寄生蜂细胞色素P450基因家族进化分析
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摘要
寄生蜂是重要的天敌昆虫,被广泛应用于生物防治,但在实际生产应用中面临诸多问题,如环境适应性和耐药性问题。细胞色素P450是真核生物中广泛存在的超基因家族酶系,参与农药、植物次生代谢物及环境有害物质等的代谢,同时也参与昆虫体内多种内源性化合物的合成与代谢。本文通过对植食性榕小蜂和9种寄生蜂基因组数据的生物信息学分析,共获得615个P450基因,分析表明不同寄生蜂P450基因家族的差异主要发生在CYP3和CYP4簇,而CYP2和Mito簇相对保守;相较于外寄生蜂,内寄生蜂的P450超基因家族有明显的收缩现象;此外,发现了2个在寄生蜂中1:1:1高度保守的P450基因,CYP18和CYP314,以及茧蜂特有的CYP304基因和内寄生蜂特有的CYP28基因。本研究从基因组水平系统地分析了寄生蜂P450超基因家族的进化,为寄生蜂的遗传改良和规模化饲养等提供理论基础。
Parasitoid wasps are important natural enemy insects and are widely used in biological control. However,their applications in pest control face many problems, such as environmental adaptability and insecticide resistance.Cytochrome P450 is a supergene family of enzymes widely found in eukaryotes. It is involved in the metabolism of pesticides, plant secondary metabolites, etc. It is also involved in the synthesis and metabolism of hormones in insects. In this study, total 615 P450 genes were obtained by bioinformatics analysis from the Ceratosolen solmsi and 9 parasitoid wasp genome data. The analysis showed that the variance of P450 gene family in different parasitoid wasps mainly occurred in CYP3 and CYP4 clans, while CYP2 and Mito clans were relatively conserved.In the ectoparasitoids, the P450 supergene family of parasitoid wasps showed significant contraction. In addition,two P450 genes, CYP18 and CYP314, were highly 1:1:1 orthologous conserved in the parasitoid wasp, as well as the Braconidae specific gene CYP304 and the endoparasitoid specific gene CYP28. This study systematically analyzed the evolution of the parasitoid wasp P450 supergene family by comparative genomic analyses, and laid the foundation for the genetic improvement and large-scale breeding of parasitoid wasps in the future.
Parasitoid wasps are important natural enemy insects and are widely used in biological control. However,their applications in pest control face many problems, such as environmental adaptability and insecticide resistance.Cytochrome P450 is a supergene family of enzymes widely found in eukaryotes. It is involved in the metabolism of pesticides, plant secondary metabolites, etc. It is also involved in the synthesis and metabolism of hormones in insects. In this study, total 615 P450 genes were obtained by bioinformatics analysis from the Ceratosolen solmsi and 9 parasitoid wasp genome data. The analysis showed that the variance of P450 gene family in different parasitoid wasps mainly occurred in CYP3 and CYP4 clans, while CYP2 and Mito clans were relatively conserved.In the ectoparasitoids, the P450 supergene family of parasitoid wasps showed significant contraction. In addition,two P450 genes, CYP18 and CYP314, were highly 1:1:1 orthologous conserved in the parasitoid wasp, as well as the Braconidae specific gene CYP304 and the endoparasitoid specific gene CYP28. This study systematically analyzed the evolution of the parasitoid wasp P450 supergene family by comparative genomic analyses, and laid the foundation for the genetic improvement and large-scale breeding of parasitoid wasps in the future.
引文
[1]Peters R S,Krogmann L,Mayer C,et al.Evolutionary history of the Hymenoptera[J].Current Biology,2017,27(7):1013-1018.
[2]Branstetter M G,Childers A K,Cox-Foster D,et al.Genomes of the Hymenoptera[J].Current Opinion in Insect Science,2018,25:65-75.
[3]Werren J H,Richards S,Desjardins C A,et al.Functional and evolutionary insights from the genomes of three parasitoid Nasonia species[J].Science,2010,327(5963):343-348.
[4]Burke G R,Walden K K,Whitfield J B,et al.Widespread genome reorganization of an obligate virus mutualist[J].PLoS Genetics,2014,10(9):e1004660.
[5]Geib S M,Liang G H,Murphy T D,et al.Whole genome sequencing of the braconid parasitoid wasp Fopius arisanus,an important biocontrol agent of pest tepritid fruit flies[J].G3(Bethesda),2017,7(8):2407-2411.
[6]Yin C,Li M,Hu J,et al.The genomic features of parasitism,polyembryony and immune evasion in the endoparasitic wasp Macrocentrus cingulum[J].BMC Genomics,2018,19(1):420.
