奇蹄目核糖核酸酶基因超家族(RNASE A)的分子进化研究
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摘要
为深入认识核糖核酸酶基因超家族(RNASE A),以奇蹄目的家马、驴、野马和白犀牛为研究对象,分析RNASE A序列、鉴定真假基因、预测等电点及构建系统发育树.结果揭示每个物种的RNASE A序列数并不相同,RNase4在该研究物种分歧之前发生1次基因复制,其中1个拷贝保留功能,另外1个拷贝发生假基因化并在不同物种中有不同程度的保留或丢失,而RNase2/3和RNase7/8经历"基因分拣"进化模式.另外,典型的RNASE A序列特征在RNase9—13中发生变异,揭示RNase9—13可能丢失核糖核酸酶活性而具有其他新功能.总之,该研究系统探讨了奇蹄目RNASE A的分子进化,增加了该基因超家族研究的多样性,为更加深入开展RNASE A研究提供了基础.
To understand the RNASE A superfamily,the authors studied the RNASE A sequences,identified function genes and pseudogenes,calculated isoelectric point and reconstructed phylogenetic tree based on the Equus caballus,Equus asinus,Equus przewalskii and Ceratotherium simum,which belonged to Perissodactyla.The results suggested that the number of the RNASE A sequences was not identical.In the RNase4,one gene duplication event occurred before the divergence of the four species,then one of the duplicates remained functional,the other one got pseudogenized and possessed differential retention and lost in different species,while the evolution pattern of "gene sorting" was detected in the RNase2/3 and RNase7/8.More typical sites were changed in the RNase9-13,which suggested these genes may lack ribonuclease activities,but have acquired new functions.In sum,the present work systematically demonstrated the molecular evolution of Perissodactyla,increased the diversity about the RNASE A superfamily studies,and established an important foundation for further studying the superfamily.
To understand the RNASE A superfamily,the authors studied the RNASE A sequences,identified function genes and pseudogenes,calculated isoelectric point and reconstructed phylogenetic tree based on the Equus caballus,Equus asinus,Equus przewalskii and Ceratotherium simum,which belonged to Perissodactyla.The results suggested that the number of the RNASE A sequences was not identical.In the RNase4,one gene duplication event occurred before the divergence of the four species,then one of the duplicates remained functional,the other one got pseudogenized and possessed differential retention and lost in different species,while the evolution pattern of "gene sorting" was detected in the RNase2/3 and RNase7/8.More typical sites were changed in the RNase9-13,which suggested these genes may lack ribonuclease activities,but have acquired new functions.In sum,the present work systematically demonstrated the molecular evolution of Perissodactyla,increased the diversity about the RNASE A superfamily studies,and established an important foundation for further studying the superfamily.
引文
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[2]MO X C,ZHANG D Q,KOU C,et al.Molecular markers in whole genome evolution of brachypodium[J].Methods Mol Biol,2018,1667:119-137.
[3]LONG M Y,THORNTON K.Gene duplication and evolution[J].Science,2001,293(5535):1551.
[4]YU L,WANG G D,RUAN J,et al.Genomic analysis of snub-nosed monkeys(Rhinopithecus)identifies genes and processes related to high-altitude adaptation[J].Nat Genet,2016,48(8):947-952.
[5]QIU Q,WANG L,WANG K,et al.Yak whole-genome resequencing reveals domestication signatures and prehistoric population expansions[J].Nat Commun,2015,6:10283.
[6]PARKER J,TSAGKOGEORGA G,COTTON J A,et al.Genome-wide signatures of convergent evolution in echolocating mammals[J].Nature,2013,502(7470):228-231.
[7]RUBIN C J,MEGENS H J,MARTINEZ BARRIO A,et al.Strong signatures of selection in the domestic pig genome[J].Proc Natl Acad Sci U S A,2012,109(48):19529-19536.
[8]ZHANG G,COWLED C,SHI Z,et al.Comparative analysis of bat genomes provides insight into the evolution of flight and immunity[J].Science,2013,339(6118):456-460.
[9]CHO S,BEINTEMA J J,ZHANG J.The ribonuclease A superfamily of mammals and birds:identifying new members and tracing evolutionary histories[J].Genomics,2005,85(2):208-220.
[10]CHO S,ZHANG J.Ancient expansion of the ribonuclease A superfamily revealed by genomic analysis of placental and marsupial mammals[J].Gene,2006,373:116-125.
[11]WHEELER T T,MAQBOOL N J,GUPTA S K.Mapping,phylogenetic and expression analysis of the RNase(RNase A)locus in cattle[J].J Mol Evol,2012,74(5/6):237-248.
