Unlimited Thirst for Genome Sequencing, Data Interpretation, and Database Usage in Genomic Era: The Road towards Fast-Track Crop Plant Improvement
Identifieur interne : 000705 ( Pmc/Curation ); précédent : 000704; suivant : 000706Unlimited Thirst for Genome Sequencing, Data Interpretation, and Database Usage in Genomic Era: The Road towards Fast-Track Crop Plant Improvement
Auteurs : Arun Prabhu Dhanapal [États-Unis] ; Mahalingam Govindaraj [Inde]Source :
- Genetics Research International [ 2090-3154 ] ; 2015.
Abstract
The number of sequenced crop genomes and associated genomic resources is growing rapidly with the advent of inexpensive next generation sequencing methods. Databases have become an integral part of all aspects of science research, including basic and applied plant and animal sciences. The importance of databases keeps increasing as the volume of datasets from direct and indirect genomics, as well as other omics approaches, keeps expanding in recent years. The databases and associated web portals provide at a minimum a uniform set of tools and automated analysis across a wide range of crop plant genomes. This paper reviews some basic terms and considerations in dealing with crop plant databases utilization in advancing genomic era. The utilization of databases for variation analysis with other comparative genomics tools, and data interpretation platforms are well described. The major focus of this review is to provide knowledge on platforms and databases for genome-based investigations of agriculturally important crop plants. The utilization of these databases in applied crop improvement program is still being achieved widely; otherwise, the end for sequencing is not far away.
Url:
DOI: 10.1155/2015/684321
PubMed: 25874133
PubMed Central: 4383144
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Unlimited Thirst for Genome Sequencing, Data Interpretation, and Database Usage in Genomic Era: The Road towards Fast-Track Crop Plant Improvement</title><author><name sortKey="Dhanapal, Arun Prabhu" sort="Dhanapal, Arun Prabhu" uniqKey="Dhanapal A" first="Arun Prabhu" last="Dhanapal">Arun Prabhu Dhanapal</name><affiliation wicri:level="1"><nlm:aff id="I1">Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Plant Sciences, University of Missouri, Columbia, MO 65211</wicri:regionArea></affiliation></author><author><name sortKey="Govindaraj, Mahalingam" sort="Govindaraj, Mahalingam" uniqKey="Govindaraj M" first="Mahalingam" last="Govindaraj">Mahalingam Govindaraj</name><affiliation wicri:level="1"><nlm:aff id="I2">International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25874133</idno><idno type="pmc">4383144</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383144</idno><idno type="RBID">PMC:4383144</idno><idno type="doi">10.1155/2015/684321</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000705</idno><idno type="wicri:Area/Pmc/Curation">000705</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Unlimited Thirst for Genome Sequencing, Data Interpretation, and Database Usage in Genomic Era: The Road towards Fast-Track Crop Plant Improvement</title><author><name sortKey="Dhanapal, Arun Prabhu" sort="Dhanapal, Arun Prabhu" uniqKey="Dhanapal A" first="Arun Prabhu" last="Dhanapal">Arun Prabhu Dhanapal</name><affiliation wicri:level="1"><nlm:aff id="I1">Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Division of Plant Sciences, University of Missouri, Columbia, MO 65211</wicri:regionArea></affiliation></author><author><name sortKey="Govindaraj, Mahalingam" sort="Govindaraj, Mahalingam" uniqKey="Govindaraj M" first="Mahalingam" last="Govindaraj">Mahalingam Govindaraj</name><affiliation wicri:level="1"><nlm:aff id="I2">International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India</nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324</wicri:regionArea></affiliation></author></analytic><series><title level="j">Genetics Research International</title><idno type="ISSN">2090-3154</idno><idno type="eISSN">2090-3162</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The number of sequenced crop genomes and associated genomic resources is growing rapidly with the advent of inexpensive next generation sequencing methods. Databases have become an integral part of all aspects of science research, including basic and applied plant and animal sciences. The importance of databases keeps increasing as the volume of datasets from direct and indirect genomics, as well as other omics approaches, keeps expanding in recent years. The databases and associated web portals provide at a minimum a uniform set of tools and automated analysis across a wide range of crop plant genomes. This paper reviews some basic terms and considerations in dealing with crop plant databases utilization in advancing genomic era. The utilization of databases for variation analysis with other comparative genomics tools, and data interpretation platforms are well described. The major focus of this review is to provide knowledge on platforms and databases for genome-based investigations of agriculturally important crop plants. