桑叶葡萄叶绿体基因组及其特征分析
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摘要
桑叶葡萄(Vitis ficifolia)是中国重要的葡萄属野生资源。以桑叶葡萄'九里沟桑4号'为试验材料,利用Illumina HiSeq PE150测序平台完成了其全基因组重测序,并组装了其叶绿体基因组。注释结果表明,桑叶葡萄叶绿体基因组全长160 751 bp,呈典型的四分体结构,其大单拷贝区(large single copy,LSC)、反向重复序列(inverted repeat,IR)和小单拷贝区(small single copy, SSC)的长度分别为88 971、26 355和19 070 bp。注释共得到133个基因,包含88个蛋白编码基因,8个rRNA基因,37个tRNA基因。在桑叶葡萄中共搜索到84个SSR位点,其中单核苷酸、二核苷酸、三核苷酸、四核苷酸和五核苷酸重复基序个数分别为55、8、9、9和3个。用MEGA软件,通过邻接法对包括5个葡萄种类的32个种的叶绿体基因组序列进行聚类分析,结果表明,桑叶葡萄与山葡萄(Vitis amurensis)、欧亚种'黑比诺'(V.vinifera'Pinot Noir')、夏葡萄(V.aestivalis)以及圆叶葡萄(V.rotundifolia)具有较近的亲缘关系。
Vitis ficifolia is an important wild resource in China. In this study,the whole genome resequencing of V. ficifolia was completed using Illumina HiSeq PE150 sequencing platform. The chloroplast genome was assembled. The results of the annotation indicated that the chloroplast genome of V. ficifolia has a total length of 160 751 bp,which is a typical tetrad structure. The length of LSC,IR and SSC regions are 88 971,26 355 and 19 070 bp,respectively. The chloroplast genome contains a total of 133 genes,including 88 protein-coding genes,8 rRNA genes,and 37 tRNA genes. We found 84 SSR loci in the V. ficifolia chloroplast genome,of which the number of mononucleotide,dinucleotide,trinucleotide,tetranucleotide and pentanucleotide repeat motifs was 55,8,9,9 and 3,respectively. The NJ tree using chloroplast genome sequences of 32 species including 5 Vitis species was contrusted by MEGA software.The results showed that V. ficifolia had a close genetic relationship with V. amurensis,Pinot Noir(V.vinifera),V. aestivalis and V. rotundifolia.
Vitis ficifolia is an important wild resource in China. In this study,the whole genome resequencing of V. ficifolia was completed using Illumina HiSeq PE150 sequencing platform. The chloroplast genome was assembled. The results of the annotation indicated that the chloroplast genome of V. ficifolia has a total length of 160 751 bp,which is a typical tetrad structure. The length of LSC,IR and SSC regions are 88 971,26 355 and 19 070 bp,respectively. The chloroplast genome contains a total of 133 genes,including 88 protein-coding genes,8 rRNA genes,and 37 tRNA genes. We found 84 SSR loci in the V. ficifolia chloroplast genome,of which the number of mononucleotide,dinucleotide,trinucleotide,tetranucleotide and pentanucleotide repeat motifs was 55,8,9,9 and 3,respectively. The NJ tree using chloroplast genome sequences of 32 species including 5 Vitis species was contrusted by MEGA software.The results showed that V. ficifolia had a close genetic relationship with V. amurensis,Pinot Noir(V.vinifera),V. aestivalis and V. rotundifolia.
引文
Asaf S,Waqas M,Khan A L,Khan M A,Kang S M,Imran Q M,Shahzad R,Bilal S,Yun B W,Lee I J.2017.The complete chloroplast genome of wild rice(Oryza minuta)and its comparison to related species.Frontiers in Plant Science,8:304.
Bankevich A,Nurk S,Antipov D,Gurevich A A,Dvorkin M,Kulikov A S,Lesin V M,Nikolenko S I,Pham S,Prjibelski A D,Pyshkin A V,Sirotkin A V,Vyahhi N,Tesler G,Alekseyev M A,Pevzner P A.2012.SPAdes:a new genome assembly algorithm and its application to single-cell sequencing.Journal of Computational Biology,19(5):455-477.
Benson G.1999.Tandem repeats finder:a program to analyze DNA sequences.Nucleic Acids Research,27(2):573-580.
