肺形侧耳线粒体基因组多态性鉴定
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摘要
线粒体是能量转化与ATP形成的重要场所,已有多种食用真菌的线粒体基因组被相继组装注释,但肺形侧耳的线粒体基因组鲜有报道。本研究对野生肺形侧耳X2菌株的线粒体基因组进行组装并注释,由野生菌株X2与主栽菌株JX线粒体大片段差异序列,构建分子标记来鉴别野生和主栽肺形侧耳菌株。结果显示X2的线粒体基因组为大小75 709bp的闭合环状结构,含有r RNA的大小亚基基因,25个负责携带氨基酸的t RNA基因以及14个常见蛋白编码基因,在cox1基因上含有9个内含子。内含子主要为IB型,包含LAGLIDADG_1 superfamily、GIY-YIG_Cterm superfamily保守结构域。位于菌株X2与JX内含子和基因间区上的大片段差异序列,是造成种内线粒体多态性的主要因素。根据两菌株的差异片段构建系统进化树的结果显示,内含子、rnl-trn X、trn D-atp6序列能够将两株野生菌株和其他主栽菌株区分开,可用于野生肺形侧耳种内鉴定,而且trn D-atp6效果最佳。
Mitochondrium is an important organelle in eukaryotic cells for energy conversion and ATP formation. Many edible fungal mitochondrial genomes have been assembled and annotated, however, the mitogenome of Pleurotus pulmonarius is rarely reported. In this study, the mitogenome of the wild type P. pulmonarius strain X2 was assembled and annotated. Molecular markers were developed based on the mitogenomes of the strain X2 and commercial strain JX to classify a wide range of wild and commercial strains. The results showed that the mitogenome of P. pulmonarius is a closed ring structure with a size up to 75 709 bp, containing small and large subunit genes of r RNA, 25 amino acids carrying t RNA genes and 14 common protein coding genes. The cox1 gene consists of nine introns mainly of IB type with conservative domain of LAGLIDADG_1 superfamily and GIY-YIG_C term superfamily. It was found that the differential fragment sequences are mainly located in the intron and intergenic regions, which are the main causes of mitochondrial polymorphism between strains X2 and JX. The phylogenetic tree was constructed with different fragment sequences, and the results indicated that the introns, rnl-trn X and trn D-atp6 sequences could be used to distinguish wild type strains from other commercial strains and could be used for the intraspecific identification of P. pulmonarius strains, however trn D-atp6 marker seemed more reliable in identification.
Mitochondrium is an important organelle in eukaryotic cells for energy conversion and ATP formation. Many edible fungal mitochondrial genomes have been assembled and annotated, however, the mitogenome of Pleurotus pulmonarius is rarely reported. In this study, the mitogenome of the wild type P. pulmonarius strain X2 was assembled and annotated. Molecular markers were developed based on the mitogenomes of the strain X2 and commercial strain JX to classify a wide range of wild and commercial strains. The results showed that the mitogenome of P. pulmonarius is a closed ring structure with a size up to 75 709 bp, containing small and large subunit genes of r RNA, 25 amino acids carrying t RNA genes and 14 common protein coding genes. The cox1 gene consists of nine introns mainly of IB type with conservative domain of LAGLIDADG_1 superfamily and GIY-YIG_C term superfamily. It was found that the differential fragment sequences are mainly located in the intron and intergenic regions, which are the main causes of mitochondrial polymorphism between strains X2 and JX. The phylogenetic tree was constructed with different fragment sequences, and the results indicated that the introns, rnl-trn X and trn D-atp6 sequences could be used to distinguish wild type strains from other commercial strains and could be used for the intraspecific identification of P. pulmonarius strains, however trn D-atp6 marker seemed more reliable in identification.
