The dataset contains a draft assembly of the common milkweed (Asclepias syriaca) nuclear genome, linkage group information, and gene family counts for Asclepias and related species. The genome assembly is accompanied by annotation of gene models, repeat models, transfer RNAs, and open reading frames, and mapping information of Asclepias transcripts, Calotropis transcripts, and Coffea proteins onto the assembled scaffolds. The linkage group information includes data input into the linkage group analysis, R scripts for processing, and a final list of scaffolds assigned to linkage groups. Additional data includes the coding sequence alignment of P5βR paralogs described in the article and a table of gene family counts in Asclepias, other Apocynaceae, coffee (Coffea), and grape (Vitis).
a) Cladogram based on ML topology, showing
support values below branches as ML bootstrap support / Bayesian posterior
probability / parsimony bootstrap support. Support values are shown only for
nodes with less than 100% bootstrap support and/or posterior probabilities less
than 1.0; single values indicate either ML bootstrap support or Bayesian
posterior probability. * indicates branch not supported in Bayesian or
b) ML Phylogram with branch lengths determined from ML
analysis; scale corresponds to probability of change per position.
Five different references from the Asclepias syriaca genome assembly were used to assemble portions of the mitochondrial genomes of species of the Sonoran Desert clade of Asclepias. This file contains a separate fasta assembly file for each individual included in the study. The masked sequence labeled with the species name in each file was used for downstream analysis.
Straub_additional_file_4.fsa: FASTA file containing 115 contigs corresponding to a partial genome sequence of the mitochondrial genome of Asclepias syriaca.
Straub_additional_file_5.fsa: FASTA file containing 6,997 contigs resulting from the de novo assembly of the nuclear genome of Asclepias syriaca.