咖啡驼孢锈菌ITS序列特征及系统发育关系
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摘要
为了了解咖啡驼孢锈菌ITS序列特征及系统发育关系,本研究对来自中国咖啡栽培区的咖啡驼孢锈菌ITS序列进行了克隆。将克隆序列与来自不同咖啡种植区的咖啡驼孢锈菌菌株序列多样性进行了比较,并于NCBI数据库中下载其他锈菌菌株ITS序列进行系统发育关系研究。结果表明,来自中国咖啡栽培区的咖啡驼孢锈菌ITS序列全长950 bp。其中ITS1长为224 bp,GC含量介于30.36%～31.25%之间;5.8S长为153 bp, GC含量为37.25%;ITS2长483～485 bp,GC含量介于24.12%～25.05%。来自不同咖啡种植区咖啡驼孢锈菌ITS核苷酸序列多态性虽然存在一定差异,但是其多样性十分低且不存在明显的区域分化。在系统发育关系方面,咖啡驼孢锈菌与其他锈菌ITS序列差异明显,能独立聚类成一个分支。
In order to study the characteristics and phylogenetic relationship of the ITS sequence of Hemileia vastatrix, in this study the ITS sequence of H. vastatrix, from the coffee growing area of China, was cloned. The diversity of cloning sequence was compared with those of the strains from different coffee growing countries, and the phylogenetic relationship was studied by downloaded ITS sequences of other rust strains from the NCBI database. The results showed that the total length of ITS sequence from Chinese coffee rust pathogen was 950 bp. Among them, the length of ITS1 was 224 bp, and the GC content was between 30.36% and 31.25%; 5.8 S length 153 bp, GC content was 37.25%; ITS2 was about 483–485 bp and GC content was between 24.12% and 25.05%. Although the polymorphisms of the ITS nucleotide sequence of coffee rust fungus from different countries had some differences, its diversity was very low and there was no obvious regional differentiation. In terms of phylogenetic relationship, the ITS sequence of coffee rust fungus and other rust fungi was significantly different, and the former could be independently clustered into one branch.
In order to study the characteristics and phylogenetic relationship of the ITS sequence of Hemileia vastatrix, in this study the ITS sequence of H. vastatrix, from the coffee growing area of China, was cloned. The diversity of cloning sequence was compared with those of the strains from different coffee growing countries, and the phylogenetic relationship was studied by downloaded ITS sequences of other rust strains from the NCBI database. The results showed that the total length of ITS sequence from Chinese coffee rust pathogen was 950 bp. Among them, the length of ITS1 was 224 bp, and the GC content was between 30.36% and 31.25%; 5.8 S length 153 bp, GC content was 37.25%; ITS2 was about 483–485 bp and GC content was between 24.12% and 25.05%. Although the polymorphisms of the ITS nucleotide sequence of coffee rust fungus from different countries had some differences, its diversity was very low and there was no obvious regional differentiation. In terms of phylogenetic relationship, the ITS sequence of coffee rust fungus and other rust fungi was significantly different, and the former could be independently clustered into one branch.
引文
[1]Hoffmann J.The world atlas of coffee:from beans to brewing-coffees explored,explained and enjoyed[M].London:James Hoffman Octopus publishing Group,2014.
[2]ICO.World coffee production.International coffee organization[EB/OL].2016.http://www.ico.org/prices/po-production.pdf.
[3]Mc Cook S.Global rust belt:Hemileia vastatrix and the ecological integration of world coffee production since 1850[J].Journal of Global History,2006,1(2):177.
[4]Zambolim L.Current status and management of coffee leaf rust in Brazil[J].Tropical Plant Pathology,2016,41(1):1-8.
[5]Mayne W W Physiological specialisation of hemileia vastatrix B.and Br[J].Nature,1932,129(3 257):510-510.
[6]Mayne W W.Annual report of the coffee scientific officer1941-1942[M].Bulletion:Mysore coffee experimental station,1942:21.
