Novel genomic resources for a climate change sensitive mammal: characterization of the American pika transcriptome

BMC Genomics

Research Article

Matthew A Lemay¹  Clayton T Lamb¹  Michael A Russello¹  Kelsey M Robson¹  Philippe Henry² 

[1] Department of Biology, University of British Columbia, Okanagan Campus 3333 University Way, V1V 1V7, Kelowna, BC, Canada;Department of Biology, University of British Columbia, Okanagan Campus 3333 University Way, V1V 1V7, Kelowna, BC, Canada;Ecosystem Science and Management Program, University of Northern British Columbia, 3333 University Way, V2N 4Z9, Prince George, BC, Canada;

关键词: Adaptation;    Elevation gradient;    Next-generation sequencing;    Ochotona princeps;    Population genomics;    Single nucleotide polymorphisms;   

DOI  :  10.1186/1471-2164-14-311

 received in 2012-12-05, accepted in 2013-05-04,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundWhen faced with climate change, species must either shift their home range or adapt in situ in order to maintain optimal physiological balance with their environment. The American pika (Ochotona princeps) is a small alpine mammal with limited dispersal capacity and low tolerance for thermal stress. As a result, pikas have become an important system for examining biotic responses to changing climatic conditions. Previous research using amplified fragment length polymorphisms (AFLPs) has revealed evidence for environmental-mediated selection in O. princeps populations distributed along elevation gradients, yet the anonymity of AFLP loci and lack of available genomic resources precluded the identification of associated gene regions. Here, we harnessed next-generation sequencing technology in order to characterize the American pika transcriptome and identify a large suite of single nucleotide polymorphisms (SNPs), which can be used to elucidate elevation- and site-specific patterns of sequence variation.ResultsWe constructed pooled cDNA libraries of O. princeps from high (1400m) and low (300m) elevation sites along a previously established transect in British Columbia. Transcriptome sequencing using the Roche 454 GS FLX titanium platform generated 780 million base pairs of data, which were assembled into 7,325 high coverage contigs. These contigs were used to identify 24,261 novel SNP loci. Using high resolution melt analysis, we developed 17 of these SNPs into genotyping assays, which were validated with independent DNA samples from British Columbia Canada and Oregon State USA. In addition, we detected haplotypes in the NADH dehydrogenase subunit 5 of the mitochondrial genome that were fixed and different among elevations, suggesting that this may be an informative target gene for studying the role of cellular respiration in local adaptation. We also identified contigs that were unique to each elevation, including a high elevation-specific contig that was a positive match with the hemoglobin alpha chain from the plateau pika, a species restricted to high elevation steppes in Asia. Elevation-specific contigs may represent candidate regions subject to differential levels of gene expression along this elevation gradient.ConclusionsTo our knowledge, this is the first broad-scale, transcriptome-level study conducted within the Ochotonidae, providing novel genomic resources for studying pika ecology, behaviour and population history.

【 授权许可】

CC BY   
© Lemay et al.; licensee BioMed Central Ltd. 2013