裂叶榆叶绿体基因组及CP-SSR位点分析
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摘要
榆树材质优良,具有良好的耐旱、耐寒和耐盐碱能力,从温带、暖温带到亚热带都有分布。本研究对榆科植物(裂叶榆)的叶绿体基因组进行De novo测序,裂叶榆叶绿体基因组序列全长为158953 bp,为典型的四段式结构,其中LSC区长度为88032 bp,SSC区长18846 bp,两个IR区长26037 bp,GC含量为35. 57%。裂叶榆叶绿体基因组总共编码139个基因,包括85个蛋白编码基因、8个r RNA和46个t RNA基因。裂叶榆的叶绿体基因组存在755个SSR位点,SSR序列长度主要以6~8 bp的短序列为主,SSR共有49个重复单元,以A/T和AT/AT为主,占所有SSR位点的66. 09%。选取42个物种叶绿体基因组的共有蛋白编码基因进行系统进化分析表明,裂叶榆与大麻科、桑科物种亲缘关系最近,榆科与大麻科、桑科均属于荨麻目,与传统分类学相吻合。本研究报道了裂叶榆的叶绿体基因组序列,对今后榆树的光合作用研究、CP-SSR引物开发、进化研究及叶绿体转基因工程等研究具有重要意义。
Elm(Ulmus) has a long history of using as high-quality hard wood and could grow in temperate,warm temperate,and subtropical regions for its strong ability to resist biotic stresses(drought,cold and salt). By de novo sequencing of the chloroplast genome of Ulmus laciniata Mayr,here we unlocked the chloroplast genome with a length of 158953 bp,which contains four distinct regions,including: a pair of inverted repeat regions(IR) of 26037 bp,large single-copy region(LSC) of 88032 bp,and small single-copy region(SSC) of 18846 bp. The chloroplast genome shows a GC content of 35. 57% and contains a total of 139 genes,consisting of 85 protein encoding genes,8 r RNA genes and 46 t RNA genes. A total of 755 SSR loci derived from 49 repeat units were found,and most of them were developed based on 6 to 8 bp short sequence. The large proportion of SSR loci was designed according to A/T and AT/AT(499,66. 09%). By phylogenetic analysis using the protein coding sequences of chloroplast genomes in 42 species,U. laciniata was found to be closely related to the plants of Cannabaceae and Moraceae,which belong to the genus Urticales,as revealed in the traditional taxonomy. Thus,this study provided a sequence of chloroplast genome in Ulmus laciniata Mayr,and this resource might be useful in understanding photosynthesis,evolution,primer development and chloroplast transgenic engineering.
Elm(Ulmus) has a long history of using as high-quality hard wood and could grow in temperate,warm temperate,and subtropical regions for its strong ability to resist biotic stresses(drought,cold and salt). By de novo sequencing of the chloroplast genome of Ulmus laciniata Mayr,here we unlocked the chloroplast genome with a length of 158953 bp,which contains four distinct regions,including: a pair of inverted repeat regions(IR) of 26037 bp,large single-copy region(LSC) of 88032 bp,and small single-copy region(SSC) of 18846 bp. The chloroplast genome shows a GC content of 35. 57% and contains a total of 139 genes,consisting of 85 protein encoding genes,8 r RNA genes and 46 t RNA genes. A total of 755 SSR loci derived from 49 repeat units were found,and most of them were developed based on 6 to 8 bp short sequence. The large proportion of SSR loci was designed according to A/T and AT/AT(499,66. 09%). By phylogenetic analysis using the protein coding sequences of chloroplast genomes in 42 species,U. laciniata was found to be closely related to the plants of Cannabaceae and Moraceae,which belong to the genus Urticales,as revealed in the traditional taxonomy. Thus,this study provided a sequence of chloroplast genome in Ulmus laciniata Mayr,and this resource might be useful in understanding photosynthesis,evolution,primer development and chloroplast transgenic engineering.
