甜酸角基因组微卫星序列特征分析
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摘要
甜酸角是干热河谷地区有多重价值的重要经济树种,对其SSR引物的开发有助于该物种的遗传学研究以及资源的利用与保护.研究通过Illumina高通量测序技术和MISA软件开发出甜酸角全基因组SSR序列,共7个类型9 447个,其中以单核苷酸重复类型最多.在不同重复类型中,A/T碱基含量显著高于G/C;在不同长度重复单元中,单核苷酸重复类型的微卫星长度变异程度最高,二核苷酸重复类型微卫星长度变异程度也较高,各重复类型微卫星的长度与微卫星出现的频率呈负相关.获得的微卫星序列以及相关分析结果,较全面地反映了甜酸角基因组微卫星的特征和潜在功能,将有助于后续的一系列遗传学研究.
Tamarindus indica Linn. is an important economic tree species in dry hot valley areas which has multiple values. Illumina high-throughput sequencing technology and MISA software were used to develop whole genome SSR sequences of the tamarind.7 types,9447 SSR sequences were obtained and most of them were single nucleotide repeat type.The content of A / T base was significantly higher than that of G / C base in different types;and the length variation of microsatellite of single nucleotide repeat type was the highest.The length of each repeat type microsatellite was negatively correlated with the frequency of microsatellites.Results obtained from microsatellite sequences and the analysis comprehensively reflect the characteristics of T. indica genomic microsatellites and the potential functions,which will contribute to a series of subsequent genetic studies of this species.
Tamarindus indica Linn. is an important economic tree species in dry hot valley areas which has multiple values. Illumina high-throughput sequencing technology and MISA software were used to develop whole genome SSR sequences of the tamarind.7 types,9447 SSR sequences were obtained and most of them were single nucleotide repeat type.The content of A / T base was significantly higher than that of G / C base in different types;and the length variation of microsatellite of single nucleotide repeat type was the highest.The length of each repeat type microsatellite was negatively correlated with the frequency of microsatellites.Results obtained from microsatellite sequences and the analysis comprehensively reflect the characteristics of T. indica genomic microsatellites and the potential functions,which will contribute to a series of subsequent genetic studies of this species.
引文
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[19]李淑娴,张新叶,王英亚,等.桉树EST序列中微卫星含量及相关特征[J].植物学报,2010,45(3):363-371.LI S X,ZHANG X Y,WANG Y Y,et al.Microsatellite content and relative characteristics in eucalyptus EST sequences[J].Chinese Bulletin of Botany,2010,45(3):363-371.
[20]许玉兰,白青松,张瑞丽,等.云南松基因组微卫星富集文库的序列特征分析[J].生物技术,2014,24(4):62-66.XV Y L,BAI Q S,ZHANG R L,et al.Sequence feature analysis of genome microsatellite enrichment library of pinus yunnanensis[J].Biotechnology,2014,24(4):62-66.
[21]LI X,SHANGGUAN L,SONG C,et al.Analysis of expressed sequence tags from Prunus mume flower and fruit and development of simple sequence repeat markers[J].Bmc Genetics,2010,11(28):66.
[22]王丽鸳,韦康,张成才,等.茶树花转录组微卫星分布特征[J].作物学报,2014,40(1):80-85.WANG L Y,WEI K,ZHANG C C,et al.The distribution characteristics of tea flower transcriptome microsatellite[J].Acta Agronomica Sinica,2014,40(1):80-85.
[23]吴敏,杜红岩,乌云塔娜,等.杜仲基因组微卫星特征及SSR标记开发[J].林业科学研究,2015,28(3):387-393.WU M,DU H Y,WU Y T N,et al.Genomic microsatellite characteristics and SSR marker development of eucommia ulmoides[J].Forest Research,2015,28(3):387-393.
[24]高亚梅,韩毅强,汤辉,等.根瘤菌基因组内简单重复序列的分析[J].中国农业科学,2008,41(10):2 992-2 998.GAO Y M,HAN Y Q,TANG H,et al.Analysis of simple repeat sequences in the genome of the nodule bacteria[J].Scientia Agricultura Sinica,2008,41(10):2 992-2 998.
[2]赵一鹤,杨时宇,李昆.世界酸角研究现状及进展[J].云南农业大学学报,2005,20(1):65-72.ZHAO Y H,YANG S Y,LI K.The research status and progress in the world of tamarind[J].Journal of Yunnan Agricultural University,2005,20(1):65-72.
[3]吴建勇.酸角生产的现状及其开发意见[J].西部林业科学,1996(4):64-66.WU J Y.The production status of tamarind and its development opinion[J].Journal of West China Forestry Science,1996(4):64-66.
[4]陈建白.酸角[J].云南热作科技,1994,17(3):46-48.CHEN J B.Tamarind[J].Journal of Yunnan Tropical Crops Science&Technology,1994,17(3):46-48.
[5]纪中华,李建增,沙毓沧,等.元谋干热河谷退化坡地罗望子人工林水土保持效益[J].水土保持学报,2001,15(4):63-65.JI Z H,LI J Z,SHA Y C,et al.The benefit of soil and water conservation of the tamarind planted forest at degraded slope land in Yuanmou Dry Hot Valley[J].Journal of Soil and Water Conservation,2001,15(4):63-65.
[6]何毓蓉,黄成敏.云南省元谋干热河谷的土壤系统分类[J].山地研究,1995(2):73-78.HE Y R,HUANG C M.The soil classification system of Yuanmou Dry Hot Valley of Yunnan[J].Journal of Mountain Research,1995(2):73-78.
