一个园艺植物基因组序列和注释的在线批量实时提取平台

doi:10.3724/SP.J.1259.2015.00388

植物学报 ›› 2015, Vol. 50 ›› Issue (3): 388-393.DOI: 10.3724/SP.J.1259.2015.00388

一个园艺植物基因组序列和注释的在线批量实时提取平台

张长青^1,^*(), 上官凌飞², 李海玲¹, 王进³

¹金陵科技学院园艺学院, 南京 210038
²南京农业大学园艺学院, 南京 210095
³南京大学生物化学系, 南京 210093

收稿日期:2014-06-18 接受日期:2014-12-26 出版日期:2015-05-01 发布日期:2015-04-08
通讯作者: 张长青
作者简介:
? 共同第一作者
基金资助:
国家自然科学基金(No.31171273)和江苏省“江苏省333高层次人才培养工程”(No.BRA2014003)

An Online, Batch, and Real-time Retrieval Platform for Genomic Sequences and Annotation of Horticultural Plants

Changqing Zhang^{1, *}, Lingfei Shangguan², Hailing Li¹, Jin Wang³

¹College of Horticulture, Jinling Institute of Technology, Nanjing 210038, China
²College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
³Department of Biochemistry, Nanjing University, Nanjing 210093, China

Received:2014-06-18 Accepted:2014-12-26 Online:2015-05-01 Published:2015-04-08
Contact: Zhang Changqing
About author:
? These authors contributed equally to this paper

摘要/Abstract

摘要： 目前, 大量园艺植物基因组测序已经完成或接近尾声, 它们的基因组序列和注释数据极大地促进了功能基因组学研究。为给科研人员提供批量下载特定的基因组区段序列和注释平台, 笔者开发了一个称为OBRRP的生物信息学工具。OBRRP具有提取葡萄(Vitis vinifera)、桃(Prunus persica)、草莓(Fragaria vesca)、黄瓜(Cucumis sativus)、西瓜(Citrullus lanatus)、番茄(Solanum lycopersicum)、甜橙(Citrus sinensis)、苹果(Malus x domestica)、猕猴桃(Actinidia chinensis)、马铃薯(Solanum tuberosum)、香蕉(Musa acuminata)和拟南芥(Arabidopsis thaliana) 12种植物基因组序列及注释数据的功能; 同时, 也具有扩展到其它Gbrowser浏览器架构的数据库功能。测试结果表明, OBRRP是一个快捷简便的在线、批量和实时提取工具, 其登录地址为http://bioinfo.jit.edu.cn/OBRRP/。

Abstract: The genomes of a large number of horticultural plants have been or are being sequenced. The genomic sequences and annotated data have greatly promoted functional genomics research. To provide a batch-retrieval platform of sub-data for researchers, we developed a bioinformatics tool called Online, Batch, and Real-time Retrieve Platform (OBRRP). The program can be used to retrieve special genomic subsequences or sub-annotations from databases for grape, peach, strawberry, cucumber, watermelon, tomato, orange, apple, kiwifruit, potato, banana, and Arabidopsis. Also, it can be extended to other species by using Gbrowser with its genomic database. OBRRP is a convenient, online, real-time, batch retrieval tool and is available at http://bioinfo.jit.edu.cn/OBRRP/.

张长青, 上官凌飞, 李海玲, 王进. 一个园艺植物基因组序列和注释的在线批量实时提取平台. 植物学报, 2015, 50(3): 388-393.

Changqing Zhang, Lingfei Shangguan, Hailing Li, Jin Wang. An Online, Batch, and Real-time Retrieval Platform for Genomic Sequences and Annotation of Horticultural Plants. Chinese Bulletin of Botany, 2015, 50(3): 388-393.

