DNA条形码在苔藓植物分子系统学中的应用
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摘要
近年来,DNA条形码已成为国际上生物研究的热点。DNA条形码技术是一种强有力的、新型的物种鉴别技术,已被大众普遍接受。本综述对叶绿体基因组、线粒体基因组和核基因组DNA条形码在苔藓植物分子系统学中的应用进展进行了归纳总结,并阐述了DNA条形码原理和技术流程。本综述将针对特定的分子系统研究选择合适的基因片段,把传统形态分类学和分子证据相结合,弥补苔藓植物的分子系统研究中的不足,为更好地推动苔藓植物系统发育与进化研究的发展提供助力。
In the recent years, DNA barcoding has become one of the hotspots in biological researches all over the world. DNA barcoding is a powerful and new-style technology in species identification, which has been widely accepted. In this review, the application progress of cpDNA, nrDNA, and mtDNA barcoding in bryophyte phylogenetics were summarized and the principle and technical process of DNA barcoding were explained. This review would select appropriate gene fragments for specific molecular systems, and combine traditional taxonomy with molecular evidence to make up for the shortcomings of the molecular system of bryophytes, so as to provide assistance to promote the development of phylogenetic and evolutionary researches of bryophytes.
In the recent years, DNA barcoding has become one of the hotspots in biological researches all over the world. DNA barcoding is a powerful and new-style technology in species identification, which has been widely accepted. In this review, the application progress of cpDNA, nrDNA, and mtDNA barcoding in bryophyte phylogenetics were summarized and the principle and technical process of DNA barcoding were explained. This review would select appropriate gene fragments for specific molecular systems, and combine traditional taxonomy with molecular evidence to make up for the shortcomings of the molecular system of bryophytes, so as to provide assistance to promote the development of phylogenetic and evolutionary researches of bryophytes.
引文
Angela E.N.,and Cymon J.C.,2000,Evolution of the major moss lineages:phylogenetic analysis based on multiple gene sequences and morphology,The Bryologist,103(2):187-211
Aront D.E.,Roper C.,and Bayoumi R.A.L.,1993,Digital codes from hypervariable tandemly repeated DNA sequences in the Plasmodium falciparum circum sporozoite gene can genetically barcode isolates,Mol.Biochem.Parasitol.,61(1):15-24
Cai Q.Y.,Wang F.X.,and Fang Y.M.,2009,A primary study of phylogeny in Mniaceae based on rbcL sequence analysis,In Nanjing Forestry University(eds.),The second Yangtze river delta regional botany symposium proce edings,Nanjing China,pp.99-106(蔡奇英,王凤仙,方炎明,2009,基于rbcL序列分析的提灯藓科(Mniaceae)分子系统发育初步研究,见:南京林业大学,编著,第二届长江三角洲地区植物学研讨会论文集,中国,南京,pp.99-106)
Che W.A.,and Zhang T.M.,2006,Research advances in bryophyte phylogenetic research,Xibei Zhiwu Xuebao(Acta Botanica Boreali-Occidentalia Sinica),26(6):1277-1281(车未艾,张铁明,2006,DNA序列在苔藓分子系统学研究中的应用,西北植物学报,26(6):1277-1281)
Eickbush T.H.,and Eickbush D.G.,2007,Finely orchestrated movements:evolution of the ribosomal RNA genes,Genetics,175(2):477-485
Fei X.T.,Ju M.M.,Lin Y.,Li B.,Li D.L.,and Xin P.Y.,2014,Application and research progress of ITS2 sequence in plant identification using DNA barcoding,Yaredai Zhiwu Kexue(Subtropical Plant Science),43(4):339-342(费希同,巨苗苗,林源,李斌,李德龙,辛培尧,2014,ITS2序列在植物DNA条形码鉴定中的应用,亚热带植物科学,43(4):339-342)