Burke S V,Wysocki W P,Zuloaga F O,Craine J M,Pires J C,Edger P P,Mayfield-Jones D,Clark L G,Kelchner S A,Duvall M R.2016.Evolutionary relationships in Panicoid grasses based on plastome phylogenomics(Panicoideae;Poaceae).BMC Plant Biology,16(1):140.
Cavalier-Smith T.2002.Chloroplast evolution:secondary symbiogenesis and multiple losses.Current Biology,12(2):62-64.
Chen H,Shao J,Zhang H,Jiang M,Huang L,Zhang Z,Yang D,Molly H,Mostafa R,Luo X,Sun B,Wu W,Liu C.2018.Sequencing and analysis of Strobilanthes cusia(Nees)kuntze chloroplast genome revealed the rare simultaneous contraction and expansion of the inverted repeat region in angiosperm.Frontiers in Plant Science,DOI:10.3389/fpls.2018.00324.
Cronn R,Liston A,Parks M,Gernandt D S,Shen R,Mockler T.2008.Multiplex sequencing of plant chloroplast genomes using solexa sequencing-by-synthesis technology.Nucleic Acids Research,36(19):e122.
Fajardo D,Senalik D,Ames M,Zhu H,Steffan S A,Harbut R,Polashock J,Vorsa N,Gillespie E,Kron K,Zalapa J E.2013.Complete plastid genome sequence of Vaccinium macrocarpon:structure,gene content,and rearrangements revealed by next generation sequencing.Tree Genetics&Genomes,9(2):489-498.
Fu J,Liu H,Hu J,Liang Y,Liang J,Wuyun T,Tan X.2016.Five complete chloroplast genome sequences from Diospyros:genome organization and comparative analysis.PLoS ONE,11(7):e0159566.
Jansen R K,Raubeson L A,Boore J L,Depamphilis C W,Chumley T W,Haberle R C,Wyman S K,Alverson A J,Peery R,Herman S J,Fourcade H M,Kuehl J V,McNeal J R,Leebens-Mack J,Cui L.2005.Methods for obtaining and analyzing whole chloroplast genome sequences.Methods in Enzymology,395(6):348.
Jansen R K,Kaittanis C,Saski C,Lee S B,Tomkins J,Alverson A J,Daniell H.2006.Phylogenetic analyses of Vitis(Vitaceae)based on complete chloroplast genome sequences:effects of taxon sampling and phylogenetic methods on resolving relationships among rosids.BMC Evolutionary Biology,6(1):32.
Keeling P J.2004.Diversity and evolutionary history of plastids and their hosts.American Journal of Botany,91(10):1481.
Kuang D Y,Wu H,Wang Y L,Gao L M,Zhang S Z,Lu L.2011.Complete chloroplast genome sequence of Magnolia kwangsiensis(Magnoliaceae):implication for dna barcoding and population genetics.Genome,54(8):663-673.
Leseberg C H,Duvall M R.2009.The complete chloroplast genome of Coix lacrymajobi and a comparative molecular evolutionary analysis of plastomes in cereals.Journal of Molecular Evolution,69(4):311-318.
Li Chao-luan.1998.Flora of China·Vitaceae.Beijing:Science Press:140-198.(in Chinese)李朝銮.1998.中国植物志·葡萄科.北京:科学出版社:140-198.
Li R,Ma P,Wen J,Yi T.2013.Complete sequencing of five Araliaceae chloroplast genomes and the phylogenetic implications.PLoS ONE,8(10):e78568.
Moore M J,Dhingra A,Soltis P S,Shaw R,Farmerie W G,Folta K M,Soltis D E.2006.Rapid and accurate pyrosequencing of angiosperm plastid genomes.BMC Plant Biology,6(1):17.
Nashima K,Terakami S,Nishitani C,Kunihisa M,Shoda M,Takeuchi M,Urasaki N,Tarora K,Yamamoto T,Katayama H.2015.Complete chloroplast genome sequence of pineapple(Ananas comosus).Tree Genetics&Genomes,11(3):60.
Nie X,Lv S,Zhang Y,Du X,Wang L,Biradar S S,Tan X,Wan F,Weining S.2012.Complete chloroplast genome sequence of a major invasive species,crofton weed(Ageratina adenophora).PLoS ONE,7(5):e36869.
