蚜蝇科昆虫比较线粒体基因组分析
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摘要
通过检索GenBank数据库(截止2018年9月)和查阅文献资料,对已知的6种蚜蝇线粒体基因组全序列进行了分析,其基本结构特点是:1)全序列在碱基组成中表现出很强的AT偏向性; 2)未出现基因重排现象; 3) tRNA基因的二级结构为典型的三叶草结构; 4)大多数线粒体蛋白编码基因的起始密码子都是ATN。同时基于8条线粒体基因组全序列(含3个外群)构建蚜蝇科系统发育关系,结果支持蚜蝇科的单系性。
Through searching NCBI( data to the end of September of 2018) and other related literature,we have analyzed the six known Syrphidae sequences of complete mitochondrial genomes. The basic structural features are as follows: 1) The entire sequence has shown a very strong AT bias in nucleotide composition; 2)no gene rearrangement emerges; 3) that all tRNA genes fold into the typical clover-leaf structure; 4) that all mitochondrial protein-coding gene start with ATN codons. Finally,the phylogenetic relationship of Syrphidae are constructed based on eight sequences of the complete mitochondrial genome( including outgroup of three species),and the results support the monophyly of Syrphidae.
Through searching NCBI( data to the end of September of 2018) and other related literature,we have analyzed the six known Syrphidae sequences of complete mitochondrial genomes. The basic structural features are as follows: 1) The entire sequence has shown a very strong AT bias in nucleotide composition; 2)no gene rearrangement emerges; 3) that all tRNA genes fold into the typical clover-leaf structure; 4) that all mitochondrial protein-coding gene start with ATN codons. Finally,the phylogenetic relationship of Syrphidae are constructed based on eight sequences of the complete mitochondrial genome( including outgroup of three species),and the results support the monophyly of Syrphidae.
引文
[1]霍科科,任国栋,郑哲民.秦巴山区蚜蝇科昆虫区系(昆虫纲,双翅目)[M].北京:中国农业科学技术出版社,2007:3.
[2] GROSSKOPF G. Biology and life history of Cheilosia urbana(Meigen)and Cheilosia psilopthalma(Becker),two sympatrichoverflies approved for the biological control of hawkweeds(Hieracium spp.)in New Zealand[J]. Biological Control,2005,35(2):142-154.
[3] FISCHER O A,MATLOVAL,DVORSKAL,et al. Various stages in the life cycle of Syrphid Flies(Eristalis tenax; Diptera:Syrphidae)as potential mechanical vectors of pathogens causing mycobacterial infections in pig herds[J]. Folia Microbiol,2006,51(2):147-153.
[4] REEMER M. Review and phylogenetic evaluation of associations between microdontinae(Diptera:Syrphidae)and ants(Hymenoptera:Formicidae)[J]. Psyche:A Journal of Entomology,2013(4):1-9.
[5] XIMO M,GUNILLA S,SANTOS R. First phylogeny of predatory flower flies(Diptera,Syrphidae,Syrphinae)using mito-chondrial COI and nuclear 28S rRNA genes:conflict and congruence with the current tribal classification[J]. Cladistics,2010,24(4):543-562.
[6] STAHLS G,HIPPA H,ROTHERAY G,et al. Phylogeny of Syrphidae(Diptera)inferred from combined analysis of molecu-lar and morphological characters[J]. Systematic Entomology,2003,28(4):433-450.
[7] MENGUAL X,STAHLS G,ROJO S. Molecular phylogeny of Allograpta(Diptera,Syrphidae)reveals diversity of lineagesand non-monophyly of phytophagous taxa[J]. Molecular Phylogenetics and Evolution,2008,49(3):715-727.
[8] CONTRERAS G M A,VIVERO R J,VELEZ I D,et al. DNA barcoding for the identification of sand fly species(Diptera,Psychodidae,Phlebotominae)in Colombia[J]. PLOS ONE,2014,9(1):e85496.
[9] CAMERON S L,LAMBKIN C L,BARKER S C,et al. A mitochondrial genome phylogeny of Diptera:whole genome se-quence data accurately resolve relationships over broad timescales with high precision[J]. Systematic Entomology,2007,32(1):40-59.
[10] WOLSTENHOLME D R. Animal mitochondrial DNA:structure and evolution[J]. International Review of Cytology,1992,141(6):173-216.
[11]尚娜,周志军.动物线粒体基因组全序列测定的研究策略[J].河池学院学报,2008,28(2):62-65.