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Genet Res Int</journal-id><journal-id journal-id-type="iso-abbrev">Genet Res Int</journal-id><journal-id journal-id-type="publisher-id">GRI</journal-id><journal-title-group><journal-title>Genetics Research International</journal-title></journal-title-group><issn pub-type="ppub">2090-3154</issn><issn pub-type="epub">2090-3162</issn><publisher><publisher-name>Hindawi Publishing Corporation</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25874133</article-id><article-id pub-id-type="pmc">4383144</article-id><article-id pub-id-type="doi">10.1155/2015/684321</article-id><article-categories><subj-group subj-group-type="heading"><subject>Review Article</subject></subj-group></article-categories><title-group><article-title>Unlimited Thirst for Genome Sequencing, Data Interpretation, and Database Usage in Genomic Era: The Road towards Fast-Track Crop Plant Improvement</article-title></title-group><contrib-group><contrib contrib-type="author"><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0002-9686-7260</contrib-id><name><surname>Dhanapal</surname><given-names>Arun Prabhu</given-names></name><xref ref-type="aff" rid="I1"><sup>1</sup></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Govindaraj</surname><given-names>Mahalingam</given-names></name><xref ref-type="aff" rid="I2"><sup>2</sup></xref></contrib></contrib-group><aff id="I1"><sup>1</sup>Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA</aff><aff id="I2"><sup>2</sup>International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India</aff><author-notes><corresp id="cor1">*Arun Prabhu Dhanapal: <email>dhanapala@missouri.edu</email></corresp><fn fn-type="other"><p>Academic Editor: Igor B. Rogozin</p></fn></author-notes><pub-date pub-type="ppub"><year>2015</year></pub-date><pub-date pub-type="epub"><day>19</day><month>3</month><year>2015</year></pub-date><volume>2015</volume><elocation-id>684321</elocation-id><history><date date-type="received"><day>17</day><month>7</month><year>2014</year></date><date date-type="rev-recd"><day>14</day><month>10</month><year>2014</year></date><date date-type="accepted"><day>3</day><month>11</month><year>2014</year></date></history><permissions><copyright-statement>Copyright © 2015 A. P. Dhanapal and M. Govindaraj.</copyright-statement><copyright-year>2015</copyright-year><license license-type="open-access"><license-p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract><p>The number of sequenced crop genomes and associated genomic resources is growing rapidly with the advent of inexpensive next generation sequencing methods. Databases have become an integral part of all aspects of science research, including basic and applied plant and animal sciences. The importance of databases keeps increasing as the volume of datasets from direct and indirect genomics, as well as other omics approaches, keeps expanding in recent years. The databases and associated web portals provide at a minimum a uniform set of tools and automated analysis across a wide range of crop plant genomes. This paper reviews some basic terms and considerations in dealing with crop plant databases utilization in advancing genomic era. The utilization of databases for variation analysis with other comparative genomics tools, and data interpretation platforms are well described. The major focus of this review is to provide knowledge on platforms and databases for genome-based investigations of agriculturally important crop plants. The utilization of these databases in applied crop improvement program is still being achieved widely; otherwise, the end for sequencing is not far away.</p></abstract></article-meta></front><floats-group><fig id="fig1" orientation="portrait" position="float"><label>Figure 1</label><caption><p>Flowchart description to integration of biological omics platforms with bioinformatics linking crop plant databases and open-access public usage.</p></caption><graphic xlink:href="GRI2015-684321.001"></graphic></fig><table-wrap id="tab1" orientation="portrait" position="float"><label>Table 1</label><caption><p>List of crop plant genomes available to public with URL information and references.</p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left" rowspan="1" colspan="1">Name of crop plant</th><th align="left" rowspan="1" colspan="1">Consortium/initiative </th><th align="left" rowspan="1" colspan="1">URL</th><th align="left" rowspan="1" colspan="1">References</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">Alfalfa (<italic>Medicago sativa</italic>)</td><td align="left" rowspan="1" colspan="1">Consortium</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.alfalfa-genome.org/www/">http://www.alfalfa-genome.org/www/</ext-link></td><td align="left" rowspan="1" colspan="1">Young et al., 2011 [<xref rid="B60" ref-type="bibr">7</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Apple (<italic>Malus domestica</italic>)</td><td align="left" rowspan="1" colspan="1">Consortium</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.rosaceae.org/species/malus/malus_spp">http://www.rosaceae.org/species/malus/malus_spp</ext-link></td><td align="left" rowspan="1" colspan="1">Velasco et al., 2010 [<xref rid="B61" ref-type="bibr">8</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Banana (<italic>Musa acuminate</italic>)</td><td align="left" rowspan="1" colspan="1">The Global Musa Genomics Consortium</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.musagenomics.org/">http://www.musagenomics.org/</ext-link></td><td align="left" rowspan="1" colspan="1">D'Hont et al., [<xref rid="B62" ref-type="bibr">9</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Barley (<italic>Hordeum vulgare</italic>)</td><td