Asparagus genus 454 reads

This tar.bz2 file contains 454 sequencing fasta files for A. aphyllus, A. asparagoides, A. densiflorus, A. falcatus, A. maritimus, A. officinalis, A. pyrimidalis, A. stipularis, and A. virgatus. There is an additional A. officinalis 454 dataset that is significantly higher coverage, named "A_officinalis_WGS_in.454.AdditionalHighCoverage.fasta"

Asparagus officinalis RepeatMasker database

This fasta file contains a custom garden asparagus RepeatMasker database. A total of 893,623 454 FLX Titanium reads were generated from leaf tissue of a doubled haploid (YY) garden asparagus individual. Reads were stringently filtered to a 150nt minimum length. RepeatExplorer was then run, and the resulting cap3 consensus assemblies for each cluster were annotated using RepeatClassifier, part of the RepeatModeler (v1.0.8) suite, with default settings. A total of 22,361 sequences greater than 150nt in length and with annotations

Hackenberg_etal_2016_Gα_RGS_protein_pairs

See README file

concat_alllegume.fsa

Concatenated nucleotide alignments for 101 orthogroups used to estimate a species tree in RAxML. This is a multifasta file

DNA alignments

cDNA alignments for all gene families in the project, made using pal2nal. These are multifasta alignment files

CDS translations

Corresponding CDS sequences for the peptide translations. These are multifasta files

Legume pairs - ksplots

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

alignments for other WGD tests

Alignments of orthogroups used to look at putative WGD events in data set. These are multifasta files

peptide translations

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

RAxML_bipartitions.concat_alllegume.fsa.raxml.out

RAxML best tree with bootstrap values estimated from concatenation of 101 orthogroups alignments. This is a Newick tree file