Peng S,Yang G,Liu C,Zhai M.2015.The complete chloroplast genome of the Juglans regia(Juglandales:Julandaceae).Mitochondrial DNA,28(3):407-408.
Qian J,Song J,Gao H,Zhu Y,Xu J,Pang X,Yao H,Sun C,Li X,Li C,Liu J,Xu H,Chen S.2013.The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza.PLoS ONE,8(2):e57607.
Raman G,Park S J.2016.The complete chloroplast genome sequence of ampelopsis:gene organization,comparative analysis,and phylogenetic relationships to other angiosperms.Frontiers in Plant Science,7:341.
Tangphatsornruang S,Sangsrakru D,Chanprasert J,Uthaipaisanwong P,Yoocha T,Jomchai N,Tragoonrung S.2009.The chloroplast genome sequence of mungbean(Vigna radiata)determined by high-throughput pyrosequencing:structural organization and phylogenetic relationships.DNA Research an International Journal for Rapid Publication of Reports on Genes&Genomes,17(1):11-22.
Su H J,Hogenhout S A,Alsadi A M,Kuo C H.2014.Complete chloroplast genome sequence of Omani Lime(Citrus aurantiifolia)and comparative analysis within the rosids.PLoS ONE,9(11):e113049.
Wan Y,Schwaninger H,Li D,Simon C J,Wang Y.2008.A review of taxonomic research on Chinese wild grapes.Vitis Journal of Grapevine Research,47(2):81-88.
Wei W,Zheng Y,Chen L,Wei,Yan Z,Yang R.2005.PCR-RFLP analysis of cpDNA and mtDNA in the genus Houttuynia,in some areas of China.Hereditas,142:24-32.
Xie H,Jiao J,Fan X,Zhang Y,Jiang J,Liu C.2016.The complete chloroplast genome sequence of Chinese wild grape Vitis amurensis(Vitaceae:Vitis L.).Conservation Genetics Resources,9(1):1-4.
Xie Hai-kun,Jiao Jian,Fan Xiu-cai,Zhang Ying,Jiang Jian-fu,Sun Hai-sheng,Liu Chong-huai.2017.Assembling and characteristic analysis of the complete chloroplast genome of Vitis vinifera cv.Cabernet Sauvignon from high-throughput sequencing data.Scientia Agricultura Sinica,50(9):1655-1665.(in Chinese)谢海坤,焦健,樊秀彩,张颖,姜建福,孙海生,刘崇怀.2017.基于高通量测序组装‘赤霞珠’叶绿体基因组及其特征分析.中国农业科学,50(9):1655-1665.
Yang Y,Tao Z,Dong D,Jia Y,Li F,Zhao G.2016.Comparative analysis of the complete chloroplast genomes of five Quercus species.Frontiers in Plant Science,7:959.
Zecca G,Abbott J R,Sun W B,Spada A,Sala F,Grassi F.2012.The timing and the mode of evolution of wild grapes(Vitis).Molecular Phylogenetics&Evolution,62(2):736-747.
Zhang Xu-tong.2012.Phylogenetic analysis of Chinese wild grapes germplasm resources[M.D.Dissertation].Yangling:Northwest A&FUniversity.(in Chinese)张旭彤.2012.中国野生葡萄种质资源的亲缘关系研究[硕士论文].杨凌:西北农林科技大学.
Zhang Yong-hui,Liu Chong-huai,Fan Xiu-cai,Zhang Ying,Sun Hai-sheng,Peng Bin,Jiang Jian-fu.2011.Application of ISSR markers in taxonomy of Chinese wild grape.Journal of Fruit Science,28(3):406-412.(in Chinese)张永辉,刘崇怀,樊秀彩,张颖,孙海生,彭斌,姜建福.2011.ISSR标记在中国野生葡萄分类中的应用.果树学报,28(3):406-412.
Bankevich A,Nurk S,Antipov D,Gurevich A A,Dvorkin M,Kulikov A S,Lesin V M,Nikolenko S I,Pham S,Prjibelski A D,Pyshkin A V,Sirotkin A V,Vyahhi N,Tesler G,Alekseyev M A,Pevzner P A.2012.SPAdes:a new genome assembly algorithm and its application to single-cell sequencing.Journal of Computational Biology,19(5):455-477.