引文
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[2]史宝胜,任子蓓,杨露,张卫东.金叶榆叶片黄色素的提取及性质研究.北方园艺,2000(16):133-136
[3] Conde P,Sousa A,Costa A,Santos C. A protocol for Ulmus minor Mill. Micro propagation and acclimatization. Plant Cell Tissue and Organ Culture,2008,92:113-119
[4] Dias M C,Monteiro C,Moutinho-Pereira J,Correia C,Gon9alves B,Santos C. Cadmium toxicity affects photosynthesis and plant growth at different levels. Acta Physiologiae Plantarum,2013,35:1281-1289
[5] Wolfe K H,Li W H,Sharp P M. Rates of nucleotide substitution vary greatly among plantmitochondrial,chloroplast,and nuclear DNAs. Proceedings of the National Academy of Sciences,1987,84(24):9054-9058
[6] Ernes M J,Neuhaus H E. Metabolism and transport in non-photosynthetic plastids. Journal of Experimental Bota,1997,48(317):1995-2005
[7] Bremer B,Bremer K,Heidari N,Erixon P,Olmstead R G,Anderberg A A,Kllersj9 M,Barkhordarian E. Phylogenetics of asterids based on 3 coding and 3 non-coding chloroplast DNA markers and the utility of non-coding DNA at higher taxonomiclevels. Molecular Phylogenetics and Evolution,2002,24(2):274-301
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[11]程慧,葛春峰,张红,乔玉山.果树叶绿体基因组测序及系统发育研究进展.核农学报,2018,32(1):58-69
[12]鄢秀芹,鲁敏,安华明.刺梨转录组SSR信息分析及其分子标记开发.园艺学报,2015,42(2):341-349
[13]李炎林,杨星星,张家银,黄三文,熊兴耀.南方红豆杉转录组SSR挖掘及分子标记的研究.园艺学报,2014,41(4):735-745
[14]李满堂,张仕林,邓鹏,侯喜林,王建军.洋葱转录组SSR信息分析及其多态性研究.园艺学报,2015,42(6):1103-1111
[15]何海,郭继云,马毅平,周梦春,王沫,舒少华.茯苓转录组SSR序列特征及其基因功能分析.中草药,2015,46(23):3558-3563
[16]李翠婷,张广辉,马春花,孟珍贵,陈军文,杨生超.野三七转录组中SSR位点信息分析及其多态性研究.中草药,2014,45(10):1468-1472
[17]刘越,岳春江,王翊,马加强,孙洪波,罗敏,马鹏举,张琳霞,马徐,陈川川,李华,唐丽.藏茵陈川西獐牙菜转录组SSR信息分析.中国中药杂志,2015,40(11):2068-2076
[18]张振,张含国,莫迟,张磊.红松转录组SSR分析及EST-SSR标记开发.林业科学,2015,51(8):114-120
[19]黄海燕,杜红岩,乌云塔娜,刘攀峰.基于杜仲转录组序列的SSR分子标记的开发.林业科学,2013,49(5):176-181
[20]文亚峰,韩文军,周宏,徐刚标.杉木转录组SSR挖掘及ESTSSR标记规模化开发.林业科学,2015,51(11):40-49
[21]宋菊,龙月红,林丽梅,尹峰,邢朝斌.五加科植物叶绿体基因组结构与进化分析.中草药,2017,48(24):5070-5075
[22]冯琛,张云婷,肖婕,汤浩茹.黑莓RuTT12-1基因密码子偏好性分析.基因组学与应用生物学,2016,35(8):2133-2144
[23]潘磊,李依,郭瑞,张凤银,曾长立,胡志辉,吴华,陈禅友.豇豆叶绿体微卫星标记的开发及其在近缘种的通用性研究.长江蔬菜,2014(6):9-15
[24]李绪英,肖炳光,高玉龙,姬广海.烟草叶绿体基因组和线粒体基因组SSR位点分析.西北植物学报,2011,31(12):2399-2405
[25]李巧丽,延娜,宋琼,郭军战.鲁桑叶绿体基因组序列及特征分析.植物学报,2018,53(1):94-103
[26]陈文超,苏琬涵,刘志高,季梦成.铁线莲属植物叶绿体微卫星引物开发及其遗传分析.浙江农业学报,2017,29(12):2023-2031
[27]王文斌,于欢,邱相坡.黄芩叶绿体基因组重复序列及密码子偏好性分析.分子植物育种,2018,16(8):2445-2452
[28]高阳,王芙蓉,刘国栋,张景霞,张传云,张军.基于陆地棉茎尖转录组序列genic-SSR标记的开发与评价.植物遗传资源学报,2015,16(4):815-822
[29]魏明明,陈钰辉,刘富中,张映,连勇.基于转录组测序的茄子SSR标记开发.植物遗传资源学报,2016,17(6):1082-1091
[30]李炎林,杨星星,张家银,黄三文,熊兴耀.南方红豆杉转录组SSR挖掘及分子标记的研究.园艺学报,2014,41(4):735-745
[2]史宝胜,任子蓓,杨露,张卫东.金叶榆叶片黄色素的提取及性质研究.北方园艺,2000(16):133-136
[3] Conde P,Sousa A,Costa A,Santos C. A protocol for Ulmus minor Mill. Micro propagation and acclimatization. Plant Cell Tissue and Organ Culture,2008,92:113-119