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链接本文: https://www.chinbullbotany.com/CN/10.3724/SP.J.1259.2015.00388

https://www.chinbullbotany.com/CN/Y2015/V50/I3/388

图/表 4

参考文献 11

1	王小非, 刘鑫, 苏玲, 孙永江, 张世忠, 郝玉金, 由春香 (2013). 番茄LBD基因家族的全基因组序列鉴定及其进化和表达分析. 中国农业科学 46, 2501-2513.
2	魏潇, 刘威生, 刘宁, 章秋平, 张玉萍, 刘硕, 刘有春 (2011). 果实软化相关PG基因的进化分析和基因组定位. 园艺学报 38, 1791-1799.
3	许瑞瑞, 张世忠, 宿红艳, 刘春香, 曹慧, 束怀瑞 (2013). 苹果锚蛋白基因ANK家族生物信息学鉴定分析. 园艺学报 40, 1021-1032.
4	袁明, 瞿礼嘉, 王小菁, 钱前, 杨维才, 王台, 孔宏智, 蒋高明, 种康 (2014). 2013年中国植物科学若干领域重要研究进展. 植物学报 49, 347-406.
5	袁伟, 顾掌根, 褚伟雄, 叶立华, 杨国志 (2014). 黄瓜转录因子TCP基因家族的鉴定及结构分析. 分子植物育种 12, 287-295.
6	张长青, 王进, 李广平, 章镇 (2005). 园艺植物分子育种相关生物信息资源及其应用. 植物学通报 22, 494-501.
7	张停林, 李季, 崔利, 苏芃, 徐建, 陈劲枫 (2013). 黄瓜细胞分裂素合成关键酶IPT基因家族序列特征及其表达分析. 园艺学报 40, 58-68.
8	张晓辉, 魏小春, 李锡香, 孙玉燕, 王冠, 常兆晶, 刘冠群, 邱杨, 宋江萍, 王海平, 沈镝, 王大江, 韩月澎 (2014). 苹果全基因组SBP-box基因家族分析及代表成员的分子克隆. 园艺学报 41, 215-226.
9	Stein LD, Mungall C, Shu SQ, Caudy M, Mangone M, Day A, Nickerson E, Stajich JE, Harris TW, Arva A, Lewis S (2002). The generic genome browser: a building block for a model organism system database.Genome Res 12, 1599-1610.
10	Zhang CQ, Li GP, Wang J, Fang JG (2012). Identification of trans-acting siRNAs and their regulatory cascades in grapevine.Bioinformatics 28, 2561-2568.
11	Zhang CQ, Li GP, Zhu SN, Zhang S, Fang JG (2014). tasiRNAdb: a database of ta-siRNA regulatory pathways.Bioinformatics 30, 1045-1046.

No.	Species in OBRRP	Website of database	Database maintainer
1	Vitis vinifera (12X)	www.genoscope.cns.fr/cgi-bin/ggb/vitis/12X/gbrowse/vitis/	French National Sequencing Center
	Vitis vinifera (8X)	www.genoscope.cns.fr/cgi-bin/ggb/vitis/gbrowse/vitis/	French National Sequencing Center
2	Prunus persica	www.rosaceae.org/gb/gbrowse/prunus_persica/	Genome Database for Rosaceae
3	Fragaria vesca	www.rosaceae.org/gb/gbrowse/fragaria_vesca_v1.0/	Genome Database for Rosaceae
4	Cucumis sativus	www.icugi.org/cgi-bin/gb2/gbrowse/cucumber_v1/	International Cucurbit Genomics Initiative
5	Citrullus lanatus	www.icugi.org/cgi-bin/gb2/gbrowse/watermelon_v1/	International Cucurbit Genomics Initiative
6	Solanum lycopersicum	solgenomics.net/gb2/gbrowse/ITAG2.3_genomic/	The Sol Genomics Network
7	Citrus sinensis	citrus.hzau.edu.cn/cgi-bin/gb2/gbrowse/orange/	Citrus Sinensis Annotation Project
8	Malus × domestica (a)	www.rosaceae.org/gb/gbrowse/malus_x_domestica_v1.0- primary/	Genome Database for Rosaceae
	Malus × domestica (b)	www.rosaceae.org/gb/gbrowse/malus_x_domestica/	Genome Database for Rosaceae
9	Actinidia chinensis	www.icugi.org/cgi-bin/gb2/gbrowse/kiwi/	International Cucurbit Genomics Initiative
10	Solanum tuberosum	solgenomics.net/gb2/gbrowse/PGSC_DM3.4/	The Sol Genomics Network
11	Musa acuminata	banana-genome.cirad.fr/cgi-bin/gbrowse/musa_acuminata/	Banana Genome Hub
12	Arabidopsis thaliana	tairvm17.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/	The Arabidopsis Information Resource

