_g1
c11158_g1
c11555_g1
c9845_g1
c15868_g1
c18613_g1
c7824_g1
c17159_g1
c10900_g2
c7337_g1
c9469_g1c9590_g1
c2810_g1
c8477_g1c13226_g1
c1582_g2
c8552_g1
c7459_g1
c9065_g1c17458_g1
c5418_g1
c1190_g1
c7897_g1
c13038_g1
c14205_g1
c15124_g1
c12145_g1
c18280_g1
c8572_g1
c14132_g1
c130_g1
c14159_g5
c8987_g1
c6387_g1
c3191_g1
c6610_g1
c8321_g1
c6728_g1
c6156_g1
c8571_g4
c8571_g3
c4386_g1
c15298_g1
c6177_g1
c2840_g1c18540_g1c18669_g1
c8280_g1
c5306_g1
c5251_g1
c12606_g1
c9102_g1
c12718_g1
c12997_g2
c12183_g2
c2863_g1
c14431_g2
c8023_g1c14666_g1
c9761_g1
c10773_g1
c7897_g2
c3853_g1
c798_g1
c16497_g1
c8356_g1
c966_g1
c11543_g2
c4456_g1c1092_g1c2842_g1
c10118_g1
c9788_g1
c6601_g1
c772_g1c17993_g1
c3675_g1
c13824_g2
c14035_g1
c5403_g1
c10769_g1
c12364_g1
c12312_g1
c13223_g1
c8631_g1c12972_g1
c8393_g2c12950_g1
c4465_g1
c10688_g1
c13626_g1
c13943_g1
c13569_g1
c14247_g1
c14859_g1
c14442_g1
c14585_g1
c14481_g1
c13076_g1
c13692_g1
c5291_g1
c5415_g1c14534_g1
c13516_g1
c14720_g1
c8656_g1
c11587_g1
c13708_g1
c6039_g1c12190_g1
c11957_g1
c9308_g1
c12001_g1
c9585_g1
c470_g1
c7182_g1
c14022_g1
c10483_g1
c14495_g1
c14764_g1
c7837_g1c18535_g1
c7234_g1c14457_g2
c14638_g1
c11478_g1
c9113_g1
c14129_g1
c14345_g1
c14840_g1
c14507_g1
c14817_g1
c6183_g1
c9937_g1
c11636_g1
c13777_g1
c12251_g1
c12918_g1
c13832_g1
c7749_g1
c9954_g1c9489_g1
c12989_g2
c13495_g1
c9263_g1
c10534_g1
c9881_g1
c13307_g2
c14586_g1
c12643_g1
c7964_g1
c12261_g1
c14457_g1
c13977_g1
c9823_g1
c12989_g1
c14818_g4
c13283_g2
c13278_g1
c14183_g3
c14888_g1
c11332_g1
c12386_g1
c12592_g1
c12457_g1
c13373_g1
c13819_g1
c12630_g1
c10357_g1
c12460_g1
c6831_g1
c14137_g1
c11273_g1
c12540_g1
c14016_g2
c11835_g1
c11102_g1
c14892_g1
c9232_g1
c14351_g1
c14421_g1
c13988_g1
c13859_g1
c10914_g1
c12699_g1
c12200_g1
c11677_g1
c12389_g1
c10842_g1
c14434_g3
c12511_g1
c12317_g1
c11334_g1
c14948_g1
c12110_g1
c10486_g1
c12908_g2

