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脆蛇转录组序列的分析和系统发育定位

祝静静 黎万顺 高虹 徐通 鲍秋颖 郑永祥 周德敏 夏钢

祝静静, 黎万顺, 高虹, 徐通, 鲍秋颖, 郑永祥, 周德敏, 夏钢. 脆蛇转录组序列的分析和系统发育定位[J]. 华东师范大学学报(自然科学版), 2014, (4): 102-112.
引用本文: 祝静静, 黎万顺, 高虹, 徐通, 鲍秋颖, 郑永祥, 周德敏, 夏钢. 脆蛇转录组序列的分析和系统发育定位[J]. 华东师范大学学报(自然科学版), 2014, (4): 102-112.
ZHU Jing-jing, LI Wan-shun, GAO Hong, XU Tong, BAO Qiu-ying, ZHENG Yong-xiang, ZHOU De-min, XIA Gang. De novo transcriptome analysis and the phylogenetic position of glass lizards[J]. Journal of East China Normal University (Natural Sciences), 2014, (4): 102-112.
Citation: ZHU Jing-jing, LI Wan-shun, GAO Hong, XU Tong, BAO Qiu-ying, ZHENG Yong-xiang, ZHOU De-min, XIA Gang. De novo transcriptome analysis and the phylogenetic position of glass lizards[J]. Journal of East China Normal University (Natural Sciences), 2014, (4): 102-112.

