Genomics / Proteomics
Straub, Shannon C.K. , Fishbein, Mark , Ovchinnikov, Sergey , Cronn, Rich C. , Liston, Aaron .
Partial characterization of the Asclepias syriaca L. (common milkweed) genome using next-generation sequencing.
Milkweeds have long been important models for studies of the evolutionary ecology of plant reproduction, plant hybridization, and plant-herbivore co-evolution. The common milkweed, Asclepias syriaca L., is the most intensively studied milkweed, and as such is an attractive target for the development of genomic resources. As a first step towards a whole genome sequence, genomic DNA from one A. syriaca individual was sequenced using massively parallel sequencing in a single lane of 40 base pair (bp) single end reads on the Illumina GAII sequencing system. The genome of A. syriaca is approximately 800 Mbp and this single run generated 10.5 million reads, yielding ~0.5X genome coverage. Even with this low coverage, several features of the common milkweed genome were successfully characterized using a combination of reference guided and de novo assembly strategies. A complete 155 kbp plastome sequence, with median read depth of 240X, was assembled using the chloroplast genome sequence of Nerium oleander L. as a reference. Other high copy regions of the genome were assembled, including a 7.5 kbp nuclear ribosomal DNA cistron with median read depth of 740X. This study represents the first step in a larger project to sequence the A. syriaca genome with 25X final coverage. The markers obtained through this sequencing effort will be applied to milkweed genetic map development and to estimate phylogenetic relationships among the 135 species of Asclepias. The genome sequence will be a community resource for studies of plant-herbivore coevolution, floral developmental genetics, chemical evolution, population genetics, and comparative genomics.
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1 - Cornell University, L.H. Bailey Hortorium, Department of Plant Biology, Ithaca, New York, 14853, USA
2 - Oklahoma State University, Department of Botany, 104 Life Sciences East, Stillwater, OK, 74078, USA
3 - Portland State University, Biology Department, PO Box 751, Portland, OR, 97207, USA
4 - USDA Forest Service, Forest Genetics, Pacific Nothwest Research Station, 3200 SW Jefferson Way, Corvallis, Oregon, 97331, USA
5 - Oregon State University, Department of Botany and Plant Pathology, 2082 Cordley Hall, Corvallis, OR, 97331, USA
Presentation Type: Oral Paper:Papers for Topics
Location: 551B/Convention Center
Date: Wednesday, August 4th, 2010
Time: 10:30 AM