Amoebozoa*

Archamoebae

Evosea64

Cutosea

Si1−TC71

ElaridaPfun−l2

99Comparative
Developmental
Transcriptomics

Echinamoebida

Si3−TC97

Micriamoeba sp.
Echinamoeba exudans
Vermamoeba vermiformis
Vermamoeba sp. [CCAP1503-5]
Rhizamoeba saxonica
Flabellula citata
Cryptodifflugia operculata
Difflugia bryophila
Arcella intermedia
Nolandella sp.
Copromyxa protea
Amoeba proteus
Sapocribrum chincoteaguense
Squamamoeba japonica
cutosean isolate [ATCC PRA-29]
Rhizomastix elongata
Pelomyxa sp.
Mastigella eilhardi
Mastigamoeba balamuthi
Mastigamoeba abducta
Entamoeba histolytica
Polysphondylium pallidum
Dictyostelium discoideum
Physarum polycephalum
Echinosteliopsis oligospora
Echinostelium minutum
Echinostelium bisporum
Protosporangium articulatum
trophozoite
pre-sporocarp
Clastostelium recurvatum
Ceratiomyxa fruticulosa
Flamella fluviatilis
Flamella aegyptia
Phalansterium solitarium
Schizoplasmodiopsis vulgaris
Tychosporium acutostipes
pre-sporocarp
Schizoplasmodiopsis pseudoendospora trophozoite
Cavostelium apophysatum
Protostelium nocturnum
Filamoeba nolandi
Soliformovum irregularis
Grellamoeba robusta
Nematostelium gracile
Ceratiomyxella tahitiensis
Acramoeba dendroida
Stenamoeba stenopodia
Stenamoeba limacina
Thecamoeba quadrilineata
trophozoite
pre-sporocarp
Thecamoeba sp.
Sappinia pedata
Thecamoebida isolate [RHP1-1]
Mayorella cantabrigiensis
Paradermamoeba levis
Dermamoeba algensis
Vermistella antarctica
Stygamoeba regulata
Vexillifera minutissima
Vexillifera bacillipedes
0.85/* 96
Vexillifera sp. [MMETSP0173]
Paramoeba atlantica
Paramoeba aestuarina
Cunea sp. [MMETSP0417]
Cunea sp. [JDS-Ruffled]
Vannella sp. [MMETSP0168]
Vannella robusta
Vannella schaefferi
trophozoite
pre-sporocarp
Vannella fimicola
Ripella sp.
Lingulamoeba sp.
Clydonella sp.
Ovalopodium desertum
Parvamoeba rugata
Cochliopodium minus
Pellita catalonica
Gocevia fonbrunei
Gocevia fonbrunei [Tekle et al. 2016]
Endostelium zonatum [PRA-191]
pre-sporocarp
Endostelium zonatum [LINKS] trophozoite
Dracoamoeba joomungandrii
Protacanthamoeba bohemica
Luapelamoeba arachisporum
Luapelamoeba hula
Acanthamoeba castellanii
Acanthamoeba pyriformis

Corycida

Tubulinea

Diplochlamys sp.
Amphizonella sp.

Trichosphaerium sp.