Ge X.J.,2015,Application of DNA barcoding in phylofloristics study,Shengwu Duoyangxing(Biodiversity Science),23(3):295-296(葛学军,2015,DNA条形码在植物系统发育区系学研究中的应用,生物多样性,23(3):295-296)
Guillon J.M.,2004,Phylogeny of horsetails(Equisetum)based on the chloroplast rps4 gene and adjacent noncoding sequences,Syst.Bot.,29(2):251-259)
Hebert P.D.N.,Cywinska A.,Ball S.L.,and deWaard J.R.,2003,Biological identifications through DNA barcodes,Proc.Biol.Sci.,270:313-321
Hedderson T.A.,Chapman R.,and Rootes W.L.,1996,Phylogenetic relationships of bryophytes infered from nuclear encoded r RNA gene sequences,Plant Syst.Evol.,200:213-224
Jiang Y.,Zhang Y.,and Guo Y.H.,2016,Research progress of DNA barcoding technique in mollusca taxonomy,Zhongguo Jishengchongxue Yu Jishengchongbing Zazhi(Chinese Journal of Parasitology and Parasitic Diseases),34(1):80-83(江颖,张仪,郭云海,2016,DNA条形码技术在软体动物分类学中的研究进展,中国寄生虫学与寄生虫病杂志,34(1):80-83)
Joly S.,Davies T.J.,Archambault A.,Bruneau A.,Derry A.,Kembel S.W.,PeresNeto P.,Vamosi J.,and Wheeler T.A.,2014,Ecology in the age of DNA barcoding:the resource,the promise and the challenges ahead,Mol.Ecol.Res.,14(2):221-232
Kress W.J.,Garcia Robledo C.,Uriarte M.,and Erickson D.L.,2015,DNA barcodes for ecology,evolution,and conservation,Trends Ecol.Evol.,30(1):25-35
Li D.Z.,and Zeng C.X.,2015,Prospects for plant DNA barcoding,Shengwu Duoyangxing(Biodiversity Science),23(3):297-298(李德铢,曾春霞,2015,植物DNA条形码研究展望,生物多样性,23(3):297-298)
Li L.J.,2013,Molecular phylogeny of the secondary host-plant mosses of Rhus Gall Aphids based on cpDNA sequences,Dissertation for Ph.D.,Shanxi University,Supervisor:Ren Z.M.,pp.13-38(李麟君,2013,五倍子蚜第二寄主苔藓cpDNA序列及其进化关系,山西大学,导师:任竹梅,pp13-38)
Li S.,and Jiang X.,2016,Comparison of agronomy properties and DNA barcoding identification in four different species of Lonicera,Beifang Yuanyi(Northern Horticulture),(5):137-140(李绍吉,蒋向辉,2016,忍冬属四种不同种质农艺学性状比较及DNA条形码鉴定研究,北方园艺,(5)137-140)
Liu Y.,Wang J.X.,Ge X.J.,and Cao T.,2011,The rps4 locus as an alternative marker for barcoding bryophytes:evaluation based on data mining from GenBank,Shengwu Duoyangxing(Biodiversity Science),19(3):311-318(刘艳,王建秀葛学军,曹同,2011,rps4作为苔藓植物候选条形码的可行性:基于GenBank数据的分析,生物多样性,19(3)311-318)
Liu Z.K.,Zhao G.H.,Liu G.H.,Song H.Y.,Li F.,and Liu Y.2012,Sequence and phylogenetic analysis of mitochondria nad5 and rrnS genes for Spirometra erinaceieuropari isolates from Hunan province,Zhongguo Shouyi Xuebao(Chinese Journal of Veterinary Science),32(2):258-261(刘自逵,赵光辉,刘国华,宋海燕,李芬,刘毅,2012,湖南省猬迭宫绦虫的线粒体nad5和rrnS基因的序列测定及种系发育分析,中国兽医学报,32(2):258-261)
Marshall E.,2005,Will DNA barcodes breathe life into classification,Science,307(5712):1037
Ning S.P.,Yan H.F.,Hao G.,and Ge X.J.,2008,Current advances of DNA barcoding study in plants,Shengwu Duoyangxing(Chinese Biodiversity),16(5):417-425(宁淑萍,颜海飞,郝刚,葛学军,2008,植物DNA条形码研究进展,生物多样性,16(5):417-425)
Palmer J.D.,1985,Comparative organization of chloroplast genome,Annu.Rev.Genet.,19:325-354