align="left" rowspan="1" colspan="1">International Barley Genome Sequencing Consortium</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.public.iastate.edu/~imagefpc/IBSC%20Webpage/IBSC%20Template-home.html">http://www.public.iastate.edu/~imagefpc/IBSC%20Webpage/IBSC%20Template-home.html</ext-link></td><td align="left" rowspan="1" colspan="1">The International Barley Genome Sequencing Consortium [<xref rid="B63" ref-type="bibr">10</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Cacao (<italic>Theobroma cacao</italic>)</td><td align="left" rowspan="1" colspan="1">Consortium</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.cacaogenomedb.org/">http://www.cacaogenomedb.org/</ext-link></td><td align="left" rowspan="1" colspan="1">Argout et al., 2011 [<xref rid="B64" ref-type="bibr">11</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Cannabis (<italic>Cannabis sativa</italic>)</td><td align="left" rowspan="1" colspan="1">Consortium</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://genome.ccbr.utoronto.ca/index.html?org=C.+sativa&db=canSat3&hgsid=11252">http://genome.ccbr.utoronto.ca/index.html?org=C.+sativa&db=canSat3&hgsid=11252</ext-link></td><td align="left" rowspan="1" colspan="1">van Bakel et al., 2011 [<xref rid="B65" ref-type="bibr">12</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Castor bean (<italic>Ricinus communis</italic>)</td><td align="left" rowspan="1" colspan="1">TIGR</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://castorbean.jcvi.org/">http://castorbean.jcvi.org/</ext-link></td><td align="left" rowspan="1" colspan="1">Chan et al., 2010 [<xref rid="B66" ref-type="bibr">13</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Chickpea (<italic>Cicer arietinum</italic>)</td><td align="left" rowspan="1" colspan="1">Consortium (ICRISAT-BGI)</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.icrisat.org/gt-bt/ICGGC/GenomeManuscript.htm">http://www.icrisat.org/gt-bt/ICGGC/GenomeManuscript.htm</ext-link></td><td align="left" rowspan="1" colspan="1">Varshney et al., 2013 [<xref rid="B67" ref-type="bibr">14</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1"> Chocolate (<italic>Theobroma cacao) </italic></td><td align="left" rowspan="1" colspan="1">Consortium</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.cacaogenomedb.org/main">http://www.cacaogenomedb.org/main</ext-link></td><td align="left" rowspan="1" colspan="1">Argout et al., 2011 [<xref rid="B64" ref-type="bibr">11</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Cotton (Gossypium <italic> raimondii</italic>)</td><td align="left" rowspan="1" colspan="1">BGI</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.cottondb.org/wwwroot/cdbhome.php">http://www.cottondb.org/wwwroot/cdbhome.php</ext-link></td><td align="left" rowspan="1" colspan="1">Wang et al., 2012 [<xref rid="B69" ref-type="bibr">15</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Common bean (<italic>Phaseolus vulgaris</italic> L.)</td><td align="left" rowspan="1" colspan="1">Consortium</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.phytozome.net/commonbean.php">http://www.phytozome.net/commonbean.php</ext-link></td><td align="left" rowspan="1" colspan="1">Schmutz et al., 2014 [<xref rid="B70" ref-type="bibr">16</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Crucifer (<italic>Thellungiella parvula</italic>)</td><td align="left" rowspan="1" colspan="1">Consortium</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.brassica.info/info/events.php">http://www.brassica.info/info/events.php</ext-link></td><td align="left" rowspan="1" colspan="1">Dassanayake et al., 2011 [<xref rid="B54" ref-type="bibr">17</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Cucumber (<italic>Cucumis sativus</italic>)</td><td align="left" rowspan="1" colspan="1">International Cucurbit Genomics Initiative (ICuGI)</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.icugi.org/">http://www.icugi.org/</ext-link></td><td align="left" rowspan="1" colspan="1">Huang et al., 2009 [<xref rid="B97" ref-type="bibr">18</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Date palm (<italic>Phoenix dactylifera</italic>)</td><td align="left" rowspan="1" colspan="1">Consortium</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://qatar-weill.cornell.edu/research/datepalmGenome/download.html">http://qatar-weill.cornell.edu/research/datepalmGenome/download.html</ext-link></td><td align="left" rowspan="1" colspan="1">Al-Dous et al., 2011 [<xref rid="B73" ref-type="bibr">19</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Wheat (<italic>Triticum aestivum</italic>)</td><td align="left" rowspan="1" colspan="1">International Wheat Genome Sequencing Consortium (IWGSC)</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.wheatgenome.org/">http://www.wheatgenome.org/</ext-link></td><td align="left" rowspan="1" colspan="1">International Wheat Genome Sequencing Consortium, 2014 [<xref rid="B74" ref-type="bibr">20</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Foxtail millet (<italic>Setaria italica</italic>)</td><td align="left" rowspan="1" colspan="1">Beijing Genomics Institute and the Joint Genomes Institute</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.phytozome.net/foxtailmillet.php">http://www.phytozome.net/foxtailmillet.php</ext-link></td><td align="left" rowspan="1" colspan="1">Zhang et al., [<xref rid="B75" ref-type="bibr">21</xref>] Bennetzen et al. [<xref rid="B98" ref-type="bibr">22</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Grape (<italic>Vitis vinifera</italic>)</td><td align="left" rowspan="1" colspan="1">Consortium</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.genoscope.cns.fr/externe/GenomeBrowser/Vitis/">http://www.genoscope.cns.fr/externe/GenomeBrowser/Vitis/</ext-link></td><td align="left" rowspan="1" colspan="1">Jaillon et al., 2007 [<xref rid="B76" ref-type="bibr">23</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Jatropha curcas</italic> L.