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首页> 外文期刊>International Journal of Molecular Sciences >Optimizing Hybrid de Novo Transcriptome Assembly and Extending Genomic Resources for Giant Freshwater Prawns ( Macrobrachium rosenbergii ): The Identification of Genes and Markers Associated with Reproduction
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Optimizing Hybrid de Novo Transcriptome Assembly and Extending Genomic Resources for Giant Freshwater Prawns ( Macrobrachium rosenbergii ): The Identification of Genes and Markers Associated with Reproduction

机译：优化杂种从头转录组组装并扩展淡水虾（罗氏沼虾）的基因组资源：与繁殖相关的基因和标记的鉴定

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The giant freshwater prawn, Macrobrachium rosenbergii , a sexually dimorphic decapod crustacean is currently the world’s most economically important cultured freshwater crustacean species. Despite its economic importance, there is currently a lack of genomic resources available for this species, and this has limited exploration of the molecular mechanisms that control the M. rosenbergii sex-differentiation system more widely in freshwater prawns. Here, we present the first hybrid transcriptome from M. rosenbergii applying RNA-Seq technologies directed at identifying genes that have potential functional roles in reproductive-related traits. A total of 13,733,210 combined raw reads (1720 Mbp) were obtained from Ion-Torrent PGM and 454 FLX. Bioinformatic analyses based on three state-of-the-art assemblers, the CLC Genomic Workbench, Trans-ABySS, and Trinity, that use single and multiple k -mer methods respectively, were used to analyse the data. The influence of multiple k -mers on assembly performance was assessed to gain insight into transcriptome assembly from short reads. After optimisation, de novo assembly resulted in 44,407 contigs with a mean length of 437 bp, and the assembled transcripts were further functionally annotated to detect single nucleotide polymorphisms and simple sequence repeat motifs. Gene expression analysis was also used to compare expression patterns from ovary and testis tissue libraries to identify genes with potential roles in reproduction and sex differentiation. The large transcript set assembled here represents the most comprehensive set of transcriptomic resources ever developed for reproduction traits in M. rosenbergii , and the large number of genetic markers predicted should constitute an invaluable resource for future genetic research studies on M . rosenbergii and can be applied more widely on other freshwater prawn species in the genus Macrobrachium .
机译：巨大的淡水虾罗氏沼虾（Macrobrachium rosenbergii），是一种有性的十足纲甲壳动物，目前是世界上经济上最重要的养殖淡水甲壳动物。尽管具有经济重要性，但目前尚缺乏该物种的基因组资源，这在控制淡水虾中更广泛地控制罗氏沼虾性别分化系统的分子机制方面受到了限制。在这里，我们介绍了罗氏沼虾的第一个杂交转录组，该研究组应用了RNA-Seq技术，旨在鉴定在生殖相关性状中具有潜在功能的基因。从Ion-Torrent PGM和454 FLX获得了总计13,733,210个合并的原始读段（1720 Mbp）。基于三个最先进的汇编程序（CLC基因组工作台，Trans-ABySS和Trinity）的生物信息学分析分别使用单个和多个k-mer方法进行了分析。评估了多个k聚体对组装性能的影响，以通过短读获得对转录组组装的了解。优化后，从头组装产生了44407个contig，平均长度为437 bp，组装的转录本进一步进行了功能注释，以检测单核苷酸多态性和简单的序列重复基序。基因表达分析还用于比较卵巢和睾丸组织文库的表达模式，以鉴定在生殖和性别分化中具有潜在作用的基因。这里组装的大量转录物代表了有史以来为罗氏沼虾繁殖性状开发的最全面的转录物资源集，预测的大量遗传标记应该构成未来对芒氏梭菌的遗传研究的宝贵资源。罗氏沼虾（Rosenbergii），可以更广泛地应用于Macrobrachium属中的其他淡水虾种。

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