[1]刘 兴,高 波,吉红九,等.鲈形目TLR1和TLR9基因的选择压力分析[J].南京师大学报(自然科学版),2022,45(03):68-78.[doi:10.3969/j.issn.1001-4616.2022.03.010]
　Liu Xing,Gao Bo,Ji Hongjiu,et al.Analysis of Selection Pressure on TLR1 and TLR9 Genes in Perciformes[J].Journal of Nanjing Normal University(Natural Science Edition),2022,45(03):68-78.[doi:10.3969/j.issn.1001-4616.2022.03.010]
点击复制

鲈形目TLR1和TLR9基因的选择压力分析()
分享到：

《南京师大学报（自然科学版）》[ISSN:1001-4616/CN:32-1239/N]

卷:
第45卷
期数:
2022年03期
页码:
68-78
栏目:
生物学
出版日期:
2022-09-15

文章信息/Info

Title:
Analysis of Selection Pressure on TLR1 and TLR9 Genes in Perciformes
文章编号:
1001-4616(2022)03-0068-11
作者:
刘 兴1; 高 波2; 吉红九2; 贾超峰2; 祝 斐2; 孟 乾2; 陈淑吟2; 张志勇2; 徐士霞1
(1.南京师范大学生命科学学院,江苏省生物多样性重点实验室,江苏 南京 210023)(2.江苏省海洋水产研究所,江苏省海水鱼类遗传育种重点实验室,江苏 南通 226007)
Author(s):
Liu Xing1; Gao Bo2; Ji Hongjiu2; Jia Chaofeng2; Zhu Fei2; Meng Qian2;  Chen Shuyin2; Zhang Zhi yong2; Xu Shixia1
(1.School of Life Sciences,Nanjing Normal University,Jiangsu Provincial Key Laboratory of Biodiversity,Nanjing 210023,China)(2.Marine Fisheries Research Institute of Jiangsu Province,Jiangsu Key Laboratory for Genetics and Breeding of Marine Fishes,Nantong 226007,China)
关键词:
鲈形目; TLR1; TLR9; 适应性进化; 先天性免疫
Keywords:
Perciformes; TLR1; TLR9; adaptive evolution; innate immunity
分类号:
Q953
DOI:
10.3969/j.issn.1001-4616.2022.03.010
文献标志码:
A
摘要:
鲈形目(Perciformes)是鱼类中物种丰富度最高的一个目,分布在多个水域,在渔业经济发展中占据着重要地位. 然而,高密度的养殖模式加剧了病原微生物引起的鱼类病害. Toll样受体(Toll-like receptors,TLRs)是先天免疫中的重要蛋白质分子,在病毒以及细菌防御中起重要作用. 本文以TLR1和LTR9为候选基因,共下载了鲈形目17个代表物种的同源序列,通过进化分析探讨该目物种先天性免疫的分子进化基础. 选择压力分析发现TLR1、TLR9基因中分别有16和8个正选择位点被两种方法同时检测到,且86%的位点位于蛋白质富含亮氨酸重复序列(Leucine rich repeat,LRR)结构域. 上述结果提示鲈形目物种面临较高的病原微生物感染的挑战,而这些正选择位点可能导致基因进化出重要的功能改变以抵抗病原体的侵袭. 另外,Free-ratio以及Branch-site模型检测发现基因的正选择具有物种特异性,如TLR1在鲷科的最近共同祖先支以及鲈科最近共同祖先支等受到显著正选择,TLR9也在鲷科的最近共同祖先支受到显著正选择,且这些谱系被报道经常受到病原体的威胁,因此,鲈形目多个谱系受到正选择可能是在长期抵抗病原微生物侵袭中进化的结果. 以上研究结果表明,在长期抵御病原微生物过程中,鲈形目物种的TLR1、TLR9基因可能发生了适应性功能改变.
Abstract:
The Perciformes is an order with the highest species richness in fish,distributed in many waters,and plays an essential role in developing the fishery economy. However,the high-density culture mode aggravates the fish diseases caused by pathogenic microorganisms. Toll-like receptors(TLRs)are essential proteins in innate immunity and play an important role in the defense against bacterial or viral infections. In this paper,TLR1 and LTR9 were used as candidate genes,and the homologous sequences of 17 representative species of Perciformes were downloaded. The molecular evolutionary basis of innate immunity of this species was discussed by evolutionary analysis. Selective pressure analysis showed that the three methods simultaneously detected 16 and 8 positive selection sites in TLR1 and TLR9,respectively. 86% of sites were located in the Leucine rich repeat(LRR)domain. These results suggest that Perciformes species face the challenge of high pathogenic microbial infection. These positive selection sites may lead to critical functional changes in gene evolution to resist pathogen invasion. In addition,free-ratio and branch-site models found that positive selection of genes was species-specific. For example,TLR1 is significantly positively selected in the last common ancestor(LCA)branch of Sparidae and Percidae,and TLR9 is also significantly positively selected in the last common ancestor branch of Sparidae. These lineages are often reported to be threatened by pathogens. Therefore,the positive selection of multiple Perciformes lineages may result from evolution in long-term resistance to pathogenic microorganisms. The above results indicated that TLR1 and TLR9 of Perciformes species may have changed their adaptive functions during the long-term resistance to pathogenic microorganisms.

