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Abstract Detail

Recent Topics Posters

Whittall, Justen B. [1], Buenrostro, Jason [1], Parks, Matthew [2], Cronn, RC [3], Liston, Aaron [4].

Finding a pine needle in a haystack: Using microread sequencing of the chloroplast genome to locate cryptic genetic diversity in the narrow endemic Pinus torreyana.

Torrey pine (Pinus torreyana) is one of the rarest pine species in the world restricted to two small populations in southern California, separated by 280 km of Pacific Ocean. Approximately 3,400 trees grow in a mainland population north of San Diego, while ca. 2000 trees occur on the northeast side of Santa Rosa Island, one of California’s Northern Channel Islands. The species is also noteworthy for very low levels of genetic diversity as measured by allozymes (157 trees were homozygous at 59 loci; two loci had fixed differences between the two populations) and cpDNA. Three cpDNA studies using 17 cpSSR loci, 150 restriction sites, and 3.4 kilobase pairs (kbp) of sequence data found no within or between population chloroplast DNA variation. Herein, we have sequenced ca. 87.5% of the chloroplast genomes of one mainland and one island accession of Torrey pine, using microread sequencing by synthesis technology (Illumina/Solexa). The source DNA was 35 PCR-amplified regions that represent the entire chloroplast genome (each region averaging 3.4 kbp each). For each accession, 1.11-1.15 million 36 bp sequence reads were obtained. Analysis with two de novo assembly programs, Edena and Velvet, resulted in 99-110 contigs that when aligned to the cp genome of Pinus ponderosa, resulted in assemblies of 108.3 and 108.6 kbp. After excluding two amplicons (one per accession) that appear to be nuclear nomad pseudogenes, ca. 98 kbp of sequence was available for comparison. Five single nucleotide polymorphisms (SNPs) were initially identified and confirmed with Sanger sequencing. Fifty to 100 trees from each population will be genotyped for these 5 SNPs using CAPs and dCAPs assays to determine the evolutionary distinctiveness of these two disjunct populations.

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Related Links:
Justen Whittall's Plant Evolution Lab
Torrey Pines State Natural Reserve
Channel Islands National Park
Pine Trees: Tree of Life

1 - Santa Clara University, Biology Department, 500 El Camino Real, Santa Clara, CA, 95053, USA
2 - Oregon State University, Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, USA
3 - USDA Forest Service, Forest Genetics, Pacific Nothwest Research Station, 3200 SW Jefferson Way, Corvallis, Oregon, 97331, USA
4 - Oregon State University, Department of Botany & Plant Pathology, 2082 Cordley Hall, Corvallis, Oregon, 97331-2902, USA

Pinus torreyana
chloroplast genome
San Diego
Santa Rosa Island
conservation genomics.

Presentation Type: Recent Topics Poster
Session: P
Location: Ball Room & Party Room/SUB
Date: Monday, July 28th, 2008
Time: 12:30 PM
Number: PRT018
Abstract ID:1146

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