Data from: Multiple polyploidy events in the early radiation of nodulating and non-nodulating legumes

Cannon SB, McKain MR, Harkess A, Nelson MN, Dash S, Deyholos MK, Peng Y, Joyce B, Stewart Jr. CN, Rolf M, Kutchan T, Tan X, Chen C, Zhang Y, Carpenter E, Wong GK, Doyle JJ, Leebens-Mack J

Date Published: October 28, 2014

DOI: http://dx.doi.org/10.5061/dryad.ff1tq

 

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Title assemblies
Downloaded 36 times
Description The filtered (>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.
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Title peptide translations
Downloaded 19 times
Description Peptide 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.
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Title CDS translations
Downloaded 17 times
Description Corresponding CDS sequences for the peptide translations. These are multifasta files.
Download cds_translations.tar.gz (48.35 Mb)
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Title trees - bipartitions
Downloaded 12 times
Description The RAxML bipartitions trees for the 3360 orthogroup alignments containing Glycine max. syntelogs. These are Newick tree files.
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Title Legume pairs - ksplots
Downloaded 8 times
Description Putative 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.
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Title alignments for other WGD tests
Downloaded 11 times
Description Alignments of orthogroups used to look at putative WGD events in data set. These are multifasta files.
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Title trees for other WGD tests
Downloaded 10 times
Description RAxML 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.
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Title single copy trees
Downloaded 11 times
Description Low-copy trees used to estimate a species phylogeny using MP-EST methods.
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Title concat_alllegume.fsa
Downloaded 18 times
Description Concatenated nucleotide alignments for 101 orthogroups used to estimate a species tree in RAxML. This is a multifasta file.
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Title RAxML_bipartitions.concat_alllegume.fsa.raxml.out
Downloaded 8 times
Description RAxML best tree with bootstrap values estimated from concatenation of 101 orthogroups alignments. This is a Newick tree file.
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Title DNA alignments
Downloaded 12 times
Description cDNA alignments for all gene families in the project, made using pal2nal. These are multifasta alignment files.
Download dna_alignments.tar.gz (52.56 Mb)
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Title protein-sequence alignments
Downloaded 16 times
Description Peptide alignments for orthogroup clusters in the project, calculated using MUSCLE. These are multifasta alignment files.
Download pep_alignments.tar.gz (42.02 Mb)
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Title trees - bipartitions
Downloaded 15 times
Description The RAxML bipartitions trees for the 3360 orthogroup alignments containing Glycine max. syntelogs. These are Newick tree files.
Download trees_bipartitions.tar.gz (4.262 Mb)
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When using this data, please cite the original publication:

Cannon SB, McKain MR, Harkess A, Nelson MN, Dash S, Deyholos MK, Peng Y, Joyce B, Stewart Jr CN, Rolf M, Kutchan T, Tan X, Chen C, Zhang Y, Carpenter E, Wong GK, Doyle JJ, Leebens-Mack J (2015) Multiple polyploidy events in the early radiation of nodulating and non-nodulating legumes. Molecular Biology and Evolution 32(1): 193-210. http://dx.doi.org/10.1093/molbev/msu296

Additionally, please cite the Dryad data package:

Cannon SB, McKain MR, Harkess A, Nelson MN, Dash S, Deyholos MK, Peng Y, Joyce B, Stewart Jr. CN, Rolf M, Kutchan T, Tan X, Chen C, Zhang Y, Carpenter E, Wong GK, Doyle JJ, Leebens-Mack J (2014) Data from: Multiple polyploidy events in the early radiation of nodulating and non-nodulating legumes. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.ff1tq
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