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油松胚珠转录组微卫星特征分析

安俊 郑彩霞 姚阳 陈彬丽

安俊, 郑彩霞, 姚阳, 陈彬丽. 油松胚珠转录组微卫星特征分析[J]. 北京林业大学学报, 2016, 38(5): 77-83. doi: 10.13332/j.1000-1522.20150033
引用本文: 安俊, 郑彩霞, 姚阳, 陈彬丽. 油松胚珠转录组微卫星特征分析[J]. 北京林业大学学报, 2016, 38(5): 77-83. doi: 10.13332/j.1000-1522.20150033
AN Jun, ZHENG Cai-xia, YAO Yang, CHEN Bin-li. Characterization of microsatellites of ovule transcriptome in Pinus tabulaeformis[J]. Journal of Beijing Forestry University, 2016, 38(5): 77-83. doi: 10.13332/j.1000-1522.20150033
Citation: AN Jun, ZHENG Cai-xia, YAO Yang, CHEN Bin-li. Characterization of microsatellites of ovule transcriptome in Pinus tabulaeformis[J]. Journal of Beijing Forestry University, 2016, 38(5): 77-83. doi: 10.13332/j.1000-1522.20150033

油松胚珠转录组微卫星特征分析

doi: 10.13332/j.1000-1522.20150033
基金项目: 

国家自然科学基金项目(31170563)

详细信息
    作者简介:

    安俊。主要研究方向:植物生长发育。 Email:anjun070124110@126.com 地址:100083 北京市海淀区清华东路35号北京林业大学生物科学与技术学院。

    责任作者:

    郑彩霞,教授,博士生导师。主要研究方向:植物生长发育的分子调控机制。 Email:zhengcx@bjfu.edu.cn 地址:同上。

Characterization of microsatellites of ovule transcriptome in Pinus tabulaeformis

  • 摘要: 为利用微卫星分子标记技术进一步研究油松胚珠发育分子调控机制以及微卫星对油松胚珠发育的影响,本文以前期高通量测序结果为基础,用MISA软件对所获得的转录组数据进行SSR位点的发掘和分析,为后续研究提供重要信息资源和数据保障。得到的1412个SSR位点存在于1274条序列中,平均每2.15kb出现一个SSR。油松胚珠转录组微卫星中存在87种重复基元,其中(A/T)n比例最高,约占45.89%;出现频率较高的重复类型是单核苷酸(46.88%)和三核苷酸(34.99%)重复。所得微卫星多为长度<20bp的短重复序列,≥20bp仅占总数的5.67%,重复序列出现频率与长度呈负相关。所得的SSR位点大部分位于非编码区,位于编码区的仅232个,有18个跨越了编码区和非编码区;编码区中占比例最高的是三核苷酸重复序列(105个,45.26%)。

     