Percy D.M.,Argus G.W.,Cronk Q.C.,Fazekas A.J.,Kesanakurt P.R.,Burgess K.S.,Husband B.C.,Newmaster S.G.,Barret S.C.H.,and Graham S.W.,2014,Understanding the spectacular failure of DNA barcoding in willows(Salix):does this result from a trans-specific selective sweep?Mol.Ecol.,23(19):4737-4756
Spagnuolo V.,Caputo P.,and Cozzolon S.,1999,Patterns of relationships in Trichostomodeae(Pottiiaceae,Musci),Plant Syst.Evol.,216:69-79
Wang Q.,and Wu P.C.,1999,The role of bryophytes in biodiversity,Shengwu Duoyangxing(Biodiversity Science),7(4)332-339(汪庆,吴鹏程,1999,苔藓植物的多样性研究,生物多样性,7(4):332-339)
Wang T.,Su Y.J.,and Zhu J.M.,1999,The application of chloroplast rbcL gene sequences to plant systemctic studies,Wuhan Zhiwuxue Yanjiu(Journal of Wuhan Botanical Research),17(S):8-14(王艇,苏应娟,朱建明,1999,叶绿体rbcL基因序列在植物系统学研究中的应用,武汉植物学研究,17(S):8-14)
Wang T.,Zhu J.M.,Su Y.J.,Fan G.K.,and Li X.Y.,2000,PCR-RFLP analysis of rbcL gene in some bryophyte,Xibei Zhiwu Xuebao(Acta Botanica Boreali-Occidentalia Sinica),20(6):968-973(王艇,朱建明,苏应娟,范国宽,李雪雁,2000,部分苔藓植物rbcL基因PCR-RFLP分析,西北植物学报,20(6):968-973)
Witt J.D.S.,Threloff D.L.,and Hebert P.D.N.,2006,DNAbarcoding reveals extraordinary cryptic diversity in an amphipod genus:implications for desert spring conservation,Mol.Ecol.,15(10):3073-3082
Wu Y.P.,Yu N.T.,Zhou Q.L.,Wang J.H.,and Liu Z.X.,2016,Cloning and sequence analysis of matK gene from cactus,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(11):3135-3140(吴育鹏,余乃通,周启林,王健华,刘志昕,2016,海南仙人掌matK基因的克隆和序列分析,基因组学与应用生物学,35(11):3135-3140)
Yang P.,Yang C.L.,Wang J.,Hu X.F.,Cheng Y.,and Zhao C.,2017,Systematic research of bryophyte(Pottiaceae)based on rps4,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),15(10):4282-4288(杨鹏,杨成龙,王健,胡贤锋,成宇,赵财,2017,基于rps4基因探讨中国丛藓科(Pottiaceae)苔藓植物系统学研究,分子植物育种,15(10):4282-4288)
Zhang A.S.,Si Q.L.,Zhang W.M.,and Chen J.,2012,Analysis of the Phylogenetic relationship among some bryophytes based on matK gene,Henan Nongye Kexue(Henan Agricul-tural Sciences),41(1):110-112(张安世,司清亮,张为民,陈娟,2012,基于matK基因的几种苔藓植物的亲缘关系分析,河南农业科学,41(1):110-112)
Zhang H.,2002,Using nuclear ribosomal DNA internal transcribed speacers(ITS)to discuss the phylogeny of Thuidiaceae(S.L.,Musci),Thesis for M.S.,Capital Normal University,Supervisor:Du G.S.,pp.19-49(张会,2002,利用细胞核核糖体DNA内转录间隔区(ITS)探讨羽藓科系统发育,硕士学位论文,首都师范大学,导师:杜桂森,pp.19-49)
Zhang L.M.,Zhang A.S.,Chen J.,and Liu Y.Y.,2012,Phylogenetic relationship in some bryophytes based on rbcL-a gene of their chloroplast,Shengwu Jishu(Biotechnology),22(1):50-52(张利民,张安世,陈娟,刘永英,2012,部分苔藓植物叶绿体DNA rbcL-a序列的亲缘关系分析,生物技术,22(1):50-52)
Aront D.E.,Roper C.,and Bayoumi R.A.L.,1993,Digital codes from hypervariable tandemly repeated DNA sequences in the Plasmodium falciparum circum sporozoite gene can genetically barcode isolates,Mol.Biochem.Parasitol.,61(1):15-24
Cai Q.Y.,Wang F.X.,and Fang Y.M.,2009,A primary study of phylogeny in Mniaceae based on rbcL sequence analysis,In Nanjing Forestry University(eds.),The second Yangtze river delta regional botany symposium proce edings,Nanjing China,pp.99-106(蔡奇英,王凤仙,方炎明,2009,基于rbcL序列分析的提灯藓科(Mniaceae)分子系统发育初步研究,见:南京林业大学,编著,第二届长江三角洲地区植物学研讨会论文集,中国,南京,pp.99-106)
