Merge pull request #4106 from solgenomics/topic/wishlist

[sgn.git] / mason / genomes / Capsicum_annuum.mas

<%args>
  $organism
</%args>
<& /page/page_title.mas, title => '<i>'.$organism->species.'</i> Genome Data' &>

<!-- <div class="page_introduction"> -->
<p>
Linked-read sequencing technology was used to create a phased assembly that was scaffolded into chromosomes for an F1 of a wide cross (UCD-10X-F1) between a landrace, Criollos de Morelos 334 (CM334) and a nonpungent blocky pepper-breeding line. Please see <a href="https://www.nature.com/articles/s41438-017-0011-0">Hulse-Kemp et al. (2017)</a> for more details. This genome is available in <a href="/tools/blast?db_id=301">blast</a> and on the <a href="ftp://ftp.solgenomics.net/genomes/Capsicum_annuum/C.annuum_UCD10X/">FTP site</a>.  
</p>
<p>
The hot pepper genome (Mexican landrace of <i>Capsicum annuum</i> cv. CM334) has been sequenced by an international group of scientists from Korea, Israel and USA.
The sequence was published in <a href="http://www.nature.com/ng/journal/v46/n3/full/ng.2877.html" target="_blank">Nature Genetics</a> in January 2014.
The official page for this genome sequences is <a href="http://peppergenome.snu.ac.kr/" target="_blank">http://peppergenome.snu.ac.kr/</a>.
</p>
<p>
The genome sequence for hot pepper. <i>C. annuum</i> cv. CM334 (Criollo de Morelos 334), a diploid and a landrace collected from the Mexican state of Morelos, was sequenced to 186.6X coverage using Illumina technology. The genome assembly was annotated with the <a href="http://www.nature.com/ng/journal/v46/n3/extref/ng.2877-S1.pdf">PGA annotation pipeline</a>. CM334 genome assembly, pseudomolecules, annotations and C. chinense genome assembly are available through the links below.<br>
</p>

<p>
The complete genomes of wild Mexican pepper accession “Chiltepin” and a Chinese inbred derivative “Zunla-1” was also sequenced and published on the same date by research groups from China and Mexico.
The genome sequence for these pepper varieties was published in <a href="http://www.pnas.org/content/111/14/5135.abstract" target="_blank">PNAS</a> in January 2014.
The official page for this genome sequences is <a href="http://peppersequence.genomics.cn/" target="_blank">http://peppersequence.genomics.cn/</a>.
</p>

<p>
<i>C. annuum</i> genome, gene and protein sequences are accessible on the SGN BLAST tool and can be downloaded from the SGN ftp site. <i>C. annuum</i> cv. CM334 genome sequence is also available on SGN JBrowse.
</p>
<!-- </div> -->

<center>
    <a id="blue_button" href="/tools/blast/?db_id=217" target="_blank">BLAST</a>&nbsp;&nbsp;
    <a id="blue_button" href="ftp://ftp.solgenomics.net/genomes/Capsicum_annuum/" target="_blank">FTP Site</a>&nbsp;&nbsp;
    <a id="blue_button" href="http://solgenomics.net/jbrowse_solgenomics/?data=data%2Fjson%2FPepper.v.1.55&loc=Pepper1.55ch01" target="_blank" style="background-image:none;">JBrowse</a>&nbsp;&nbsp;
</center>

<!-- <&| /page/info_section.mas, title => 'CM334 genome' &> -->
  <!-- The genome sequence for hot pepper. <i>C. annuum</i> cv. CM334 (Criollo de Morelos 334), a dipoloid and a landrace collected from the Mexican state of Morelos, was sequenced to 186.6X coverage using Illumina technology. The genome assembly was annotated with the <a href="http://www.nature.com/ng/journal/v46/n3/extref/ng.2877-S1.pdf">PGA annotation pipeline</a>.  CM334 genome assembly, pseudomolecules, annotations and C. chinense genome assembly are available through the links below.<br> -->


  <!-- <% info_table_html(
                     __border   => 0,
                     __multicol => 2,
                     'Bulk Datasets (via FTP)' =>
                     '<a href="ftp://ftp.solgenomics.net/genomes/Capsicum_annuum/">Genome sequence and Annotation</a>',
                     BLAST => '<a href="/tools/blast/?db_id=219">Genomic sequence</a>',
                     'Genome browser' => '<a href="/jbrowse/JBrowse-1.11.4/?data=data/json/Pepper1.55/">Jbrowse</a>'
                    )
  %> -->
<!-- </&> -->



<&| /page/info_section.mas,
      title       => 'Sequence datasets',
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      hide_if_empty => 1
 &>
  <& /genomes/default/genome_builds.mas, %ARGS &>
</&>


<&| /page/info_section.mas,
      title       => 'Browsable annotations',
      collapsible => 1,
      hide_if_empty => 1,
 &>

  <& /gbrowse/list_sources.mas, organism => $organism &>

</&>

<&| /page/info_section.mas,
      title       => 'Annotation datasets',
      collapsible => 1,
      hide_if_empty => 1,
 &>

  <& /genomes/default/annotation_sets.mas, %ARGS &>

</&>

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