[12] JUNQUEIRA A C M,AZEREDOESPIN A M L,PAULO D F,et al. Large-scale mitogenomics enables insights into Schizo-phora(Diptera)radiation and population diversity[J]. Scientific Reports,2016(6):1-13.
[13] TANG M,TAN M,MENG G,et al. Multiplex sequencing of pooled mitochondrial genomes-a crucial step toward biodiversi-ty analysis using mito-metagenomics[J]. Nucleic Acids Reseasrch,2014,42(22):e166.
[14] PU D Q,LIU H L,GONG Y Y,et al. Mitochondrial genomes of the hoverflies Episyrphus balteatus and Eupeodes corollae(Diptera:Syrphidae),with a phylogenetic analysis of Muscomorpha[J]. Scientific Reports,2017(7):44300.
[15] LI X,DING S,LI X,et al. The complete mitochondrial genome analysis of Eristalis tenax(Diptera,Syrphidae)[J]. Mito-chondrial DNA Part B,2017,2(2):654-655.
[16] TAUTZ D,ARCTANDER P,MINELLI A,et al. A plea for DNA taxonomy[J]. Trends in Ecology and Evolution,2003,18(2):70-74.
[17] COSTA F O,DEWAARD J R,BOUTILLIER J,et al. Biological identifications through DNA barcodes:the case of theCrustacea[J]. Canadian Journal of Fisheries and Aquatic Sciences,2007,64(2):272-295.
[18] NICHOLS S A. An evaluation of support for order-level monophyly and interrelationships within the class Demospongiae u-sing partial data from the large subunit r DNA and cytochrome oxidase subunit I[J]. Molecular Phylogenetics and Evolu-tion,2005,34(1):81-96.
[19] DURAN S,PASCUAL M,TURON X. Low levels of genetic variation in mt DNA sequences over the western Mediterraneanand Atlantic range of the sponge Crambe crambe(Poecilosclerida)[J]. Marine Biology,2004,144(1):31-35.
[20] LIU L N,WANG C Y. Complete mitochondrial genome of yellow meal worm(Tenebrio molitor)[J]. Zoological Research,2014,35(6):537-545.
[21]张敏,赵盼,尹洁,等.小红珠绢蝶线粒体基因组特征及基于线粒体基因组的蝶类高级阶元系统发育关系分析[J].昆虫学报,2017,60(11):1324-1338.
[22]杨洪,汪佳佳,戴仁怀,等.烟蚜线粒体基因组全序列及系统发育分析[J].昆虫学报,2017,60(1):84-94.
[23] TIMMERMANS M J,DODSWORTH S,CULVERWELL C L,et al. Why barcode? high-throughput multiplex sequencing ofmitochondrial genomes for molecular systematics[J]. Nucleic Acids Research,2010,38(21):e197.
[24]杨秀帅.线粒体基因组在夜蛾总科高级阶元系统发育研究中的应用[D].北京:中国科学院大学,2013.
[25]张乃心,张玉娟,余果,等.双翅目昆虫线粒体基因组结构特点及其测序通用引物的设计和应用[J].昆虫学报,2013,56(4):398-407.
[26]魏书军,陈学新.昆虫比较线粒体基因组学研究进展[J].应用昆虫学报,2011,48(6):1573-1585.
[27] PERNA N T,KOCHER T D. Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial ge-nomes[J]. Journal of Molecular Evolution,1995,41(3):353-358.
[28] CAMERON S L,WHITING M F. The complete mitochondrial genome of the tobacco hornworm,Manduca sexta(Insecta:Lepidoptera:Sphingidae)and an examination of mitochondrial gene variability within butterflies and moths[J]. Gene,2008,408(1/2):112-123.
[29] LI H,LIU H,CAO L,et al. The Complete mitochondrial genome of the Damsel Bug Alloeorhynchus bakeri(Hemiptera:Na-bidae)[J]. International Journal of Biological Sciences,2012,8(1):93-107.
[30] SHAO R,BARKER S C. The highly rearranged mitochondrial genome of the Plague Thrips,Thrips imaginis(Insecta:Thys-anoptera):convergence of two novel gene boundaries and an extraordinary arrangement of rRNA genes[J]. Molecular Bi-ology&Evolution,2003,20(3):362-370.
[31]王维,孟智启,石放雄,等.鳞翅目昆虫比较线粒体基因组学研究进展[J].科学通报,2013,58(30):3017-3029.
[32] VARE V Y,ERUYSAL E R,NARENDRAN A,et al. Chemical and conformational diversity of modified nucleosides affectstrna structure and function[J]. Biomolecules,2017,7(1):29.
