DOI: 10.5061/dryad.ff1tq
title: Data from: Multiple polyploidy events in the early radiation of nodulating and non-nodulating legumes

description: Unresolved questions about evolution of the large and diverse legume
 family include the timing of polyploidy (whole-genome duplication; WGDs)
 relative to the origin of the major lineages within the Fabaceae and to
 the origin of symbiotic nitrogen fixation. Previous work has established
 that a WGD affects most lineages in the Papilionoideae and occurred some
 time after the divergence of the papilionoid and mimosoid clades, but the
 exact timing has been unknown. The history of WGD has also not been
 established for legume lineages outside the Papilionoideae. We
 investigated the presence and timing of WGDs in the legumes by querying
 thousands of phylogenetic trees constructed from transcriptome and genome
 data from 20 diverse legumes and 17 outgroup species. The timing of
 duplications in the gene trees indicates that the papilionoid WGD occurred
 in the common ancestor of all papilionoids. The earliest diverging
 lineages of the Papilionoideae include both nodulating taxa such as the
 genistoids (e.g. lupin), dalbergioids (e.g. peanut), phaseoloids (e.g.
 beans), and galegoids (= Hologalegina, e.g. clovers), and clades with
 non-nodulating taxa including Xanthocercis and Cladrastis (evaluated in
 this study). We also found evidence for several independent WGDs near the
 base of other major legume lineages, including the
 Mimosoid-Cassiinae-Caesalpinieae (MCC), Detarieae, and Cercideae clades.
 Nodulation is found in the MCC and papilionoid clades, both of which
 experienced ancestral WGDs. However, there are numerous non-nodulating
 lineages in both clades, making it unclear whether the phylogenetic
 distribution of nodulation is due to independent gains or a single origin
 followed by multiple losses.
description: assembliesThe filtered (&gt;1% per-component read representation) Trinity assemblies of legume transcriptomes used in this study, as part of the Thousand Plant Transcriptome (1kp) project. These are multifasta files.peptide translationsPeptide translations based on a blastx of the filtered Trinity assemblies to the 22 genome dataset (Amborella Genome Consortium, 2013) and conceptually translated using Genewise. These are multifasta files.pep_translations.tar.gzCDS translationsCorresponding CDS sequences for the peptide translations. These are multifasta files.cds_translations.tar.gztrees - bipartitionsThe RAxML bipartitions trees for the 3360 orthogroup alignments containing Glycine max. syntelogs. These are Newick tree files.trees_bipartitions.tar.gzLegume pairs - ksplotsPutative paralog pairs estimated from Ks plots for multiple species from study. These were used to test for other WGD events (other than PWGD). This is a tab delimited file with the first and second columns being Ks plot identified putative paralogs and the third column being a designation for the putative event.Legume_pairs_ksplots.txt.gzalignments for other WGD testsAlignments of orthogroups used to look at putative WGD events in data set. These are multifasta files.alignments_for_other_WGD_tests.tar.gztrees for other WGD testsRAxML best trees with bootstrap values added (bipartitions) for orthogroups used to test for putative WGD events in data set identified through Ks plots that are not PWGD. These are Newick tree files.trees_for_other_WGD_tests.tar.gzsingle copy treesLow-copy trees used to estimate a species phylogeny using MP-EST methods.single_copy_trees.tar.gzconcat_alllegume.fsaConcatenated nucleotide alignments for 101 orthogroups used to estimate a species tree in RAxML. This is a multifasta file.RAxML_bipartitions.concat_alllegume.fsa.raxml.outRAxML best tree with bootstrap values estimated from concatenation of 101 orthogroups alignments. This is a Newick tree file.DNA alignmentscDNA alignments for all gene families in the project, made using pal2nal. These are multifasta alignment files.dna_alignments.tar.gzprotein-sequence alignmentsPeptide alignments for orthogroup clusters in the project, calculated using MUSCLE. These are multifasta alignment files.pep_alignments.tar.gztrees - bipartitionsThe RAxML bipartitions trees for the 3360 orthogroup alignments containing Glycine max. syntelogs. These are Newick tree files.trees_bipartitions.tar.gz