No.	Species in OBRRP	Website of database	Database maintainer
1	Vitis vinifera (12X)	www.genoscope.cns.fr/cgi-bin/ggb/vitis/12X/gbrowse/vitis/	French National Sequencing Center
	Vitis vinifera (8X)	www.genoscope.cns.fr/cgi-bin/ggb/vitis/gbrowse/vitis/	French National Sequencing Center
2	Prunus persica	www.rosaceae.org/gb/gbrowse/prunus_persica/	Genome Database for Rosaceae
3	Fragaria vesca	www.rosaceae.org/gb/gbrowse/fragaria_vesca_v1.0/	Genome Database for Rosaceae
4	Cucumis sativus	www.icugi.org/cgi-bin/gb2/gbrowse/cucumber_v1/	International Cucurbit Genomics Initiative
5	Citrullus lanatus	www.icugi.org/cgi-bin/gb2/gbrowse/watermelon_v1/	International Cucurbit Genomics Initiative
6	Solanum lycopersicum	solgenomics.net/gb2/gbrowse/ITAG2.3_genomic/	The Sol Genomics Network
7	Citrus sinensis	citrus.hzau.edu.cn/cgi-bin/gb2/gbrowse/orange/	Citrus Sinensis Annotation Project
8	Malus × domestica (a)	www.rosaceae.org/gb/gbrowse/malus_x_domestica_v1.0- primary/	Genome Database for Rosaceae
	Malus × domestica (b)	www.rosaceae.org/gb/gbrowse/malus_x_domestica/	Genome Database for Rosaceae
9	Actinidia chinensis	www.icugi.org/cgi-bin/gb2/gbrowse/kiwi/	International Cucurbit Genomics Initiative
10	Solanum tuberosum	solgenomics.net/gb2/gbrowse/PGSC_DM3.4/	The Sol Genomics Network
11	Musa acuminata	banana-genome.cirad.fr/cgi-bin/gbrowse/musa_acuminata/	Banana Genome Hub
12	Arabidopsis thaliana	tairvm17.tacc.utexas.edu/cgi-bin/gb2/gbrowse/arabidopsis/	The Arabidopsis Information Resource

No.	Tool name	Parameters						Number	Used time (s)
1	Cucumber	Gene IDs:						8	147
1	Cucumber	Csa000066; Csa001021; Csa004014; Csa006964; Csa018435; Csa021143; Csa022290; Csa025189;						8	147
2	Tomato	Gene IDs:						46	172
	Tomato	Solyc01g044520.1.1; Solyc01g091400.1.1; Solyc01g091420.1.1; Solyc01g098220.1.1; Solyc01g107190.1.1; Solyc01g109240.1.1; Solyc02g065150.1.1; Solyc02g067800.1.1; Solyc02g069440.1.1; Solyc02g077380.1.1; Solyc02g085910.1.1; Solyc02g086480.1.1;	Solyc02g087570.1.1; Solyc02g090410.1.1; Solyc02g092550.1.1; Solyc03g063140.1.1; Solyc03g095940.1.1; Solyc03g112430.1.1; Solyc03g113360.1.1; Solyc03g119530.1.1; Solyc04g050010.1.1; Solyc04g077990.1.1; Solyc05g009320.1.1; Solyc05g048740.1.1;		Solyc06g005090.1.1; Solyc06g007390.1.1; Solyc06g050430.1.1; Solyc06g050950.1.1; Solyc06g062630.1.1; Solyc06g064540.1.1; Solyc06g071660.1.1; Solyc06g082310.1.1; Solyc06g082430.1.1; Solyc06g082770.1.1; Solyc06g083930.1.1;		Solyc08g065130.1.1; Solyc09g010490.1.1; Solyc09g014690.1.1; Solyc09g014700.1.1; Solyc09g066260.1.1; Solyc09g066270.1.1; Solyc11g008830.1.1; Solyc11g045530.1.1; Solyc11g072470.1.1; Solyc12g010810.1.1; Solyc12g100150.1.1;	46	172
	MyOBRRP	(1) Species Website: http://solgenomics.net/gb2/gbrowse/ITAG2_genomic/ (2) Test Gene: Solyc01g044520.1.1							469
3	Genoscope (12X)	Genomic locations:						5	15
3	Genoscope (12X)	Chr5:359214..359381; Chr14:21607855..21608085;		Chr9:3017668..3018077; Chr5:22564235..22564791;		Chr19:5718801..5719546;		5	15
4	Cucumber	Genomic locations:						22	27
		Chr5:20276908..20278927;		Chr5:27486172..27487465;		Chr4:18785112..18787609;		22	27
		Chr6:9759628..9760584;		Chr1:2917372..2918787;		Chr1:2214334..2223145;
		Chr1:4095889..4097124;		Chr1:3476246..3478078;		Chr6:8956474..8957034;
		Scaffold000100:527374..528264;		Chr4:5358347..5359240;		Chr6:6316016..6317507;
		Scaffold000164:128613..129407;		Chr5:449956..450726;		Chr6:18756255..18756878;
		Scaffold000195:22087..23115;		Chr6:5180192..5180920;		Chr1:1848674..1849114;
		Chr1:3837106..3837585;		Chr1:7967784..7968414;		Chr1:1434222..1435145;
		Chr3:15413475..15414623;

