DOI: 10.5061/dryad.1k5s048
title: Data from: Whole chloroplast genome and gene locus phylogenies reveal the taxonomic placement and relationship of Tripidium (Panicoideae: Andropogoneae) to sugarcane

description: Background: For over 50 years, attempts have been made to introgress
 agronomically useful traits from Erianthus sect. Ripidium (Tripidium)
 species into sugarcane based on both genera being part of the ‘Saccharum
 Complex’, an interbreeding group of species believed to be involved in the
 origins of sugarcane. However, recent low copy number gene studies
 indicate that Tripidium and Saccharum are more divergent than previously
 thought. The extent of genus Tripidium has not been fully explored and
 many species that should be included in Tripidium are still classified as
 Saccharum. Moreover, Tripidium is currently defined as incertae sedis
 within the Andropogoneae, though it has been suggested that members of
 this genus are related to the Germainiinae. Results: Eight newly-sequenced
 chloroplasts from potential Tripidium species were combined in a
 phylogenetic study with 46 members of the Panicoideae, including seven
 Saccharum accessions, two Miscanthidium and three Miscanthus species. A
 robust chloroplast phylogeny was generated and comparison with a gene
 locus phylogeny clearly places a monophyletic Tripidium clade outside the
 bounds of the Saccharinae. A key to the currently identified Tripidium
 species is presented. Conclusion: For the first time, we have undertaken a
 large-scale whole plastid study of eight newly assembled Tripidium
 accessions and a gene locus study of five Tripidium accessions. Our
 findings show that Tripidium and Saccharum are eight million years
 divergent, last sharing a common ancestor 12 million years ago. We
 demonstrate that four species should be removed from Saccharum/Erianthus
 and included in genus Tripidium. In a genome context, we show that
 Tripidium evolved from a common ancestor with and extended Germainiinae
 clade formed from Germainia, Eriochrysis, Apocopis, Pogonatherum and
 Imperata. We re-define the ‘Saccharum complex’ to a group of genera that
 can interbreed in the wild and extend the Saccharinae to include Sarga
 along with Sorghastrum, Microstegium vimineum and Polytrias (but excluding
 Sorghum). Monophyly of genus Tripidium is confirmed and the genus is
 expanded to include Tripidium arundinaceum, Tripidium procerum, Tripidium
 kanashiroi and Tripidium rufipilum. As a consequence, these species are
 excluded from genus Saccharum. Moreover, we demonstrate that genus
 Tripidium is distinct from the Germainiinae.
description: Low copy number gene
 loci assembled for the projectA tarball (tar.gz) file
 containing the readme, along with individual assemblies of 5 low copy
 number gene regions for the following species: Miscanthidium_junceum
 Sarga_versicolor Miscanthus_sacchariflorus Sorghum_propinquum
 Miscanthus_sinensis_Andante Andropogon_virginicus
 Miscanthus_transmorrisonensis Tripidium_arundinaceum-2
 Miscanthus_x_giganteus Sorghum_bicolor-BTx623 Saccharum_hybrid_LCP85-384
 Sorghum_arundinaceum Saccharum_hybrid-SP80-3280 Tripidium_procerum
 Saccharum_spontaneum Tripidium_rufipilum Sarga_timorense Coix_lacryma-jobi
 (ep2-ex7 and ep2-ex8 only) The assemblies can be found in individual
 multi-fasta corresponding to the gene name and exon of the region
 assembled: apo1 d8 ep2-ex7 ep2-ex8 rep1gene-loci.tar.gzAlignment of low copy number gene loci employed in this studyConcatenated alignment for the five low copy number gene regions employed in the study. Alignment file is: low-copy-number-alignment.fas as well as sequences derived from the paper of Estep et al: Estep MC, McKain MR, Diaz DV, Zhong J, Hodge JG, Hodkinson TR, et al. Allopolyploidy, diversification, and the Miocene grassland expansion. Proc Natl Acad Sci USA. 2014; 111:15149-54 The Estep et al. datasets can be obtained from the Dryad digital repository: http://datadryad.org/resource/doi:10.5061/dryad.5kf38 The following data partitions were employed apo1.fsa d8.fsa ep2-ex7.fsa ep2-ex8.fsa rep1.fsa In addition to data from the Estep et al. publication, the Sorghum laxiflorum dataset (lacking rep1) of et al: Hawkins, J.S., Ramachandran, D., Henderson, A., Freeman, J., Carlise, M., Harris, A. and Willison-Headley, Z., 2015. Phylogenetic reconstruction using four low-copy nuclear loci strongly supports a polyphyletic origin of the genus Sorghum. Annals of botany, 116(2), pp.291-299. was also emplogyed. The alignment files include the following additional species data assembled from SRA datasets: Miscanthidium junceum Miscanthus_transmorrisonensis Miscanthus_sacchariflorus Miscanthus_x_giganteus Saccharum_hybrid_LCP85-384 Saccharum_hybrid_SP80-3280 Saccharum_spontaneum_RB Sarga_versicolor Sarga_timorense Sorghum_propinquum Sorguhum_bicolor_BTx623 Sorghum_arundinaceum Miscanths sinensis cv Andanta and Andropogon virginicus whole genome datasets as well as Tripidium arundinaceum 2, Tripidium procerum and Tripidium rufipilum datasets were sequenced for this study. The alignment is partitioned as follows locus partition apo1 1-674 d8 675-1816 ep2-ex7 1817-2818 ep2-ex8 2819-3640 rep1 3641-4426low-copy-number-gene-align-phylogeny.tar.gzLow copy gene locus alignment and phylogenyAlignment of the five low copy number gene loci analyzed in the paper, along with a maximum likelihood phylogeny derived from the alignment matrix. The alignment matrix is divided into the following gene region partitions: apo1.fsa d8.fsa ep2-ex7.fsa ep2-ex8.fsa rep1.fsa The alignment is divided into partitions as follows: locus partition apo1 1-674 d8 675-1816 ep2-ex7 1817-2818 ep2-ex8 2819-3640 rep1 3641-4426 Partitions were alanyzed independently to generate the reference phylogeny.low-copy-number-gene-align-phylogeny.tar.gzchloroplast-align-phylogeny.tarTarball contains the files: README-CP.txt, tripidium-rearranged.fasta and Tripidium-cp-rooted.phy. The tripidium-rearranged.fasta file contains the alignment of whole chloroplasts from 54 species from the Andropogoneae focussing on Tripidium and Saccharum. The alignment is divided into LSC, IRA and SSC partitions. These partitions were further divided into protein-coding gene, RNA-coding gene and non-coding regions. The regions were isolated with the BeforePhylo.pl script and merged into separate partitions which are joined together in this file. The partitions are: p1 = 1-40026 p2 = 40027-41716 p3 = 41717-85819 p4 = 85820-94385 p5 = 94386-99135 p6 = 99136-105301 p7 = 105302-104847 p8 = 104848-123717 Best-fit evolutionary models for each partition were selected using JModelTest2 and the AICc criterion. The best-fit models were as follows: LSC protein coding: TPM1uf+I+Gamma, LSC RNA genes: TVM+Gamma; LSC non-coding: TVM+Gamma; IRA protein coding: TVM+I+Gamma; IRA non-coding: TVM+Gamma; SSC protein coding: TPM1uf+I+Gamma; SSC RNA-gene: TrN+I+Gamma and SSC non-coding: TVM+I+Gamma. The alignment was analyzed with RAxML using the above partitions and the most likely tree is given in Tripidium-cp-rooted.phy which is the tree topology presented in the BMC Evolutionary Biology paper.