[7]Lindsey A R I,Kelkar Y D,Wu X,et al.Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum[J].BMC Biology,2018,16(1):54.
[8]Xiao J H,Yue Z,Jia L Y,et al.Obligate mutualism within a host drives the extreme specialization of a fig wasp genome[J].Genome Biology,2013,14(12):R141.
[9]Feyereisen R.Insect CYP genes and P450 enzymes[M]//Insect Molecular Biology and Biochemistry.Academic Press,2012,236-316.
[10]艾均文,孟繁利,贾孟周,等.昆虫细胞色素P450的研究进展[C].中国蚕学会第六届青年学术研讨会论文集,2009,10.
[11]杨帆,王进军.昆虫细胞色素P450与抗药性关系研究进展[J].四川动物,2008(3):460-463.
[12]刘金定,李飞.丽蝇蛹集金小蜂P450基因家族的发现和分子进化分析[J].中国生物防治学报,2013,29(4):490-496.
[13]El-Gebali S,Mistry J,Bateman A,et al.The Pfam protein families database in 2019[J].Nucleic Acids Research,2018,47(D1):D427-D432.
[14]Sayers E W,Agarwala R,Bolton E E,et al.Database resources of the National Center for Biotechnology Information[J].Nucleic Acids Research,2019,47(D1):D23-D28.
[15]Yin C,Shen G,Guo D,et al.InsectBase:a resource for insect genomes and transcriptomes[J].Nucleic Acids Research,2016,44(D1):D801-807.
[16]Birney E,Clamp M,Durbin R.GeneWise and genomewise[J].Genome Research,2004,14(5):988-995.
[17]Katoh K,Misawa K,Kuma K,et al.MAFFT:a novel method for rapid multiple sequence alignment based on fast Fourier transform[J].Nucleic Acids Research,2002,30(14):3059-3066.
[18]Capella-Gutierrez S,Silla-Martinez J M,Gabaldon T.trimAl:a tool for automated alignment trimming in large-scale phylogenetic analyses[J].Bioinformatics,2009,25(15):1972-1973.
[19]Nguyen L T,Schmidt H A,von Haeseler A,et al.IQ-TREE:a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies[J].Molecular Biology and Evolution,2015,32(1):268-274.
[20]Kalyaanamoorthy S,Minh B Q,Wong T K F,et al.ModelFinder:fast model selection for accurate phylogenetic estimates[J].Nature Methods,2017,14(6):587-589.
[21]Stamatakis A.RAxML version 8:a tool for phylogenetic analysis and post-analysis of large phylogenies[J].Bioinformatics,2014,30(9):1312-1313.
[22]Wang F,Fang Q,Wang B,et al.A novel negative-stranded RNA virus mediates sex ratio in its parasitoid host[J].PLOS Pathogens,2017,13(3):e1006201.
[23]Yan Z,Fang Q,Liu Y,et al.A venom serpin splicing isoform of the endoparasitoid wasp Pteromalus puparum suppresses host prophenoloxidase cascade by forming complexes with host hemolymph proteinases[J].Journal of Biological Chemistry,2017,292(3):1038-1051.
[24]Teng Z W,Xu G,Gan S Y,et al.Effects of the endoparasitoid Cotesia chilonis(Hymenoptera:Braconidae)parasitism,venom,and calyx fluid on cellular and humoral immunity of its host Chilo suppressalis(Lepidoptera:Crambidae)larvae[J].Journal of Insect Physiology,2016,85(1):46-56.
[25]Wang Z Z,Ye X Q,Shi M,et al.Parasitic insect-derived miRNAs modulate host development[J].Nature Communications,2018,9(1):2205.
[26]Tan C W,Peiffer M,Hoover K,et al.Symbiotic polydnavirus of a parasite manipulates caterpillar and plant immunity[J].Proceedings of the National Academy of Sciences of the United States of America,2018,115(20):5199-5204.
[27]Zhu F,Cusumano A,Bloem J,et al.Symbiotic polydnavirus and venom reveal parasitoid to its hyperparasitoids[J].Proceedings of the National Academy of Sciences of the United States of America,2018,115(20):5205-5210.
[28]Kubota A,Stegeman J J,Goldstone J V,et al.Cytochrome P450 CYP2 genes in the common cormorant:Evolutionary relationships with 130 diapsid CYP2 clan sequences and chemical effects on their expression[J].Comparative Biochemistry and Physiology Part C:Toxicology and Pharmacology,2011,153(3):280-289.
