cgi-bin/markers/cosii_markers.pl

   1 use strict;
   2 use CXGN::Page;
   3 my $page=CXGN::Page->new('cosii_markers.html','html2pl converter');
   4 $page->header('Conserved Ortholog Set II (COSII) markers');
   5 print<<END_HEREDOC;
   6
   7   <center>
   8
   9
  10     <table summary="" width="100\%" cellpadding="0" cellspacing="0"
  11     border="0">
  12       <tr>
  13         <td>
  14           <center>
  15             <h3>Conserved Ortholog Set II (COSII) markers</h3>
  16           </center>
  17
  18           <p>COSII markers are PCR-based markers developed from a
  19           set of single-copy conserved orthologous genes (COSII
  20           genes) in Asterid species. Each COSII gene (representing
  21           a group of Asterid unigenes) matches only one single-copy
  22           Arabidopsis gene. In comparison with COS markers reported
  23           by Fulton et al. (2002), COSII markers/genes have the
  24           following new properties:</p>
  25
  26           <ol>
  27             <li>Multiple EST-assembled unigene databases, tomato,
  28             potato, pepper and coffee, as well as the Arabidopsis
  29             CDS database, were screened computationally and the
  30             method for establishing orthology was more robust.</li>
  31
  32             <li>Phylogenetic analyses support their classification
  33             as orthologs.</li>
  34
  35             <li>They occur as single-copy genes in these
  36             species.</li>
  37
  38             <li>Designed "Universal Primers" were able to amplify
  39             orthologous counterparts (exons and/or introns) from
  40             other related solanaceous species including those lack
  41             of sequence data.</li>
  42           </ol>
  43
  44           <p>Therefore, this set of COSII genes as well as
  45           Universal Primers is a powerful tool for establishing a
  46           syntenic network between Solanaceae and Arabidopsis, and
  47           for elucidating phylogenies, genome evolution and genome
  48           organization of Solanaceae. Moreover, one can establish
  49           similar orthologs sets and Universal Primers for other
  50           plant families (especially dicots), and connect them with
  51           COSII genes by the common Arabidopsis orthologs.</p>
  52
  53           <p>The computational screen for identifying COSII genes
  54           is described in <a href="/documents/img/cosii.png">this diagram</a>.</p>
  55
  56           <p>In this section of SGN, you will find sequence
  57           information of each COSII gene as well as the mapping
  58           information of those mapped COSII genes (so called COSII
  59           markers). We\'ve mapped more than 300 COSII markers in
  60           tomato and will map more in the future, up to at least
  61           500, and in the meanwhile, these COSII markers will be
  62           mapped in major solanaceous species (e.g. eggplant,
  63           pepper, Nicotiana, etc.). All the information in this
  64           section will be updated as new data are generated, so
  65           please come back and check from time to time.</p>
  66
  67           <h4>Universal Primers developed from COSII genes (iUPA
  68           and eUPA)</h4>
  69
  70           <p><em>Universal Primers for Asterid species</em> (UPA)
  71           were designed on the consensus sequence of a COSII
  72           gene/group, which amplify both exonic and intronic
  73           regions in most, if not all, solanaceous species and
  74           related taxa in the Asterid I clade of dicot plant
  75           species, and which are therefore useful for comparative
  76           mapping and phylogenetics.</p>
  77
  78           <p><em>Intronic UPA</em> (iUPA) amplify an intron with a
  79           short stretch of the flanking exons and hence are useful
  80           for genome/comparative mapping, and phylogenetics of
  81           closely related species. Many iUPAs have been tested in
  82           various solanaceous species as well as coffee, and primer
  83           sequences, PCR conditions and product sizes are
  84           available.</p>
  85
  86           <p><em>Exonic UPA</em>S (eUPA) amplify at least 400bp exonic
  87           sequences with/without an intervening intron and hence
  88           are useful for phylogenetics of distantly related
  89           species. Some eUPAs have been tested in various
  90           solanaceous species as well as coffee, and primer
  91           sequences, PCR conditions and product sizes are
  92           available.</p>
  93
  94           <h4>How to read COSII marker information pages</h4>
  95
  96           <p>Arabidopsis CDS is not edited. The unigenes were
  97           edited based on their alignment with the CDS, by trimming
  98           the UTRs and correcting sequencing errors. Peptide
  99           sequence is translated from from edited sequence in frame
 100           1 (for unigenes) or downloaded from <a href=
 101           "http://www.arabidopsis.org">TAIR</a> (for Arabidopsis).
 102           Intron locations of unigenes were predicted from
 103           alignment with the Arabidopsis CDS, whose intron
 104           locations were downloaded from <a href=
 105           "http://www.arabidopsis.org">TAIR</a>. "=====" indicates
 106           introns from <a href=
 107           "http://www.arabidopsis.org">TAIR</a> (for Arabidopsis)
 108           or predicted intron location in the sequence (for
 109           unigenes).</p>
 110
 111           <h4>Functional annotation of COSII genes</h4>
 112
 113           <p>Each of the COSII genes was assigned a functional
 114           annotation based on the <a href=
 115           "http://www.arabidopsis.org/info/ontologies/go/">Gene
 116           Ontology (GO) annotation</a> of the matching Arabidopsis
 117           gene member.</p>
 118
 119           <h4>Mapping PCR-based COSII markers in major solanaceous
 120           species</h4>
 121
 122           <p>All mapped COSII markers can be found in these
 123           <a href="/search/markers/markersearch.pl?submit=search&amp;types=COSII&amp;mapped=on">
 124           marker search results</a>.</p>
 125
 126           <h4>Complete listing of COSII genes</h4>
 127
 128           <p>Complete listings of COSII genes and markers can be
 129           found in our <a href=
 130           "/search/markers/markersearch.pl?submit=search&amp;types=COSII">marker
 131           search results</a> or in this <a href="/documents/markers/cosii.xls">.xls
 132           spreadsheet</a>. The spreadsheet is sometimes more up-to-date than the search results.
 133           Sequence text files and other associated COSII data can be downloaded from our
 134           <a href="ftp://ftp.sgn.cornell.edu/COSII/">FTP site</a>.</p>
 135
 136           <ol>
 137             <li><span class="tinytype">Fulton T, van der Hoeven R,
 138             Eannetta N, Tanksley S (2002). Identification, Analysis
 139             and Utilization of a Conserved Ortholog Set (COS)
 140             Markers for Comparative Genomics in Higher Plants. The
 141             Plant Cell 14: 1457-1467</span></li>
 142
 143             <li><span class="tinytype">Wu F, Mueller LA, Crouzillat D, Petiard V, Tanksley SD (2006).
 144 Combining Bioinformatics and Phylogenetics to Identify Large Sets of
 145 Single Copy, Orthologous Genes (COSII) for Comparative, Evolutinonary
 146 and Systematics Studies: A Test Case in the Euasterid Plant Clade (2006).
 147 Genetics, 2006 Nov;174(3):1407-20. <a href="http://www.genetics.org/cgi/content/abstract/genetics.106.062455v1">Genetics</a> | <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&term=16951058">PubMed</a> | <a href="ftp://ftp.sgn.cornell.edu/COSII/COSII-Genetics-suppl/">[access supplement information on SGN FTP site]</a>
 148 </span></li>
 149           </ol>
 150         </td>
 151       </tr>
 152     </table>
 153   </center>
 154 END_HEREDOC
 155 $page->footer();