脆蛇转录组序列的分析和系统发育定位

详细信息
  • 中图分类号: Q111

De novo transcriptome analysis and the phylogenetic position of glass lizards

  • 摘要: 脆蛇是一种类似于蛇但是又具有蜥蜴的特征的爬行动物, 这些矛盾的特性与脆蛇的系统发育分类学有密切的关系. 脆蛇在传统中药中也有很多治疗作用. 基于这些方面, 本研究利用高通量测序方法对脆蛇胃肠道的转录组序列进行检测, 组装和注释. 最终获得4.6~Gbp高质量的数据, 组装获得58 959个单一的基因, 其中35 708(60.56{\%})个单一基因与数据库的基因相匹配. 为了确定脆蛇与蛇和蜥蜴的同源进化关系, 对同源基因家族和系统进化树进行了分析, 结果显示脆蛇的转录组序列更接近于蛇而不是蜥蜴. 除此之外还鉴定了10 613 cSSR标签, 其中\linebreak1 644个标签根据严格的标准能够用至少一个引物获得. 本研究第一次揭示了脆蛇胃肠道的转录组序列, 确定其在系统发育学上的定位. 这些序列和标签为脆蛇的研究提供了重要的资源.
  • [1] {1} SECOR S M. Digestive physiology of the Burmese python: broad regulation of integrated performance [J]. J Exp Biol, 2008, 211(24): 3767-3774.
    {2} WIENS J J, SLINGLUFF J L. How lizards turn into snakes: a phylogenetic analysis of body-form evolution in anguid lizards [J]. Evolution, 2001, 55(11): 2303-2318.
    {3} BRANDLEY M C, HUELSENBECK J P, WIENS J J. Rates and patterns in the evolution of snake-like body form in squamate reptiles: evidence for repeated re-evolution of lost digits and long-term persistence of intermediate body forms [J]. Evolution, 2008, 62(8): 2042-2064.
    {4} CASTOE T A, de KONING J A, HALL K T, et al. Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes [J]. Genome Biol, 2011, 12(7): 406.
    {5} VIDAL N, HEDGES S B. The phylogeny of squamate reptiles (lizards, snakes, and amphisbaenians) inferred from nine nuclear protein-coding genes [J]. C R Biol, 2005, 328(10-11): 1000-1008.
    {6} LI S Z. Compendium of Materia Medica (Bencao Gangmu) [M]. LUO X W translator. Beijing: Foreign Languages Press, 2004.
    {7} NENE V, WORTMAN J R, LAWSON D, et al. Genome sequence of Aedes aegypti, a major arbovirus vector [J]. Science, 2007, 316(5832): 1718-1723.
    {8} FARKAS S L, BENKO M, ELO P, et al. Genomic and phylogenetic analyses of an adenovirus isolated from a corn snake (Elaphe guttata) imply a common origin with members of the proposed new genus Atadenovirus [J]. J Gen Virol, 2002, 83(Pt 10): 2403-2410.
    {9} ALFOLDI J, DI PALMA F, Grabherr M, et al. The genome of the green anole lizard and a comparative analysis with birds and mammals [J]. Nature, 2011, 477(7366): 587-591.
    {10} MARDIS E R. Next-generation DNA sequencing methods [J]. Annu Rev Genomics Hum Genet, 2008(9): 387-402.
    {11} GRABHERR M G, HAAS B J, YASSOUR M, et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome [J]. Nat Biotechnol, 2011, 29(7): 644-652.
    {12} PERTEA G, HUANG X, LIANG F, et al. TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets [J]. Bioinformatics, 2003, 19(5): 651-652.
    {13} KANEHISA M, GOTO S, KAWASHIMA S, et al. The KEGG resource for deciphering the genome [J]. Nucleic Acids Res, 2004, 32(Database issue): D277-280.
    {14} ISELI C, JONGENEEL C V, BUCHER P. ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences [J]. Proc Int Conf Intell Syst Mol Biol, 1999, : 138-148.
    {15} CONESA A, GOTZ S, GARCIA-GOMEZ J M, et al. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research [J]. Bioinformatics, 2005, 21(18): 3674-3676.
    {16} MORTAZAVI A, WILLIAMS B A, MCCUE K, et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq [J]. Nat Methods, 2008, 5(7): 621-628.
    {17} YU X J, ZHENG H K, WANG J, et al. Detecting lineage-specific adaptive evolution of brain-expressed genes in human using rhesus macaque as outgroup [J]. Genomics, 2006, 88(6): 745-751.
    {18} HUELSENBECK J P, RONQUIST F. MRBAYES: Bayesian inference of phylogenetic trees [J]. Bioinformatics, 2001, 17(8): 754-755.
    {19} POSADA D, CRANDALL K A. MODELTEST: testing the model of DNA substitution [J]. Bioinformatics, 1998, 14(9): 817-818.
    {20} UNTERGASSER A, CUTCUTACHE I, KORESSAAR T, et al. FAIRCLOTH B C, REMM M, ROZEN S G. Primer3--new capabilities and interfaces [J]. Nucleic Acids Res, 2012, 40(15): e115.
    {21} CASTOE T A, FOX S E, JASON de KONING A, et al. A multi-organ transcriptome resource for the Burmese Python (Python molurus bivittatus) [J]. BMC Res Notes, 2011(4): 310.
    {22} SCHWARTZ T S, TAE H, YANG Y, et al. A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences [J]. BMC Genomics, 2010(11): 694.
    {23} Consortium ICGS. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution [J]. Nature, 2004, 432(7018): 695-716.
    {24} HELLSTEN U, HARLAND R M, GILCHRIST M J, et al. The genome of the Western clawed frog Xenopus tropicalis [J]. Science, 2010, 328(5978): 633-636.
    {25} DU H, BAO Z, HOU R, et al. Transcriptome sequencing and characterization for the sea cucumber Apostichopus japonicus (Selenka, 1867) [J]. PLoS One, 2012, 7(3): e33311.
    {26} GARG R, PATEL R K, TYAGI A K, et al. De novo assembly of chickpea transcriptome using short reads for gene discovery and marker identification [J]. DNA Res, 2011, 18(1): 53-63.
    {27} CASTOE T A, GU W, de KONING A P, et al. Dynamic nucleotide mutation gradients and control region usage in squamate reptile mitochondrial genomes [J]. Cytogenet Genome Res, 2009, 127(2-4): 112-127.
    {28} DUBEY S, SHINE R. Evolutionary diversification of the lizard genus Bassiana (Scincidae) across Southern Australia [J]. PLoS One, 2010, 5(9): e12982.
    {29} KOCOT K M, CANNON J T, TODT C, et al. Phylogenomics reveals deep molluscan relationships [J]. Nature, 2011, 477(7365): 452-456.
    {30} LI H, COGHLAN A, RUAN J, et al. TreeFam: a curated database of phylogenetic trees of animal gene families [J]. Nucleic Acids Res, 2006, 34(Database issue): D572-580.
    {31} Carroll R L. Patterns and processes of vertebrate evolution. Cambridge Univ. New York1997.
    {32} NISHYAMA T, FUJITA T, SHIN T, et al. Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution [J]. Proc Natl Acad Sci U S A, 2003, 100, 13: 8007-8012.
    {33} BOURDON V, NAEF F, RAO P H, et al. Genomic and expression analysis of the 12p11-p12 amplicon using EST arrays identifies two novel amplified and overexpressed genes [J]. Cancer Res, 2002, 62(21): 6218-6223.
    {34} PARCHMAN T L, GEIST K S, GRAHNEN J A, et al. Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery [J]. BMC Genomics, 2010(11): 180.
    {35} 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 Res, 2001, 11(8): 1441-1452.
  • [1] 吴威, 李彩霞, 陈雪初.  基于生态系统服务的海岸带生态修复工程成效评估 . 华东师范大学学报(自然科学版), 2020, (3): 98-108. doi: 10.3969/j.issn.1000-5641.201941027
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出版历程
  • 收稿日期:  2013-10-01
  • 修回日期:  2014-01-01
  • 刊出日期:  2014-07-25

