碧桃花瓣转录组微卫星特征分析

doi:10.3969/j.issn.1000-2006.2015.03.007

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南京林业大学学报（自然科学版） ›› 2015, Vol. 39 ›› Issue (03): 34-38.doi: 10.3969/j.issn.1000-2006.2015.03.007

碧桃花瓣转录组微卫星特征分析

马秋月,廖卓毅,张得芳,戴晓港,陈赢男,李淑娴^*

南京林业大学南方现代林业协同创新中心,江苏南京 210037

出版日期:2015-05-30 发布日期:2015-05-30
基金资助:
收稿日期:2014-05-12 修回日期:2014-07-02
基金项目:国家林业公益性行业科研专项重大项目(201304102); 国家自然科学基金项目(31270711); 江苏高校优势学科建设工程资助项目(PAPD)
第一作者:马秋月,博士生; 廖卓毅,硕士生。*通信作者:李淑娴,研究员。E-mail: shuxianli@njfu.com.cn。
引文格式:马秋月,廖卓毅,张得芳,等. 碧桃花瓣转录组微卫星特征分析[J]. 南京林业大学学报:自然科学版,2015,39(3):34-38.

Deep sequenced-based transcriptome analysis of microsatellites in peach(Prunus persica cv. duplex) flowers

MA Qiuyue, LIAO Zhuoyi, ZHANG Defang, DAI Xiaogang, CHEN Yingnan, LI Shuxian^*

Co-Innovation Center for the Sustainable Forestry in Southern China,Nanjing Forestry University, Nanjing 210037, China

Online:2015-05-30 Published:2015-05-30

摘要/Abstract

摘要： 为开发碧桃转录组微卫星信息,利用454高通量测序技术,对其花瓣转录组序列进行SSR位点发掘,结果发现含SSR的序列4 705条,共得到5 668个SSR,平均每3.49 kb出现1个SSR。微卫星序列主要以三碱基重复为主,约占总数的42.66%。笔者共发现516种碱基重复基元,所占比例最高的为(AG/CT)_n(18.34%),其次是(AAG/CTT)_n(12.42%)。微卫星多为重复长度小于20 bp 的短序列, 长度大于20 bp 的微卫星仅占总数的12.13%。研究还发现碧桃花瓣微卫星的频率和长度呈显著负相关(P<0.05),相关系数为-0.246。

Abstract: To obtain information of Prunus persica cv. duplex, the transcriptome of peach flowers were sequenced by 454 high-throughput sequencing technology. A total of 5 668 SSRs were identified in 4 705 sequences, with an average density of one SSR per 3.49 kb. Tri-nucleotide repeats were the most abundant, accounted for 42.66% of all SSRs. Among all the 516 SSR motifs,(AG/CT)_n was the most frequent repeat motif(18.34%), followed by the(AAG/CTT)_n(12.42%). The microsatellites in length below 20 bp were in maximum proportion, while the microsatellites over 20 bp were only 12.13%. There were significant negative correlation(P<0.05)between the frequency of microsatellites and the length, the correlation coefficient was -0.246.

中图分类号:

Q948
Q78

马秋月,廖卓毅,张得芳,等. 碧桃花瓣转录组微卫星特征分析[J]. 南京林业大学学报（自然科学版）, 2015, 39(03): 34-38.

MA Qiuyue, LIAO Zhuoyi, ZHANG Defang, DAI Xiaogang, CHEN Yingnan, LI Shuxian. Deep sequenced-based transcriptome analysis of microsatellites in peach(Prunus persica cv. duplex) flowers[J].Journal of Nanjing Forestry University (Natural Science Edition), 2015, 39(03): 34-38.DOI: 10.3969/j.issn.1000-2006.2015.03.007.