</td><td align="left" rowspan="1" colspan="1">Consortium</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.kazusa.or.jp/jatropha/">http://www.kazusa.or.jp/jatropha/</ext-link></td><td align="left" rowspan="1" colspan="1">Sato et al., 2011 [<xref rid="B77" ref-type="bibr">24</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Lotus (<italic>Lotus japonicas</italic>)</td><td align="left" rowspan="1" colspan="1">Consortium</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.kazusa.or.jp/lotus/">http://www.kazusa.or.jp/lotus/</ext-link></td><td align="left" rowspan="1" colspan="1">Sato et al., 2008 [<xref rid="B78" ref-type="bibr">25</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Maize (<italic>Zea mays</italic>)</td><td align="left" rowspan="1" colspan="1">Consortium</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.maizegdb.org/">http://www.maizegdb.org/</ext-link></td><td align="left" rowspan="1" colspan="1">Schnable et al., 2009 [<xref rid="B79" ref-type="bibr">26</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Model Grass (<italic>Brachypodium distachyon</italic>)</td><td align="left" rowspan="1" colspan="1">Consortium</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.brachypodium.org/">http://www.brachypodium.org/</ext-link></td><td align="left" rowspan="1" colspan="1">International Brachypodium Initiative, 2010 [<xref rid="B80" ref-type="bibr">27</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Mosses (<italic>Physcomitrella patens</italic>)</td><td align="left" rowspan="1" colspan="1">JGI</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://genome.jgi-psf.org/Phypa1_1/Phypa1_1.home.html">http://genome.jgi-psf.org/Phypa1_1/Phypa1_1.home.html</ext-link></td><td align="left" rowspan="1" colspan="1">Rensing et al., 2008 [<xref rid="B81" ref-type="bibr">28</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Mouse ear cress (<italic>Arabidopsis thaliana</italic>,<italic> Arabidopsis lyrata</italic>)</td><td align="left" rowspan="1" colspan="1">The Arabidopsis Genome Initiative (2000)</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.arabidopsis.org/">http://www.arabidopsis.org/</ext-link></td><td align="left" rowspan="1" colspan="1">The Arabidopsis Genome Initiative, 2000 [<xref rid="B82" ref-type="bibr">29</xref>]; Cao et al., 2011 [<xref rid="B8" ref-type="bibr">30</xref>]; Hu et al., 2011 [<xref rid="B9" ref-type="bibr">31</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Papaya (<italic>Carica papaya</italic>)</td><td align="left" rowspan="1" colspan="1">Consortium</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.plantgdb.org/CpGDB/">http://www.plantgdb.org/CpGDB/</ext-link></td><td align="left" rowspan="1" colspan="1">Ming et al., 2008 [<xref rid="B84" ref-type="bibr">32</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Peach (<italic>Prunus persica</italic>)</td><td align="left" rowspan="1" colspan="1">International Peach Genome Initiative</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.rosaceae.org/peach/genome">http://www.rosaceae.org/peach/genome</ext-link></td><td align="left" rowspan="1" colspan="1">International Peach genome initiative 2013 [<xref rid="B85" ref-type="bibr">33</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Pigeon pea (<italic>Cajanus cajan</italic>) </td><td align="left" rowspan="1" colspan="1">International Initiative for Pigeonpea Genomics (IIPG)</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.icrisat.org/gt-bt/iipg/Home.html">http://www.icrisat.org/gt-bt/iipg/Home.html</ext-link></td><td align="left" rowspan="1" colspan="1">Varshney et al., 2011 [<xref rid="B102" ref-type="bibr">34</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Poplar (<italic>Populus trichocarpa</italic>)</td><td align="left" rowspan="1" colspan="1">JGI</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://genome.jgi-psf.org/Poptr1_1/Poptr1_1.home.html">http://genome.jgi-psf.org/Poptr1_1/Poptr1_1.home.html</ext-link></td><td align="left" rowspan="1" colspan="1">Tuskan et al., 2006 [<xref rid="B86" ref-type="bibr">35</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Potato (<italic>Solanum tuberosum</italic>)</td><td align="left" rowspan="1" colspan="1">Consortium (PGSC)</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.potatogenome.net/index.php/Main_Page">http://www.potatogenome.net/index.php/Main_Page</ext-link></td><td align="left" rowspan="1" colspan="1">The Potato Genome Sequencing Consortium, 2011 [<xref rid="B87" ref-type="bibr">36</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Rape seed (<italic>Brassica napus</italic>)</td><td align="left" rowspan="1" colspan="1">Consortium (MGBP)</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.plantgdb.org/BrGDB/">http://www.plantgdb.org/BrGDB/</ext-link></td><td align="left" rowspan="1" colspan="1">Wang et al., 2011 [<xref