Synchronization of Sporocarpic Amoebae
erutLiquid
luC )dilCultureos( ragA

Agarerutl(solid)
uC diuCultureqiL

Vannella fimicola

Felicity Kleitz-Singleton

laDevelopmental
tnempoleveD
scTranscriptomics
imotpircsnarT
G

mRNA

ANRm

G

Vannellafimicola

trophozoite

25.5hr time lapse
1 sec = 15minpre-sporocarp

rising sporocarp

sporocarp

Cutosea

Archamoebae

64

2

OUTGROUP TAXA

*Orthogroups Represented in OrthoMCL v5

3Time and computationally intensive task
−50Color Key

samples vs. features
diffExpr.P0.001_C2.matrix.log2.centered

5

−5

0

RS

RS

PSC

trophozoite

pre-sporocarp

rising sporocarp

5

Value

PSC

TC

TC
TR5788|c1_g1
TR5788|c1_g2
TR208|c1_g1
TR5788|c3_g7
TR5064|c0_g1
TR1897|c0_g1
TR4917|c0_g2
TR2591|c0_g1
TR5748|c2_g1
TR1897|c0_g2
TR2236|c0_g1
TR5057|c0_g1
TR2543|c0_g1
TR8800|c0_g1
TR7457|c0_g2
TR4917|c0_g1
TR5822|c0_g1
TR5788|c3_g8
TR5081|c0_g1
TR8750|c6096_g1
TR2274|c1_g1
TR9387|c0_g1
TR6095|c1_g1
TR7527|c0_g1
TR5137|c0_g1
TR2127|c0_g1
TR7391|c0_g2
TR4407|c0_g1
TR4601|c0_g1
TR889|c0_g1
TR9340|c0_g1
TR6026|c0_g2
TR6271|c0_g1
TR113|c1_g1
TR110|c1_g1
TR7224|c0_g1
TR1932|c0_g1
TR7169|c1_g1
TR170|c0_g3
TR3417|c0_g2
TR5437|c0_g1
TR4932|c0_g3
TR8933|c0_g1
TR9168|c0_g1
TR150|c0_g1
TR8015|c0_g1
TR8015|c0_g2
TR7634|c0_g1
TR170|c0_g2
TR4895|c0_g2
TR8750|c6195_g1
TR5788|c2_g1
TR5788|c3_g5
TR4968|c0_g1
TR663|c0_g1
TR2801|c1_g1
TR5711|c7_g2
TR9359|c0_g1
TR4895|c0_g1
TR8750|c4327_g1
TR2653|c0_g1
TR996|c0_g1
TR6225|c0_g1
TR1951|c0_g2
TR8750|c602_g1
TR8750|c6154_g1
TR2598|c0_g15
TR6650|c0_g1
TR1951|c0_g1
TR617|c0_g1
TR7550|c0_g2
TR7457|c0_g1
TR6295|c0_g1
TR5444|c0_g1
TR7193|c0_g2
TR4659|c0_g2
TR5702|c1_g1
TR4659|c0_g1
TR2557|c0_g1
TR4901|c0_g2
TR8750|c6140_g1
TR8750|c6284_g1
TR143|c1_g1
TR8750|c6113_g1
TR8750|c6103_g1
TR7451|c0_g1
TR4236|c0_g2
TR8750|c5609_g1
TR4980|c3_g4
TR5711|c3_g1
TR2515|c0_g1
TR9162|c0_g2
TR8750|c6324_g2
TR2789|c0_g2
TR5102|c0_g1
TR6666|c0_g1
TR4556|c0_g1
TR4622|c2_g2
TR152|c0_g1
TR4433|c0_g2
TR5804|c0_g1
TR5837|c0_g14
TR8767|c0_g2
TR8875|c0_g2
TR9236|c0_g1
TR7474|c0_g2
TR5022|c0_g4
TR9317|c1_g1
TR143|c1_g3
TR143|c0_g1
TR6065|c0_g1
TR9317|c1_g2
TR329|c0_g1
TR5829|c0_g1
TR2848|c0_g1
TR2701|c1_g1
TR2789|c0_g1
TR2665|c0_g1
TR5368|c0_g1
TR4562|c1_g2
TR6661|c2_g1
TR2832|c0_g1
TR7735|c0_g1
TR4901|c0_g1
TR6661|c0_g1
TR8750|c5375_g1
TR143|c1_g2
TR4967|c6_g1
TR9368|c0_g1
TR2427|c0_g1
TR4433|c0_g1
TR7428|c2_g1
TR2516|c0_g1
TR992|c0_g1
TR4821|c0_g2
TR2980|c0_g1
TR8692|c0_g1
TR169|c1_g2
TR5678|c0_g1
TR8620|c0_g1
TR2308|c0_g9
TR9162|c0_g1
TR6091|c1_g1
TR5711|c7_g1
TR2587|c0_g2
TR4616|c0_g1
TR5711|c7_g4
TR8993|c0_g1
TR856|c1_g1
TR6208|c1_g1
TR856|c1_g2
TR5711|c6_g1
TR3043|c0_g1
TR2587|c0_g3
TR1251|c0_g1
TR4925|c0_g3
TR8754|c0_g1
TR3737|c0_g2
TR2587|c0_g1
TR7451|c0_g2
TR650|c0_g1
TR5893|c0_g1
TR2835|c0_g1
TR6087|c0_g1
TR2572|c1_g1
TR8750|c6126_g1
TR4266|c0_g2
TR5047|c0_g2
TR4713|c0_g1
TR8829|c0_g1
TR430|c0_g1
TR5787|c0_g1
TR3544|c0_g1