No.	Tool name	Parameters						Number	Used time (s)
1	Cucumber	Gene IDs:						8	147
1	Cucumber	Csa000066; Csa001021; Csa004014; Csa006964; Csa018435; Csa021143; Csa022290; Csa025189;						8	147
2	Tomato	Gene IDs:						46	172
	Tomato	Solyc01g044520.1.1; Solyc01g091400.1.1; Solyc01g091420.1.1; Solyc01g098220.1.1; Solyc01g107190.1.1; Solyc01g109240.1.1; Solyc02g065150.1.1; Solyc02g067800.1.1; Solyc02g069440.1.1; Solyc02g077380.1.1; Solyc02g085910.1.1; Solyc02g086480.1.1;	Solyc02g087570.1.1; Solyc02g090410.1.1; Solyc02g092550.1.1; Solyc03g063140.1.1; Solyc03g095940.1.1; Solyc03g112430.1.1; Solyc03g113360.1.1; Solyc03g119530.1.1; Solyc04g050010.1.1; Solyc04g077990.1.1; Solyc05g009320.1.1; Solyc05g048740.1.1;		Solyc06g005090.1.1; Solyc06g007390.1.1; Solyc06g050430.1.1; Solyc06g050950.1.1; Solyc06g062630.1.1; Solyc06g064540.1.1; Solyc06g071660.1.1; Solyc06g082310.1.1; Solyc06g082430.1.1; Solyc06g082770.1.1; Solyc06g083930.1.1;		Solyc08g065130.1.1; Solyc09g010490.1.1; Solyc09g014690.1.1; Solyc09g014700.1.1; Solyc09g066260.1.1; Solyc09g066270.1.1; Solyc11g008830.1.1; Solyc11g045530.1.1; Solyc11g072470.1.1; Solyc12g010810.1.1; Solyc12g100150.1.1;	46	172
	MyOBRRP	(1) Species Website: http://solgenomics.net/gb2/gbrowse/ITAG2_genomic/ (2) Test Gene: Solyc01g044520.1.1							469
3	Genoscope (12X)	Genomic locations:						5	15
3	Genoscope (12X)	Chr5:359214..359381; Chr14:21607855..21608085;		Chr9:3017668..3018077; Chr5:22564235..22564791;		Chr19:5718801..5719546;		5	15
4	Cucumber	Genomic locations:						22	27
		Chr5:20276908..20278927;		Chr5:27486172..27487465;		Chr4:18785112..18787609;		22	27
		Chr6:9759628..9760584;		Chr1:2917372..2918787;		Chr1:2214334..2223145;
		Chr1:4095889..4097124;		Chr1:3476246..3478078;		Chr6:8956474..8957034;
		Scaffold000100:527374..528264;		Chr4:5358347..5359240;		Chr6:6316016..6317507;
		Scaffold000164:128613..129407;		Chr5:449956..450726;		Chr6:18756255..18756878;
		Scaffold000195:22087..23115;		Chr6:5180192..5180920;		Chr1:1848674..1849114;
		Chr1:3837106..3837585;		Chr1:7967784..7968414;		Chr1:1434222..1435145;
		Chr3:15413475..15414623;

一个园艺植物基因组序列和注释的在线批量实时提取平台

An Online, Batch, and Real-time Retrieval Platform for Genomic Sequences and Annotation of Horticultural Plants

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