  • [1] 李凤兰,沈熙环,李悦. 油松雌性不育无性系的发现及其原因分析[J]. 河北林学院学报,1992,7(2):93-98.
    [1] LI F L,SHEN X H,LI Y. Discovery and analysis of female infertility of clone No.28 in seed orchard of Pinus tabulaeformis Carr.[J]. Journal of Hebei Forestry College,1992,7(2):93-98.
    [2] 丁坤善,郑彩霞,包仁艳. 油松雌性不育系的POD同工酶和蛋白质多肽分析[J]. 西北植物学报,2004,24(1):17-20.
    [2] DING K S,ZHENG C X,BAO R Y. Analyses of peroxidase isozyme and protein polypeptides in female sterile Pinus tabulaeformis [J]. Acta Botanica Boreali-Occidentalia Sinica,2004,24(1):17-20.
    [3] LI M L,ZHENG C X. RAPD analysis in female sterility (Clone 28) of Pinus tabulaeformis Carr.[J]. Journal of Beijing Forestry University,2002,24(4):35-38.
    [3] BAO R Y,ZHENG C X. Content changes of several endogenous plant hormones in female-sterile Pinus tabulaeformis Carr. [J]. Forestry Studies in China,2005,7(4):16-19.
    [4] GUO C L,GENG Y M,WANG S C. Identification of main crops should combine new and old methods[J]. China Seed Industry,2013(7):24-26.
    [4] 李敏俐,郑彩霞. 油松雌性不育系(28号无性系)的RAPD分析[J]. 北京林业大学学报,2002,24(4):35-38.
    [5] LI M Q,GAO P X,ZHU Y L,et al. Research progress of in cotton variety identification SSR molecular marker in protection of threatened plant[J]. Journal of Jiangxi Forestry Science and Technology,2011(2):24-28.
    [5] KASHI Y,KING D,SOLLER M. Simple sequence repeats as a source of quantitative genetic variation[J]. Trends in Genetics,1997,13(2):74-78.
    [6] JEWELL E,ROBINSON A,SAVAGE D,et al. SSR primer and SSR taxonomy tree: biome SSR discovery[J]. Nucleic Acids Research, 2006,34(Web Server):W656-W659.
    [6] TIAN L M,CAO Y F,DONG X G,et al. Application of SSR molecular marker in pear germplasm resources[J]. Journal of Biology,2013,30(6):91-94.
    [7] POWELL W,MACHRAY G C,PROVAN J. Polymorphism revealed by simple sequence repeats[J]. Trends in Plant Science,1996,1(7):215-222.
    [7] ZHOU L,LIU J X,GUI J F. Exploration genetic diversity in Carassius auratus gibelio bloch of gynogenesis using microsatellites marker[J]. Zoological Research,2001,22(4):257-264.
    [8] 郭承亮,耿月明,王世才. 主要农作物品种鉴定方法要“新、老”结合[J]. 中国种业,2013(7):24-26.
    [8] SHI Y F,YING J Z,WANG L,et al. Screening SSR markers for rice variety identification[J]. Chinese Journal of Rice Science,2005,19(3):195-201.
    [9] 李美琼,高浦新,朱友林,等. 微卫星(SSR)分子标记应用于濒危植物保护的研究进展[J]. 江西林业科技,2011(2):24-28.
    [9] ZHANG L L. The development of the microsatellitics in the functional genes[J]. Progress in Modern Biomedicine,2008,8(9):1783-1785.
    [10] 田路明,曹玉芬,董星光,等. SSR分子标记在梨种质资源研究中的应用[J]. 生物学杂志,2013,30(6):91-94.
    [10] CHENG X M,HUANG X X. Development and application of SSR markers in plants[J]. Chinese Agricultural Science Bulletin,2011,27(5):304-307.
    [11] CHEN L N,MA Q G,ZHANG J P,et al. Development of BAC-SSR markers in walnut and its application in genetic diversity analysis[J]. Journal of Beijing Forestry University,2014,36(6):24-29.
    [11] HOU C,LI M,ZHANG Y,et al. Analysis of SSR fingerprints in introduced silkworm germplasm resources[J]. Agricultural Sciences in China,2007,6(5):620-627.