[12]GOO S M,CHO S.The expansion and functional diversification of the mammalian ribonuclease a superfamily epitomizes the efficiency of multigene families at generating biological novelty[J].Genome Biol Evol,2013,5(11):2124-2140.
[13]郎大田,张亚平,于黎.核糖核酸酶基因超家族分子进化[J].遗传,2014,36(4):316-326.
[14]ZHANG J,ZHANG Y P,ROSENBERG H F.Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey[J].Nat Genet,2002,30(4):411-415.
[15]YU L,ZHANG Y.The unusual adaptive expansion of pancreatic ribonuclease gene in carnivora[J].Mol Biol Evol,2006,23(12):2326-2335.
[16]ZHANG J.Parallel adaptive origins of digestive RNases in Asian and African leaf monkeys[J].Nat Genet,2006,38(7):819-823.
[17]LIU J,WANG X P,CHO S,et al.Evolutionary and functional novelty of pancreatic ribonuclease:a study of Musteloidea(order Carnivora)[J].Sci Rep,2014,4:5070.
[18]ZHANG J,ZHANG Y P.Pseudogenization of the tumor-growth promoter angiogenin in a leaf-eating monkey[J].Gene,2003,308:95-101.
[19]CODONER F M,ALFONSO-LOECHES S,FARES M A.Mutational dynamics of murine angiogenin duplicates[J].BMC Evol Biol,2010,10:310.
[20]ZHANG J,DYER K D,ROSENBERG H F.Evolution of the rodent eosinophil-associated RNase gene family by rapid gene sorting and positive selection[J].Proc Natl Acad Sci USA,2000,97(9):4701-4706.
[21]DYER K D,ROSENBERG H F,ZHANG J.Isolation,characterization,and evolutionary divergence of mouse RNase 6:evidence for unusual evolution in rodents[J].J Mol Evol,2004,59(5):657-665.
[22]DEMING M S,DYER K D,BANKIER A T,et al.Ribonuclease K6:chromosomal mapping and divergent rates of evolution within the RNase A gene superfamily[J].Genome Res,1998,8(6):599-607.
[23]PIETROWSKI D,FORSTER M.Complete cDNA sequence and amino acid analysis of a bovine ribonuclease K6gene[J].DNA Seq,2000,11(3/4):365-371.
[24]ROSE K D,HOLBROOK L T,RANA R S,et al.early eocene fossils suggest that the mammalian order Perissodactyla originated in India[J].Nat Commun,2014,5:5570.
[25]GINGERICH P D.Environment and evolution through the Paleocene-Eocene thermal maximum[J].Trends Ecol Evol,2006,21(5):246-253.
[26]WANG Z,XU S,DU K,et al.Evolution of digestive enzymes and RNASE1provides insights into dietary switch of cetaceans[J].Mol Biol Evol,2016,33(12):3144-3157.
[27]BARNARD E A.Biological function of pancreatic ribonuclease[J].Nature,1969,221(5178):340-344.
[28]HUANG J,ZHAO Y,SHIRAIGOL W,et al.Analysis of horse genomes provides insight into the diversification and adaptive evolution of karyotype[J].Sci Rep,2014,4:4958.
[29]HUANG J,ZHAO Y,BAI D,et al.Corrigendum:donkey genome and insight into the imprinting of fast karyotype evolution[J].Sci Rep,2015,5:17124.
[30]HUANG J,ZHAO Y,BAI D,et al.Donkey genome and insight into the imprinting of fast karyotype evolution[J].Sci Rep,2015,5:14106.
[31]KUMAR S,STECHER G,TAMURA K.Mega7:molecular evolutionary genetics analysis Version 7.0for bigger datasets[J].Mol Biol Evol,2016,33(7):1870-1874.
[32]LARKIN M A,BLACKSHIELDS G,BROWN N P,et al.Clustal W and Clustal X version 2.0[J].Bioinformatics,2007,23(21):2947-2948.
[33]BJELLQVIST B,HUGHES G J,PASQUALI C,et al.The focusing positions of polypeptides in immobilized pH gradients can be predicted from their amino acid sequences[J].Electrophoresis,1993,14(10):1023-1031.
[34]BJELLQVIST B,BASSE B,OLSEN E,et al.Reference points for comparisons of two-dimensional maps of proteins from different human cell types defined in a pH scale where isoelectric points correlate with polypeptide compositions[J].Electrophoresis,1994,15(3/4):529-539.
[35]LANG D T,WANG X P,WANG L,et al.Molecular evolution of pancreatic ribonuclease gene(RNase1)in Rodentia[J].J Genet Genomics,2017,44(4):219-222.