引文
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Al-Reedy RM,Malireddy R,Dillman CB,Kennell JC,2012.Comparative analysis of Fusarium mitochondrial genomes reveals a highly variable region that encodes an exceptionally large open reading frame.Fungal Genetics and Biology,49(1):2-14
Bao D,Aimi T,Kitamoto Y,2005.Cladistic relationships among the Pleurotus ostreatus complex,the Pleurotus pulmonarius complex,and Pleurotus eryngii based on the mitochondrial small subunit ribosomal DNAsequence analysis.Journal of Wood Science,51(1):77-82
Bullerwell CE,Lang BF,2005.Fungal evolution:the case of the vanishing mitochondrion.Current Opinion in Microbiology,8(4):362-369
Burger G,Gray MW,Lang BF,2003.Mitochondrial genomes:anything goes.Trends in Genetics,19(12):709-716
Chen B,He W,Li HT,Wu P,Xiao YZ,LüXL,He J,2017.Identification and phylogenetic analysis of Sagittidae(Chaetognatha)in the South China Sea based on mitochondrial COⅠgene*.Journal of Tropical Oceanography,36(6):100-108(in Chinese)
Deng YJ,Zhang QH,Ming R,Lin LJ,Lin XZ,Lin YY,Li X,Wen ZQ,2016.Analysis of the mitochondrial genome in Hypomyces aurantius reveals a novel Tw intron complex in fungi.International Journal of Molecular Sciences,17(7):1049
Felsenstein J,1985.Confidence limits on phylogenies:all approach using the bootstrap.Evolution,39(4):783-791
Formey D,Molès M,Haouy A,Savelli B,Bouchez O,Becard G,Roux C,2012.Comparative analysis of mitochondrial genomes of Rhizophagus irregularis-syn.Glomus irregulare-reveals a polymorphism induced by variability generating elements.New Phytologist,196(4):1217-1227
Gong YY,Li W,Zhao J,Chen HG,Wang YK,Zhu XP,2017.Identification and classification application of mitochondrial COⅠgene in ornamental fish.Genomics and Applied Biology,36(9):3728-3734(in Chinese)
Kang LY,Cui HF,Zhang YF,Zhang ZJ,Yu XP,Ye ZH,2017.Identification and ISSR polymorphism analysis of Ustilago esculenta isolated from Zizania latifolia.Mycosystema,36(9):1210-1221(in Chinese)
Kovalenko SA,Kopsidas G,Kelso J,Rosenfeldt F,Linnane AW,1998.T issue-specific distribution of multiple mitochondrial DNA rearrangements during human aging.Annuals of the New York Academy of Sciences,854(1):171-181
Larkin MA,Blackshields G,Brown NP,Chenna R,Mc Gettigan PA,Mc William H,Valentin F,Wallace IM,Wilm A,Lopez R,Thompson JD,Gibson TJ,Higgins DG,2007.Clustal Wand Clustal X version 2.0.Bioinformatics,23(21):2947-2948
Li Y,Hu XD,Yang RH,Hsiang T,Wang K,Liang DQ,Liang F,Cao DM,Zhou F,Wen G,Yao YJ,2015.Complete mitochondrial genome of the medicinal fungus Ophiocordyceps sinensis.Scientific Reports,5:13892
Li J,Zhang J,Chen H,Chen XD,Lan J,Liu C,2013.Complete mitochondrial genome of the medicinal mushroom Ganoderma lucidum.PLo S One,8(8):e72038
Liu PH,Lin Q,Wei RH,Wang XR,Zhou MY,2016.Genetic characterization of Phytophthora nicotianae by the analysis of intergenic regions of the mitochondrial DNA.Bulletin of Agricultural Science and Technology,8:102-104(in Chinese)
