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.

生物学家正通过研究转录组（Transcriptome）——即特定组织内被转录的基因全集——来解析模式生物的基因表达复杂性。然而，由于环境会影响基因表达，目前尚无法确定模式系统的研究结果能否推广至非模式生物。此外，目前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程度。本研究针对3只虎螈（Tiger Salamander）幼体的肺与鳃组织，开展了基因表达的转录组分析（Transcriptomic profiling），并采用层级化实验设计以捕捉基因间、组织间以及个体间的表达变异。本研究采用454焦磷酸测序（454 Pyrosequencing）技术，生成了59兆碱基的高质量序列数据，并将约20万条测序读段（Reads）组装为19501个重叠群（Contigs）。上述重叠群经BLAST比对后，匹配到3599个转录本，其中721个在两种组织中均有表达，1668个仅在鳃组织中特异性表达，1210个仅在肺组织中特异性表达。本研究数据显示，基因表达水平呈现组织特异性模式，且不同转录本与个体间均存在表达变异。本研究鉴定出与呼吸作用相关的基因及基因本体（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性基因证据，并鉴定出约1400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）。鉴于本研究在转录组中观察到的组织特异性差异，上述数据进一步佐证了：基因表达变化是表型可塑性（Phenotypic plasticity）背后的核心调控机制。