[7]Várzea V M P,Marques D V.Resistance,population variability of Hemileia vastatrix vs.coffee durable[M]//Zambolim L,Zambolim E,Várzea V M P.eds.Durable resistance to coffee leaf rust.Vicsa:UFV Press,2005:53-74.
[8]Cabral P G C,Zambolim E M,Zambolim L,et al.Identification of a new race of Hemileia vastatrix in Brazil[J].Australasian Plant Disease Notes,2009,4:129-130.
[9]Capucho A S,Zambolim E M,Freitas R L,et al.Identification of race XXXIII of Hemileia vastatrix on coffea arabica catimor derivatives in Brazil[J].Australasian Plant Disease Notes,2012,7(1):189-191.
[10]Gouveia M M C,Ribeiro A,Várzea V M P,et al.Genetic diversity in Hemileia vastatrix based on RAPD markers[J].Mycologia,2005,97(2):396-404.
[11]Cristancho M,Escobar C,Ocampo J.Evolución de razas de Hemileia vastatrix en Colombia[J].Cenicafé,2007,58(4):340-359.
[12]Alaei H,De Backer M,Nuytinck J,et al.Phylogenetic relationships of Puccinia horiana and other rust pathogens of Chrysanthemum×morifolium based on rDNA ITS sequence analysis[J].Mycological Research,2009,113(6-7):668-683.
[13]Abbasi M,Goodwin S B,Scholler M.Taxonomy,phylogeny,and distribution of Puccinia graminis,the black stem rust:new insights based on rDNA sequence data[J].Mycoscience,2005,46(4):241-247.
[14]Chatasiri S,Kitade O,Ono Y.Phylogenetic relationships among Puccinia hemerocallidis,P.funkiae,and P.patriniae(Uredinales)inferred from ITS sequence data[J].Mycoscience,2006,47(3):123-129.
[15]陈振佳,Rodrigues Jr C J.中国咖啡锈菌(H.vastatrix)生理小种研究[J].菌物系统,1998,17(l):21-28.
[16]白学慧,Varzea V M P,郭铁英,等.云南咖啡锈菌小种鉴定[C]//2018全国天然香料产业品牌高峰论坛暨香料饮料作物学术年会.2018:45-54.
[17]White T J,Bruns T,Lee S,et al.Amplification and direct sequencing of fungal ribosomal RNA genes for phylogeneties[M]//White T J,Bruns T,Lee S,et al.eds.PCR Protocols.Elsevier,1990:315-322.
[18]Librado P,Rozas J.Dnasp V5:a software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,2009,25(11):1 451-1 452.
[19]黄家雄,吕玉兰,李贵平,等.咖啡产业发展形势分析研究[C]//2017年亚洲咖啡年会论文集.2017:2-13.
[20]Cristancho and Escobar.Transferability of SSR markers from related Uredinales species to the coffee rust Hemileia vastatrix[J].Genetics and Molecular Research,2008,7(5):1 186-1 192.
[21]Rozo Y,Escobar C,Gaitan A,et al,Aggressiveness and genetic diversity of Hemileia vastatrix during an epidemic in Colombia[J].Journal of Phytopathology,2012,160(11-12):732-740.
[22]Cabral P G C,Maciel-Zambolim E,Oliveira S A S,et al.Genetic diversity and structure of Hemileia vastatrix population on Coffea spp.[J].Plant Pathology,2016,65(2):196-204.
[23]Aime M C.Toward resolving family-level relationships in rust fungi(Uredinales)[J].Mycoscience,2006,47(3):112-122.
[2]ICO.World coffee production.International coffee organization[EB/OL].2016.http://www.ico.org/prices/po-production.pdf.
[3]Mc Cook S.Global rust belt:Hemileia vastatrix and the ecological integration of world coffee production since 1850[J].Journal of Global History,2006,1(2):177.
[4]Zambolim L.Current status and management of coffee leaf rust in Brazil[J].Tropical Plant Pathology,2016,41(1):1-8.