Liu R,2016.The discovery and the origins hypothesis of mitochondria.Biology Teaching,41(11):9-11(in Chinese)
Lu ZH,2008.SRAP analysis of cultivation strains of Pleurotus pulmonarius and it’s sibling varieties.Acta Agriculturae Jiangxi,20(11):8-10(in Chinese)
Mouhamadou B,Ferandon C,Barroso G,Labarere J,2006.The mitochondrial apocytochrome b genes of two Agrocybe species suggest lateral transfers of group Ihoming introns among phylogenetically distant fungi.Fungal Genetics and Biology,43(3):135-145
Nuno R,Lei S,Shutt TE,Cotney J,Guan MX,Gilliland TC,Hohuan D,Santos-Sacchi J,Shadel GS,2012.Mitochondrial stress engages E2F1 apoptotic signaling to cause deafness.Cell,148(4):716
Qiu YG,Shi YL,2008.Progress in the study of mitochondrial DNA and aging.Journal of Bethune Military Medical College,6(1):27-28(in Chinese)
Song HQ,Ai L,Mo YM,Zhou JQ,Lin RQ,Yuan ZG,Zhu XQ,2009.Sequencing of mitochondrial NADHdehydrogenase subunit 1(nad1)gene among Fasciola spp.and phylogenetic reconstruction.Veterinary Science in China,39(6):487-491(in Chinese)
Xin Y,Ruan SL,Wang SH,Ma HS,Wang WK,Wang SZ,2008.Cluster analysis of ten Pleurotus geesteranus strains based on random amplification of polymorphic DNA(RAPD)and expressed sequence tag-single sequence repeats(EST-SSR)markers.Acta Edulis Fungi,15(4):20-25(in Chinese)
Xiong Q,Liu ZY,YU ZS,2002.Progresses in studies and application of mitochondrial DNA.Southwest China Journal of Agricultural Sciences,15(3):111-115(in Chinese)
Yang D,Mi F,Dong JY,Zhang YR,Wu JY,2016.Changes of genome size of fungal mitochondria.Journal of Anhui Agricultural Sciences,44(1):36-39(in Chinese)
Yi X,Wang PP,Wang J,Su YQ,Mao Y,2018.The research of COⅠ-based DNA barcoding in Penaeidaes’identification.Journal of Fisheries of China,42(1):1-9(in Chinese)
Yin JH,Zhang P,Gong QF,Chen ZH,2008.Sequence analysis of the internal transcribed spacer of gene coding for r DNA in Russula subnigricans and R.nigricans.Mycosystema,27(2):237-242(in Chinese)
Yoon H,Kong WS,Kim YJ,Kim JG,2016.Complete mitochondrial genome of the ectomycorrhizal fungus Tricholoma matsutake.Mitochondrial DNA Part A,27(6):3855-3857
Yoon H,You YH,Woo JR,Park YJ,Kong WS,2012.The mitochondrial genome of the white-rot fungus Flammulina velutipes.The Journal of General and Applied Microbiology,58(4):331-337
Zeng FY,Zhang YZ,1998.Analyses of mushroom mitochondrial DNA by four-gc-cutter restriction enzyme.Microbiology China,25(1):5-9(in Chinese)
Zeng FR,Wang J,Zhou KL,You XX,Mao Y,2010.Genetic structure and population differentiation in four wild populations of Marsupenaeus japonicus based on cytochrome b gene segment sequence of mitochondrial DNA.Journal of Xiamen University(Natural Science),49(5):701-706(in Chinese)
Zerbino DR,Birney E,2008.Velvet:algorithms for de novo short read assembly using de Bruijn graphs.Genome Research,18(5):821-829
Zhang Y,Liu X,Wang C,Xu J,2015.Comparison of mitochondrial genomes provides insights into intron dynamics and evolution in the caterpillar fungus Cordyceps militaris.Fungal Genetics and Biology,77:95-107