参考文献/References:

[1]陈大刚,张美昭. 中国海洋鱼类[M]. 山东:中国海洋大学出版社,2015.
[2]LAFFERTY K D,HOFMANN E E. Marine disease impacts,diagnosis,forecasting,management and policy[J]. Philosophical transactions of the royal society b:biological sciences,2016,371(1689):20150200.
[3]AKIRA S,UEMATSU S,TAKEUCHI O. Pathogen recognition and innate immunity[J]. Cell,2006,124(4):783-801.
[4]IWASAKI A,MEDZHITOV R. Regulation of adaptive immunity by the innate immune system. [J]. Science,2010,327(5963):291-295.
[5]王卫卫. 牙鲆免疫系统的结构及其部分免疫细胞的功能研究[D]. 青岛:中国海洋大学,2009.
[6]MACLEOD C,BRYANT C E. Visualising pattern recognition receptor signalling[J]. Biochemical society transactions,2017,45(5):1077-1085.
[7]PIETRETTI D,WIEGERTJES G F. Ligand specificities of Toll-like receptors in fish:indications from infection studies[J]. Developmental & comparative immunology,2014,43(2):205-222.
[8]WANG Y,BI X,CHU Q,et al. Discovery of toll-like receptor 13 exists in the teleost fish:Miiuy croaker(Perciformes,Sciaenidae)[J]. Developmental & comparative immunology,2016,61:25-33.
[9]REYES-BECERRIL M,LPEZ-MEDINA T,ASCENCIO-VALLE F,et al. Immune response of gilthead seabream(Sparus aurata)following experimental infection with Aeromonas hydrophila[J]. Fish & shellfish immunology,2011,31(4):564-570.
[10]MU Y,DING F,CUI P,et al. Transcriptome and expression profiling analysis revealed changes of multiple signaling pathways involved in immunity in the large yellow croaker during Aeromonas hydrophila infection[J]. BMC genomics,2010,11(1):1-14.
[11]MEIJER A H,KRENS S G,RODRIGUEZ I A M,et al. Expression analysis of the Toll-like receptor and TIR domain adaptor families of zebrafish[J]. Molecular immunology,2004,40(11):773-783.
[12]KLASCHIK S,GURSEL I,KLINMAN D M. CpG-mediated changes in gene expression in murine spleen cells identified by microarray analysis[J]. Molecular immunology,2007,44(6):1095-1104.
[13]WU X Y,XIANG L X,HUANG L,et al. Characterization,expression and evolution analysis of Toll-like receptor 1 gene in pufferfish(Tetraodon nigroviridis)[J]. International journal of immunogenetics,2008,35(3):215-225.
[14]QUINIOU S M,BOUDINOT P,BENGTÉN E. Comprehensive survey and genomic characterization of Toll-like receptors(TLRs)in channel catfish,Ictalurus punctatus:identification of novel fish TLRs[J]. Immunogenetics,2013,65(7):511-530.
[15]CAMACHO C,COULOURIS G,AVAGYAN V,et al. BLAST+:architecture and applications[J]. BMC bioinformatics,2009,10(1):1-9.
[16]LÖYTYNOJA A,GOLDMAN N. Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis[J]. Science,2008,320(5883):1632-1635.
[17]CASTRESANA J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis[J]. Molecular biology and evolution,2000,17(4):540-552.