[4] Dias M C,Monteiro C,Moutinho-Pereira J,Correia C,Gon9alves B,Santos C. Cadmium toxicity affects photosynthesis and plant growth at different levels. Acta Physiologiae Plantarum,2013,35:1281-1289
[5] Wolfe K H,Li W H,Sharp P M. Rates of nucleotide substitution vary greatly among plantmitochondrial,chloroplast,and nuclear DNAs. Proceedings of the National Academy of Sciences,1987,84(24):9054-9058
[6] Ernes M J,Neuhaus H E. Metabolism and transport in non-photosynthetic plastids. Journal of Experimental Bota,1997,48(317):1995-2005
[7] Bremer B,Bremer K,Heidari N,Erixon P,Olmstead R G,Anderberg A A,Kllersj9 M,Barkhordarian E. Phylogenetics of asterids based on 3 coding and 3 non-coding chloroplast DNA markers and the utility of non-coding DNA at higher taxonomiclevels. Molecular Phylogenetics and Evolution,2002,24(2):274-301
[8]田欣,李德铢. DNA序列在植物系统学研究中的应用.云南植物研究,2002(2):170-184
[9] Leliaert F,Smith D R,Moreau H,Herron M D,Verbruggen H,Delwiche C F,Clerck O D. Phylogeny and molecular evolution of the green algae. Critical Reviews Plant Sciences,2012,31:1-46
[10] Zuo L H,Shang A Q,Zhang S,Yu X Y,Ren Y C,Yang M S,Wang J M. The first complete chloroplast genome sequences of Ulmus species by de novo sequencing:Genome comparative and taxonomic position analysis. PLo S One,2017,12(2):1-19. DOI:10. 1371/journal. pone. 0171264
[11]程慧,葛春峰,张红,乔玉山.果树叶绿体基因组测序及系统发育研究进展.核农学报,2018,32(1):58-69
[12]鄢秀芹,鲁敏,安华明.刺梨转录组SSR信息分析及其分子标记开发.园艺学报,2015,42(2):341-349
[13]李炎林,杨星星,张家银,黄三文,熊兴耀.南方红豆杉转录组SSR挖掘及分子标记的研究.园艺学报,2014,41(4):735-745
[14]李满堂,张仕林,邓鹏,侯喜林,王建军.洋葱转录组SSR信息分析及其多态性研究.园艺学报,2015,42(6):1103-1111
[15]何海,郭继云,马毅平,周梦春,王沫,舒少华.茯苓转录组SSR序列特征及其基因功能分析.中草药,2015,46(23):3558-3563
[16]李翠婷,张广辉,马春花,孟珍贵,陈军文,杨生超.野三七转录组中SSR位点信息分析及其多态性研究.中草药,2014,45(10):1468-1472
[17]刘越,岳春江,王翊,马加强,孙洪波,罗敏,马鹏举,张琳霞,马徐,陈川川,李华,唐丽.藏茵陈川西獐牙菜转录组SSR信息分析.中国中药杂志,2015,40(11):2068-2076
[18]张振,张含国,莫迟,张磊.红松转录组SSR分析及EST-SSR标记开发.林业科学,2015,51(8):114-120
[19]黄海燕,杜红岩,乌云塔娜,刘攀峰.基于杜仲转录组序列的SSR分子标记的开发.林业科学,2013,49(5):176-181
[20]文亚峰,韩文军,周宏,徐刚标.杉木转录组SSR挖掘及ESTSSR标记规模化开发.林业科学,2015,51(11):40-49
[21]宋菊,龙月红,林丽梅,尹峰,邢朝斌.五加科植物叶绿体基因组结构与进化分析.中草药,2017,48(24):5070-5075
[22]冯琛,张云婷,肖婕,汤浩茹.黑莓RuTT12-1基因密码子偏好性分析.基因组学与应用生物学,2016,35(8):2133-2144
[23]潘磊,李依,郭瑞,张凤银,曾长立,胡志辉,吴华,陈禅友.豇豆叶绿体微卫星标记的开发及其在近缘种的通用性研究.长江蔬菜,2014(6):9-15
[24]李绪英,肖炳光,高玉龙,姬广海.烟草叶绿体基因组和线粒体基因组SSR位点分析.西北植物学报,2011,31(12):2399-2405
[25]李巧丽,延娜,宋琼,郭军战.鲁桑叶绿体基因组序列及特征分析.植物学报,2018,53(1):94-103
[26]陈文超,苏琬涵,刘志高,季梦成.铁线莲属植物叶绿体微卫星引物开发及其遗传分析.浙江农业学报,2017,29(12):2023-2031
[27]王文斌,于欢,邱相坡.黄芩叶绿体基因组重复序列及密码子偏好性分析.分子植物育种,2018,16(8):2445-2452
[28]高阳,王芙蓉,刘国栋,张景霞,张传云,张军.基于陆地棉茎尖转录组序列genic-SSR标记的开发与评价.植物遗传资源学报,2015,16(4):815-822
[29]魏明明,陈钰辉,刘富中,张映,连勇.基于转录组测序的茄子SSR标记开发.植物遗传资源学报,2016,17(6):1082-1091
[30]李炎林,杨星星,张家银,黄三文,熊兴耀.南方红豆杉转录组SSR挖掘及分子标记的研究.园艺学报,2014,41(4):735-745
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