Genome-wide integrated analysis reveals functions of lncRNA-miRNA-mRNA interactions in Atlantic salmon challenged by Aeromonas salmonicida

Yu-Qing Xia; Jian-Xin Cheng; Ya-Fang Liu; Cheng-Hua Li; Ying Liu; Peng-Fei Liu

doi:10.1016/j.ygeno.2021.12.013

Genome-wide integrated analysis reveals functions of lncRNA-miRNA-mRNA interactions in Atlantic salmon challenged by Aeromonas salmonicida

Genomics. 2022 Jan;114(1):328-339. doi: 10.1016/j.ygeno.2021.12.013. Epub 2021 Dec 18.

Authors

Yu-Qing Xia¹, Jian-Xin Cheng², Ya-Fang Liu³, Cheng-Hua Li⁴, Ying Liu⁵, Peng-Fei Liu⁶

Affiliations

¹ School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China; Key Laboratory of Environment Controlled Aquaculture (KLECA), Ministry of Education, 52 Heishijiao Street, Dalian 116023, China.
² Key Laboratory of Environment Controlled Aquaculture (KLECA), Ministry of Education, 52 Heishijiao Street, Dalian 116023, China; College of Life Science, Liaoning Normal University, Dalian 116081, China.
³ College of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China.
⁴ School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China.
⁵ Key Laboratory of Environment Controlled Aquaculture (KLECA), Ministry of Education, 52 Heishijiao Street, Dalian 116023, China; College of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China.
⁶ Key Laboratory of Environment Controlled Aquaculture (KLECA), Ministry of Education, 52 Heishijiao Street, Dalian 116023, China; College of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China. Electronic address: liupengfei@dlou.edu.cn.

PMID: 34933071
DOI: 10.1016/j.ygeno.2021.12.013

Abstract

Aeromonas salmonicida (A. salmonicida) is a pathogenic bacterium that causes serious problems in the global Atlantic salmon aquaculture industry. In this study, we comprehensively analyzed the profiles of lncRNAs, miRNAs and mRNAs in gills of Atlantic salmon at high-dose A. salmonicida infection (3.06 × 10⁸ CFU/mL), low-dose A. salmonicida infection (3.06 × 10⁵ CFU/mL), and a PBS (100 μL) control. We identified 65 differentially expressed lncRNAs, 41 miRNAs, and 512 mRNAs between the control group and infection groups. Functional analysis showed that these genes were significantly enriched in the p53 signaling pathway, Wnt signaling pathway, mTOR signaling pathway, JAK-STAT signaling pathway, and Toll-like receptor signaling pathway. In addition, we predicted key genes in immune-related pathways and constructed a lncRNA-miRNA-mRNA network based on whole transcriptomic analysis. We further predicted three lncRNA-miRNA-mRNA axes as potential novel biomarkers in regulating the immune response of Atlantic salmon against A. salmonicida infection.

Keywords: Aeromonas salmonicida; Atlantic salmon; Immune response; Non-coding RNA; ceRNA network.

Publication types

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

MeSH terms

Aeromonas salmonicida* / genetics
Aeromonas salmonicida* / metabolism
Animals
MicroRNAs* / genetics
RNA, Long Noncoding* / genetics
RNA, Messenger / genetics
RNA, Messenger / metabolism
Salmo salar* / genetics
Salmo salar* / metabolism

Substances

MicroRNAs
RNA, Long Noncoding
RNA, Messenger