叶尔羌高原鳅鳃组织TLRs基因家族成员鉴定及生物信息学分析

Identification and bioinformatics analysis of Toll-like receptor gene family members in Triplophysa yarkandensis

为探究叶尔羌高原鳅(Triplophysa yearkandensis)免疫系统中TLRs基因家族的多样性、进化关系和功能特征,基于该物种鳃组织的高通量二代转录组测序数据进行了生物信息学分析,在对该物种TLRs基因家族进行鉴定的基础上分析了其系统发育和蛋白功能。结果表明,叶尔羌高原鳅鳃组织中存在11个TLRs基因家族成员,分别为TLR1、TLR2、TLR3、TLR5、TLR7、TLR8、TLR9、TLR13、TLR18、TLR22和TLR25,其中TLR7、TLR9和TLR13缺失5′端序列,而其余序列均完整。TLRs基因家族成员系统发育分析发现,可以将11个基因分为5个亚家族。蛋白功能分析发现,各个TLR基因都含有富含亮氨酸重复结构域以及TIR结构域。物种间系统发育分析显示,叶尔羌高原鳅与西藏高原鳅(Triplophysa tibetana)和玫瑰高原鳅(Triplophysa rosa)在TLRs基因家族成员方面分别聚为一类,说明3个物种亲缘关系相近。研究结果有助于深入了解叶尔羌高原鳅TLRs基因家族的进化关系和免疫功能,同时也为该物种的遗传资源保护和养殖利用提供理论基础。

The innate immune system of fish is composed of a series of pattern recognition receptors(PRRs)that can activate the immune system upon recognition of pathogen-associated molecular patterns(PAMPs),leading to immune responses and defense against pathogen invasion.Toll-like receptors(TLRs),located on the cell membranes of fish,are the most important class of recognition receptors for pathogen-associated molecular patterns.Yarkant schizothoracin(Triplophysa yearkandensis),primarily inhabiting the Tarim River Basin,is a migratory fish species and one of the highest-altitude species in cyprinid family.The unique habitat of high-altitude environments characterized by low temperature,low oxygen level,and intense ultraviolet radiation directly impacts the survival of the species.In this environment,aquatic organisms have evolved corresponding adaptations and tolerances.Furthermore,both in the wild and under artificial breeding conditions,Triplophysa yearkandensis is frequently attacked by pathogenic factors such as native organisms and pathogens.To explore the diversity,evolutionary relationships,and functional characteristics of Toll-like receptor(TLR)gene family in the immune system of Triplophysa yearkandensis,this study conducted bioinformatics analysis based on high-throughput second-generation transcriptome sequencing data from the gill tissue of Triplophysa yearkandensis.The seed alignments file of Toll-like receptors was searched in Pfam database,and hidden Markov models(HMM)were used to identify similar sequences in TLR gene protein sequences of other species.After removing redundancies,the Trinity-assembled transcripts from the high-throughput second-generation transcriptome sequencing data of Triplophysa yearkandensis gill tissue were aligned using the local TBLASTN program to identify the TLR gene family.Based on identification of the TLR gene family in this species,protein domain and gene family phylogenetic analysis of TLRs in Triplophysa yearkandensis were conducted.The results revealed the presence of 11 TLR gene family members in the gill tissue of Triplophysa yearkandensis,including TLR1,TLR2,TLR3,TLR5,TLR7,TLR8,TLR9,TLR13,TLR18,TLR22,and TLR25.Among them,TLR7,TLR9,and TLR13 were found to lack 5′end sequence,while the remaining sequences were complete.Phylogenetic analysis of TLR gene family members classified the 11 genes into 5 subfamilies.Protein functional analysis revealed the presence of leucine-rich repeat domains and Toll/interleukin-1 receptor(TIR)domains in each TLR gene.Inter-species phylogenetic analysis demonstrated that Triplophysa yearkandensis,Triplophysa tibetana,and Triplophysa rosa formed distinct clusters in terms of TLR gene family members,indicating a close evolutionary relationship among these three species.This study focused on Triplophysa yearkandensis,a fish species adapted to high-altitude cold environments,and identified the Toll-like receptor(TLR)gene family members in the gill tissue of Triplophysa yearkandensis.The findings contribute to a deeper understanding of the evolutionary relationships and immune function of TLRs in Triplophysa yearkandensis,providing valuable data for the study of Toll-like receptor gene biological evolution.Additionally,this research provides a theoretical foundation for the conservation of genetic resources and utilization of Triplophysa yearkandensis in aquaculture.It also serves as a fundamental database support for species gene family and molecular differentiation studies,explaining species evolution,adaptation of aquatic organisms to high-altitude hypoxia and salinity,and other related research areas.