Full-length transcriptome analysis of Litopenaeus vannamei reveals transcript variants involved in the innate immune system

Xiujuan Zhang; Guanyu Li; Haiying Jiang; Linmiao Li; Jinge Ma; Huiming Li; Jinping Chen

doi:10.1016/j.fsi.2019.01.023

Full-length transcriptome analysis of Litopenaeus vannamei reveals transcript variants involved in the innate immune system

Fish Shellfish Immunol. 2019 Apr:87:346-359. doi: 10.1016/j.fsi.2019.01.023. Epub 2019 Jan 21.

Authors

Xiujuan Zhang¹, Guanyu Li¹, Haiying Jiang¹, Linmiao Li¹, Jinge Ma¹, Huiming Li¹, Jinping Chen²

Affiliations

¹ Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, 510260, China.
² Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, Guangdong, 510260, China. Electronic address: Chenjp@giabr.gd.cn.

PMID: 30677515
DOI: 10.1016/j.fsi.2019.01.023

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.

Keywords: Immune molecules; Isoform sequencing; Litopenaeus vannamei; The Pacific white shrimp.

MeSH terms

Animals
Gene Expression Profiling
Immunity, Innate / genetics*
Penaeidae / genetics*
Penaeidae / immunology*
Real-Time Polymerase Chain Reaction
Transcriptome / immunology*