rid="B88" ref-type="bibr">37</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Rice (<italic>Oryza sativa </italic>ssp<italic>. indica and japonica</italic>)</td><td align="left" rowspan="1" colspan="1">Consortium (IRGSP)</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://rgp.dna.affrc.go.jp/E/IRGSP/index.html">http://rgp.dna.affrc.go.jp/E/IRGSP/index.html</ext-link></td><td align="left" rowspan="1" colspan="1">Yu et al., 2002 [<xref rid="B89" ref-type="bibr">38</xref>]; Goff et al., 2002 [<xref rid="B90" ref-type="bibr">39</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Sorghum (<italic>Sorghum bicolor</italic>)</td><td align="left" rowspan="1" colspan="1">JGI</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.plantgdb.org/SbGDB/">http://www.plantgdb.org/SbGDB/</ext-link></td><td align="left" rowspan="1" colspan="1">Paterson et al., 2009 [<xref rid="B91" ref-type="bibr">40</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Soybeans (<italic>Glycine max</italic>)</td><td align="left" rowspan="1" colspan="1">JGI</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.phytozome.net/soybean_er.php">http://www.phytozome.net/soybean_er.php</ext-link></td><td align="left" rowspan="1" colspan="1">Schmutz et al., 2010 [<xref rid="B92" ref-type="bibr">41</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Strawberry (<italic>Fragaria vesca</italic>)</td><td align="left" rowspan="1" colspan="1">Consortium</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.strawberrygenome.org/">http://www.strawberrygenome.org/</ext-link></td><td align="left" rowspan="1" colspan="1">Shulaev et al., 2011 [<xref rid="B93" ref-type="bibr">42</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Tomato (<italic>Solanum lycopersicum</italic>)</td><td align="left" rowspan="1" colspan="1">Consortium</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://solgenomics.net/organism/Solanum_lycopersicum/genome">http://solgenomics.net/organism/Solanum_lycopersicum/genome</ext-link></td><td align="left" rowspan="1" colspan="1">The Tomato Genome Consortium 2012 [<xref rid="B94" ref-type="bibr">43</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Watermelon (<italic>Citrullus lanatus</italic>)</td><td align="left" rowspan="1" colspan="1">International Watermelon Genomics Initiative</td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://www.iwgi.org/">http://www.iwgi.org/</ext-link></td><td align="left" rowspan="1" colspan="1">Guo et al., 2013 [<xref rid="B95" ref-type="bibr">44</xref>]</td></tr><tr><td align="center" colspan="4" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Mung bean (<italic>Vigna radiata</italic>)</td><td align="left" rowspan="1" colspan="1">Not available </td><td align="left" rowspan="1" colspan="1"><ext-link ext-link-type="uri" xlink:href="http://vigra.comparative-legumes.org/">http://vigra.comparative-legumes.org/</ext-link></td><td align="left" rowspan="1" colspan="1">Kang et al., 2014 [<xref rid="B96" ref-type="bibr">45</xref>]</td></tr></tbody></table></table-wrap><table-wrap id="tab2" orientation="portrait" position="float"><label>Table 2</label><caption><p>List of databases and their information of application to crop plant research community. </p></caption><table frame="hsides" rules="groups"><thead><tr><th align="left" rowspan="1" colspan="1">Name of databases</th><th align="left" rowspan="1" colspan="1">Application</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">AgBase—a unified resource for functional analysis in agriculture</td><td align="left" rowspan="1" colspan="1">Search and analyze functional genomics datasets in agricultural species</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">AutoSNPdb—an annotated single nucleotide polymorphism database for crop plants</td><td align="left" rowspan="1" colspan="1">Identify SNPs from assembled EST sequences for the crops rice, barley, and <italic>Brassica </italic></td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">BarleyBase—an expression profiling database for plant genomics</td><td align="left" rowspan="1" colspan="1">Analyze and visualize plant microarray data</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">BBGD—an online database for blueberry genomic data.</td><td align="left" rowspan="1" colspan="1">It stores both EST and microarray data and allows scientists to correlate expression profiles with gene function</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">BIOGEN BASE—CASSAVA</td><td align="left" rowspan="1" colspan="1">A web accessible resource for investigating cassava phenomics and genomics information</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">CastorDB—a comprehensive knowledge base for Ricinus communis.