[18]KEANE T M,CREEVEY C J,PENTONY M M,et al. Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified[J]. BMC evolutionary biology,2006,6(1):1-17.
[19]STAMATAKIS A. RAxML version 8:a tool for phylogenetic analysis and post-analysis of large phylogenies[J]. Bioinformatics,2014,30(9):1312-1313.
[20]HUELSENBECK J P,RONQUIST F. MRBAYES:Bayesian inference of phylogenetic trees[J]. Bioinformatics,2001,17(8):754-755.
[21]YANG Z. PAML 4:phylogenetic analysis by maximum likelihood[J]. Molecular biology and evolution,2007,24(8):1586-1591.
[22]SLOSS B L,BILLINGTON N,BURR B M. A molecular phylogeny of the Percidae(Teleostei,Perciformes)based on mitochondrial DNA sequence[J]. Molecular phylogenetics and evolution,2004,32(2):545-562.
[23]POND S L K,FROST S D. Datamonkey:rapid detection of selective pressure on individual sites of codon alignments[J]. Bioinformatics,2005,21(10):2531-2533.
[24]YANG Z,WONG W S,NIELSEN R. Bayes empirical Bayes inference of amino acid sites under positive selection[J]. Molecular biology and evolution,2005,22(4):1107-1118.
[25]吴金炉,曾志南. 鱼类病毒病与鱼类病毒疫苗[J]. 海洋科学,1999(4):6.
[26]LIU W,XIE Y,MA J,et al. IBS:an illustrator for the presentation and visualization of biological sequences[J]. Bioinformatics,2015(20):3359.
[27]ALCAIDE M,EDWARDS S V. Molecular evolution of the toll-like receptor multigene family in birds[J]. Molecular biology and evolution,2011,28(5):1703-1715.
[28]FORNUSKOVÁ A,VINKLER M,PAGÈS M,et al. Contrasted evolutionary histories of two Toll-like receptors(Tlr4 and Tlr7)in wild rodents(MURINAE)[J]. BMC evolutionary biology,2013,13(1):1-17.
[29]GOUNDASHEVA D,ANDONOVA M,IVANOV V. Changes in some parameters of the immune response in rats after cold stress[J]. Journal of veterinary medicine,series b,1994,41(1-10):670-674.
[30]冯东岳,温周瑞. 鱼类病毒病的研究进展及其展望[J]. 养殖与饲料,2011(6):4.
[31]WU M H,LI G Y. Structure and function of the leucine—rich repeat as a protein recognition motif[J]. International journal of pathology and clinical medicine,2006,26(1):35-38.
[32]LI L,HE J,MORI K I,et al. Mass mortalities associated with viral nervous necrosis in hatchery-reared groupers in the People's Republic of China[J]. Fish pathology,2001,36(3):186-188.
[33]SKALL H F,OLESEN N J,MELLERGAARD S. Viral haemorrhagic septicaemia virus in marine fish and its implications for fish farming-A review[J]. Journal of fish diseases,2005,28(9):509-529.

备注/Memo

备注/Memo:
收稿日期:2022-01-27.
基金项目:江苏省农业重大新品种创制项目(PZCZ201744)、江苏省种业振兴“揭榜挂帅”项目(JBGS〔2021〕034).
通讯作者:陈淑吟,研究员,研究方向:鱼类分子遗传与育种. E-mail:shuyinchen89@163.com
更新日期/Last Update: 2022-09-15