Full-length transcriptome sequencing and comparative transcriptome analysis of Eriocheir sinensis in response to infection by the microsporidian Hepatospora eriocheir

Libo Hou; Mengdi Wang; Lei Zhu; Mingxiao Ning; Jingxiu Bi; Jie Du; Xianghui Kong; Wei Gu; Qingguo Meng

doi:10.3389/fcimb.2022.997574

Full-length transcriptome sequencing and comparative transcriptome analysis of Eriocheir sinensis in response to infection by the microsporidian Hepatospora eriocheir

Front Cell Infect Microbiol. 2022 Dec 1:12:997574. doi: 10.3389/fcimb.2022.997574. eCollection 2022.

Authors

Libo Hou¹, Mengdi Wang¹, Lei Zhu¹, Mingxiao Ning², Jingxiu Bi², Jie Du³, Xianghui Kong¹, Wei Gu⁴, Qingguo Meng⁴

Affiliations

¹ Engineering Lab of Henan Province for Aquatic Animal Disease Control, College of Fisheries, Henan Normal University, Xinxiang, China.
² Institution of Quality Standard and Testing Technology for Agro-product, Shandong Academy of Agricultural Science, Jinan, Shandong, China.
³ Animal Husbandry and Veterinary College, Jiangsu Vocational College of Agriculture and Forestry, Jurong, Jiangsu, China.
⁴ Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, Jiangsu, China.

Abstract

As a new generation of high-throughput sequencing technology, PacBio Iso-Seq technology (Iso-Seq) provides a better alternative sequencing method for the acquisition of full-length unigenes. In this study, a total of 22.27 gigabyte (Gb) subread bases and 128,614 non-redundant unigenes (mean length: 2,324 bp) were obtained from six main tissues of Eriocheir sinensis including the heart, nerve, intestine, muscle, gills and hepatopancreas. In addition, 74,732 unigenes were mapped to at least one of the following databases: Non-Redundant Protein Sequence Database (NR), Gene Ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG), KEGG Orthology (KO) and Protein family (Pfam). In addition, 6696 transcription factors (TFs), 28,458 long non-coding RNAs (lncRNAs) and 94,230 mRNA-miRNA pairs were identified. Hepatospora eriocheir is the primary pathogen of E. sinensis and can cause hepatopancreatic necrosis disease (HPND); the intestine is the main target tissue. Here, we attempted to identify the key genes related to H. eriocheir infection in the intestines of E. sinensis. By combining Iso-Seq and Illumina RNA-seq analysis, we identified a total of 12,708 differentially expressed unigenes (DEUs; 6,696 upregulated and 6,012 downregulated) in the crab intestine following infection with H. eriocheir. Based on the biological analysis of these DEUs, several key processes were identified, including energy metabolism-related pathways, cell apoptosis and innate immune-related pathways. Twelve selected genes from these DEUs were subsequently verified by quantitative real-time PCR (qRT-PCR) analysis. Our findings enhance our understanding of the E. sinensis transcriptome and the specific association between E. sinensis and H. eriocheir infection.

Keywords: Eriocheir sinensis; hepatopancreatic necrosis disease; intestine; microsporidian; third-generation sequencing technology.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Brachyura* / genetics
Gene Expression Profiling
Microsporidia* / genetics
Transcriptome

Supplementary concepts

Hepatospora eriocheir