</td><td align="left" rowspan="1" colspan="1">CastorDB provides a user friendly comprehensive resource on castor with particular emphasis on its genome, transcriptome, and proteome and on protein domains, pathways, protein localization, presence of sumoylation sites, expression data, and protein interacting partners</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">ChromDB—The Chromatin Database</td><td align="left" rowspan="1" colspan="1">Locate chromatin-associated proteins, including RNAi-associated proteins, for a broad range of organisms</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">CR-EST—a resource for crop ESTs</td><td align="left" rowspan="1" colspan="1">Search for sequence, classification, clustering, and annotation data of crop EST projects</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">CSRDB—a small RNA integrated database and browser resource for cereals</td><td align="left" rowspan="1" colspan="1">Search for sequence information on rice, maize, and other cereal crops small RNAs</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">DEBDOM—Database Exploring Banana Diversity of Manipur</td><td align="left" rowspan="1" colspan="1">The database DEBDOM provides a sophisticated web base access to the details of the taxonomy, morphological characteristics, utility, and sites of collection of Musa genotypes</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">DRASTIC—Database Resource for the Analysis of Signal Transduction in Cells</td><td align="left" rowspan="1" colspan="1">Search for information of plant gene expression in response to pathogens and environmental changes</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">FLAGdb++—A Database for the Functional Analysis of the Arabidopsis Genome</td><td align="left" rowspan="1" colspan="1">Search and visualize data for high-throughput functional analysis of <italic>Arabidopsis</italic>, rice, and other plant genomes</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">GabiPD—a plant integrative “omics” database</td><td align="left" rowspan="1" colspan="1">Search for comprehensive and extensive information on various plant genomes generated by a German collaborative network of plant genomics research</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">GCP—The Generation Challenge Programme</td><td align="left" rowspan="1" colspan="1">An online resource documenting stress-responsive genes comparatively across plant species</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">GDR—Genome Database for Rosaceae</td><td align="left" rowspan="1" colspan="1">A central repository of curated and integrated genetics and genomics data of Rosaceae, which includes apple, cherry, peach, pear, raspberry, rose, and strawberry</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">GeneCAT—gene co-expression analysis toolbox</td><td align="left" rowspan="1" colspan="1">Novel web tools that combine BLAST and coexpression analyses</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">GeneSeqer@PlantGDB—gene structure prediction in plant genomes</td><td align="left" rowspan="1" colspan="1">Predict gene structures of plant genomes</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">GERMINATE</td><td align="left" rowspan="1" colspan="1">A generic database for integrating genotypic and phenotypic information for plant genetic resource collections</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">GGT—Graphical GenoTypes</td><td align="left" rowspan="1" colspan="1">Software for visualization and analysis of genetic data</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">GrainGenes—The genome database for small-grain crops</td><td align="left" rowspan="1" colspan="1">Search for molecular and phenotypic information on wheat, barley, rye, triticale, and oats</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Gramene—a resource for comparative grass genomics</td><td align="left" rowspan="1" colspan="1">Curated resource for genetic, genomic, and comparative genomics data for the major crop species, including rice, maize, wheat, and many other plant (mainly grass) species</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">MaizeGDB—the Community Database for Maize Genetics and Genomics</td><td align="left" rowspan="1" colspan="1">Search genetic and genomic information about maize</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">MANET—The Molecular Ancestry Network</td><td align="left" rowspan="1" colspan="1">Tracing evolution of protein architecture in metabolic networks</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Medicago—A database for personalized data mining of the model legume Medicago truncatula transcriptome</td><td align="left" rowspan="1" colspan="1">Search for integrated genomic, genetic, and biological information on cool season legume <italic>Medicago truncatula</italic> (Mt)</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">MetaCrop—a detailed database of crop plant metabolism</td><td align="left" rowspan="1" colspan="1">A database that summarizes diverse information about metabolic pathways in crop plants and allows automatic export of information for the creation of detailed metabolic models</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">MetaCrop 2.0—managing and exploring information about crop plant metabolism.</td><td align="left" rowspan="1" colspan="1">It contains information about seven major crop plants with high agronomical importance and two model plants; MetaCrop is intended to support research aimed at the improvement of crops for both nutrition and industrial use</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Narcisse—a mirror view of conserved syntenies</td><td align="left" rowspan="1" colspan="1">A database dedicated to the study of genome conservation</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">NIASGBdb—National Institute of Agrobiological Sciences Gene Bank DataBase</td><td align="left" rowspan="1" colspan="1">Find information about agricultural plant genetics and diseases</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">P3DB—Plant Protein Phosphorylation Database</td><td