    [12] YAN M M,DAI X G,LI S X,et al. Sequence analysis and comparison of EST-SSRs in pine,poplar and eucalyptus[J]. Genomics and Applied Biology,2011,30(1):103-109.
    [12] KANTARTZI S K,UIIOA M,SACKS E,et al. Assessing genetic diversity in Gossypium arboreum L. cultivars using genomic and EST-derived microsatellites[J]. Genetica,2009,136:141-147.
    [13] WANG L Y,WEI K,ZHANG C C,et al. Characterization of micorsatellites in tea ( Camellia sinensis ) floral transcriptome[J]. Acta Agronomica Sinica,2014,40(1):80-85.
    [13] 周莉,刘静霞,桂建芳. 应用微卫星标记对雌核发育银鲫的遗传多样性初探[J]. 动物学研究,2001,22(4):257-264.
    [14] LI Y L,YANG X X,ZHANG J Y,et al. Studies on SSR molecular markers based on transcriptome of Taxus chinensis var. mairei [J]. Acta Horticulturae Sinica,2014,41(4):735-745.
    [14] 施勇烽,应杰政,王磊,等. 鉴定水稻品种的微卫星标记筛选[J]. 中国水稻科学,2005,19(3):195-201.
    [15] RODER M S,WENDEHAKE K,KORZUN V,et al. Construction and analysis of a microsatellite-based database of European wheat varieties[J]. Theoretical and Applied Genetics,2002,106:67-73.
    [15] FAN H H,LI Y C,LI Z P,et al. Characteristics of EST-SSR distribution in ginkgo ESTs[J]. Genomics and Applied Biology,2009,28(5):869-873.
    [16] WANG X F,HE W L,CAI W J,et al. Analysis on transcriptome sequenced for Pinus massoniana [J].Molecular Plant Breeding,2013,11(3):385-392.
    [16] 张琳琳. 功能基因中的微卫星序列[J]. 现代生物医学进展,2008,8(9):1783-1785.
    [17] MA Q Y,DAI X G,CHEN Y N,et al. Characterization of microsatellites in the genome of Ziziphus jujuba [J]. Scientia Silvae Sinicae,2013,49(12):81-87.
    [17] 程小毛,黄晓霞. SSR标记开发及其在植物中的应用[J]. 中国农学通报,2011,27(5):304-307.
    [18] KONG F M,WANG X L,CHEN Y N,et al. Characterization of microsatellites in coding genes and functional analysis of these genes in pines[J]. Journal of Nanjing Forestry University (Natural Sciences Edition),2014,38(2):47-51.
    [18] WEBER J L. Informativeness of human (dC-dA)n.(dG-dT)n polymorphisms[J]. Genomics,1990,7:524-530.
    [19] JENA S N,SRIVASTAVA A,RAI K M,et al. Development and characterization of genomic and expressed SSRs for levant cotton ( Gossypium herbaceum L.)[J]. Theoretical and Applied Genetics,2012,124:565-576.
    [19] YUAN Y Y,WANG Q F,CHEN J M. Development of SSR markers in aquatic plant Nymphoides peltata (Menyanthaceae) based on information from transcriptome sequencing[J].Plant Science Journal,2013,31(5):485-492.
    [20] HE P. Abundance, polymorphism and applications of microsatellite in eukaryote[J]. Hereditas,1998,20(4):42-47.
    [20] 陈凌娜,马庆国,张俊佩,等. 核桃BES-SSR的开发及在遗传多样性分析中的应用[J]. 北京林业大学学报,2014,36(6):24-29.
    [21] LI X B,ZHANG M L,CUI H R. Analysis of SSR information in EST resource of oilseed rape[J]. Chinese Journal of Oil Crop Sciences,2007,29(1):20-25.
    [21] 阎毛毛,戴晓港,李淑娴,等. 松树、杨树及桉树表达基因序列微卫星比对分析[J]. 基因组学与应用生物学,2011,30(1):103-109.
    [22] XU Y L,BAI Q S,ZHANG R L,et al. Characteristics of microsatellite enrichment pool from Pinus yunnanensis genomic DNA[J]. Biotechnology,2014,24(4):62-66.
    [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.
    [23] 李炎林,杨星星,张家银,等. 南方红豆杉转录组SSR挖掘及分子标记的研究[J]. 园艺学报,2014,41(4):735-745.