Zhang YJ,Guo LH,Zhang S,Liu XZ,2015.Determining mitochondrial molecular markers suitable for genetic diversity analysis of Cordyceps militaris.Acta Microbiologica Sinica,55(7):826-833(in Chinese)
Zhu J,Liu XR,Xie BG,Liu FY,Deng YJ,Xiong F,2009.Analysis of germplasm resources of Pleurotus geesteranus by ITS-RFLP.Journal of Fujian Agriculture and Forestry University(Philosophy and Social Sciences),38(2):186-191(in Chinese)
陈斌,何薇,李海涛,吴鹏,肖瑜璋,吕向立,何静,2017.基于线粒体COⅠ基因对南海毛颚动物箭虫科的鉴定及系统发育初探.热带海洋学报,36(6):100-108
公月月,李伟,赵建,陈海港,王亚坤,朱新平,2017.线粒体COⅠ基因在观赏鱼中物种鉴定与分类应用.基因组学与应用生物学,36(9):3728-3734
康璐瑶,崔海峰,张雅芬,张子杰,俞晓平,叶子弘,2017.不同茭白品种中菰黑粉菌的鉴定及ISSR多态性分析.菌物学报,36(9):1210-1221
刘萍花,林起,魏如翰,王雄荣,周敏亚,2016.基于线粒体基因间区的烟草黑胫病菌遗传多样性研究.农业科技通讯,8:102-104
仇艳光,史玉兰,2008.线粒体DNA与衰老的研究进展.白求恩军医学院学报,6(1):27-28
宋慧群,艾琳,莫伊梦,周嘉琦,林瑞庆,袁子国,朱兴全,2009.片形吸虫线粒体nad1基因的序列分析及种系发育.中国兽医科学,39(6):487-491
忻雅,阮松林,王世恒,马华升,王伟科,王淑珍,2008.基于RAPD和EST-SSR标记的秀珍菇菌株聚类分析.食用菌学报,15(4):20-25
熊庆,刘作易,喻子牛,2002.线粒体DNA的研究与应用.西南农业学报,15(3):111-115
尹军华,张平,龚庆芳,陈作红,2008.亚稀褶黑菇和稀褶黑菇的ITS序列分析.菌物学报,27(2):237-242
易啸,王攀攀,王军,苏永全,毛勇,2018.基于线粒体COⅠ的DNA条形码在对虾科种类鉴定中的研究.水产学报,42(1):1-9
杨丹,米飞,董建勇,张云润,吴金燕,2016.真菌线粒体基因组大小变化.安徽农业科学,44(1):36-39
曾凡亚,张义正,1998.食用真菌线粒体DNA的直接分析.微生物学通报,25(1):5-9
曾凡荣,王军,周孔霖,游欣欣,毛勇,2010.基于线粒体Cytb基因探讨我国日本囊对虾4个地理群体的遗传结构及种群分化.厦门大学学报(自然版),49(5):701-706
张永杰,郭丽宏,张姝,刘杏忠,2015.适于蛹虫草遗传多样性研究的线粒体分子标记的筛选.微生物学报,55(7):826-833
朱坚,刘新锐,谢宝贵,刘福阳,邓优锦,熊芳,2009.秀珍菇种质资源的ITS-RFLP分析.福建农林大学学报(自然科学版),38(2):186-191
Al-Reedy RM,Malireddy R,Dillman CB,Kennell JC,2012.Comparative analysis of Fusarium mitochondrial genomes reveals a highly variable region that encodes an exceptionally large open reading frame.Fungal Genetics and Biology,49(1):2-14
Bao D,Aimi T,Kitamoto Y,2005.Cladistic relationships among the Pleurotus ostreatus complex,the Pleurotus pulmonarius complex,and Pleurotus eryngii based on the mitochondrial small subunit ribosomal DNAsequence analysis.Journal of Wood Science,51(1):77-82
Bullerwell CE,Lang BF,2005.Fungal evolution:the case of the vanishing mitochondrion.Current Opinion in Microbiology,8(4):362-369
Burger G,Gray MW,Lang BF,2003.Mitochondrial genomes:anything goes.Trends in Genetics,19(12):709-716
Chen B,He W,Li HT,Wu P,Xiao YZ,LüXL,He J,2017.Identification and phylogenetic analysis of Sagittidae(Chaetognatha)in the South China Sea based on mitochondrial COⅠgene*.Journal of Tropical Oceanography,36(6):100-108(in Chinese)
Deng YJ,Zhang QH,Ming R,Lin LJ,Lin XZ,Lin YY,Li X,Wen ZQ,2016.Analysis of the mitochondrial genome in Hypomyces aurantius reveals a novel Tw intron complex in fungi.International Journal of Molecular Sciences,17(7):1049
Felsenstein J,1985.Confidence limits on phylogenies:all approach using the bootstrap.Evolution,39(4):783-791
Formey D,Molès M,Haouy A,Savelli B,Bouchez O,Becard G,Roux C,2012.Comparative analysis of mitochondrial genomes of Rhizophagus irregularis-syn.Glomus irregulare-reveals a polymorphism induced by variability generating elements.New Phytologist,196(4):1217-1227
