Characterization of the miiuy croaker (Miichthys miiuy) transcriptome and development of immune-relevant genes and molecular markers.
Characterization of the miiuy croaker (Miichthys miiuy) transcriptome and development of immune-relevant genes and molecular markers.
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Miiuy Croaker (Miichthys miiuy) 转录组的表征以及免疫相关基因和分子标记的开发
DOI：
10.1371/journal.pone.0094046
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发表时间：
2014
期刊：
影响因子：
3.7
通讯作者：
Xu T
中科院分区：
文献类型：
--
作者：
Che R;Sun Y;Sun D;Xu T
黄花鱼（Miichthys miiuy）是支持捕捞渔业和水产养殖的重要海鱼种。目前，由于病原体和寄生虫引起的疾病限制了该物种的生产和商业价值，限制了该物种的商业规模养殖。由于转录组学和基因组学信息的缺乏，限制了研究人员研究该物种的发病机制和免疫系统的能力。本研究构建了肝脏、脾脏和肾脏的cDNA文库，并利用Illumina配对端测序技术对其进行测序，以进行基因发现和分子标记开发。本研究共获得69,071个unigenes，平均长度为572 bp。其中，45,676篇（66.13%）在公共数据库中被成功标注。用Gene Ontology、Clusters of Orthologous Groups和KEGG pathways对这些unique基因进行了注释。此外，还鉴定和分类了498个免疫相关基因。此外，从69,071个单基因中鉴定出14,885个假定的简单序列重复序列（cSSRs）和8,510个假定的单核苷酸多态性（snp）。结论miuy croaker （Miichthys miiuy）转录组数据为鉴定参与病原体和疾病应答等许多过程的新基因提供了大量资源。此外，本研究发现的数千个潜在的cSSR和SNP标记，对于未来发展分子标记辅助育种计划是重要的资源。
Background The miiuy croaker (Miichthys miiuy) is an important species of marine fish that supports capture fisheries and aquaculture. At present commercial scale aquaculture of this species is limited due to diseases caused by pathogens and parasites which restrict production and limit commercial value. The lack of transcriptomic and genomic information for the miiuy croaker limits the ability of researchers to study the pathogenesis and immune system of this species. In this study we constructed a cDNA library from liver, spleen and kidney which was sequenced using Illumina paired-end sequencing to enable gene discovery and molecular marker development. Principal Findings In our study, a total of 69,071 unigenes with an average length of 572 bp were obtained. Of these, 45,676 (66.13%) were successfully annotated in public databases. The unigenes were also annotated with Gene Ontology, Clusters of Orthologous Groups and KEGG pathways. Additionally, 498 immune-relevant genes were identified and classified. Furthermore, 14,885 putative simple sequence repeats (cSSRs) and 8,510 putative single nucleotide polymorphisms (SNPs) were identified from the 69,071 unigenes. Conclusion The miiuy croaker (Miichthys miiuy) transcriptome data provides a large resource to identify new genes involved in many processes including those involved in the response to pathogens and diseases. Furthermore, the thousands of potential cSSR and SNP markers found in this study are important resources with respect to future development of molecular marker assisted breeding programs for the miiuy croaker.
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