A draft genome and transcriptome of common milkweed ( Asclepias syriaca ) as resources for evolutionary, ecological, and molecular studies in milkweeds and Apocynaceae

• Published in: PeerJ (San Francisco, CA) CA), 2019-09, Vol.7, p.e7649, Article e7649
• Main Authors: Weitemier, Kevin, Straub, Shannon C K, Fishbein, Mark, Bailey, C Donovan, Cronn, Richard C, Liston, Aaron
• Format: Article
• Language: English
• Subjects: Apocynaceae; Artificial chromosomes; Asclepias; Asclepias syriaca; Cardenolide; Chloroplasts; Chromosome evolution; Chromosomes; Coevolution; Deoxyribonucleic acid; DNA; Evolution; Evolutionary biology; Evolutionary Studies; Future predictions; Gene expression; Gene mapping; Gene rearrangement; Genes; Genetic aspects; Genome; Genomes; Genomics; Herbivores; Investigations; Metabolites; Milkweed; Mitochondria; Peptide mapping; Plant evolution; Plant reproduction; Plant Science; Pollination; Povidone; Progesterone; Proteins; Reductase; Sex hormones; Transcription
• ISSN: 2167-8359; 2167-8359
• DOI: 10.7717/peerj.7649

Milkweeds ( ) are used in wide-ranging studies including floral development, pollination biology, plant-insect interactions and co-evolution, secondary metabolite chemistry, and rapid diversification. We present a transcriptome and draft nuclear genome assembly of the common milkweed, . This reconstruction of the nuclear genome is augmented by linkage group information, adding to existing chloroplast and mitochondrial genomic resources for this member of the Apocynaceae subfamily Asclepiadoideae. The genome was sequenced to 80.4× depth and the draft assembly contains 54,266 scaffolds ≥1 kbp, with N50 = 3,415 bp, representing 37% (156.6 Mbp) of the estimated 420 Mbp genome. A total of 14,474 protein-coding genes were identified based on transcript evidence, closely related proteins, and ab initio models, and 95% of genes were annotated. A large proportion of gene space is represented in the assembly, with 96.7% of transcripts, 88.4% of transcripts from the related genus , and 90.6% of proteins from mapping to the assembly. Scaffolds covering 75 Mbp of the assembly formed 11 linkage groups. Comparisons of these groups with pseudochromosomes in found that six chromosomes show consistent stability in gene content, while one may have a long history of fragmentation and rearrangement. The progesterone 5β-reductase gene family, a key component of cardenolide production, is likely reduced in relative to other Apocynaceae. The genome and transcriptome of common milkweed provide a rich resource for future studies of the ecology and evolution of a charismatic plant family.