Che W.A.,and Zhang T.M.,2006,Research advances in bryophyte phylogenetic research,Xibei Zhiwu Xuebao(Acta Botanica Boreali-Occidentalia Sinica),26(6):1277-1281(车未艾,张铁明,2006,DNA序列在苔藓分子系统学研究中的应用,西北植物学报,26(6):1277-1281)
Eickbush T.H.,and Eickbush D.G.,2007,Finely orchestrated movements:evolution of the ribosomal RNA genes,Genetics,175(2):477-485
Fei X.T.,Ju M.M.,Lin Y.,Li B.,Li D.L.,and Xin P.Y.,2014,Application and research progress of ITS2 sequence in plant identification using DNA barcoding,Yaredai Zhiwu Kexue(Subtropical Plant Science),43(4):339-342(费希同,巨苗苗,林源,李斌,李德龙,辛培尧,2014,ITS2序列在植物DNA条形码鉴定中的应用,亚热带植物科学,43(4):339-342)
Ge X.J.,2015,Application of DNA barcoding in phylofloristics study,Shengwu Duoyangxing(Biodiversity Science),23(3):295-296(葛学军,2015,DNA条形码在植物系统发育区系学研究中的应用,生物多样性,23(3):295-296)
Guillon J.M.,2004,Phylogeny of horsetails(Equisetum)based on the chloroplast rps4 gene and adjacent noncoding sequences,Syst.Bot.,29(2):251-259)
Hebert P.D.N.,Cywinska A.,Ball S.L.,and deWaard J.R.,2003,Biological identifications through DNA barcodes,Proc.Biol.Sci.,270:313-321
Hedderson T.A.,Chapman R.,and Rootes W.L.,1996,Phylogenetic relationships of bryophytes infered from nuclear encoded r RNA gene sequences,Plant Syst.Evol.,200:213-224
Jiang Y.,Zhang Y.,and Guo Y.H.,2016,Research progress of DNA barcoding technique in mollusca taxonomy,Zhongguo Jishengchongxue Yu Jishengchongbing Zazhi(Chinese Journal of Parasitology and Parasitic Diseases),34(1):80-83(江颖,张仪,郭云海,2016,DNA条形码技术在软体动物分类学中的研究进展,中国寄生虫学与寄生虫病杂志,34(1):80-83)
Joly S.,Davies T.J.,Archambault A.,Bruneau A.,Derry A.,Kembel S.W.,PeresNeto P.,Vamosi J.,and Wheeler T.A.,2014,Ecology in the age of DNA barcoding:the resource,the promise and the challenges ahead,Mol.Ecol.Res.,14(2):221-232
Kress W.J.,Garcia Robledo C.,Uriarte M.,and Erickson D.L.,2015,DNA barcodes for ecology,evolution,and conservation,Trends Ecol.Evol.,30(1):25-35
Li D.Z.,and Zeng C.X.,2015,Prospects for plant DNA barcoding,Shengwu Duoyangxing(Biodiversity Science),23(3):297-298(李德铢,曾春霞,2015,植物DNA条形码研究展望,生物多样性,23(3):297-298)
Li L.J.,2013,Molecular phylogeny of the secondary host-plant mosses of Rhus Gall Aphids based on cpDNA sequences,Dissertation for Ph.D.,Shanxi University,Supervisor:Ren Z.M.,pp.13-38(李麟君,2013,五倍子蚜第二寄主苔藓cpDNA序列及其进化关系,山西大学,导师:任竹梅,pp13-38)
Li S.,and Jiang X.,2016,Comparison of agronomy properties and DNA barcoding identification in four different species of Lonicera,Beifang Yuanyi(Northern Horticulture),(5):137-140(李绍吉,蒋向辉,2016,忍冬属四种不同种质农艺学性状比较及DNA条形码鉴定研究,北方园艺,(5)137-140)
Liu Y.,Wang J.X.,Ge X.J.,and Cao T.,2011,The rps4 locus as an alternative marker for barcoding bryophytes:evaluation based on data mining from GenBank,Shengwu Duoyangxing(Biodiversity Science),19(3):311-318(刘艳,王建秀葛学军,曹同,2011,rps4作为苔藓植物候选条形码的可行性:基于GenBank数据的分析,生物多样性,19(3)311-318)
Liu Z.K.,Zhao G.H.,Liu G.H.,Song H.Y.,Li F.,and Liu Y.2012,Sequence and phylogenetic analysis of mitochondria nad5 and rrnS genes for Spirometra erinaceieuropari isolates from Hunan province,Zhongguo Shouyi Xuebao(Chinese Journal of Veterinary Science),32(2):258-261(刘自逵,赵光辉,刘国华,宋海燕,李芬,刘毅,2012,湖南省猬迭宫绦虫的线粒体nad5和rrnS基因的序列测定及种系发育分析,中国兽医学报,32(2):258-261)
