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

PeerJ

article

Kevin Weitemier¹  Shannon C.K. Straub²  Mark Fishbein³  C. Donovan Bailey⁴  Richard C. Cronn⁵  Aaron Liston⁶ 

[1] Department of Fisheries and Wildlife, Oregon State University;Department of Biology, Hobart and William Smith Colleges;Department of Plant Biology, Ecology, and Evolution, Oklahoma State University;Department of Biology, New Mexico State University;Pacific Northwest Research Station;Department of Botany & Plant Pathology, Oregon State University

关键词: Asclepias;    Milkweed;    Apocynaceae;    Cardenolide;    Chromosome evolution;    Genome;    Gentianales;    Linkage mapping;    Plant genome;   

DOI  :  10.7717/peerj.7649

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

Milkweeds (Asclepias) 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, Asclepias syriaca. 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 Asclepias transcripts, 88.4% of transcripts from the related genus Calotropis, and 90.6% of proteins from Coffea mapping to the assembly. Scaffolds covering 75 Mbp of the Asclepias assembly formed 11 linkage groups. Comparisons of these groups with pseudochromosomes in Coffea 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 Asclepias 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.

【 授权许可】

CC BY