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首页> 外文期刊>RSC Advances >De novo assembly of Schizothorax waltoni transcriptome to identify immune-related genes and microsatellite markers
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De novo assembly of Schizothorax waltoni transcriptome to identify immune-related genes and microsatellite markers

机译：从头开始的Schizothorax waltoni转录组的组装，以识别免疫相关基因和微卫星标记

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Schizothorax waltoni ( S. waltoni ) is one kind of the subfamily Schizothoracinae and an indigenous economic tetraploid fish to Tibet in China. It is rated as a vulnerable species in the Red List of China's Vertebrates , owing to overexploitation and biological invasion. S. waltoni plays an important role in ecology and local fishery economy, but little information is known about genetic diversity, local adaptation, immune system and so on. Functional gene identification and molecular marker development are the first and essential step for the following biological function and genetics studies. For this purpose, the transcriptome from pooled tissues of three adult S. waltoni was sequenced and analyzed. Using paired-end reads from the Illumina Hiseq4000 platform, 83?103 transcripts with an N50 length of 2337 bp were assembled, which could be further clustered into 66?975 unigenes with an N50 length of 2087 bp. The majority of the unigenes (58?934, 87.99%) were successfully annotated by 7 public databases, and 15 KEGG pathways of immune-related genes were identified for the following functional research. Furthermore, 19?497 putative simple sequence repeats (SSRs) of 1–6 bp unit length were detected from 14?690 unigenes (21.93%) with an average distribution density of 1?:?3.28 kb. We identified 3590 unigenes (5.36%) containing more than one SSR, providing abundant potential polymorphic markers in functional genes. This is the first reported high-throughput transcriptome analysis of S. waltoni , and it would provide valuable genetic resources for the functional genes involved in multiple biological processes, including the immune system, genetic conservation, and molecular marker-assisted breeding of S. waltoni .
机译：沃氏Schizothorax waltoni（S. waltoni）是Schizothoracinae的一种亚科，是中国西藏自治区的一种经济四倍体鱼类。由于过度开发和生物入侵，它被列为《中国脊椎动物红色名录》中的脆弱物种。沃尔顿链球菌在生态和当地渔业经济中起着重要作用，但是关于遗传多样性，当地适应性，免疫系统等方面的信息知之甚少。功能基因鉴定和分子标记开发是随后生物学功能和遗传学研究的第一步，也是必不可少的步骤。为此，对来自三个成年沃尔顿链球菌的合并组织的转录组进行了测序和分析。使用来自Illumina Hiseq4000平台的成对末端读取，组装了N50长度为2337 bp的83？103个转录本，可以将其进一步聚类为N50长度为2087 bp的66？975个单基因。大多数单基因（58？934，87.99％）已通过7个公共数据库成功注释，并确定了15种KEGG免疫相关基因的途径，用于以下功能研究。此外，从14个690个单基因（21.93％）中检测到19个497个单位长度为1-6 bp的简单序列重复（SSR），平均分布密度为1个：3.28 kb。我们鉴定了3590个单基因（5.36％），其中包含一个以上的SSR，在功能基因中提供了丰富的潜在多态性标记。这是首次报道沃尔顿链球菌的高通量转录组分析，它将为参与多个生物学过程的功能基因提供有价值的遗传资源，包括免疫系统，遗传保护和沃尔顿链球菌的分子标记辅助育种。 。

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