参考文献

[1] 何平. 真核生物中的微卫星及其应用[J]. 遗传, 1998, 20(4): 42-47. He P.Abundance, polymorphism and applications of microsatellite in eukaryote [J]. Hereditas, 1998, 20(4): 42-47.
[2] Mrázek J, Guo X, Shah A. Simple sequence repeats in prokaryotic genomes[J]. Proceedings of the National Academy of Sciences, 2007, 104(20): 8472-8477.
[3] Tóth G, Gáspári Z, Jurka J. Microsatellites in different eukaryotic genomes: survey and analysis[J]. Genome Research, 2000, 10(7): 967-981.
[4] 杨纪青,杨硕,杨莉,等. Tomato leaf curl Bangladesh病毒完整基因组上微卫星分布[J].中国农学通报,2010,26(24):20-27.Yang J Q, Yang S, Yang L, et al.The microsatellite distribution in the complete genomes of the tomato leaf curl Bangladesh virus[J]. Chinese Agricultural Science Bulletin, 2010, 26(24):20-27.
[5] Selkoe K A, Toonen R J. Microsatellites for ecologists: a practical guide to using and evaluating microsatellite markers [J]. Ecology Letters, 2006, 9(5): 615-629.
[6] Beheregaray L B, Ciofi C, Geist D, et al. Genes record a prehistoric volcano eruption in the Galapagos [J]. Science, 2003, 302(5642): 75.
[7] 杨华,陈琪,韦朝领,等. 茶树转录组中SSR 位点的信息分析 [J]. 安徽农业大学学报,2011,38(6):882-886.Yang H, Chen Q, Wei Z L, et al.Analysis on SSR information in Camellia sinensis transcriptome[J]. Journal of Anhui Agricultural University, 2011, 38(6): 882-886.
[8] 李小白,向林,罗洁,等. 转录组测序(RNA-seq)策略及其数据在分子标记开发上的应用[J]. 中国细胞生物学报,2013,35(5):1-8.Li X B, Xiang L, Luo J, et al.The strategy of RNA-seq, application and development of molecular marker derived from RNA-seq[J]. Chinese Journal of Cell Biology, 2013, 35(5): 1-8.
[9] 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.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]. Journal of Plant Sciences, 2013, 31(5):485-492.
[10] 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.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.
[11] 张文娥,潘学军,杨仕国,等. 碧桃组织培养中褐化及其抑制研究[J]. 贵州农业科学,2009, 37(1): 11-12.Zhang W E, Pan X J, Yang S G, et al. Inhibition effects of different sterilized methods, inoculation times and antioxidants on browning in tissue culture of Prunus persica var. duplex[J]. Guizhou Agricultural Science, 2009, 37(1): 11-12.
[12] Chen Y, Mao Y, Liu H, et al. Transcriptome analysis of differentially expressed genes relevant to variegation in Peach flowers[J]. PloS one, 2014, 9(3): e90842.
[13] Verde I, Abbott A G, Scalabrin S, et al. The high-quality draft genome of peach(Prunus persica)identifies unique patterns of genetic diversity, domestication and genome evolution [J]. Nature Genetics, 2013, 45(5): 487-494.
[14] 李雄伟,贾惠娟,高中山. 桃基因组学及全基因组关联分析研究进展[J].遗传,2013, 35(10):1167-1178.Li X W, Jia H J, Gao Z S.Peach genomics and genome-wide association study: a review [J]. Hereditas, 2013, 35(10): 1167-1178.
[15] 曹珂, 王力荣, 朱更瑞, 等. 桃遗传图谱的构建及两个花性状的分子标记[J]. 园艺学报, 2009, 36(2): 179-186.Cao K, Wang L R, Zhu G R, et al. Genetic linkage maps constructing and markers linked with pistil development and double petal gene in peach[J]. Acta Horticulturae Sinica, 2009, 36(2): 179-186.
[16] Weber J L. Informativeness of human(dC-dA)n·(dG-dT)n polymorphisms[J]. Genomics,1990,7(4): 524-530.
[17] Biet E, Sun J, Dutreix M. Conserved sequence preference in DNA binding among recombination proteins: an effect of ssDNA secondary structure[J]. Nucleic Acids Research, 1999, 27(2), 596-600.
[18] Wang L, Zhao S, Gu C, et al. Deep RNA-Seq uncovers the peach transcriptome landscape [J]. Plant Molecular Biology, 2013, 83(4-5): 365-377.