Benson G.1999.Tandem repeats finder:a program to analyze DNA sequences.Nucleic Acids Research,27(2):573-580.
Burke S V,Wysocki W P,Zuloaga F O,Craine J M,Pires J C,Edger P P,Mayfield-Jones D,Clark L G,Kelchner S A,Duvall M R.2016.Evolutionary relationships in Panicoid grasses based on plastome phylogenomics(Panicoideae;Poaceae).BMC Plant Biology,16(1):140.
Cavalier-Smith T.2002.Chloroplast evolution:secondary symbiogenesis and multiple losses.Current Biology,12(2):62-64.
Chen H,Shao J,Zhang H,Jiang M,Huang L,Zhang Z,Yang D,Molly H,Mostafa R,Luo X,Sun B,Wu W,Liu C.2018.Sequencing and analysis of Strobilanthes cusia(Nees)kuntze chloroplast genome revealed the rare simultaneous contraction and expansion of the inverted repeat region in angiosperm.Frontiers in Plant Science,DOI:10.3389/fpls.2018.00324.
Cronn R,Liston A,Parks M,Gernandt D S,Shen R,Mockler T.2008.Multiplex sequencing of plant chloroplast genomes using solexa sequencing-by-synthesis technology.Nucleic Acids Research,36(19):e122.
Fajardo D,Senalik D,Ames M,Zhu H,Steffan S A,Harbut R,Polashock J,Vorsa N,Gillespie E,Kron K,Zalapa J E.2013.Complete plastid genome sequence of Vaccinium macrocarpon:structure,gene content,and rearrangements revealed by next generation sequencing.Tree Genetics&Genomes,9(2):489-498.
Fu J,Liu H,Hu J,Liang Y,Liang J,Wuyun T,Tan X.2016.Five complete chloroplast genome sequences from Diospyros:genome organization and comparative analysis.PLoS ONE,11(7):e0159566.
Jansen R K,Raubeson L A,Boore J L,Depamphilis C W,Chumley T W,Haberle R C,Wyman S K,Alverson A J,Peery R,Herman S J,Fourcade H M,Kuehl J V,McNeal J R,Leebens-Mack J,Cui L.2005.Methods for obtaining and analyzing whole chloroplast genome sequences.Methods in Enzymology,395(6):348.
Jansen R K,Kaittanis C,Saski C,Lee S B,Tomkins J,Alverson A J,Daniell H.2006.Phylogenetic analyses of Vitis(Vitaceae)based on complete chloroplast genome sequences:effects of taxon sampling and phylogenetic methods on resolving relationships among rosids.BMC Evolutionary Biology,6(1):32.
Keeling P J.2004.Diversity and evolutionary history of plastids and their hosts.American Journal of Botany,91(10):1481.
Kuang D Y,Wu H,Wang Y L,Gao L M,Zhang S Z,Lu L.2011.Complete chloroplast genome sequence of Magnolia kwangsiensis(Magnoliaceae):implication for dna barcoding and population genetics.Genome,54(8):663-673.
Leseberg C H,Duvall M R.2009.The complete chloroplast genome of Coix lacrymajobi and a comparative molecular evolutionary analysis of plastomes in cereals.Journal of Molecular Evolution,69(4):311-318.
Li Chao-luan.1998.Flora of China·Vitaceae.Beijing:Science Press:140-198.(in Chinese)李朝銮.1998.中国植物志·葡萄科.北京:科学出版社:140-198.
Li R,Ma P,Wen J,Yi T.2013.Complete sequencing of five Araliaceae chloroplast genomes and the phylogenetic implications.PLoS ONE,8(10):e78568.
Moore M J,Dhingra A,Soltis P S,Shaw R,Farmerie W G,Folta K M,Soltis D E.2006.Rapid and accurate pyrosequencing of angiosperm plastid genomes.BMC Plant Biology,6(1):17.
Nashima K,Terakami S,Nishitani C,Kunihisa M,Shoda M,Takeuchi M,Urasaki N,Tarora K,Yamamoto T,Katayama H.2015.Complete chloroplast genome sequence of pineapple(Ananas comosus).Tree Genetics&Genomes,11(3):60.
