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Abstract Detail


Recent Topics Posters

Cronn, RC [1], Liston, Aaron [2], Syring, John V. [3], Whittall, Justen B. [4], Parks, Matthew [5], Buenrostro, Jason [4], Grachico, Ismael [3].

Chloroplast Population Genomics In Narrowly-Endemic And Widespread Species Of Pinus .

Recent, dramatic improvements in next-generation sequencing make it possible to acquire entire simple genomes at a fraction of the time and cost of traditional approaches. These high-throughput platforms, when used in conjunction with multiplex sequencing tags, can be used to obtain organelle genome sequences to provide unprecedented insights into population and evolutionary history. Here, we highlight results of three studies in Pinus that were enabled by Multiplex Sequencing-By-Synthesis (MSBS) on the Illumina Genome Analyzer: (1) identifying population specific polymorphisms in the chloroplast genome of the narrowly endemic Torrey pine (Pinus torreyana); (2) characterizing regional chloroplast genome diversity in the widespread western white pine (Pinus monticola); and (3) conducting phylogenetic analysis in Pinus using whole chloroplast genomes. Previous studies of cpDNA variation in P. torreyana have failed to detect variation, despite the interrogation of 17 cpSSR loci, 150 restriction sites, and 3.4 kbp of sequence data. Sequencing of chloroplast genomes from two individuals (San Diego, CA; Santa Rosa Island, CA) resulted in assemblies of ~105 kbp/genome (87% complete). We identified five nucleotide polymorphisms, and these differences are fixed between island and mainland populations in a sample of 170 trees. In the second study, range wide chloroplast genome variation was assessed from 31 individuals of P. monticola across a 40 kbp contiguous segment. This screen revealed polymorphism with limited geographic structure—a pattern that is shown to be distinctive from the nuclear genome and provides insight into the post-Pleistocene history of this species. Finally, full-length chloroplast genomes were used in a phylogenetic analysis of 35 species of Pinus representing ca. one-third of the overall diversity. Results show robust differences for all tested species and a tree with ≥ 95% bootstrap support at 33/36 nodes. The assembled genomes in these three studies provide a wealth of information on the pace of molecular evolution.


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1 - USDA Forest Service, Forest Genetics, Pacific Nothwest Research Station, 3200 SW Jefferson Way, Corvallis, Oregon, 97331, USA
2 - Oregon State University, Department of Botany & Plant Pathology, 2082 Cordley Hall, Corvallis, Oregon, 97331-2902, USA
3 - Linfield College, Biology, 900 SE Baker St., McMinnville, OR, 97128, USA
4 - Santa Clara University, Biology Department, 500 El Camino Real, Santa Clara, CA, 95053, USA
5 - Oregon State University, Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, 97331, USA

Keywords:
next-gen
MSBS
multiplex
Pinus
pine
organellar
Chloroplast
population genetics.

Presentation Type: Recent Topics Poster
Session: P2
Location: Event Tent/Cliff Lodge
Date: Tuesday, July 28th, 2009
Time: 5:30 PM
Number: P2RT002
Abstract ID:1203


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