Chin Bull Bot ›› 2015, Vol. 50 ›› Issue (3): 388-393.doi: 10.3724/SP.J.1259.2015.00388

• TECHNIQUES AND METHODS • Previous Articles     Next Articles

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

Changqing Zhang1, *, Lingfei Shangguan2, Hailing Li1, Jin Wang3   

  1. 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:2015-04-08 Published:2015-05-01
  • Contact: Zhang Changqing E-mail:zcq@jit.edu.cn
  • About author:

    ? These authors contributed equally to this paper

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/.

Table 1

The sources of species in OBRRP"

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

Figure 1

The workflow of OBRRP"

Figure 2

An interface example of OBRRP"

Table 2

Evaluation of OBRRP effectiveness"

No. Tool name Parameters Number Used
time
(s)
1 Cucumber Gene IDs: 8 147
Csa000066; Csa001021; Csa004014; Csa006964; Csa018435; Csa021143; Csa022290; Csa025189;
2 Tomato Gene IDs: 46 172
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;
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
Chr5:359214..359381;
Chr14:21607855..21608085;
Chr9:3017668..3018077;
Chr5:22564235..22564791;
Chr19:5718801..5719546;
4 Cucumber Genomic locations: 22 27
Chr5:20276908..20278927; Chr5:27486172..27487465; Chr4:18785112..18787609;
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;
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