align="left" rowspan="1" colspan="1">Find information about protein phosphorylation in plants</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Panzea—a database and resource for molecular and functional diversity in the maize genome</td><td align="left" rowspan="1" colspan="1">Search for information on relationship between genotype and functional phenotype variations</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Pepper EST database—in silico exploitation of EST data to extensively score genes of Capsicum annuum</td><td align="left" rowspan="1" colspan="1">Comprehensive in silico tool for analyzing the chili pepper (<italic>Capsicum annuum</italic>) transcriptome</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">PIP—a database of potential intron polymorphism markers</td><td align="left" rowspan="1" colspan="1">A database of potential intron polymorphism markers in plants</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">PLACE—plant cis-acting regulatory DNA elements</td><td align="left" rowspan="1" colspan="1">Search for documented motifs found in plant cis-acting regulatory DNA elements</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Plant snoRNA database</td><td align="left" rowspan="1" colspan="1">Search for comprehensive information on small nucleolar RNAs in plants</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">PlantCARE—a database of plant cis-acting elements</td><td align="left" rowspan="1" colspan="1">Search for information on plant cis-acting regulatory elements, transcription sites, enhancers, and repressors</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">PlantTFDB—Plant Transcription Factor Databases</td><td align="left" rowspan="1" colspan="1">A comprehensive plant transcription factor database</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">PlantTribes—a gene and gene family resource for comparative genomics in plants</td><td align="left" rowspan="1" colspan="1">A plant gene family database based on the inferred proteomes of five sequenced plant species: <italic>Arabidopsis thaliana</italic>, <italic>Carica papaya</italic>, <italic>Medicago truncatula</italic>, <italic>Oryza sativa</italic>, and <italic>Populus trichocarpa </italic></td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">PLecDom—Plant Lectin Domains server</td><td align="left" rowspan="1" colspan="1">Find information about plant lectin domains</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">PlnTFDB—Plant Transcription Factor Database</td><td align="left" rowspan="1" colspan="1">Find information about transcription factors in plants</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">PmiRKB—Plant MicroRNA Knowledge Base</td><td align="left" rowspan="1" colspan="1">Find information about plant microRNAs</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">PMRD—Plant MicroRNA Database</td><td align="left" rowspan="1" colspan="1">Find information about microRNA sequences and targets in plants</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">PODB—the Plant Organelles Database</td><td align="left" rowspan="1" colspan="1">Search a collection of visualized plant organelles and protocols for plant organelle research</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">POGs/PlantRBP—a resource for comparative genomics in plants</td><td align="left" rowspan="1" colspan="1">Search for information on putative orthologous proteins among rice, maize, and <italic>Arabidopsis</italic> with emphasis on RNA-binding proteins</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">PoMaMo—a comprehensive database for potato genome data</td><td align="left" rowspan="1" colspan="1">Search for comprehensive genomic information on potato</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">PREP Suite—Predictive RNA Editor for Plants</td><td align="left" rowspan="1" colspan="1">Use to predict sites of RNA editing in plants</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">PRGDB—Plant Resistance Genes DataBase</td><td align="left" rowspan="1" colspan="1">Find information about genes involved in plant defense mechanisms</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">pssRNAMiner—a plant short small RNA regulatory cascade analysis server</td><td align="left" rowspan="1" colspan="1">Identify both the clusters of phased small RNAs as well as the potential phase-initiator</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">RadishBase—a database for genomics and genetics of radish.</td><td align="left" rowspan="1" colspan="1">A database containing radish pathways predicted from unigene sequences is also included in RadishBase</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">RoBuST—an integrated genomics resource for the root and bulb crop families Apiaceae and Alliaceae.