Gong YY,Li W,Zhao J,Chen HG,Wang YK,Zhu XP,2017.Identification and classification application of mitochondrial COⅠgene in ornamental fish.Genomics and Applied Biology,36(9):3728-3734(in Chinese)
Kang LY,Cui HF,Zhang YF,Zhang ZJ,Yu XP,Ye ZH,2017.Identification and ISSR polymorphism analysis of Ustilago esculenta isolated from Zizania latifolia.Mycosystema,36(9):1210-1221(in Chinese)
Kovalenko SA,Kopsidas G,Kelso J,Rosenfeldt F,Linnane AW,1998.T issue-specific distribution of multiple mitochondrial DNA rearrangements during human aging.Annuals of the New York Academy of Sciences,854(1):171-181
Larkin MA,Blackshields G,Brown NP,Chenna R,Mc Gettigan PA,Mc William H,Valentin F,Wallace IM,Wilm A,Lopez R,Thompson JD,Gibson TJ,Higgins DG,2007.Clustal Wand Clustal X version 2.0.Bioinformatics,23(21):2947-2948
Li Y,Hu XD,Yang RH,Hsiang T,Wang K,Liang DQ,Liang F,Cao DM,Zhou F,Wen G,Yao YJ,2015.Complete mitochondrial genome of the medicinal fungus Ophiocordyceps sinensis.Scientific Reports,5:13892
Li J,Zhang J,Chen H,Chen XD,Lan J,Liu C,2013.Complete mitochondrial genome of the medicinal mushroom Ganoderma lucidum.PLo S One,8(8):e72038
Liu PH,Lin Q,Wei RH,Wang XR,Zhou MY,2016.Genetic characterization of Phytophthora nicotianae by the analysis of intergenic regions of the mitochondrial DNA.Bulletin of Agricultural Science and Technology,8:102-104(in Chinese)
Liu R,2016.The discovery and the origins hypothesis of mitochondria.Biology Teaching,41(11):9-11(in Chinese)
Lu ZH,2008.SRAP analysis of cultivation strains of Pleurotus pulmonarius and it’s sibling varieties.Acta Agriculturae Jiangxi,20(11):8-10(in Chinese)
Mouhamadou B,Ferandon C,Barroso G,Labarere J,2006.The mitochondrial apocytochrome b genes of two Agrocybe species suggest lateral transfers of group Ihoming introns among phylogenetically distant fungi.Fungal Genetics and Biology,43(3):135-145
Nuno R,Lei S,Shutt TE,Cotney J,Guan MX,Gilliland TC,Hohuan D,Santos-Sacchi J,Shadel GS,2012.Mitochondrial stress engages E2F1 apoptotic signaling to cause deafness.Cell,148(4):716
Qiu YG,Shi YL,2008.Progress in the study of mitochondrial DNA and aging.Journal of Bethune Military Medical College,6(1):27-28(in Chinese)
Song HQ,Ai L,Mo YM,Zhou JQ,Lin RQ,Yuan ZG,Zhu XQ,2009.Sequencing of mitochondrial NADHdehydrogenase subunit 1(nad1)gene among Fasciola spp.and phylogenetic reconstruction.Veterinary Science in China,39(6):487-491(in Chinese)
Xin Y,Ruan SL,Wang SH,Ma HS,Wang WK,Wang SZ,2008.Cluster analysis of ten Pleurotus geesteranus strains based on random amplification of polymorphic DNA(RAPD)and expressed sequence tag-single sequence repeats(EST-SSR)markers.Acta Edulis Fungi,15(4):20-25(in Chinese)
Xiong Q,Liu ZY,YU ZS,2002.Progresses in studies and application of mitochondrial DNA.Southwest China Journal of Agricultural Sciences,15(3):111-115(in Chinese)
