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

摘要: Variations in gene expression are essential for the evolution of novel phenotypes and speciation. Studying allelic specific (ASGE) within interspecies hybrids provides a unique opportunity to reveal underlying mechanisms genetic variation. Using Xiphophorus hybrid fishes high-throughput next generation sequencing technology, we were able assess variations between two closely related vertebrate species, maculatus couchianus, their F(1) hybrids. We constructed transcriptome-wide SNP polymorphism sets highly inbred X. lines (JP 163 A B), second couchianus. The JP B parental have been separated laboratory ≈70 years identify SNPs at resolution 1 per 49 kb transcriptome. In contrast, polymorphisms couchianus which diverged ≈5-10 million ago, identified about every 700 bp. 6524 transcripts with species (X. couchianus), mapped RNA-seq reads determine ASGE developed an silico transcriptome by replacing 90,788 bases consensus provide evidence that this procedure overcomes read mapping biases. Employment reference tolerating 5 mismatches during allow direct assessment Overall, these results show is tractable experimental model investigate how occur speciation may affect interactions regulation expression.