[33] HARDY C M,COURT L N,MORGAN M J. The complete mitochondrial DNA genome of Aedes vigilax(Diptera:Culici-dae)[J]. Mitochondrial DNA:The Journal of DNA Mapping,Sequencing,and Analysis,2016,27(4):2552-2553.
[34]郭仲龙,袁明龙.半翅目昆虫线粒体基因组学研究进展[J].中国科学:生命科学,2016,46(2):151-166.
[35] YOKOBORI S I,PAABO S. Polyadenylation creates the discriminator nucleotide of chicken mitochondrial tRNATyr[J].Journal of Molecular Biology,1997,265(2):95-99.
[36]张卓,胡建楠,王晓昕,等.基于线粒体COI~COII序列的黑带食蚜蝇(Episyrphus balteatus)遗传多样性初探[J].沈阳大学学报(自然科学版),2015,27(2):116-119.
[37]张宏杰,霍科科.管蚜蝇族7种食蚜蝇Cty b基因序列差异及系统进化关系[J].汉中师范学院学报,2004,22(6):54-59.
[2] GROSSKOPF G. Biology and life history of Cheilosia urbana(Meigen)and Cheilosia psilopthalma(Becker),two sympatrichoverflies approved for the biological control of hawkweeds(Hieracium spp.)in New Zealand[J]. Biological Control,2005,35(2):142-154.
[3] FISCHER O A,MATLOVAL,DVORSKAL,et al. Various stages in the life cycle of Syrphid Flies(Eristalis tenax; Diptera:Syrphidae)as potential mechanical vectors of pathogens causing mycobacterial infections in pig herds[J]. Folia Microbiol,2006,51(2):147-153.
[4] REEMER M. Review and phylogenetic evaluation of associations between microdontinae(Diptera:Syrphidae)and ants(Hymenoptera:Formicidae)[J]. Psyche:A Journal of Entomology,2013(4):1-9.
[5] XIMO M,GUNILLA S,SANTOS R. First phylogeny of predatory flower flies(Diptera,Syrphidae,Syrphinae)using mito-chondrial COI and nuclear 28S rRNA genes:conflict and congruence with the current tribal classification[J]. Cladistics,2010,24(4):543-562.
[6] STAHLS G,HIPPA H,ROTHERAY G,et al. Phylogeny of Syrphidae(Diptera)inferred from combined analysis of molecu-lar and morphological characters[J]. Systematic Entomology,2003,28(4):433-450.
[7] MENGUAL X,STAHLS G,ROJO S. Molecular phylogeny of Allograpta(Diptera,Syrphidae)reveals diversity of lineagesand non-monophyly of phytophagous taxa[J]. Molecular Phylogenetics and Evolution,2008,49(3):715-727.
[8] CONTRERAS G M A,VIVERO R J,VELEZ I D,et al. DNA barcoding for the identification of sand fly species(Diptera,Psychodidae,Phlebotominae)in Colombia[J]. PLOS ONE,2014,9(1):e85496.
[9] CAMERON S L,LAMBKIN C L,BARKER S C,et al. A mitochondrial genome phylogeny of Diptera:whole genome se-quence data accurately resolve relationships over broad timescales with high precision[J]. Systematic Entomology,2007,32(1):40-59.
[10] WOLSTENHOLME D R. Animal mitochondrial DNA:structure and evolution[J]. International Review of Cytology,1992,141(6):173-216.
[11]尚娜,周志军.动物线粒体基因组全序列测定的研究策略[J].河池学院学报,2008,28(2):62-65.
[12] JUNQUEIRA A C M,AZEREDOESPIN A M L,PAULO D F,et al. Large-scale mitogenomics enables insights into Schizo-phora(Diptera)radiation and population diversity[J]. Scientific Reports,2016(6):1-13.
[13] TANG M,TAN M,MENG G,et al. Multiplex sequencing of pooled mitochondrial genomes-a crucial step toward biodiversi-ty analysis using mito-metagenomics[J]. Nucleic Acids Reseasrch,2014,42(22):e166.
[14] PU D Q,LIU H L,GONG Y Y,et al. Mitochondrial genomes of the hoverflies Episyrphus balteatus and Eupeodes corollae(Diptera:Syrphidae),with a phylogenetic analysis of Muscomorpha[J]. Scientific Reports,2017(7):44300.
[15] LI X,DING S,LI X,et al. The complete mitochondrial genome analysis of Eristalis tenax(Diptera,Syrphidae)[J]. Mito-chondrial DNA Part B,2017,2(2):654-655.
[16] TAUTZ D,ARCTANDER P,MINELLI A,et al. A plea for DNA taxonomy[J]. Trends in Ecology and Evolution,2003,18(2):70-74.
