Full-length transcriptome analysis of Litopenaeus vannamei reveals transcript variants involved in the innate immune system. Issue 87 (April 2019)

• Record Type: Journal Article
• Authors: Zhang, Xiujuan; Li, Guanyu; Jiang, Haiying; Li, Linmiao; Ma, Jinge; Li, Huiming; Chen, Jinping
• Is Part Of: Fish & shellfish immunology. Issue 87(2019)
• Page Start: 346
• Page End: 359
• Publication Date: 2019-04
• Subjects: The Pacific white shrimp -- Litopenaeus vannamei -- Isoform sequencing -- Immune molecules; Fishes -- Immunology -- Periodicals; Shellfish -- Immunology -- Periodicals; Poissons -- Immunologie -- Périodiques; Crustacés -- Immunologie -- Périodiques; 571.9617
• DOI: 10.1016/j.fsi.2019.01.023
• Languages: English
• ISSNs: 1050-4648

Abstract

Abstract: 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. Highlights: The full-length transcriptome analysis of Litopenaeus vannamei provided comprehensive insight in the innate immune system. 72, 648 full-length transcripts with an average length of 2, 545 bp provided new genetic resource. 5, 279 full-length transcripts involved in the innate immune system were successfully identified. Transcript variants increased the number and function complexity of immune molecules. 480 DEGs were significantly higher or tissue-specific expression patterns in the hepatopancreas.