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

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1 Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon, United States
2 Department of Biology, Hobart and William Smith Colleges, Geneva, New York, United States
3 Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, Oklahoma, United States
4 Department of Biology, New Mexico State University, Las Cruces, New Mexico, United States
5 Pacific Northwest Research Station, USDA Forest Service, Corvallis, Oregon, United States
6 Department of Botany & Plant Pathology, Oregon State University, Corvallis, Oregon, United States
DOI
10.7287/peerj.preprints.26488v2
Published
Accepted
Subject Areas
Evolutionary Studies, Genomics, Plant Science
Keywords
Asclepias, milkweed, Apocynaceae, cardenolide, chromosome evolution, genome, Gentianales, linkage mapping
Licence
This is an open access article, free of all copyright, made available under the Creative Commons Public Domain Dedication. This work may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose.
Cite this article
Weitemier K, Straub SC, Fishbein M, Bailey CD, Cronn RC, Liston A. 2019. A draft genome and transcriptome of common milkweed (Asclepias syriaca) as resources for evolutionary, ecological, and molecular studies in milkweeds and Apocynaceae. PeerJ Preprints 7:e26488v2

Abstract

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 = 3415 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 eleven 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.

Author Comment

The primary changes to version 2 include adding Calotropis to the analysis of gene family evolution, adding sequences from Calotropis and Rhazya to the P5βR gene tree, and incorporating the methods from the supplemental text into the main text.

Supplemental Information

Supplementary Materials

Supplementary figures and tables.

DOI: 10.7287/peerj.preprints.26488v2/supp-1