[19] Cavagnaro P F, Senalik D A, Yang L, et al. Genome-wide characterization of simple sequence repeats in cucumber(Cucumis sativus L.)[J]. BMC Genomics, 2010, 11:569.
[20] 陈军方,任正隆,高丽锋,等. 从小麦EST 序列中开发新的SSR 引物[J].作物学报,2005,31(2):154-158.Chen J F, Ren Z L, Gao L F, et al. Developing new SSR marker from EST of wheat [J]. Acta Agronomica Sinica, 2005,31(2): 154-158.
[21] 江东,钟广炎,洪棋斌. 柑橘EST-SSR分子标记分析[J].遗传学报, 2006, 33(4): 345-353. Jiang D, Zhong G Y, Hong Q B. Analysis of microsatellites in citrus unigenes[J]. Acta Genetica Sinica, 2006, 33(4):345-353.
[22] 杨素丽,明军,刘春,等. 基于EST信息的百合SSR标记的建立[J]. 园艺学报,2008, 35(7):1069-1074.Yang S L, Ming J, Liu C, et al. Data mining for simple sequence repeats marker development in Expressed Sequence Tags from Lilium L.[J]. Acta Horticulturae Sinica, 2008, 35(7):1069-1074.
[23] 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. Characterization of microsatellites in tea(Camellia sinensis)floral transcriptome [J]. Acta Agronomica Sinica, 2014, 40(1): 80-85.
[24] 王艳敏,魏志刚,杨传平. 白桦EST-SSR 信息分析与标记的开发[J]. 林业科学,2008, 44(2):78-84Wang Y M, Wei Z G, Yang C P. Data mining for SSRs in ESTs and EST-SSR marker development in Betula platyphylla[J]. Scientia Silvae Sinicae, 2008, 44(2): 78-84.
[25] 朱艳,郝艳宾,王克建,等. 核桃EST-SSR 信息分析与标记的初步建立[J].果树学报,2009,26(3):394-398.Zhu Y, Hao Y B, Wang K J, et al. Analysis of SSRs information and development of SSR markers from walnut ESTs[J]. Journal of Fruit Science,2009, 26(3): 394-398.
[26] 姜春芽,徐小彪,廖娇,等. 猕猴桃EST 序列的SSR 信息分析[J].中国农学通报,2009, 25(13):37-39.Jiang C Y, Xu X B, Liao J, et al. Analysis of SSR information in EST resources of kiwifruit(Actinidia ssp.)[J]. Chinese Agricultural Science Bulletin, 2009,25(13): 37-39.
[27] 张新叶,宋丛文,张亚东,等. 杨树EST-SSR 标记的开发[J]. 林业科学,2009, 45(9):53-59.Zhang X Y, Song C W, Zhang Y D, et al. Development of EST-SSR in Populus deltodes and P. euramericana [J]. Scientia Silvae Sinicae, 2009, 45(9): 53-59.
[28] Aggarwal R K, Hendre P S, Varshney R K, et al. Identification, characterization and utilization of EST-derived genic microsatellite markers for genome analyses of coffee and related species[J]. Theoretical and Applied Genetics, 2007, 114(2): 359-372.
[29] Blanca J, Ca?izares J, Roig C, et al. Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo(Cucurbitaceae)[J]. BMC Genomics, 2011, 12(1): 104.
[30] 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.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.
[31] Kantety R V,La Rota M, Matthews D E, et al, Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat [J]. Plant Molecular Biology, 2002, 48(5-6):501-510.
[32] Schorderet D F, Gartler S M. Analysis of CpG suppression in methylated and nonmethylated species [J]. PNAS, 1992, 89(3): 957-961.
[33] Gao L, Tang J, Li H, et al. Analysis of microsatellites in major crops assessed by computational and experimental approaches[J]. Molecular Breeding, 2003, 12(3): 245-261.
[34] 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.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.
[35] Sharopova N. Plant simple sequence repeats: distribution, variation, and effects on gene expression[J]. Genome, 2008, 51(2): 79-90.
[36] 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(8): 1441-1452.
[37] 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.

碧桃花瓣转录组微卫星特征分析

Deep sequenced-based transcriptome analysis of microsatellites in peach(Prunus persica cv. duplex) flowers

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