NDLI: Identification of transcriptome SNPs between Xiphophorus lines and species for assessing allele specific gene expression within F1 interspecies hybrids☆

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Identification of transcriptome SNPs between Xiphophorus lines and species for assessing allele specific gene expression within F1 interspecies hybrids☆

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Identification of transcriptome SNPs between Xiphophorus lines and species for assessing allele specific gene expression within F1 interspecies hybrids☆

Content Provider	PubMed Central
Author	Shen, Yingjia Julian, Catchen Garcia, Tzintzuni Amores, Angel Ion, Beldroth Wagner, Jonathon R. Zhang, Ziping Postlethwait, John Warren, Wes Manfred, Schartl Walter, Ronald B.
Copyright Year	2010
Abstract	Variations in gene expression are essential for the evolution of novel phenotypes and for speciation. Studying allelic specific gene expression (ASGE) within interspecies hybrids provides a unique opportunity to reveal underlying mechanisms of genetic variation. Using Xiphophorus interspecies hybrid fishes and high-throughput next generation sequencing technology, we were able to assess variations between two closely related vertebrate species, X. maculatus and X. couchianus, and their F1 interspecies hybrids. We constructed transcriptome-wide SNP polymorphism sets between two highly inbred X. maculatus lines (JP 163 A and B), and between X. maculatus and a second species, X. couchianus. The X. maculatus JP 163 A and B parental lines have been separated in the laboratory for ≈ 70 years and we were able to identify SNPs at a resolution of 1 SNP per 49 kb of transcriptome. In contrast, SNP polymorphisms between X. couchianus and X. maculatus species, which diverged ≈ 5–10 million years ago, were identified about every 700 bp. Using 6,524 transcripts with identified SNPs between the two parental species (X. maculatus and X. couchianus), we mapped RNA-seq reads to determine ASGE within F1 interspecies hybrids. We developed an in silico X. couchianus transcriptome by replacing 90,788 SNP bases for X. maculatus transcriptome with the consensus X. couchianus SNP bases and provide evidence that this procedure overcomes read mapping biases. Employment of the insilico reference transcriptome and tolerating 5 mismatches during read mapping allow direct assessment of ASGE in the F1 interspecies hybrids. Overall, these results show that Xiphophorus is a tractable vertebrate experimental model to investigate how genetic variations that occur during speciation may affect gene interactions and the regulation of gene expression.
Related Links	http://dx.doi.org/10.1016/j.cbpc.2011.03.012
Ending Page	108
Page Count	7
Starting Page	102
File Format	PDF
ISSN	15320456
Journal	Comparative biochemistry and physiology. Toxicology & pharmacology : CBP
Issue Number	1
Volume Number	155
Language	English
Publisher Date	2012-01-01
Access Restriction	Open
Subject Keyword	Toxicology Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Cell Biology Physiology Health, Toxicology and Mutagenesis Medicine Aquatic Science Biochemistry Toxicology Animal Science and Zoology

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