TR1893|c0_g1
TR2365|c0_g1
TR5670|c0_g1
TR9357|c0_g1
TR2251|c0_g1
TR4580|c1_g2
TR732|c0_g1
TR6423|c0_g1
TR4399|c0_g1
TR1891|c0_g1
TR4362|c0_g1
TR4612|c1_g1
TR1904|c0_g1
TR8843|c0_g1
TR7221|c0_g1
TR103|c0_g3
TR3719|c0_g1
TR3057|c0_g1
TR4567|c0_g2
TR4770|c0_g1
TR3761|c0_g1
TR5780|c1_g1
TR4932|c0_g1
TR4250|c0_g1
TR4327|c0_g1
TR3584|c0_g1
TR1215|c1_g1
TR4541|c1_g1
TR141|c1_g1
TR2857|c0_g1
TR1249|c0_g2
TR7389|c0_g2
TR3845|c0_g1
TR172|c0_g1
TR6896|c0_g2
TR6103|c1_g1
TR2248|c0_g1
TR868|c0_g1
TR5739|c1_g14
TR1921|c0_g1
TR6152|c0_g1
TR8071|c0_g1
TR3552|c0_g1
TR882|c0_g1
TR4610|c0_g1
TR2564|c0_g1
TR3590|c1_g1
TR87|c0_g1
TR3152|c0_g1
TR3194|c0_g1
TR9167|c0_g3
TR1657|c0_g1
TR1936|c0_g1
TR6143|c0_g1
TR4105|c0_g1
TR9186|c0_g1
TR1746|c0_g1
TR4834|c0_g1
TR3804|c0_g1
TR6364|c0_g1
TR3614|c0_g1
TR8926|c0_g1
TR3305|c0_g1
TR4904|c0_g1
TR6137|c0_g1
TR7337|c0_g1
TR5756|c1_g1
TR9299|c0_g1
TR9012|c0_g1
TR977|c0_g1
TR3039|c0_g1
TR960|c1_g1
TR3659|c0_g1
TR3318|c0_g1
TR4218|c0_g1
TR6926|c0_g1
TR3292|c0_g1
TR6350|c0_g1
TR7773|c0_g1
TR1313|c0_g1
TR5634|c0_g1
TR8673|c0_g1
TR2612|c0_g1
TR764|c0_g1
TR9160|c0_g1
TR7207|c1_g1
TR857|c0_g1
TR3132|c0_g1
TR5774|c1_g2
TR156|c0_g1
TR4542|c1_g1
TR2105|c0_g1
TR7192|c0_g1
TR6151|c1_g1
TR3136|c0_g1
TR7207|c1_g2
TR5727|c0_g1
TR8978|c0_g1
TR5860|c0_g1
TR2895|c0_g2
TR3983|c0_g1
TR6184|c0_g2
TR6184|c0_g1
TR3545|c0_g8
TR6112|c0_g1
TR8326|c0_g1
TR4800|c0_g1
TR4302|c0_g2
TR6960|c0_g1
TR5859|c2_g1
TR855|c1_g1
TR1072|c0_g1
TR7495|c0_g1
TR9274|c0_g1
TR8833|c0_g1
TR3965|c0_g2
TR9361|c0_g1
TR975|c0_g1
TR443|c0_g1
TR8561|c0_g1
TR3820|c0_g1
TR3671|c0_g1
TR8833|c0_g2
TR2811|c0_g1
TR1134|c0_g1
TR5954|c0_g1
TR8653|c0_g1
TR1330|c0_g11
TR4538|c0_g1
TR8743|c0_g1
TR4998|c2_g1
TR5735|c1_g1
TR2049|c0_g1
TR5271|c0_g2
TR8583|c0_g1
TR5133|c2_g1
TR9190|c0_g1
TR4229|c0_g1
TR109|c0_g1
TR8781|c0_g1
TR4664|c0_g1
TR6031|c0_g1
TR5323|c0_g1
TR3311|c0_g1
TR898|c0_g1
TR5456|c0_g1
TR7599|c0_g1
TR9252|c0_g1
TR1425|c0_g1
TR3820|c0_g3
TR1761|c1_g1
TR1211|c0_g1
TR6937|c0_g1
TR816|c0_g1
TR1761|c1_g2
TR6676|c0_g1
TR7260|c0_g1
TR5460|c0_g1
TR6408|c0_g1
TR7848|c1_g1
TR3829|c0_g1
TR7501|c2_g1
TR2419|c0_g1
TR135|c0_g1
TR8883|c0_g1
TR7462|c0_g1
TR2737|c0_g1
TR6109|c2_g7
TR5642|c0_g44
TR3145|c0_g1
TR6939|c0_g1
TR474|c0_g1
TR6109|c2_g10
TR8129|c0_g1
TR1051|c0_g1
TR7627|c0_g1
TR7590|c0_g1
TR5914|c0_g1
TR3300|c0_g1
TR8703|c0_g1
TR5181|c0_g1
TR4482|c0_g1
TR3015|c0_g1
TR8980|c0_g1
TR7701|c0_g1
TR3501|c0_g1
TR9268|c2_g1
TR536|c0_g1
TR2369|c0_g2
TR4487|c0_g1
TR240|c0_g1
TR6564|c0_g1
TR4489|c0_g2
TR5642|c0_g19
TR863|c0_g1
TR412|c0_g1
TR1748|c0_g1
TR9029|c0_g2
TR655|c1_g1
TR3403|c0_g1
TR7019|c0_g1
TR7023|c0_g1
TR3733|c0_g1
TR8593|c0_g1
TR1039|c0_g1
TR7402|c0_g1
TR4068|c0_g1
TR7376|c0_g1
TR7497|c0_g1
TR184|c0_g1
TR809|c0_g1
TR1048|c0_g1
TR1303|c0_g1
TR5336|c0_g1
TR1637|c0_g1
TR1927|c0_g1
TR5791|c0_g1
TR7729|c0_g1
TR789|c0_g1
TR2937|c0_g1
TR4893|c0_g1
TR8010|c0_g1
TR6112|c0_g2
TR7425|c0_g1
TR2912|c0_g1