[7]赵静,冯叙桥,吴永娴.酸角的营养成分分析[J].营养学报,2001,23(4):378-379.ZHAO J,FENG X Q,WU Y X.Analysis of nutritional components of tamarind[J].Acta Nutrimenta Sinica,2001,23(4):378-379.
[8]赵一鹤,杨时宇,李昆.泰国甜角不同品种果实营养成分分析[J].植物资源与环境学报,2005,14(3):57-58.ZHAO Y H,YANG S Y,LI K.Analysis of nutritional components in different varieties of Thailand sweet tamarind fruit[J].Journal of Plant Resources and Environment,2005,14(3):57-58.
[9]邵金良,黎其万,刘宏程,等.酸角保健软糖的加工工艺技术研究[J].中国食品添加剂,2010(2):201-205.SHAO J L,LI Q W,LIU H C,et al.Study on the processing technology of tamarind softsweets[J].China Food Additives,2010(2):201-205.
[10]任红,曹兵,李劲松.酸豆的营养价值及开发利用[J].广西热带农业,2007(5):23-24.REN H,CAO B,LI J S.The nutritional value and exploitation and utilization of tamarind[J].Agricultural Research and Application,2007(5):23-24.
[11]顾志平,陈四保,王晓光.罗望子的综合利用开发[J].天然产物研究与开发,1994,6(2):84-87.GU Z P,CHEN S B,WANG X G.The development of comprehensive utilization of tamarind[J].Natural Product Research and Development,1994,6(2):84-87.
[12]张家华,肖太菊.酸角对肠道致病菌的抑制作用研究[J].攀枝花医药,1994,16(1):1-2.ZHANG J H,XIAO T J.Study on the inhibitory effect of tamarind to intestinal pathogenic bacteria[J].Journal of Panzhihua Medicine,1994,16(1):1-2.
[13]MAITI R,JANA D,DAS U K,et al.Antidiabetic effect of aqueous extract of seed of Tamarindus indica in streptozotocin-induced diabetic rats.[J].Journal of Ethnopharmacology,2004,92(1):85-91.
[14]王兵益,杨光映,李体初,等.酸角及3个甜角品种的果实形态特征及营养成分分析[J].云南大学学报:自然科学版,2014,36(2):294-298.WANG B Y,YANG G Y,LI T C,et al.Analysis of fruit morphological characteristics and nutrient composition of tamarind and 3 varieties of sweet tamarind[J].Journal of Yunnan University:Natural Sciences Edition,2014,36(2):294-298.
[15]王元兰,李忠海.罗望子胶及其在食品工业中的应用[J].食品研究与开发,2006,27(9):179-182.WANG Y L,LI Z H.Tamarind gum and its application in the food industry[J].Food Research and Development,2006,27(9):179-182.
[16]赵一鹤,杨时宇,王兵益,等.泰国甜角嫁接繁殖技术研究[J].云南大学学报:自然科学版,2006,28(6):547-553.ZHAO Y H,YANG S Y,WANG B Y,et al.Study on grafting propagation technique of Thailand sweet tamarind[J].Journal of Yunnan University:Natural Sciences Edition,2006,28(6):547-553.
[17]ALGABAL A Q A Y,PAPANNA N,SIMON L.Amplified fragment length polymorphism marker-based genetic diversity in tamarind(Tamarindus indica)[J].International Journal of Fruit Science,2011,11(1):1-16.
[18]杨时宇,何承忠,赵一鹤,等.引进泰国甜角基因资源多样性的RAPD分析[J].林业科学研究,2008,21(1):60-63.YANG S Y,HE C Z,ZHAO Y H,et al.RAPD analysis of genetic resources diversity in introduced Thailand sweet tamarind[J].Forest Research,2008,21(1):60-63.
[19]李淑娴,张新叶,王英亚,等.桉树EST序列中微卫星含量及相关特征[J].植物学报,2010,45(3):363-371.LI S X,ZHANG X Y,WANG Y Y,et al.Microsatellite content and relative characteristics in eucalyptus EST sequences[J].Chinese Bulletin of Botany,2010,45(3):363-371.
[20]许玉兰,白青松,张瑞丽,等.云南松基因组微卫星富集文库的序列特征分析[J].生物技术,2014,24(4):62-66.XV Y L,BAI Q S,ZHANG R L,et al.Sequence feature analysis of genome microsatellite enrichment library of pinus yunnanensis[J].Biotechnology,2014,24(4):62-66.
[21]LI X,SHANGGUAN L,SONG C,et al.Analysis of expressed sequence tags from Prunus mume flower and fruit and development of simple sequence repeat markers[J].Bmc Genetics,2010,11(28):66.
[22]王丽鸳,韦康,张成才,等.茶树花转录组微卫星分布特征[J].作物学报,2014,40(1):80-85.WANG L Y,WEI K,ZHANG C C,et al.The distribution characteristics of tea flower transcriptome microsatellite[J].Acta Agronomica Sinica,2014,40(1):80-85.
[23]吴敏,杜红岩,乌云塔娜,等.杜仲基因组微卫星特征及SSR标记开发[J].林业科学研究,2015,28(3):387-393.WU M,DU H Y,WU Y T N,et al.Genomic microsatellite characteristics and SSR marker development of eucommia ulmoides[J].Forest Research,2015,28(3):387-393.
[24]高亚梅,韩毅强,汤辉,等.根瘤菌基因组内简单重复序列的分析[J].中国农业科学,2008,41(10):2 992-2 998.GAO Y M,HAN Y Q,TANG H,et al.Analysis of simple repeat sequences in the genome of the nodule bacteria[J].Scientia Agricultura Sinica,2008,41(10):2 992-2 998.