</td><td align="left" rowspan="1" colspan="1">The RoBuST database has been developed to initiate a platform for collecting and organizing genomic information useful for RBV (root and bulb vegetables) researchers </td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">SALAD—Surveyed contained motif ALignment diagram and the Associating Dendrogram</td><td align="left" rowspan="1" colspan="1">Perform systematic comparison of proteome data among species</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">SGN—SOL Genomics Network</td><td align="left" rowspan="1" colspan="1">A comparative map viewer dedicated to the biology of the Solanaceae family</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Shanghai RAPESEED Database—a resource for functional genomics studies of seed development and fatty acid metabolism of <italic>Brassica </italic></td><td align="left" rowspan="1" colspan="1">Find information on EST, gene expression profiles, and bioresources for the promotion of functional genomics studies and quality breeding of <italic>Brassica</italic> crops</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">SolRgene—an online database to explore disease resistance genes in tuber-bearing Solanum species</td><td align="left" rowspan="1" colspan="1">The SolRgene database contains data on resistance to <italic>P. infestans</italic> and presence of R genes and R gene homologues in Solanum section Petota</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">SoyBase—USDA-ARS soybean genetics and genomics database</td><td align="left" rowspan="1" colspan="1">Find genetic information about soybeans</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1"> SoyTEdb—a comprehensive database of transposable elements in the soybean genome. </td><td align="left" rowspan="1" colspan="1">SoyTEdb provides resources and information related to transposable elements in the soybean genome, representing the most comprehensive and the largest manually curated transposable element database for any individual plant genome completely sequenced to date</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">SoyXpress—a database for exploring the soybean transcriptome</td><td align="left" rowspan="1" colspan="1">A soybean gene expression and transcription database</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">Sputnik—a database platform for comparative plant genomics</td><td align="left" rowspan="1" colspan="1">Search for ESTs from over 20 different plant species</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">TFGD—Tomato Functional Genomics Database</td><td align="left" rowspan="1" colspan="1">Find information about tomato genes</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">The Adaptive Evolution Database (TAED)—a phylogeny based tool for comparative genomics</td><td align="left" rowspan="1" colspan="1">Search for information on adaptive evolution in gene families of higher plants and chordate</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">The Legume Information System (LIS)—an integrated information resource for comparative legume biology</td><td align="left" rowspan="1" colspan="1">Search for integrated genetic and molecular data from multiple legume species</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">The Plant DNA <italic>C</italic>-values Database</td><td align="left" rowspan="1" colspan="1">Search for information on plant DNA <italic>C</italic>-values and genome sizes</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">The Plant Ontology Database—a resource for plant structure and developmental stages</td><td align="left" rowspan="1" colspan="1">View, search, and query plant ontology terms</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">The PlantsP Functional Genomics Database</td><td align="left" rowspan="1" colspan="1">Search for information on plant kinases and phosphatases</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">The TIGR Maize Database</td><td align="left" rowspan="1" colspan="1">Search for annotated genomic sequences of maize</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">The TIGR Plant Repeat Databases—A Collective Resource for the Identification of Repetitive Sequences in Plants</td><td align="left" rowspan="1" colspan="1">Identify, classify, and analyze repetitive sequences in plant genomes</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">TomatEST database—in silico exploitation of EST data to explore expression patterns in tomato species</td><td align="left" rowspan="1" colspan="1">Find expressed sequence tag (EST)/cDNA sequence information from different libraries of multiple tomato species</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">TriMEDB—a database to integrate transcribed markers and facilitate genetic studies of the tribe Triticeae.</td><td align="left" rowspan="1" colspan="1">The Triticeae mapped expressed sequence tag (EST) database</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">TropGENE-DB—A Multi-tropical Crop Information System</td><td align="left" rowspan="1" colspan="1">Search for genetic, molecular, and phenotypic data of tropical crop species</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">TropGENE-DB—A Multi-tropical Crop Information System</td><td align="left" rowspan="1" colspan="1">Search for genetic, molecular, and phenotypic data of tropical crop species</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">UK CropNet—a collection of databases and bioinformatics resources for crop plant genomics</td><td align="left" rowspan="1" colspan="1">Search sequences and genomic information on crop plants</td></tr><tr><td align="center" colspan="2" rowspan="1"><hr></hr></td></tr><tr><td align="left" rowspan="1" colspan="1">WhETS—Wheat Estimated Transcript Server</td><td align="left" rowspan="1" colspan="1">A tool to provide the best estimate of hexaploid wheat transcript sequence</td></tr></tbody></table></table-wrap></floats-group></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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