Spreadsheet: 430dc988-0600-45ca-bbf8-a59a211226f0
Sheet: Sheet1

Table S3. Summary list of genes inactivated or lost in [NAME] genomes of the Aphidinae. | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6 | Unnamed: 7 | Unnamed: 8
 |  |  | Buchnera
Gene | Functional category & description |  | Ua | Ak | Tokyo | 5A | Tuc7 | [NAME]
rnfA | Cp | oxidative stress | – | + | + | + | + | +
rnfB | Cp | oxidative stress | – | + | + | + | + | +
rnfC | Cp | oxidative stress | – | + | + | + | + | -1A (10A)
rnfD | Cp | oxidative stress | – | + | + | + | + | +
rnfG | Cp | oxidative stress | – | + | + | + | + | +
rnfE | Cp | oxidative stress | – | + | + | + | + | +
smpA | Cs | inner membrane | – | + | + | + | + | +
mutT | [NAME] | DNA repair and recombination | – | + | + | + | + | +
mutS | [NAME] | DNA repair and recombination | – | + | + | + | + | +
mutL | [NAME] | DNA repair and recombination | – | + | + | + | + | +
argE | Met | biosynthesis of ARG (ornithine) | – | + | + | + | + | +
argC | Met | biosynthesis of ARG (ornithine) | – | + | + | + | + | +
argB | Met | biosynthesis of ARG (ornithine) | – | + | + | + | + | +
argA | Met | biosynthesis of ARG (ornithine) | – | + | + | + | + | +
argD | Met | biosynthesis of ARG (ornithine) | – | + | + | + | + | +
speE | Met | spermidine | – | + | + | + | + | +
speD | Met | spermidine | – | + | + | + | + | +
panB | Met | pantothenate | – | + | + | + | + | +
panC | Met | pantothenate | – | + | + | + | + | +
pyrC | Met | pyrimidine biosynthesis | – | + | + | + | + | +
pyrD | Met | pyrimidine biosynthesis | – | + | + | + | + | +
pyrB | Met | pyrimidine biosynthesis | – | + | + | + | + | +
pyrI | Met | pyrimidine biosynthesis | – | + | + | + | + | +
yba4 | Unk | unknown | – | + | + | + | + | +
yggS | Unk | unknown | – | + | + | + | + | +
yfjF | Unk | unknown | – | + | + | + | + | +
queA | [NAME] | RNA modification | – | Large indel | + | + | + | +
apbE | Met | thiamine | – | +1A (12A) | -1A (10A) | -1A (10A) | -1A (10A) | -1T (9T)
ansA | Met | introconversion of ASN and ASP | – | + | ≥3 | ≥3 | ≥3 | +1A (12A)
cmk | Met | Pyrimidine salvage | – | + | -1A (9A) | -1A (9A) | -1A (9A) | ≥3
metR | Reg | transcriptional dual regulator | – | + | ≥3 | ≥3 | ≥3 | +
alx | Cs | inner membrane | – | ≥3 | ≥3 | ≥3 | ≥3 | +
queC | [NAME] | RNA modification | – | ≥3 | ≥3 | ≥3 | ≥3 | +
folE | Met | tetrahydrafolate | – | – | ≥3 | ≥3 | ≥3 | +
lolE | Tr | [NAME] transporter | -1bp | + | -1T (9T) | -1T (9T) | -1T (9T) | +
ftsB | Cp | Cell division | -1A (9A) | + | + | + | + | +
ispA | Met | isoprenoid biosynthesis | -1A (13A) | + | + | + | + | +
yeaZ | Met | Proteins/peptides/glycopeptides | -2A (11A) or +1T (4T) | + | + | + | + | +
ribF | Met | flavin | -1A (6A), +1A (6A) | + | + | + | + | +
metK | Met | S-adenosylmethionine (SAM) | ≥3 | + | + | + | + | +
thiL | Met | thiamine | ≥3 | + | + | + | + | +
bolA | Reg | cell division | -1A (7A) | + | + | + | + | +
rsmC | [NAME] | RNA modification | + | -1A (10A) | + | + | + | +
ispE | Met | isoprenoid biosynthesis | + | -1A (10A) | + | + | + | +
murA | Met | peptidoglycan | + | -1A (12A) | + | + | + | +
recC | [NAME] | DNA repair and recombination | + | -1A (10A) | + | + | + | +
priA | [NAME] | DNA replication | + | -1A (10A) | + | + | + | +
endA | Met | DNA regulation | + | ≥3 | + | + | + | -1A (8A)
ycfM | Unk | unknown | + | ≥3 | + | + | + | ≥3
mrcB | Met | peptidoglycan | + | + | + | + | + | ≥3
cysI | Met | Sulfate assimilation | + | + | + | + | + | -1A (5A),     1 nonsense
cysH | Met | Sulfate assimilation | + | + | + | + | + | ≥3
