Full‐length transcriptome analysis of Litopenaeus vannamei reveals transcript variants involved in the innate immune system
Full‐length transcriptome analysis of Litopenaeus vannamei reveals transcript variants involved in the innate immune system
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DOI：
10.1016/j.fsi.2019.01.023
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发表时间：
2019-04
影响因子：
4.7
通讯作者：
Xiujuan Zhang;Guanyu Li;Haiying Jiang;Linmiao Li;Jing-e Ma;Huiming Li;Jinping Chen
中科院分区：
文献类型：
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作者：
Xiujuan Zhang;Guanyu Li;Haiying Jiang;Linmiao Li;Jing-e Ma;Huiming Li;Jinping Chen
为了更好地了解对虾的免疫系统，本研究结合PacBio异构体测序(Iso-Seq)和Illumina Pair-End Short-Read测序方法，从肝胰腺、心脏胃、心脏、肌肉和幽门胃等5个主要组织中获得了72,648个非冗余全长转录本(Uniges)，平均长度为2545bp。与NR、NT、Swiss-Prot、Pfam、GO、KEGG和COG数据库相比，这些Uniges的注释率较高(62,164，85.57%)。共检测到7544个假定的长非编码RNA(LncRNAs)，1164个非冗余全长转录本(449个UniTransModel)参与了选择性剪接(AS)事件。重要的是，共成功鉴定了5279个非冗余全长Uniges，它们参与了天然免疫系统，包括9个免疫相关过程，19个免疫相关途径和10个其他免疫相关系统。我们还发现了广泛的转录变异体，这增加了免疫分子的数量和功能复杂性；例如，Toll样受体(TLRs)和干扰素调节因子(IRF)。480个差异表达基因(DEG)在肝胰腺组织中的表达模式显著高于在其他四个组织中的表达模式(FDR<；0.05)。此外，使用实时荧光聚合酶链式反应技术验证了选定的六个免疫相关DEG和可能的IRF的表达水平，证实了PacBio Iso-seq结果的可靠性。综上所述，我们的研究结果为鉴定免疫相关基因提供了新的遗传资源，特别是为进一步探索对虾的先天免疫和防御机制提供了宝贵的基因组参考资料。
To better understand the immune system of shrimp, this study combined PacBio isoform sequencing (Iso-Seq) and Illumina paired-end short reads sequencing methods to discover full-length immune-related molecules of the Pacific white shrimp,Litopenaeus vannamei.A total of 72,648 nonredundant full-length transcripts (unigenes) were generated with an average length of 2545 bp from five main tissues, including the hepatopancreas, cardiac stomach, heart, muscle, and pyloric stomach. These unigenes exhibited a high annotation rate (62,164, 85.57%) when compared against NR, NT, Swiss-Prot, Pfam, GO, KEGG and COG databases. A total of 7544 putative long noncoding RNAs (lncRNAs) were detected and 1164 nonredundant full-length transcripts (449 UniTransModels) participated in the alternative splicing (AS) events. Importantly, a total of 5279 nonredundant full-length unigenes were successfully identified, which were involved in the innate immune system, including 9 immune-related processes, 19 immune-related pathways and 10 other immune-related systems. We also found wide transcript variants, which increased the number and function complexity of immune molecules; for example, toll-like receptors (TLRs) and interferon regulatory factors (IRFs). The 480 differentially expressed genes (DEGs) were significantly higher or tissue-specific expression patterns in the hepatopancreas compared with that in other four tested tissues (FDR<0.05). Furthermore, the expression levels of six selected immune-related DEGs and putative IRFs were validated using real-time PCR technology, substantiating the reliability of the PacBio Iso-seq results. In conclusion, our results provide new genetic resources of long-read full-length transcripts data and information for identifying immune-related genes, which are an invaluable transcriptomic resource as genomic reference, especially for further exploration of the innate immune and defense mechanisms of shrimp.