sporocarp

Centramoebia

S

S

C

C

C

C

C

C

S

Sporocarpic Life Cycle Stages Sampled

Color Key

samples vs. features
diffExpr.P0.005_C2.matrix.log2.centered

−5

0

Value

5

RS
PSC
TC
c3849_g1_i1
c8527_g1_i2
c9175_g1_i1
c7756_g1_i1
c10978_g1_i1
c8321_g1_i1
c8780_g1_i1
c5774_g1_i2
c5959_g2_i1
c7252_g1_i2
c7465_g1_i2
c6528_g1_i3
c4228_g1_i1
c5503_g1_i2
c13489_g1_i1
c7741_g1_i1
c8913_g1_i1
c6849_g1_i1
c10376_g1_i1
c10195_g1_i4
c2570_g1_i1
c2520_g1_i1
c7742_g1_i2
c10706_g1_i1
c6955_g2_i1
c9247_g2_i1
c7115_g1_i2
c9441_g1_i1
c9816_g1_i2
c5521_g1_i2
c4218_g1_i1
c9714_g1_i1
c5043_g1_i3
c7849_g1_i1
c4550_g1_i2
c7181_g1_i2
c9062_g1_i3
c7561_g1_i1
c13718_g1_i1
c10355_g1_i2
c7400_g1_i2
c9729_g1_i2
c10819_g1_i1
c5327_g1_i2
c144_g1_i1
c5362_g1_i1
c6993_g1_i1c1893_g1_i2
c8827_g1_i1
c8849_g1_i1
c10400_g3_i10
c2842_g1_i1
c6565_g1_i1
c12140_g1_i1
c4908_g1_i1
c9761_g1_i1
c5755_g1_i2
c8307_g1_i1
c55_g1_i2
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c11222_g1_i1
c4652_g1_i1
c5337_g1_i1
c5387_g1_i1
c4071_g1_i1
c10903_g1_i1
c13169_g1_i1
c2558_g1_i2
c2676_g1_i1
c12827_g1_i1
c7135_g1_i2
c3236_g1_i2
c4732_g1_i1
c2515_g1_i1
c13187_g1_i1
c13786_g1_i1
c12704_g1_i1
c7802_g1_i3
c5290_g1_i1
c6570_g1_i1
c11801_g1_i1
c3233_g1_i1
c8003_g1_i2
c4673_g1_i3
c4677_g1_i1
c2294_g1_i1
c8603_g1_i1
c13378_g1_i1
c5266_g1_i2
c9290_g1_i3
c10822_g1_i1
c11964_g1_i1
c7440_g1_i2
c4696_g1_i1
c14119_g1_i1
c2351_g1_i1
c11410_g1_i1
c3934_g1_i2
c9604_g1_i1
c12602_g1_i1
c1287_g1_i1
c3545_g1_i1
c8065_g1_i1
c6015_g1_i1
c3207_g1_i2
c9090_g1_i2
c7894_g1_i1
c5326_g1_i1
c4427_g1_i3
c10400_g6_i3
c7686_g1_i1
c1122_g1_i2
c2821_g1_i1
c5861_g1_i2
c13234_g1_i1
c9859_g2_i3
c2874_g1_i1
c5453_g1_i1
c6725_g1_i2
c14005_g1_i1
c9302_g1_i1
c10230_g1_i3
c9477_g1_i1
c9073_g3_i1
c10400_g6_i2
c9623_g1_i1
c3448_g1_i2
c2716_g1_i1
c11112_g1_i1
c11823_g1_i1
c2510_g1_i1
c6432_g1_i1
c8919_g1_i3
c2567_g1_i1
c6560_g1_i2
c13952_g1_i1
c5862_g1_i2
c13334_g1_i1
c9072_g1_i1
c9350_g1_i1
c7210_g1_i2
c11861_g1_i1
c9645_g1_i2
c7374_g1_i1
c7874_g1_i1
c2505_g1_i1
c9624_g1_i3
c3554_g1_i2
c6594_g1_i1
c294_g1_i1
c3084_g1_i2
c9938_g1_i3
c3554_g1_i1
c2416_g1_i1
c12415_g1_i1
c6482_g1_i2
c11878_g1_i1
c9299_g1_i2
c8536_g1_i1
c9023_g1_i1
c200_g1_i1
c5227_g1_i3
c5040_g1_i2
c8283_g1_i3
c7492_g1_i1
c4825_g1_i1
c11318_g1_i1
c7260_g1_i2
c4655_g1_i3
c8063_g1_i4
c13206_g1_i1
c9613_g1_i2
c12134_g1_i1
c5564_g1_i1
c13986_g1_i1
c5488_g1_i1
c10173_g1_i1
c11267_g1_i1
c3455_g1_i1
c9043_g1_i6
c8286_g1_i3
c8535_g1_i3
c12686_g1_i1
c8078_g1_i1
c8734_g1_i2
c5600_g1_i2
c7207_g1_i4
c13743_g1_i1
c8635_g1_i2
c4145_g1_i1
c5907_g1_i1
c6270_g1_i1
c7087_g1_i1
c10234_g1_i3
c10221_g1_i1
c7614_g1_i2
c10303_g1_i2
c12470_g1_i1
c9887_g1_i1
c5024_g1_i2
c5621_g1_i3
c4141_g1_i1
c6907_g1_i1
c8454_g1_i1
c9979_g1_i2
c1346_g1_i1
c9955_g1_i2
c7351_g1_i1
c6589_g1_i2
c9526_g1_i1
c6411_g1_i1
c2960_g1_i1
c9093_g1_i2
c9857_g1_i2
c1686_g1_i1
c9359_g1_i2
c13030_g1_i1
c8123_g1_i1
c3560_g1_i1
c1656_g1_i1
c7471_g1_i1
c6282_g1_i1
c7956_g1_i3
c5516_g1_i1
c10159_g1_i4
c10503_g1_i1
c7508_g1_i2
c2591_g1_i1
c9359_g1_i1
c10446_g3_i7
c8029_g1_i2
c10261_g1_i3
c76_g1_i1
c7244_g1_i2
c9620_g1_i4
c11457_g1_i1
c9910_g1_i4
c8138_g1_i1
c3491_g1_i1
c7740_g1_i1
c4993_g1_i1
c13753_g1_i1
c11377_g1_i1
c7950_g1_i1
c7763_g1_i2
c6910_g1_i1
c10158_g1_i4
c3254_g1_i2
c5339_g1_i1
c7386_g1_i1
c9673_g1_i2
c11760_g1_i1
c7321_g1_i1
c13050_g1_i1
c7620_g1_i1
c8860_g1_i1c1958_g1_i2
c6171_g1_i1
c8489_g1_i3
c3125_g1_i1
c6407_g1_i1
c264_g1_i1
c7994_g1_i2
c6344_g1_i1
c10475_g1_i1
c12514_g1_i1
c3664_g1_i1
c9663_g1_i5
c7222_g1_i2
c6584_g1_i2
c8434_g1_i1
c9169_g1_i2
c5300_g1_i4
c114_g1_i1
c10441_g2_i1
c8576_g1_i2
c10089_g1_i2
c7244_g1_i1
c10283_g1_i3
c5116_g1_i1
c9137_g1_i3
c8377_g1_i1
c5323_g1_i1
c7593_g1_i2
c12050_g1_i1
c7593_g1_i1
c7749_g2_i1
c8499_g1_i1
c11960_g1_i1
c3405_g1_i1
c3518_g1_i2
c13822_g1_i1
c2605_g1_i1
c13041_g1_i1
c597_g1_i1
c7363_g1_i1
c5352_g1_i1
c9957_g1_i2
c10825_g1_i1
c3469_g1_i1
c5621_g1_i1
c7232_g1_i2
c186_g1_i1
c8910_g1_i1
c4651_g1_i1
c6823_g1_i1
c5023_g1_i1
c8181_g1_i1
c8217_g1_i1
c60_g1_i1
c7566_g1_i2
c10186_g1_i1
c7216_g1_i1
c3750_g1_i1
c7798_g1_i1
c11764_g1_i1
c10372_g1_i6
c10218_g1_i1
c6753_g1_i1
c8552_g1_i1
c10494_g1_i1
c9624_g1_i2
c10409_g1_i2
c10409_g1_i4
c8024_g1_i3
c6335_g1_i1
c7360_g1_i1
c3672_g1_i1
c8192_g1_i3
c7872_g1_i1
c6452_g1_i2
c7820_g1_i1
c9573_g1_i1
c9673_g1_i3
c10410_g3_i1
c7820_g1_i2
c11989_g1_i1
c8826_g1_i1
c10486_g1_i1
c8862_g1_i3
c6854_g1_i1
c5621_g1_i2

