Comprehensive transcripts analysis based on single-molecule real-time sequencing and Illumina sequencing provides insights into the mining of Toll-like receptor family in Schizothorax lissolabiatus

Qian Duan; Qi Luo; Qian Tang; Lei Deng; Renyi Zhang; Yanping Li

doi:10.1016/j.fsi.2023.108963

Comprehensive transcripts analysis based on single-molecule real-time sequencing and Illumina sequencing provides insights into the mining of Toll-like receptor family in Schizothorax lissolabiatus

Fish Shellfish Immunol. 2023 Sep:140:108963. doi: 10.1016/j.fsi.2023.108963. Epub 2023 Jul 21.

Authors

Qian Duan¹, Qi Luo¹, Qian Tang¹, Lei Deng¹, Renyi Zhang², Yanping Li³

Affiliations

¹ School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China.
² School of Life Sciences, Guizhou Normal University, Guiyang, 550025, China. Electronic address: zhangrenyi@gznu.edu.cn.
³ Key Laboratory of Sichuan Province for Fishes Conservation and Utilization in the Upper Reaches of the Yangtze River, College of Life Sciences, Neijiang Normal University, Neijiang, 641100, China. Electronic address: liyanping@njtc.edu.cn.

PMID: 37481099
DOI: 10.1016/j.fsi.2023.108963

Abstract

Schizothorax lissolabiatus is an economically important cold-water fish species in southwestern China. Because of water pollution and habitat destruction, the number of wild populations has dramatically decreased. In this study, we used PacBio single-molecule real-time (SMRT) sequencing and Illumina sequencing to generate the first full-length transcriptome and transcriptome, respectively. A total of 19 310 polished consensus reads (PC) were obtained, with an average length of 1379 bp and an N50 length of 1485 bp. Meanwhile, 12 253 transcripts were successfully annotated as known homologous genes. The pathway annotation indicated that the enrichment and expression of most genes were mainly related to membrane, signal transduction and binding, and immune response. Furthermore, we identified 16 Toll-like receptors (TLRs) by mining the data from the transcripts. Phylogeny analysis showed that S. lissolabiatus TLR genes (slTLRs) supported the classification of TLRs into six families as in other vertebrates. Selection pressure analyses showed that 16 slTLRs revealed purification selection at the overall evolutionary selection. Further, positive selection signals were still detected in eight slTLRs, and most of the positive selection sites were located in the leucine-rich repeat region (LRR domain) associated with the recognition of pathogenic microorganisms, indicating that the function of these slTLR genes may be affected. Tissue specific expression analysis showed all slTLRs are present in kidney, spleen and liver but the relative expression varied among tissues. In conclusion, this study not only provided a valuable resource of transcripts for further research on S. lissolabiatus, but also contributed to improve the current understanding of the evolutionary history of immune-related genes and the TLR gene family in S. lissolabiatus.

Keywords: Evolution; Innate immune; RNA-Seq; Schizothorax lissolabiatus; Toll-like receptors.

MeSH terms

Animals
Cyprinidae* / genetics
Cyprinidae* / metabolism
Gene Expression Profiling / veterinary
High-Throughput Nucleotide Sequencing
Signal Transduction
Toll-Like Receptors* / genetics
Toll-Like Receptors* / metabolism
Transcriptome

Substances

Toll-Like Receptors