cysG | Met | Sulfate assimilation | + | + | + | + | + | ≥3
cysD | Met | Sulfate assimilation | + | + | + | + | + | ≥3
cysN | Met | Sulfate assimilation | + | + | + | + | + | ≥3
cysQ | Met | Sulfur metabolism | + | + | + | + | + | ≥3
bioD | Met | [NAME] | + | + | + | + | + | -1A (13A)
glmM | Met | UDP-N-acetyl-D-glucosamine | + | + | + | + | + | -2A (11A)
cvpA | Cs | inner membrane | + | -1T (4T) | -1T (2T) | -1T (2T) | -1T (2T) | -1T (9T)
fabD | Met | fatty acid biosynthesis | -1A (9A) | -1A (10A) | -1A (10A) | -1A (10A) | -1A (10A) | +
rnhA | [NAME] | DNA replication | + | + | -1A (9A) | -1A (9A) | -1A (9A) | +
ribD2 | Met | riboflavin | + | + | + | -1A (6A) | -1A (6A) | +
sbcB | IT | DNA degredation | +1T (8T) | + | +1T (7T) | + | + | +
ynfM | Tr | unknown substrate | + | + | -1A (8A) | + | + | +
rnpA | [NAME] | RNA modification | + | + | + | -1A (11A) | -1A (11A) | +
rlmE | [NAME] | RNA modification | + | + | + | -1A (10A) | -1A (10A) | +
flgB | Cs | Flagellum | + | + | -1A (2A) | + | + | +
fliK | Cs | Flagellum | + | + | 1 nonsense | + | + | +
bamA | Cs | outer membrane | + | + | indel | + | + | +
[NAME] | Met | fatty acid biosynthesis | + | + | indel | + | + | +
yigL | Met | unknown | + | + | indel | + | + | +
nlpD | Cs | outer membrane | + | + | + | + | + | ≥3
lig | [NAME] | DNA repair and recombination | + | + | + | + | + | -1bp
mfd | [NAME] | DNA repair and recombination | + | + | + | + | + | ≥3
phr | [NAME] | DNA repair and recombination | + | + | + | + | + | -1A, (5A)
yfaE | [NAME] | Fe-S cluster - maintenance | + | + | + | + | + | -1A (11A)
miaA | [NAME] | Heat Shock Regulon | + | + | + | + | + | -1A (10A)
rsmD | [NAME] | RNA modification | + | + | + | + | + | -1A (14A)
poxA | [NAME] | tRNA synthetase | + | + | + | + | + | -1A (11A)
[NAME] | Met | heme, siroheme | + | + | + | + | + | 2 nonsense
hemD | Met | heme, siroheme | +1T (8T) | -1T (8T) | -1T (5T) | -1T (5T) | -1T (5T) | ≥3
murC | Met | peptidoglycan | + | + | + | + | + | -1A (10A)
murE | Met | peptidoglycan | + | + | + | + | + | -1A (10A)
murF | Met | peptidoglycan | -1A (11A) | -1A (11A) | + | +1A (9A) | +1A (9A) | -1T (8T)
mraY | Met | peptidoglycan | + | + | + | + | + | -1A (10A)
emtA | Met | peptidoglycan | + | + | + | + | + | -1 bp
pyrE | Met | pyrimidine biosynthesis | + | + | + | + | + | -1A (9A), +1A (2A)
yba3 | Unk | unknown | + | + | + | + | + | -1bp,             1 nonsense
ung | [NAME] | DNA repair and recombination | + | + | + | -1A (12A) | + | -2T (4T)
ddlB | Met | peptidoglycan | + | + | -1A (11A) | -1A (11A) | -1A (11A) | +
cspC | Reg | Transcription related | + | + | + | + | + | –
hflD | Cs | inner membrane | ≥3 | + | + | + | + | –
[NAME] | Reg | transcriptional dual regulator | – | ≥3 | + | + | + | –
dam | [NAME] | DNA restriction/modification | – | ≥3 | – | – | – | –
bioH | Met | [NAME] | + | ≥3 | – | – | – | +1A (11A)
bcp | Cp | Detoxification | – | – | – | – | – | +
ygfA | Cp | Drug resistance/sensitivity | – | – | – | – | – | +
queF | [NAME] | RNA modification | – | – | – | – | – | +
queD | Met | nucleotides | – | – | – | – | – | +
yjeK | Met | unknown | – | – | – | – | – | +
znuA | Tr | Zn2+ transporter | – | – | – | – | – | +
yidD | Unk | unknown | – | – | – | – | – | +
yebA | Unk | unknown | – | – | – | – | – | +
ygcF | Unk | unknown | – | – | – | – | – | +
Inferred number of deleted '-' or inserted '+' and current homopolymer length' (XN)'
Functional category abbr. are as follows: cell processes (Cp) , cell structure (Cs),  metabolism (Met), regulation ([NAME]), information transfer ([NAME]), transport (Tr), unknown (Unk)