De novo assembly of mud loach (Misgurnus anguillicaudatus) skin transcriptome to identify putative genes involved in immunity and epidermal mucus secretion.
De novo assembly of mud loach (Misgurnus anguillicaudatus) skin transcriptome to identify putative genes involved in immunity and epidermal mucus secretion.
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从头组装泥鳅（Misgurnus anguillicaudatus）皮肤转录组以鉴定参与免疫和表皮粘液分泌的推定基因
DOI：
10.1371/journal.pone.0056998
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Cui Z
中科院分区：
文献类型：
--
作者：
Long Y;Li Q;Zhou B;Song G;Li T;Cui Z
鱼皮是抵御各种化学、物理和生物应激源的第一道防线。粘液的分泌是鱼皮最显着的特征之一，表皮粘液中已鉴定出许多先天免疫因子。然而，由于缺乏大多数经济上重要的鱼类的基因组和转录组数据，鱼皮粘液分泌和免疫活性的分子机制仍不清楚。在本研究中，我们使用 Illumia 双端测序对泥鳅的皮肤转录组进行了表征。总共 40364 个 unigenes 由 8660 万（3.07 GB）过滤读数组装而成。组装转录本的平均长度、N50 大小和最大长度分别为 387、611 和 8670 bp。通过对 NCBI 非冗余蛋白数据库进行 Blast 搜索，总共注释了 17336 个（43.76%）unigenes。基因本体映射将总共 108513 个 GO 术语分配给 15369 个（38.08%）unigenes。 KEGG 直系同源图谱注释了 9337 个（23.23%）unigenes。在已确定的KO类别中，免疫系统是最大的类别，包含趋化因子信号传导、白细胞跨内皮迁移和T细胞受体信号传导等多种免疫途径的各个组成部分，这表明鱼皮免疫机制的复杂性。至于粘蛋白生物合成，37个unigenes被定位到粘蛋白型O-聚糖生物合成途径的7种酶，并鉴定出多肽N-乙酰半乳糖氨基转移酶家族的8个成员。此外，38个unigenes被映射到囊泡运输途径中SNARE相互作用的23个因子，表明该途径的活性是表皮粘液储存和释放过程所必需的。此外，在 1564 个单基因中检测到 1754 个简单序列重复（SSR），其中二核苷酸重复代表了最丰富的类型。这些发现为进一步了解泥鳅皮肤粘液的分泌过程和免疫功能奠定了基础。
Fish skin serves as the first line of defense against a wide variety of chemical, physical and biological stressors. Secretion of mucus is among the most prominent characteristics of fish skin and numerous innate immune factors have been identified in the epidermal mucus. However, molecular mechanisms underlying the mucus secretion and immune activities of fish skin remain largely unclear due to the lack of genomic and transcriptomic data for most economically important fish species. In this study, we characterized the skin transcriptome of mud loach using Illumia paired-end sequencing. A total of 40364 unigenes were assembled from 86.6 million (3.07 gigabases) filtered reads. The mean length, N50 size and maximum length of assembled transcripts were 387, 611 and 8670 bp, respectively. A total of 17336 (43.76%) unigenes were annotated by blast searches against the NCBI non-redundant protein database. Gene ontology mapping assigned a total of 108513 GO terms to 15369 (38.08%) unigenes. KEGG orthology mapping annotated 9337 (23.23%) unigenes. Among the identified KO categories, immune system is the largest category that contains various components of multiple immune pathways such as chemokine signaling, leukocyte transendothelial migration and T cell receptor signaling, suggesting the complexity of immune mechanisms in fish skin. As for mucin biosynthesis, 37 unigenes were mapped to 7 enzymes of the mucin type O-glycan biosynthesis pathway and 8 members of the polypeptide N-acetylgalactosaminyltransferase family were identified. Additionally, 38 unigenes were mapped to 23 factors of the SNARE interactions in vesicular transport pathway, indicating that the activity of this pathway is required for the processes of epidermal mucus storage and release. Moreover, 1754 simple sequence repeats (SSRs) were detected in 1564 unigenes and dinucleotide repeats represented the most abundant type. These findings have laid the foundation for further understanding the secretary processes and immune functions of loach skin mucus.
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4.7
作者：
Aranishi, F
通讯作者：
Aranishi, F
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