Nie X,Lv S,Zhang Y,Du X,Wang L,Biradar S S,Tan X,Wan F,Weining S.2012.Complete chloroplast genome sequence of a major invasive species,crofton weed(Ageratina adenophora).PLoS ONE,7(5):e36869.
Peng S,Yang G,Liu C,Zhai M.2015.The complete chloroplast genome of the Juglans regia(Juglandales:Julandaceae).Mitochondrial DNA,28(3):407-408.
Qian J,Song J,Gao H,Zhu Y,Xu J,Pang X,Yao H,Sun C,Li X,Li C,Liu J,Xu H,Chen S.2013.The complete chloroplast genome sequence of the medicinal plant Salvia miltiorrhiza.PLoS ONE,8(2):e57607.
Raman G,Park S J.2016.The complete chloroplast genome sequence of ampelopsis:gene organization,comparative analysis,and phylogenetic relationships to other angiosperms.Frontiers in Plant Science,7:341.
Tangphatsornruang S,Sangsrakru D,Chanprasert J,Uthaipaisanwong P,Yoocha T,Jomchai N,Tragoonrung S.2009.The chloroplast genome sequence of mungbean(Vigna radiata)determined by high-throughput pyrosequencing:structural organization and phylogenetic relationships.DNA Research an International Journal for Rapid Publication of Reports on Genes&Genomes,17(1):11-22.
Su H J,Hogenhout S A,Alsadi A M,Kuo C H.2014.Complete chloroplast genome sequence of Omani Lime(Citrus aurantiifolia)and comparative analysis within the rosids.PLoS ONE,9(11):e113049.
Wan Y,Schwaninger H,Li D,Simon C J,Wang Y.2008.A review of taxonomic research on Chinese wild grapes.Vitis Journal of Grapevine Research,47(2):81-88.
Wei W,Zheng Y,Chen L,Wei,Yan Z,Yang R.2005.PCR-RFLP analysis of cpDNA and mtDNA in the genus Houttuynia,in some areas of China.Hereditas,142:24-32.
Xie H,Jiao J,Fan X,Zhang Y,Jiang J,Liu C.2016.The complete chloroplast genome sequence of Chinese wild grape Vitis amurensis(Vitaceae:Vitis L.).Conservation Genetics Resources,9(1):1-4.
Xie Hai-kun,Jiao Jian,Fan Xiu-cai,Zhang Ying,Jiang Jian-fu,Sun Hai-sheng,Liu Chong-huai.2017.Assembling and characteristic analysis of the complete chloroplast genome of Vitis vinifera cv.Cabernet Sauvignon from high-throughput sequencing data.Scientia Agricultura Sinica,50(9):1655-1665.(in Chinese)谢海坤,焦健,樊秀彩,张颖,姜建福,孙海生,刘崇怀.2017.基于高通量测序组装‘赤霞珠’叶绿体基因组及其特征分析.中国农业科学,50(9):1655-1665.
Yang Y,Tao Z,Dong D,Jia Y,Li F,Zhao G.2016.Comparative analysis of the complete chloroplast genomes of five Quercus species.Frontiers in Plant Science,7:959.
Zecca G,Abbott J R,Sun W B,Spada A,Sala F,Grassi F.2012.The timing and the mode of evolution of wild grapes(Vitis).Molecular Phylogenetics&Evolution,62(2):736-747.
Zhang Xu-tong.2012.Phylogenetic analysis of Chinese wild grapes germplasm resources[M.D.Dissertation].Yangling:Northwest A&FUniversity.(in Chinese)张旭彤.2012.中国野生葡萄种质资源的亲缘关系研究[硕士论文].杨凌:西北农林科技大学.
Zhang Yong-hui,Liu Chong-huai,Fan Xiu-cai,Zhang Ying,Sun Hai-sheng,Peng Bin,Jiang Jian-fu.2011.Application of ISSR markers in taxonomy of Chinese wild grape.Journal of Fruit Science,28(3):406-412.(in Chinese)张永辉,刘崇怀,樊秀彩,张颖,孙海生,彭斌,姜建福.2011.ISSR标记在中国野生葡萄分类中的应用.果树学报,28(3):406-412.