c12327_g1
c7290_g1c17328_g1
c12108_g1
c14315_g1
c12095_g1
c14874_g1
c14723_g1
c13987_g1
c12032_g1
c14815_g1
c14241_g1
c13259_g1
c13928_g1
c11993_g1
c14629_g1
c14069_g1
c13180_g1
c12639_g1
c14868_g1
c12291_g1
c9443_g1
c11822_g1
c12139_g1
c12762_g1
c10113_g1
c8608_g1
c10644_g1
c8610_g1c11471_g1
c12859_g1
c8347_g1
c12416_g2
c12164_g1
c11440_g1
c11111_g1
c8353_g1c10828_g1
c14750_g1
c11074_g1
c9563_g1
c8081_g1
c14923_g1
c11939_g1
c14728_g1
c14302_g1
c14722_g1
c7982_g1
c14946_g6
c14754_g1
c14780_g5
c141_g1
c6860_g1
c11158_g1
c11555_g1
c9845_g1
c15868_g1
c18613_g1
c7824_g1
c17159_g1
c10900_g2
c7337_g1
c9469_g1c9590_g1
c2810_g1
c8477_g1c13226_g1
c1582_g2
c8552_g1
c7459_g1
c9065_g1c17458_g1
c5418_g1
c1190_g1
c7897_g1
c13038_g1
c14205_g1
c15124_g1
c12145_g1
c18280_g1
c8572_g1
c14132_g1
c130_g1
c14159_g5
c8987_g1
c6387_g1
c3191_g1
c6610_g1
c8321_g1
c6728_g1
c6156_g1
c8571_g4
c8571_g3
c4386_g1
c15298_g1
c6177_g1
c2840_g1c18540_g1c18669_g1
c8280_g1
c5306_g1
c5251_g1
c12606_g1
c9102_g1
c12718_g1
c12997_g2
c12183_g2
c2863_g1
c14431_g2
c8023_g1c14666_g1
c9761_g1
c10773_g1
c7897_g2
c3853_g1
c798_g1
c16497_g1
c8356_g1
c966_g1
c11543_g2
c4456_g1c1092_g1c2842_g1
c10118_g1
c9788_g1
c6601_g1
c772_g1c17993_g1
c3675_g1
c13824_g2
c14035_g1
c5403_g1
c10769_g1
c12364_g1
c12312_g1
c13223_g1
c8631_g1c12972_g1
c8393_g2c12950_g1
c4465_g1
c10688_g1
c13626_g1
c13943_g1
c13569_g1
c14247_g1
c14859_g1
c14442_g1
c14585_g1
c14481_g1
c13076_g1
c13692_g1
c5291_g1
c5415_g1c14534_g1
c13516_g1
c14720_g1
c8656_g1
c11587_g1
c13708_g1
c6039_g1c12190_g1
c11957_g1
c9308_g1
c12001_g1
c9585_g1
c470_g1
c7182_g1
c14022_g1
c10483_g1
c14495_g1
c14764_g1
c7837_g1c18535_g1
c7234_g1c14457_g2
c14638_g1
c11478_g1
c9113_g1
c14129_g1
c14345_g1
c14840_g1
c14507_g1
c14817_g1
c6183_g1
c9937_g1
c11636_g1
c13777_g1
c12251_g1
c12918_g1
c13832_g1
c7749_g1
c9954_g1c9489_g1
c12989_g2
c13495_g1
c9263_g1
c10534_g1
c9881_g1
c13307_g2
c14586_g1
c12643_g1
c7964_g1
c12261_g1
c14457_g1
c13977_g1
c9823_g1
c12989_g1
c14818_g4
c13283_g2
c13278_g1
c14183_g3
c14888_g1
c11332_g1
c12386_g1
c12592_g1
c12457_g1
c13373_g1
c13819_g1
c12630_g1
c10357_g1
c12460_g1
c6831_g1
c14137_g1
c11273_g1
c12540_g1
c14016_g2
c11835_g1
c11102_g1
c14892_g1
c9232_g1
c14351_g1
c14421_g1
c13988_g1
c13859_g1
c10914_g1
c12699_g1
c12200_g1
c11677_g1
c12389_g1
c10842_g1
c14434_g3
c12511_g1
c12317_g1
c11334_g1
c14948_g1
c12110_g1
c10486_g1
c12908_g2

