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Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery
Thomas L Parchman1, Katherine S Geist, Johan A Grahnen
1Department of Botany, University of Wyoming, Laramie, WY 82071, USA. tparchma@uwyo.edu
BMC Genomics
|March 18, 2010
Summary
This study generated a large sequence collection for lodgepole pine (P. contorta), identifying thousands of genetic markers. This resource aids population genomics and molecular marker development for non-model pine species.
Area of Science:
- Genomics
- Molecular Biology
- Ecology
Background:
- Large, complex pine genomes (Pinus spp.) hinder genomic resource development.
- Lodgepole pine (P. contorta) is ecologically vital and shows adaptive variation.
- Existing genomic resources are insufficient for non-model pine ecological genomics.
Purpose of the Study:
- To characterize expressed genes in lodgepole pine (P. contorta).
- To develop molecular markers for population and association genetic studies.
- To establish a genomic resource for P. contorta and related pine species.
Main Methods:
- Utilized 454 GS XLR70 Titanium pyrosequencing for cDNA.
- Performed reference-based and de novo assembly of sequencing reads.
- Identified and characterized simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs).
Main Results:
- Generated 586,732 sequencing reads, assembled into 63,657 contigs.
- Identified approximately 17,000 unique genes.
- Characterized thousands of SSRs and SNPs, with successful primer design and amplification for many SSR loci.
Conclusions:
- The generated sequence collection is a significant genomic resource for P. contorta.
- The identified genetic markers will advance research in population and association genetics.
- Next-generation sequencing is effective for marker development in non-model species.
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