Marshall E.,2005,Will DNA barcodes breathe life into classification,Science,307(5712):1037
Ning S.P.,Yan H.F.,Hao G.,and Ge X.J.,2008,Current advances of DNA barcoding study in plants,Shengwu Duoyangxing(Chinese Biodiversity),16(5):417-425(宁淑萍,颜海飞,郝刚,葛学军,2008,植物DNA条形码研究进展,生物多样性,16(5):417-425)
Palmer J.D.,1985,Comparative organization of chloroplast genome,Annu.Rev.Genet.,19:325-354
Percy D.M.,Argus G.W.,Cronk Q.C.,Fazekas A.J.,Kesanakurt P.R.,Burgess K.S.,Husband B.C.,Newmaster S.G.,Barret S.C.H.,and Graham S.W.,2014,Understanding the spectacular failure of DNA barcoding in willows(Salix):does this result from a trans-specific selective sweep?Mol.Ecol.,23(19):4737-4756
Spagnuolo V.,Caputo P.,and Cozzolon S.,1999,Patterns of relationships in Trichostomodeae(Pottiiaceae,Musci),Plant Syst.Evol.,216:69-79
Wang Q.,and Wu P.C.,1999,The role of bryophytes in biodiversity,Shengwu Duoyangxing(Biodiversity Science),7(4)332-339(汪庆,吴鹏程,1999,苔藓植物的多样性研究,生物多样性,7(4):332-339)
Wang T.,Su Y.J.,and Zhu J.M.,1999,The application of chloroplast rbcL gene sequences to plant systemctic studies,Wuhan Zhiwuxue Yanjiu(Journal of Wuhan Botanical Research),17(S):8-14(王艇,苏应娟,朱建明,1999,叶绿体rbcL基因序列在植物系统学研究中的应用,武汉植物学研究,17(S):8-14)
Wang T.,Zhu J.M.,Su Y.J.,Fan G.K.,and Li X.Y.,2000,PCR-RFLP analysis of rbcL gene in some bryophyte,Xibei Zhiwu Xuebao(Acta Botanica Boreali-Occidentalia Sinica),20(6):968-973(王艇,朱建明,苏应娟,范国宽,李雪雁,2000,部分苔藓植物rbcL基因PCR-RFLP分析,西北植物学报,20(6):968-973)
Witt J.D.S.,Threloff D.L.,and Hebert P.D.N.,2006,DNAbarcoding reveals extraordinary cryptic diversity in an amphipod genus:implications for desert spring conservation,Mol.Ecol.,15(10):3073-3082
Wu Y.P.,Yu N.T.,Zhou Q.L.,Wang J.H.,and Liu Z.X.,2016,Cloning and sequence analysis of matK gene from cactus,Jiyinzuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),35(11):3135-3140(吴育鹏,余乃通,周启林,王健华,刘志昕,2016,海南仙人掌matK基因的克隆和序列分析,基因组学与应用生物学,35(11):3135-3140)
Yang P.,Yang C.L.,Wang J.,Hu X.F.,Cheng Y.,and Zhao C.,2017,Systematic research of bryophyte(Pottiaceae)based on rps4,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),15(10):4282-4288(杨鹏,杨成龙,王健,胡贤锋,成宇,赵财,2017,基于rps4基因探讨中国丛藓科(Pottiaceae)苔藓植物系统学研究,分子植物育种,15(10):4282-4288)
Zhang A.S.,Si Q.L.,Zhang W.M.,and Chen J.,2012,Analysis of the Phylogenetic relationship among some bryophytes based on matK gene,Henan Nongye Kexue(Henan Agricul-tural Sciences),41(1):110-112(张安世,司清亮,张为民,陈娟,2012,基于matK基因的几种苔藓植物的亲缘关系分析,河南农业科学,41(1):110-112)
Zhang H.,2002,Using nuclear ribosomal DNA internal transcribed speacers(ITS)to discuss the phylogeny of Thuidiaceae(S.L.,Musci),Thesis for M.S.,Capital Normal University,Supervisor:Du G.S.,pp.19-49(张会,2002,利用细胞核核糖体DNA内转录间隔区(ITS)探讨羽藓科系统发育,硕士学位论文,首都师范大学,导师:杜桂森,pp.19-49)
Zhang L.M.,Zhang A.S.,Chen J.,and Liu Y.Y.,2012,Phylogenetic relationship in some bryophytes based on rbcL-a gene of their chloroplast,Shengwu Jishu(Biotechnology),22(1):50-52(张利民,张安世,陈娟,刘永英,2012,部分苔藓植物叶绿体DNA rbcL-a序列的亲缘关系分析,生物技术,22(1):50-52)
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