[5]Mayne W W Physiological specialisation of hemileia vastatrix B.and Br[J].Nature,1932,129(3 257):510-510.
[6]Mayne W W.Annual report of the coffee scientific officer1941-1942[M].Bulletion:Mysore coffee experimental station,1942:21.
[7]Várzea V M P,Marques D V.Resistance,population variability of Hemileia vastatrix vs.coffee durable[M]//Zambolim L,Zambolim E,Várzea V M P.eds.Durable resistance to coffee leaf rust.Vicsa:UFV Press,2005:53-74.
[8]Cabral P G C,Zambolim E M,Zambolim L,et al.Identification of a new race of Hemileia vastatrix in Brazil[J].Australasian Plant Disease Notes,2009,4:129-130.
[9]Capucho A S,Zambolim E M,Freitas R L,et al.Identification of race XXXIII of Hemileia vastatrix on coffea arabica catimor derivatives in Brazil[J].Australasian Plant Disease Notes,2012,7(1):189-191.
[10]Gouveia M M C,Ribeiro A,Várzea V M P,et al.Genetic diversity in Hemileia vastatrix based on RAPD markers[J].Mycologia,2005,97(2):396-404.
[11]Cristancho M,Escobar C,Ocampo J.Evolución de razas de Hemileia vastatrix en Colombia[J].Cenicafé,2007,58(4):340-359.
[12]Alaei H,De Backer M,Nuytinck J,et al.Phylogenetic relationships of Puccinia horiana and other rust pathogens of Chrysanthemum×morifolium based on rDNA ITS sequence analysis[J].Mycological Research,2009,113(6-7):668-683.
[13]Abbasi M,Goodwin S B,Scholler M.Taxonomy,phylogeny,and distribution of Puccinia graminis,the black stem rust:new insights based on rDNA sequence data[J].Mycoscience,2005,46(4):241-247.
[14]Chatasiri S,Kitade O,Ono Y.Phylogenetic relationships among Puccinia hemerocallidis,P.funkiae,and P.patriniae(Uredinales)inferred from ITS sequence data[J].Mycoscience,2006,47(3):123-129.
[15]陈振佳,Rodrigues Jr C J.中国咖啡锈菌(H.vastatrix)生理小种研究[J].菌物系统,1998,17(l):21-28.
[16]白学慧,Varzea V M P,郭铁英,等.云南咖啡锈菌小种鉴定[C]//2018全国天然香料产业品牌高峰论坛暨香料饮料作物学术年会.2018:45-54.
[17]White T J,Bruns T,Lee S,et al.Amplification and direct sequencing of fungal ribosomal RNA genes for phylogeneties[M]//White T J,Bruns T,Lee S,et al.eds.PCR Protocols.Elsevier,1990:315-322.
[18]Librado P,Rozas J.Dnasp V5:a software for comprehensive analysis of DNA polymorphism data[J].Bioinformatics,2009,25(11):1 451-1 452.
[19]黄家雄,吕玉兰,李贵平,等.咖啡产业发展形势分析研究[C]//2017年亚洲咖啡年会论文集.2017:2-13.
[20]Cristancho and Escobar.Transferability of SSR markers from related Uredinales species to the coffee rust Hemileia vastatrix[J].Genetics and Molecular Research,2008,7(5):1 186-1 192.
[21]Rozo Y,Escobar C,Gaitan A,et al,Aggressiveness and genetic diversity of Hemileia vastatrix during an epidemic in Colombia[J].Journal of Phytopathology,2012,160(11-12):732-740.
[22]Cabral P G C,Maciel-Zambolim E,Oliveira S A S,et al.Genetic diversity and structure of Hemileia vastatrix population on Coffea spp.[J].Plant Pathology,2016,65(2):196-204.
[23]Aime M C.Toward resolving family-level relationships in rust fungi(Uredinales)[J].Mycoscience,2006,47(3):112-122.