脆蛇转录组序列的分析和系统发育定位

  • 中图分类号: Q111

摘要: 脆蛇是一种类似于蛇但是又具有蜥蜴的特征的爬行动物, 这些矛盾的特性与脆蛇的系统发育分类学有密切的关系. 脆蛇在传统中药中也有很多治疗作用. 基于这些方面, 本研究利用高通量测序方法对脆蛇胃肠道的转录组序列进行检测, 组装和注释. 最终获得4.6~Gbp高质量的数据, 组装获得58 959个单一的基因, 其中35 708(60.56{\%})个单一基因与数据库的基因相匹配. 为了确定脆蛇与蛇和蜥蜴的同源进化关系, 对同源基因家族和系统进化树进行了分析, 结果显示脆蛇的转录组序列更接近于蛇而不是蜥蜴. 除此之外还鉴定了10 613 cSSR标签, 其中\linebreak1 644个标签根据严格的标准能够用至少一个引物获得. 本研究第一次揭示了脆蛇胃肠道的转录组序列, 确定其在系统发育学上的定位. 这些序列和标签为脆蛇的研究提供了重要的资源.

English Abstract

祝静静, 黎万顺, 高虹, 徐通, 鲍秋颖, 郑永祥, 周德敏, 夏钢. 脆蛇转录组序列的分析和系统发育定位[J]. 华东师范大学学报(自然科学版), 2014, (4): 102-112.
引用本文: 祝静静, 黎万顺, 高虹, 徐通, 鲍秋颖, 郑永祥, 周德敏, 夏钢. 脆蛇转录组序列的分析和系统发育定位[J]. 华东师范大学学报(自然科学版), 2014, (4): 102-112.
ZHU Jing-jing, LI Wan-shun, GAO Hong, XU Tong, BAO Qiu-ying, ZHENG Yong-xiang, ZHOU De-min, XIA Gang. De novo transcriptome analysis and the phylogenetic position of glass lizards[J]. Journal of East China Normal University (Natural Sciences), 2014, (4): 102-112.
Citation: ZHU Jing-jing, LI Wan-shun, GAO Hong, XU Tong, BAO Qiu-ying, ZHENG Yong-xiang, ZHOU De-min, XIA Gang. De novo transcriptome analysis and the phylogenetic position of glass lizards[J]. Journal of East China Normal University (Natural Sciences), 2014, (4): 102-112.
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