Data from: Comparative transcriptomics and gene expression in larval tiger salamander (Ambystoma tigrinum) gill and lung tissues as revealed by pyrosequencing

Biologists are beginning to unravel the complexities of gene expression in model organisms by studying the transcriptome, the complement of genes that are transcribed in a given tissue. It is unclear, however, if findings from model systems apply to non-model organisms because of environmental effects on gene expression. Furthermore, there have been few efforts to quantify how transcriptome or gene expression varies across individuals and across tissues in natural environments. Herein, we describe transcriptomic profiling of gene expression in lung and gill tissue of three larval tiger salamanders. We do so with a hierarchical experimental design that captures variation in expression among genes, among tissues, and among individuals. Using 454 pyrosequencing, we produced high-quality sequence data of 59 megabases and assembled ~200,000 reads into 19,501 contigs. These contigs BLASTed to 3,599 transcripts, of which 721 were expressed in both tissues, 1,668 were unique to gill, and 1,210 unique to lung. Our data showed tissue-specific patterns in gene expression level with variation among transcripts and individuals. We identified genes and gene ontology terms related to respiration and compared their relative expression levels between gill and lung tissues. We also found evidence of exogenous genes associated with larval salamanders, and we identified ~1400 potential molecular markers (microsatellites and single nucleotide polymorphisms) that are associated with expressed genes. Given the tissue-specific differences we observed in transcriptomes, these data reinforce the idea that changes in gene expression serve as a primary mechanism underlying phenotypic plasticity.

生物学家已开始通过研究转录组（transcriptome）——即特定组织中被转录的基因集合——来解析模式生物基因表达的复杂机制。然而，由于环境对基因表达的影响，目前尚不清楚模式生物系统中的研究结果是否适用于非模式生物。此外，鲜有研究尝试量化自然环境中，转录组或基因表达在不同个体与不同组织间的变异情况。本研究针对3只虎螈幼体的肺与鳃组织开展了基因表达转录组分析，采用层级实验设计以捕捉基因间、组织间以及个体间的表达变异。本研究借助454焦磷酸测序技术，获得了59兆碱基的高质量序列数据，并将约200,000条读段（reads）组装为19,501个重叠群（contigs）。这些重叠群经BLAST比对后匹配到3,599个转录本，其中721个在两种组织中均有表达，1,668个仅在鳃组织中表达，1,210个仅在肺组织中表达。本研究数据显示，基因表达水平存在组织特异性模式，且不同转录本与个体间均存在表达变异。我们鉴定出了与呼吸作用相关的基因及基因本体论（gene ontology, GO）条目，并比较了鳃与肺组织中这些基因的相对表达水平。本研究还发现了与虎螈幼体相关的外源基因证据，并鉴定出约1,400个与表达基因相关的潜在分子标记，包括微卫星（microsatellites）与单核苷酸多态性（single nucleotide polymorphisms, SNPs）。鉴于本研究观察到的转录组组织特异性差异，本数据进一步证实：基因表达变化是表型可塑性背后的核心调控机制。