6

92

5

*

Discosea

OrthoMCL, OrthoFinder, Flabellinia
ProteinOrtho, OMA

4

*

Diffe
in Li rential
fe CEycle xpress
ion

Pfam, SignalP, TMHMM
Variosea

9

63

98

7

Transcripts

*

69

8

60

Eumycetozoa

Amoebozoa

*

99

Diffe
in Li rential
fe CEycle xpression

Sporocarpic Life Cycle

Evosea*1

ocarpic Life Cycle

Protein Functional
Prediction

Sample Similarity

71

OEBOZOA

L v5

Ortholog Prediction

2

99

ElaridaTranscripts

Differential Expression Assays

Comparative
Developmental
AMOEBOZOA
Transcriptomics

Echinamoebida1

notype of Interest

Micriamoeba sp.
Echinamoeba exudans
Vermamoeba vermiformis
Vermamoeba sp. [CCAP1503-5]
Rhizamoeba saxonica
Flabellula citata
Cryptodifflugia operculata
Difflugia bryophila
Arcella intermedia
Nolandella sp.
Copromyxa protea
Amoeba proteus
Sapocribrum chincoteaguense
Squamamoeba japonica
cutosean isolate [ATCC PRA-29]
Rhizomastix elongata
Pelomyxa sp.
Mastigella eilhardi
Mastigamoeba balamuthi
Mastigamoeba abducta
Entamoeba histolytica
Polysphondylium pallidum
Dictyostelium discoideum
Physarum polycephalum
Echinosteliopsis oligospora
Echinostelium minutum
Echinostelium bisporum
Protosporangium articulatum
Clastostelium recurvatum
Ceratiomyxa fruticulosa
Flamella fluviatilis
Flamella aegyptia
Phalansterium solitarium
Schizoplasmodiopsis vulgaris
Tychosporium acutostipes
Schizoplasmodiopsis pseudoendospora
Cavostelium apophysatum
Protostelium nocturnum
Filamoeba nolandi
Soliformovum irregularis
Grellamoeba robusta
Nematostelium gracile
Ceratiomyxella tahitiensis
Acramoeba dendroida
Stenamoeba stenopodia
Stenamoeba limacina
Thecamoeba quadrilineata
Thecamoeba sp.
Sappinia pedata
Thecamoebida isolate [RHP1-1]
Mayorella cantabrigiensis
Paradermamoeba levis
Dermamoeba algensis
Vermistella antarctica
Stygamoeba regulata
Vexillifera minutissima
Vexillifera bacillipedes
0.85/* 96
Vexillifera sp. [MMETSP0173]
Paramoeba atlantica
Paramoeba aestuarina
Cunea sp. [MMETSP0417]
Cunea sp. [JDS-Ruffled]
Vannella sp. [MMETSP0168]
Vannella robusta
Vannella schaefferi
Color Key
Vannella fimicola
Ripella sp.
Lingulamoeba sp.
Clydonella sp.
Value
Ovalopodium desertum
Parvamoeba rugata
Cochliopodium minus
Pellita catalonica
Gocevia fonbrunei
Gocevia fonbrunei [Tekle et al. 2016]
Endostelium zonatum [PRA-191]
Endostelium zonatum [LINKS]
Dracoamoeba joomungandrii
Protacanthamoeba bohemica
Luapelamoeba arachisporum
Luapelamoeba hula
Acanthamoeba castellanii
Acanthamoeba pyriformis