Yang D,Mi F,Dong JY,Zhang YR,Wu JY,2016.Changes of genome size of fungal mitochondria.Journal of Anhui Agricultural Sciences,44(1):36-39(in Chinese)
Yi X,Wang PP,Wang J,Su YQ,Mao Y,2018.The research of COⅠ-based DNA barcoding in Penaeidaes’identification.Journal of Fisheries of China,42(1):1-9(in Chinese)
Yin JH,Zhang P,Gong QF,Chen ZH,2008.Sequence analysis of the internal transcribed spacer of gene coding for r DNA in Russula subnigricans and R.nigricans.Mycosystema,27(2):237-242(in Chinese)
Yoon H,Kong WS,Kim YJ,Kim JG,2016.Complete mitochondrial genome of the ectomycorrhizal fungus Tricholoma matsutake.Mitochondrial DNA Part A,27(6):3855-3857
Yoon H,You YH,Woo JR,Park YJ,Kong WS,2012.The mitochondrial genome of the white-rot fungus Flammulina velutipes.The Journal of General and Applied Microbiology,58(4):331-337
Zeng FY,Zhang YZ,1998.Analyses of mushroom mitochondrial DNA by four-gc-cutter restriction enzyme.Microbiology China,25(1):5-9(in Chinese)
Zeng FR,Wang J,Zhou KL,You XX,Mao Y,2010.Genetic structure and population differentiation in four wild populations of Marsupenaeus japonicus based on cytochrome b gene segment sequence of mitochondrial DNA.Journal of Xiamen University(Natural Science),49(5):701-706(in Chinese)
Zerbino DR,Birney E,2008.Velvet:algorithms for de novo short read assembly using de Bruijn graphs.Genome Research,18(5):821-829
Zhang Y,Liu X,Wang C,Xu J,2015.Comparison of mitochondrial genomes provides insights into intron dynamics and evolution in the caterpillar fungus Cordyceps militaris.Fungal Genetics and Biology,77:95-107
Zhang YJ,Guo LH,Zhang S,Liu XZ,2015.Determining mitochondrial molecular markers suitable for genetic diversity analysis of Cordyceps militaris.Acta Microbiologica Sinica,55(7):826-833(in Chinese)
Zhu J,Liu XR,Xie BG,Liu FY,Deng YJ,Xiong F,2009.Analysis of germplasm resources of Pleurotus geesteranus by ITS-RFLP.Journal of Fujian Agriculture and Forestry University(Philosophy and Social Sciences),38(2):186-191(in Chinese)
陈斌,何薇,李海涛,吴鹏,肖瑜璋,吕向立,何静,2017.基于线粒体COⅠ基因对南海毛颚动物箭虫科的鉴定及系统发育初探.热带海洋学报,36(6):100-108
公月月,李伟,赵建,陈海港,王亚坤,朱新平,2017.线粒体COⅠ基因在观赏鱼中物种鉴定与分类应用.基因组学与应用生物学,36(9):3728-3734
康璐瑶,崔海峰,张雅芬,张子杰,俞晓平,叶子弘,2017.不同茭白品种中菰黑粉菌的鉴定及ISSR多态性分析.菌物学报,36(9):1210-1221
刘萍花,林起,魏如翰,王雄荣,周敏亚,2016.基于线粒体基因间区的烟草黑胫病菌遗传多样性研究.农业科技通讯,8:102-104
仇艳光,史玉兰,2008.线粒体DNA与衰老的研究进展.白求恩军医学院学报,6(1):27-28
宋慧群,艾琳,莫伊梦,周嘉琦,林瑞庆,袁子国,朱兴全,2009.片形吸虫线粒体nad1基因的序列分析及种系发育.中国兽医科学,39(6):487-491
忻雅,阮松林,王世恒,马华升,王伟科,王淑珍,2008.基于RAPD和EST-SSR标记的秀珍菇菌株聚类分析.食用菌学报,15(4):20-25
熊庆,刘作易,喻子牛,2002.线粒体DNA的研究与应用.西南农业学报,15(3):111-115
尹军华,张平,龚庆芳,陈作红,2008.亚稀褶黑菇和稀褶黑菇的ITS序列分析.菌物学报,27(2):237-242
易啸,王攀攀,王军,苏永全,毛勇,2018.基于线粒体COⅠ的DNA条形码在对虾科种类鉴定中的研究.水产学报,42(1):1-9
杨丹,米飞,董建勇,张云润,吴金燕,2016.真菌线粒体基因组大小变化.安徽农业科学,44(1):36-39
曾凡亚,张义正,1998.食用真菌线粒体DNA的直接分析.微生物学通报,25(1):5-9
曾凡荣,王军,周孔霖,游欣欣,毛勇,2010.基于线粒体Cytb基因探讨我国日本囊对虾4个地理群体的遗传结构及种群分化.厦门大学学报(自然版),49(5):701-706
张永杰,郭丽宏,张姝,刘杏忠,2015.适于蛹虫草遗传多样性研究的线粒体分子标记的筛选.微生物学报,55(7):826-833
朱坚,刘新锐,谢宝贵,刘福阳,邓优锦,熊芳,2009.秀珍菇种质资源的ITS-RFLP分析.福建农林大学学报(自然科学版),38(2):186-191