| 基于Perl脚本的大豆核苷酸序列高通量提取 |
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| 引用本文： | 张大勇,王长彪,易金鑫,何晓兰,马鸿翔.基于Perl脚本的大豆核苷酸序列高通量提取[J].南京农业大学学报,2012,35(1):7-13. |
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| 作者姓名： | 张大勇 王长彪 易金鑫 何晓兰 马鸿翔 |
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| 作者单位： | 1. 江苏省农业科学院江苏省农业生物学重点实验室,江苏南京,210014
2. 山西省农业科学院棉花研究所,山西运城044000;山西省农业科学院生物技术研究中心,山西太原030032 |
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| 基金项目： | 国家自然科学基金项目，山西省青年科技研究基金项目，江苏省农业科技自主创新资金项目，江苏省自然科学基金项目 |
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| 摘 要： | 自从大豆全基因组测序完成和序列公布之后,阐明每个基因的生物学功能和调控网络成为当前的主要任务。基于Perl脚本开发了一套可以高通量、快速提取序列的程序,该程序可以批量提取大豆染色体某个区间的核苷酸序列并利用其他工具进行批量分析,还可用于某个基因在全基因组中的所有序列分析。本研究分别对大豆第4染色体Glyma04g00930.1～Glyma04g01740.1区间的基因序列和水通道蛋白基因家族成员TIP(液泡膜水通道蛋白)序列进行提取。结果发现:Glyma04g00930.1～Glyma04g01740.1区间共含有112个基因序列;大豆全基因组共有91个TIP基因,在20条染色体上均有分布,且在第12染色体上分布最多,多达10个,暗示该染色体可能对大豆的水分利用效率起着重要作用,基因所含内含子数为1～8个。序列提取所用的2个脚本程序可以从http://www.zlhyd.com/sxbi/soybean_strict.rar下载。
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| 关 键 词： | 大豆全基因组 序列提取 序列分析 液泡膜水通道蛋白 Perl程序 |
Perl-based high-throughput nucleotide sequence extraction in soybean( Glycine max L.Merri) |
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| ZHANG Da-yong
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WANG Chang-biao
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YI Jin-xin
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HE Xiao-lan
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MA Hong-xiang.Perl-based high-throughput nucleotide sequence extraction in soybean( Glycine max L.Merri)[J].Journal of Nanjing Agricultural University,2012,35(1):7-13. |
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| Authors: | ZHANG Da-yong WANG Chang-biao YI Jin-xin HE Xiao-lan MA Hong-xiang |
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| Institution: | 1(1.Key Laboratory of Agrobiology of Jiangsu Province,Jiangsu Academy of Agricultural Sciences,Nanjing 210014,China; 2.Cotton Research Institute,Shanxin Academy of Agricultural Sciences,Yuncheng 044000,China;3.Biotechnology Research Center,Shanxi Academy of Agricultural Sciences,Taiyuan 030032,China) |
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| Abstract: | With the completely sequencing and publishing of soybean genome sequence,elucidating the biological function and regulation web of each gene become an important project currently.In this study,the program for high-throughput nucleotide or amino acids sequence extraction for specific blocks and gene families in soybean whole genome was developed based on Perl program,which could analyze gene numbers included,the sequences and functions of genes in this region.For example,the genes contained between the region of Glyma04g00930.1-Glyma04g01740.1 on the chromosome 4 and the TIP(tonoplast intrinsic protein) genes which is a member of aquaporin gene family was extracted in this study.The result showed that the region of Glyma04g00930.1-Glyma04g01740.1 contained 112 genes and totally 91 different TIP genes existed in whole soybean genome respectively,and were distributed on each chromosome,among which,the largest of number was up to 10 on chromosome 12,implying they may play important roles in water use efficiency.Moreover,the number of intron of these genes ranged from 1-8.The extraction programs can be downloaded from the website:http://www.zlhyd.com/sxbi/soybean_strict.rar. |
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| Keywords: | soybean genome sequence extraction sequence analysis tonoplast intrinsic protein(TIP) Perl program |
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