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首页> 外文期刊>BMC Genomics >Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing
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Characterisation of the transcriptome of a wild great tit Parus major population by next generation sequencing

机译：野生山雀大山雀主要种群的转录组的下一代测序

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Background The recent development of next generation sequencing technologies has made it possible to generate very large amounts of sequence data in species with little or no genome information. Combined with the large phenotypic databases available for wild and non-model species, these data will provide an unprecedented opportunity to "genomicise" ecological model organisms and establish the genetic basis of quantitative traits in natural populations. Results This paper describes the sequencing, de novo assembly and analysis from the transcriptome of eight tissues of ten wild great tits. Approximately 4.6 million sequences and 1.4 billion bases of DNA were generated and assembled into 95,979 contigs, one third of which aligned with known Taeniopygia guttata (zebra finch) and Gallus gallus (chicken) transcripts. The majority (78%) of the remaining contigs aligned within or very close to regions of the zebra finch genome containing known genes, suggesting that they represented precursor mRNA rather than untranscribed genomic DNA. More than 35,000 single nucleotide polymorphisms and 10,000 microsatellite repeats were identified. Eleven percent of contigs were expressed in every tissue, while twenty one percent of contigs were expressed in only one tissue. The function of those contigs with strong evidence for tissue specific expression and contigs expressed in every tissue was inferred from the gene ontology (GO) terms associated with these contigs; heart and pancreas had the highest number of highly tissue specific GO terms (21.4% and 28.5% respectively). Conclusions In summary, the transcriptomic data generated in this study will contribute towards efforts to assemble and annotate the great tit genome, as well as providing the markers required to perform gene mapping studies in wild populations.
机译：背景技术下一代测序技术的最新发展使得有可能在几乎没有或没有基因组信息的物种中产生大量的序列数据。结合可用于野生和非模式物种的大型表型数据库，这些数据将为“生态”模式生物的“基因组化”和建立自然种群数量性状的遗传基础提供前所未有的机会。结果本文描述了从十只野生大山雀的八种组织的转录组中测序，从头组装和分析。产生了大约460万个序列和14亿个DNA碱基，并将其组装成95,979个重叠群，其中三分之一与已知的Taeniopygia guttata（斑雀雀）和Gallus gallus（鸡）转录本对齐。其余重叠群中的大多数（78％）在含有已知基因的斑马雀科基因组区域内排列或非常接近，这表明它们代表前体mRNA而非未转录的基因组DNA。鉴定出超过35,000个单核苷酸多态性和10,000个微卫星重复。重叠群的11％在每个组织中表达，而重叠群的21％仅在一个组织中表达。从与这些重叠群相关的基因本体论（GO）术语可以推断出这些重叠群的功能，这些重叠群具有明显的组织特异性表达和在每个组织中表达的重叠群。心脏和胰腺具有最高的组织特异性GO术语数量（分别为21.4％和28.5％）。结论总之，本研究产生的转录组数据将有助于组装和注释大山雀基因组，并提供在野生种群中进行基因作图研究所需的标记。

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