[29]Zhu F,Moural T W,Shah K,et al.Integrated analysis of cytochrome P450 gene superfamily in the red flour beetle,Tribolium castaneum[J].BMCGenomics,2013,14(1):174.
[30]王小青,刘婷.昆虫CYP4基因家族多样性和进化[J].山西农业科学,2012,40(5):559-562.
[31]Feyereisen R.Evolution of insect P450[J].Biochemical Society Transactions,2006,34(6):1252-1255.
[32]Bassett M H,McCarthy J L,Waterman M R,et al.Sequence and developmental expression of Cyp18,a member of a new cytochrome P450 family from Drosophila[J].Molecular and Cellular Endocrinology,1997,131(1):39-49.
[33]艾均文,王根洪,李艳红,等.家蚕P450基因CYP18A1的克隆、序列分析及转录活性[J].昆虫学报,2008,51(3):237-245.
[34]Rewitz K F,O’Connor M B,Gilbert L I.Molecular evolution of the insect Halloween family of cytochrome P450s:phylogeny,gene organization and functional conservation[J].Insect Biochemistry and Molecular Biology,2007,37(8):741-753.
[35]Daimon T,Shinoda T.Function,diversity,and application of insect juvenile hormone epoxidases(CYP15)[J].Biotechnology and Applied Biochemistry,2013,60(1):82-91.
[36]Minakuchi C,Ishii F,Washidu Y,et al.Expressional and functional analysis of CYP15A1,a juvenile hormone epoxidase,in the red flour beetle Tribolium castaneum[J].Journal of Insect Physiology,2015,80(1):61-70.
[37]Hudson S A,Mashalidis E H,Bender A,et al.Biofragments:an approach towards predicting protein function using biologically related fragments and its application to Mycobacterium tuberculosis CYP126[J].ChemBioChem,2014,15(4):549-555.
[2]Branstetter M G,Childers A K,Cox-Foster D,et al.Genomes of the Hymenoptera[J].Current Opinion in Insect Science,2018,25:65-75.
[3]Werren J H,Richards S,Desjardins C A,et al.Functional and evolutionary insights from the genomes of three parasitoid Nasonia species[J].Science,2010,327(5963):343-348.
[4]Burke G R,Walden K K,Whitfield J B,et al.Widespread genome reorganization of an obligate virus mutualist[J].PLoS Genetics,2014,10(9):e1004660.
[5]Geib S M,Liang G H,Murphy T D,et al.Whole genome sequencing of the braconid parasitoid wasp Fopius arisanus,an important biocontrol agent of pest tepritid fruit flies[J].G3(Bethesda),2017,7(8):2407-2411.
[6]Yin C,Li M,Hu J,et al.The genomic features of parasitism,polyembryony and immune evasion in the endoparasitic wasp Macrocentrus cingulum[J].BMC Genomics,2018,19(1):420.
[7]Lindsey A R I,Kelkar Y D,Wu X,et al.Comparative genomics of the miniature wasp and pest control agent Trichogramma pretiosum[J].BMC Biology,2018,16(1):54.
[8]Xiao J H,Yue Z,Jia L Y,et al.Obligate mutualism within a host drives the extreme specialization of a fig wasp genome[J].Genome Biology,2013,14(12):R141.
[9]Feyereisen R.Insect CYP genes and P450 enzymes[M]//Insect Molecular Biology and Biochemistry.Academic Press,2012,236-316.
[10]艾均文,孟繁利,贾孟周,等.昆虫细胞色素P450的研究进展[C].中国蚕学会第六届青年学术研讨会论文集,2009,10.
[11]杨帆,王进军.昆虫细胞色素P450与抗药性关系研究进展[J].四川动物,2008(3):460-463.
[12]刘金定,李飞.丽蝇蛹集金小蜂P450基因家族的发现和分子进化分析[J].中国生物防治学报,2013,29(4):490-496.
[13]El-Gebali S,Mistry J,Bateman A,et al.The Pfam protein families database in 2019[J].Nucleic Acids Research,2018,47(D1):D427-D432.
[14]Sayers E W,Agarwala R,Bolton E E,et al.Database resources of the National Center for Biotechnology Information[J].Nucleic Acids Research,2019,47(D1):D23-D28.
[15]Yin C,Shen G,Guo D,et al.InsectBase:a resource for insect genomes and transcriptomes[J].Nucleic Acids Research,2016,44(D1):D801-807.
[16]Birney E,Clamp M,Durbin R.GeneWise and genomewise[J].Genome Research,2004,14(5):988-995.
