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Abstract Detail

Genomics / Proteomics

Weitemier, Kevin [1], Straub, Shannon [2], Parks, Matt [3], Cronn, Richard [4], Fishbein, Mark [5], Liston, Aaron [6].

The challenge of assembling highly heterozygous genomes from short read sequences.

As genome sequencing efforts expand to a broad range of plant species, multiple challenges have arisen, including the assembly of highly heterozygous genomes from short read sequences. The common milkweed, Asclepias syriaca, is a diploid with an estimated genome size of 820 Mbp. The species is strongly self-incompatible, and thus is predicted to have high levels of heterozygosity. The genome was sequenced to a depth of ca. 40X using the Illumina GAIIx. De novo assembly with ABySS of 132 million paired end reads resulted in 685 million bp of sequence in 6 million contigs with an N50 of 112 bp. Plotting the distribution of sequencing depth per contig reveals a strong peak at 22X coverage, and this appears to represent haplotypes derived from highly heterozygous regions of the genome. A total of 114 million bp of the assembly comprise contigs longer than 1 kbp (N50=3408 bp). These 42830 contigs have a mean sequencing depth of 38X, corresponding to the expected coverage of the diploid genome. Although representing only 14% of the genome, these contigs contain 95% of 923 Asterid conserved orthologous sequences, and 64% of 9266 Catharanthus EST-derived unigenes. These results suggest that the well-assembled portion of the genome contains a significant fraction of the gene space, and provides a large amount of data for the development of sequence-capture probes. We plan to use these markers in linkage mapping of Asclepias syriaca, and population genetic and phylogenetic analyses of Asclepias.

Broader Impacts:

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Related Links:
Milkweed Genome Project

1 - Oregon State University, Botany And Plant Pathology, Cordley Hall 2082, Corvallis, OR, 97331, USA
2 - Oregon State University, Department Of Plant Biology, 2082 Cordley Hall, Corvallis, OR, 97331, USA
3 - Oregon State University, Botany and Plant Pathology, 2082 Cordley Hall, Corvallis, OR, 97331-2902, USA
4 - USDA Forest Service, 3200 SW Jefferson Way, Corvallis, OR, 97330, USA
5 - Oklahoma State University, Dept Of Botany, 301 Physical Science, Stillwater, OK, 74078, USA
6 - Oregon State University, Department Of Botany & Plant Pathology, 2082 Cordley Hall, Corvallis, OR, 97331-2902, USA, 541/737-5301

Genome Assembly
SNP detection
Sequence capture.

Presentation Type: Oral Paper:Papers for Topics
Session: 44
Location: Union B/Hyatt
Date: Wednesday, July 11th, 2012
Time: 11:15 AM
Number: 44013
Abstract ID:329

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