A draft genome and transcriptome of common milkweed (Asclepias syriaca) as resources for evolutionary, ecological, and molecular studies in milkweeds and Apocynaceae
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, Asclep...
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PeerJ Inc.
2019-09-01
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| Online Access: | https://peerj.com/articles/7649.pdf |
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| author | Kevin Weitemier Shannon C.K. Straub Mark Fishbein C. Donovan Bailey Richard C. Cronn Aaron Liston |
| author_facet | Kevin Weitemier Shannon C.K. Straub Mark Fishbein C. Donovan Bailey Richard C. Cronn Aaron Liston |
| author_sort | Kevin Weitemier |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T06:54:43Z |
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| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:54:43Z |
| publishDate | 2019-09-01 |
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| series | PeerJ |
| spelling | doaj.art-006ed2529f374150a2739b2b228ab58a2023-12-03T10:05:18ZengPeerJ Inc.PeerJ2167-83592019-09-017e764910.7717/peerj.7649A draft genome and transcriptome of common milkweed (Asclepias syriaca) as resources for evolutionary, ecological, and molecular studies in milkweeds and ApocynaceaeKevin Weitemier0Shannon C.K. Straub1Mark Fishbein2C. Donovan Bailey3Richard C. Cronn4Aaron Liston5Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, USADepartment of Biology, Hobart and William Smith Colleges, Geneva, NY, USADepartment of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, OK, USADepartment of Biology, New Mexico State University, Las Cruces, NM, USAPacific Northwest Research Station, USDA Forest Service, Corvallis, OR, USADepartment of Botany & Plant Pathology, Oregon State University, Corvallis, OR, USAMilkweeds (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.https://peerj.com/articles/7649.pdfAsclepiasMilkweedApocynaceaeCardenolideChromosome evolutionGenome |
| spellingShingle | Kevin Weitemier Shannon C.K. Straub Mark Fishbein C. Donovan Bailey Richard C. Cronn Aaron Liston A draft genome and transcriptome of common milkweed (Asclepias syriaca) as resources for evolutionary, ecological, and molecular studies in milkweeds and Apocynaceae PeerJ Asclepias Milkweed Apocynaceae Cardenolide Chromosome evolution Genome |
| title | A draft genome and transcriptome of common milkweed (Asclepias syriaca) as resources for evolutionary, ecological, and molecular studies in milkweeds and Apocynaceae |
| title_full | A draft genome and transcriptome of common milkweed (Asclepias syriaca) as resources for evolutionary, ecological, and molecular studies in milkweeds and Apocynaceae |
| title_fullStr | A draft genome and transcriptome of common milkweed (Asclepias syriaca) as resources for evolutionary, ecological, and molecular studies in milkweeds and Apocynaceae |
| title_full_unstemmed | A draft genome and transcriptome of common milkweed (Asclepias syriaca) as resources for evolutionary, ecological, and molecular studies in milkweeds and Apocynaceae |
| title_short | A draft genome and transcriptome of common milkweed (Asclepias syriaca) as resources for evolutionary, ecological, and molecular studies in milkweeds and Apocynaceae |
| title_sort | draft genome and transcriptome of common milkweed asclepias syriaca as resources for evolutionary ecological and molecular studies in milkweeds and apocynaceae |
| topic | Asclepias Milkweed Apocynaceae Cardenolide Chromosome evolution Genome |
| url | https://peerj.com/articles/7649.pdf |
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