title: Identification of transcriptome SNPs between Xiphophorus lines and species for assessing allele specific gene expression within F₁ interspecies hybrids.
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, Xiphophorus maculatus and Xiphophorus couchianus, and their F(1) 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 6524 transcripts with identified SNPs between the two parental species (X. maculatus and X. couchianus), we mapped RNA-seq reads to determine ASGE within F(1) 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 in silico reference transcriptome and tolerating 5 mismatches during read mapping allow direct assessment of ASGE in the F(1) 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.
authors.affiliation: Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA.
authors.forename: Yingjia
authors.initials: Y
authors.lastname: Shen
authors.forename: Julian
authors.initials: J
authors.lastname: Catchen
authors.forename: Tzintzuni
authors.initials: T
authors.lastname: Garcia
authors.forename: Angel
authors.initials: A
authors.lastname: Amores
authors.forename: Ion
authors.initials: I
authors.lastname: Beldorth
authors.forename: Jonathan
authors.initials: J
authors.lastname: Wagner
authors.forename: Ziping
authors.initials: Z
authors.lastname: Zhang
authors.forename: John
authors.initials: J
authors.lastname: Postlethwait
authors.forename: Wes
authors.initials: W
authors.lastname: Warren
authors.forename: Manfred
authors.initials: M
authors.lastname: Schartl
authors.forename: Ronald B
authors.initials: RB
authors.lastname: Walter
mesh_terms: D000483:Alleles; D000818:Animals; D002678:Chimera / Q000235:genetics* / Q000378:metabolism; D016384:Consensus Sequence; D003532:Cyprinodontiformes / Q000235:genetics* / Q000378:metabolism; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods; D005786:Gene Expression Regulation; D049810:Genetic Speciation; D008297:Male; D020641:Polymorphism, Single Nucleotide; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D013045:Species Specificity; D059467:Transcriptome
chemical_list: D012333:RNA, Messenger