    [23] LIU Q Q,DAI X G,WANG J,et al. Effect of microsatellites on gene expression level and characteristics of expressed SSRs in poplars[J]. Journal of Nanjing Forestry University (Natural Sciences Edition),2011,35(1):11-14.
    [24] 樊洪泓,李廷春,李正鹏,等. 银杏EST序列中微卫星的分布特征[J]. 基因组学与应用生物学,2009,28(5):869-873.
    [24] LI S X,ZHANG X Y,WANG Y Y,et al. Content and characteristics of microsatellites in eucalyptus EST sequences[J]. Chinese Bulletin of Botany,2010,45(3):363-371.
    [25] 王晓锋,何卫龙,蔡卫佳,等. 马尾松转录组测序和分析[J]. 分子植物育种,2013,11(3):385-392.
    [26] BAI T D,XU L A,WANG Z R,et al. Characterization of masson pine ( Pinus massoniana Lamb.) microsatellite DNA by 454 genome shotgun sequencing[J]. Tree Genetics & Genomes,2014,10:429-437.
    [27] REDDY P S,HOUSMAN D. The complex pathology of trinucleotide repeats[J]. Current Opinion in Cell Biology,1997,9(3):364-372.
    [28] 马秋月,戴晓港,陈赢男,等. 枣基因组的微卫星特征[J]. 林业科学,2013,49(12):81-87.
    [29] WU J,CAI C F,CHENG F Y,et al. Characterisation and development of EST-SSR markers in tree peony using transcriptome sequences[J]. Molecular Breeding,2014,34:1853-1866.
    [30] WANG L X,ELBAIDOURI M,ABERNATHY B,et al. Distribution and analysis of SSR in mung bean ( Vigna radiata L.) genome based on an SSR-enriched library[J]. Molecular Breeding,2015,35:25-35.
    [31] 孔凡明,王小龙,陈赢男,等. 松属编码区微卫星特征和相应基因功能分析[J]. 南京林业大学学报(自然科学版),2014,38(2):47-51.
    [32] 袁阳阳,王青锋,陈进明. 基于转录组测序信息的水生植物莕菜SSR标记开发[J]. 植物科学学报,2013,31(5):485-492.
    [33] HENDRE P S,AGGARWAL R K. Development of genic and genomic SSR markers of robusta coffee ( Coffea canephora Pierre Ex A. Froehner)[J]. PLoS One,2014,9(12):0113661.
    [34] SCHORDERET D F,GARTLER S M. Analysis of CpG suppression in methylated and nonmethylated species[J]. Proceedings of the National Academy of the Sciences of the United States of America,1992,89:957-961.
    [35] 何平. 真核生物中的微卫星及其应用[J]. 遗传,1998,20(4):42-47.
    [36] 李小白,张明龙,崔海瑞. 油菜EST资源的SSR信息分析[J]. 中国油料作物学报,2007,29(1):20-25.
    [37] SHAROPOVA N,FRANCKI M. Plant simple sequence repeats: distribution,variation,and effects on gene expression[J]. Genome,2008,51:79-90.
    [38] 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.
    [39] 刘菁菁,戴晓港,王洁,等. 杨树微卫星序列对基因表达频率的影响及表达序列中微卫星特征的分析[J]. 南京林业大学学报(自然科学版),2011,35(1):11-14.
    [40] TEMNYKH S,DECLERCK G,LUKASHOVA A,et al. Computational and experimental analysis of microsatellites in rice ( Oryza sativa L.):frequency,length variation,transposon associations,and genetic marker potential[J]. Genome Research,2001,11:1441-1452.
    [41] 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.
    [42] SAMADI S,ARTIGUEBIELLE E,ESTOUP A,et al. Density and variability of dinucleotide microsatellites in the parthenogenetic polyploid snail Melanoides tuberculata [J]. Molecular Ecology,1998,7(9):1233-1236.
    [43] STREELMAN J T,KOCHER T D. Microsatellite variation associated with prolactin expression and growth of salt-challenged tilapia[J]. Physiol Genomics,2002,9:1-4.
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出版历程
  • 收稿日期:  2015-01-29
  • 修回日期:  2015-01-29
  • 刊出日期:  2016-05-31

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