[17]Katoh K,Misawa K,Kuma K,et al.MAFFT:a novel method for rapid multiple sequence alignment based on fast Fourier transform[J].Nucleic Acids Research,2002,30(14):3059-3066.
[18]Capella-Gutierrez S,Silla-Martinez J M,Gabaldon T.trimAl:a tool for automated alignment trimming in large-scale phylogenetic analyses[J].Bioinformatics,2009,25(15):1972-1973.
[19]Nguyen L T,Schmidt H A,von Haeseler A,et al.IQ-TREE:a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies[J].Molecular Biology and Evolution,2015,32(1):268-274.
[20]Kalyaanamoorthy S,Minh B Q,Wong T K F,et al.ModelFinder:fast model selection for accurate phylogenetic estimates[J].Nature Methods,2017,14(6):587-589.
[21]Stamatakis A.RAxML version 8:a tool for phylogenetic analysis and post-analysis of large phylogenies[J].Bioinformatics,2014,30(9):1312-1313.
[22]Wang F,Fang Q,Wang B,et al.A novel negative-stranded RNA virus mediates sex ratio in its parasitoid host[J].PLOS Pathogens,2017,13(3):e1006201.
[23]Yan Z,Fang Q,Liu Y,et al.A venom serpin splicing isoform of the endoparasitoid wasp Pteromalus puparum suppresses host prophenoloxidase cascade by forming complexes with host hemolymph proteinases[J].Journal of Biological Chemistry,2017,292(3):1038-1051.
[24]Teng Z W,Xu G,Gan S Y,et al.Effects of the endoparasitoid Cotesia chilonis(Hymenoptera:Braconidae)parasitism,venom,and calyx fluid on cellular and humoral immunity of its host Chilo suppressalis(Lepidoptera:Crambidae)larvae[J].Journal of Insect Physiology,2016,85(1):46-56.
[25]Wang Z Z,Ye X Q,Shi M,et al.Parasitic insect-derived miRNAs modulate host development[J].Nature Communications,2018,9(1):2205.
[26]Tan C W,Peiffer M,Hoover K,et al.Symbiotic polydnavirus of a parasite manipulates caterpillar and plant immunity[J].Proceedings of the National Academy of Sciences of the United States of America,2018,115(20):5199-5204.
[27]Zhu F,Cusumano A,Bloem J,et al.Symbiotic polydnavirus and venom reveal parasitoid to its hyperparasitoids[J].Proceedings of the National Academy of Sciences of the United States of America,2018,115(20):5205-5210.
[28]Kubota A,Stegeman J J,Goldstone J V,et al.Cytochrome P450 CYP2 genes in the common cormorant:Evolutionary relationships with 130 diapsid CYP2 clan sequences and chemical effects on their expression[J].Comparative Biochemistry and Physiology Part C:Toxicology and Pharmacology,2011,153(3):280-289.
[29]Zhu F,Moural T W,Shah K,et al.Integrated analysis of cytochrome P450 gene superfamily in the red flour beetle,Tribolium castaneum[J].BMCGenomics,2013,14(1):174.
[30]王小青,刘婷.昆虫CYP4基因家族多样性和进化[J].山西农业科学,2012,40(5):559-562.
[31]Feyereisen R.Evolution of insect P450[J].Biochemical Society Transactions,2006,34(6):1252-1255.
[32]Bassett M H,McCarthy J L,Waterman M R,et al.Sequence and developmental expression of Cyp18,a member of a new cytochrome P450 family from Drosophila[J].Molecular and Cellular Endocrinology,1997,131(1):39-49.
[33]艾均文,王根洪,李艳红,等.家蚕P450基因CYP18A1的克隆、序列分析及转录活性[J].昆虫学报,2008,51(3):237-245.
[34]Rewitz K F,O’Connor M B,Gilbert L I.Molecular evolution of the insect Halloween family of cytochrome P450s:phylogeny,gene organization and functional conservation[J].Insect Biochemistry and Molecular Biology,2007,37(8):741-753.
[35]Daimon T,Shinoda T.Function,diversity,and application of insect juvenile hormone epoxidases(CYP15)[J].Biotechnology and Applied Biochemistry,2013,60(1):82-91.
[36]Minakuchi C,Ishii F,Washidu Y,et al.Expressional and functional analysis of CYP15A1,a juvenile hormone epoxidase,in the red flour beetle Tribolium castaneum[J].Journal of Insect Physiology,2015,80(1):61-70.
[37]Hudson S A,Mashalidis E H,Bender A,et al.Biofragments:an approach towards predicting protein function using biologically related fragments and its application to Mycobacterium tuberculosis CYP126[J].ChemBioChem,2014,15(4):549-555.