3

Transcripts

97

Corycida

Tubulinea

Diplochlamys sp.
Amphizonella sp.

Trichosphaerium sp.

SEX - Meiosis
Hoffstater, Brown, Lahr. 2019. GBE

GENERALIZEDSporocarpic
LIFE CYCLE
TYPESA
Simple Amoeba
Sorocarpic
sporocarp
C
A
B
spore

spore

amoebacyst

sorocarp

flagellate

Strict Flagellate D
B

test
TestateArcella E

E

Shell Variation

F

Sex

Reference Genome Targets
Species Delineation
Targets (Genome & Transcriptome)
Genome Available

El

ar

di

Cryptodifflugia E
Copromyxa CaSorocarpy (gain)

65

Echinamoeba A
Armaparvus A
Cavostelium B

79

Nematostelium B

81

Flagellates (loss)

Phalansterium D
Echinostelium B

99

Flagellates (loss)

74

74

70

yc

id

Ec

ia

hi
C nam
ut
os oe
ea bi
di
a
Va
rio
se
a

Eu

TevosaTrichosphaerium E Cor

Rab GTPases
Porfírio-Sousa et al. 2021.
Small GTPases

m

43

yc

et

Ar

oz

ch

oa

am

oe

99

A vs. B Cen
tra
Acanthamoeba
Sporocarpy (loss?)

ba

e

m

bi

99

83

Sappinia F
Vannella A vs. B
Sporocarpy (loss?)

99

Vexillifera A

Fresh vs. Marine

Fl

ab

el

lin

ia

a

Discoseaoe

GENOMES!

Conclusions• Fully resolved phylogeny of a deep eukaryotic group• Amoebozoa• Complex last common ancestor• Genomically

dida

AMO

OBA

RPHE

A

oe

via

bo
zo

a

tea

ZOA

m

s

M
Ru

A

Bre

ona
Apu
som

a

Stramenopiles

tist

Alveolatap
Cry

Rhizaria

a

ta
hy

ia

id

op

nem

SAR

od

Telo

st

a
yt

la

ph
co

ro
p

• Developmental Expression Profiling, a low input tool
• Sporocarpic amoebae - Homologous?

ula• More diversity will change views

G• PhyloFisher tool for phylogenomics

AR
Ch
lo

Rh

E

A
CH

tista
Hap

A
PL

Opistho

A

ID
ST

K
a+SUM
Ancor

Hemi+

• Sampling diversity deeply is now possible

konta• Life History

C

o
cyr

An

da

adi

n
mo

Mal

a

adid

on
awim

EXCAVATA

Discoba
Metamonada

Acknowledgments• Alexander Tice, Ph.D.

• Emily Foreman• Quentin Blandenier, Ph.D.

• Robert Berry• Seungho Kang• Sammira Rais-Rohani• Robert Jones• Priya Patel• Tomáš Pánek, Ph.D.

• Pamela Watson• Fulbright• Tristan Henderson• Stephanie Sorrell• Nicholas Fry• David Žihala• College of Arts & Sciences• Gabriel Schuler• Emily Dale

• Kina Martin• Felicity Kleitz-Singleton• Alfredo de Sousa• Maggie Shepherd• Institute for Genomics,
Biocomputing & Biotechnology• Chris Lebeau• Violet Jira

• Peter Kooienga• Nick Gibson• Department of Biological Sciences• National Science Foundation(DEB-SBS)– SRI• Texas EcoLab• Frederick W. Spiegel, Ph.D.
• Daniel J. G. Lahr, Ph.D.
• Brendan Zurweller, Ph.D.

QUESTIONS?

Felicity Kleitz-Singleton