Identification of transcriptome SNPs between Xiphophorus lines and species for assessing allele specific gene expression within F₁ interspecies hybrids.
Identification of transcriptome SNPs between Xiphophorus lines and species for assessing allele specific gene expression within F₁ interspecies hybrids.
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DOI：
10.1016/j.cbpc.2011.03.012
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发表时间：
2012-01
影响因子：
3.9
通讯作者：
Walter, Ronald B.
中科院分区：
文献类型：
--
作者：
Shen, Yingjia;Catchen, Julian;Garcia, Tzintzuni;Amores, Angel;Beldorth, Ion;Wagner, Jonathan;Zhang, Ziping;Postlethwait, John;Warren, Wes;Schartl, Manfred;Walter, Ronald B.
关键词：
基因表达的变异对于新表型的进化和物种形成至关重要。研究种间杂种内的等位基因特异性基因表达（ASGE）为揭示遗传变异的潜在机制提供了独特的机会。利用剑尾鱼种间杂交鱼和高通量下一代测序技术，我们能够评估两种密切相关的脊椎动物物种 X. maculatus 和 X. couchianus 及其 F1 种间杂交鱼之间的变异。我们在两个高度近交的 X. maculatus 品系（JP 163 A 和 B）之间以及 X. maculatus 和第二个物种 X. couchianus 之间构建了全转录组 SNP 多态性集。 X. maculatus JP 163 A 和 B 亲本系已在实验室中分离约 70 年，我们能够以每 49 kb 转录组 1 个 SNP 的分辨率识别 SNP。相比之下，X. couchianus 和 X. maculatus 物种之间的 SNP 多态性在约 5-1000 万年前发生分歧，大约每 700 bp 就被鉴定出一次。使用两个亲本物种（X. maculatus 和 X. couchianus）之间已识别的 SNP 的 6,524 个转录本，我们绘制了 RNA-seq 读数以确定 F1 种间杂种内的 ASGE。我们通过用共有的 X. couchianus SNP 碱基替换 X. maculatus 转录组的 90,788 个 SNP 碱基，开发了计算机 X. couchianus 转录组，并提供了证据证明该过程克服了读取映射偏差。使用 insilico 参考转录组并在读取映射过程中容忍 5 个错配，可以直接评估 F1 种间杂交中的 ASGE。总的来说，这些结果表明剑尾鱼是一种易于处理的脊椎动物实验模型，用于研究物种形成过程中发生的遗传变异如何影响基因相互作用和基因表达的调节。
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.
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影响因子：
2
作者：
Kallman, Klaus D.;Kazianis, Steven
通讯作者：
Kazianis, Steven
影响因子：
4.9
作者：
Fontanillas P;Landry CR;Wittkopp PJ;Russ C;Gruber JD;Nusbaum C;Hartl DL
通讯作者：
Hartl DL
影响因子：
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作者：
Tirosh I;Barkai N;Verstrepen KJ
通讯作者：
Verstrepen KJ
影响因子：
4.4
作者：
Main, Bradley J.;Bickel, Ryan D.;Nuzhdin, Sergey V.
通讯作者：
Nuzhdin, Sergey V.
影响因子：
7
作者：
Emerson, J. J.;Hsieh, Li-Ching;Li, Wen-Hsiung
通讯作者：
Li, Wen-Hsiung