[17] COSTA F O,DEWAARD J R,BOUTILLIER J,et al. Biological identifications through DNA barcodes:the case of theCrustacea[J]. Canadian Journal of Fisheries and Aquatic Sciences,2007,64(2):272-295.
[18] NICHOLS S A. An evaluation of support for order-level monophyly and interrelationships within the class Demospongiae u-sing partial data from the large subunit r DNA and cytochrome oxidase subunit I[J]. Molecular Phylogenetics and Evolu-tion,2005,34(1):81-96.
[19] DURAN S,PASCUAL M,TURON X. Low levels of genetic variation in mt DNA sequences over the western Mediterraneanand Atlantic range of the sponge Crambe crambe(Poecilosclerida)[J]. Marine Biology,2004,144(1):31-35.
[20] LIU L N,WANG C Y. Complete mitochondrial genome of yellow meal worm(Tenebrio molitor)[J]. Zoological Research,2014,35(6):537-545.
[21]张敏,赵盼,尹洁,等.小红珠绢蝶线粒体基因组特征及基于线粒体基因组的蝶类高级阶元系统发育关系分析[J].昆虫学报,2017,60(11):1324-1338.
[22]杨洪,汪佳佳,戴仁怀,等.烟蚜线粒体基因组全序列及系统发育分析[J].昆虫学报,2017,60(1):84-94.
[23] TIMMERMANS M J,DODSWORTH S,CULVERWELL C L,et al. Why barcode? high-throughput multiplex sequencing ofmitochondrial genomes for molecular systematics[J]. Nucleic Acids Research,2010,38(21):e197.
[24]杨秀帅.线粒体基因组在夜蛾总科高级阶元系统发育研究中的应用[D].北京:中国科学院大学,2013.
[25]张乃心,张玉娟,余果,等.双翅目昆虫线粒体基因组结构特点及其测序通用引物的设计和应用[J].昆虫学报,2013,56(4):398-407.
[26]魏书军,陈学新.昆虫比较线粒体基因组学研究进展[J].应用昆虫学报,2011,48(6):1573-1585.
[27] PERNA N T,KOCHER T D. Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial ge-nomes[J]. Journal of Molecular Evolution,1995,41(3):353-358.
[28] CAMERON S L,WHITING M F. The complete mitochondrial genome of the tobacco hornworm,Manduca sexta(Insecta:Lepidoptera:Sphingidae)and an examination of mitochondrial gene variability within butterflies and moths[J]. Gene,2008,408(1/2):112-123.
[29] LI H,LIU H,CAO L,et al. The Complete mitochondrial genome of the Damsel Bug Alloeorhynchus bakeri(Hemiptera:Na-bidae)[J]. International Journal of Biological Sciences,2012,8(1):93-107.
[30] SHAO R,BARKER S C. The highly rearranged mitochondrial genome of the Plague Thrips,Thrips imaginis(Insecta:Thys-anoptera):convergence of two novel gene boundaries and an extraordinary arrangement of rRNA genes[J]. Molecular Bi-ology&Evolution,2003,20(3):362-370.
[31]王维,孟智启,石放雄,等.鳞翅目昆虫比较线粒体基因组学研究进展[J].科学通报,2013,58(30):3017-3029.
[32] VARE V Y,ERUYSAL E R,NARENDRAN A,et al. Chemical and conformational diversity of modified nucleosides affectstrna structure and function[J]. Biomolecules,2017,7(1):29.
[33] HARDY C M,COURT L N,MORGAN M J. The complete mitochondrial DNA genome of Aedes vigilax(Diptera:Culici-dae)[J]. Mitochondrial DNA:The Journal of DNA Mapping,Sequencing,and Analysis,2016,27(4):2552-2553.
[34]郭仲龙,袁明龙.半翅目昆虫线粒体基因组学研究进展[J].中国科学:生命科学,2016,46(2):151-166.
[35] YOKOBORI S I,PAABO S. Polyadenylation creates the discriminator nucleotide of chicken mitochondrial tRNATyr[J].Journal of Molecular Biology,1997,265(2):95-99.
[36]张卓,胡建楠,王晓昕,等.基于线粒体COI~COII序列的黑带食蚜蝇(Episyrphus balteatus)遗传多样性初探[J].沈阳大学学报(自然科学版),2015,27(2):116-119.
[37]张宏杰,霍科科.管蚜蝇族7种食蚜蝇Cty b基因序列差异及系统进化关系[J].汉中师范学院学报,2004,22(6):54-59.