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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
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<i style="font-weight: bold;">Grupo de Biologia Computacional, Evolutiva e de Sistemas</i>
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<h1>Sugarcane leaf development</h1>
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<p>One of our goals is to generate a public catalogue/atlas of sugarcane transcripts. Currently there are only ~240K EST available in GenBank, and there is not much genomic information publicly available. Here at the <a href="http://ctbe.cnpem.br/">CTBE</a>, we have been generating data in the form of transcriptome and genome sequencing and we are commited to release that data, assemblies and annotation, to the public. We are convinced that making large genomics and functional genomics datasets avaiable for the sugarcane cammunity, will aid in the understanding of C4 photosynthesis, complex polyploid genomes and in the adoption of molecular breeding approaches.
</p><p><!--break-->
</p><p>One of our first projects, contributing towards the Sugarcane gene catalogue, is a study of the leaf development in Sugarcane, genotype SP80-3280. The leaf of C4 plants, such as sugarcane have a developmental gradient along the leaf. We have studied the sugarcane leaf +1 (First leaf from top to bottom with the delawp fully exposed), examining four different segments, as show in the following figure. More details are available in <a href="http://www.ncbi.nlm.nih.gov/pubmed/26714767">Mattiello <em>et al</em>., 2015</a>.
</p><p><span style="font-size: 12.16px; line-height: 20.672px;"> </span><img alt="Sugarcane leaf+1 segments" src="./pixs/SugarcaneLeafSegments_0.png" style="font-size: 12.16px; line-height: 20.672px; width: 446px; height: 108px;">
</p><p>For each region we collected total RNA, from several individuals. RNA was processed with the total mRNA library preparation kit from Illumina (stranded-chemistry) and sequenced on a HiSeq2500 instrument using paired-end reads (2x100bp). The following table has a summary of the sequencing and quality evaluation.
</p><table class="inline" style="margin-top: 0px; margin-bottom: 0px; padding: 0px; border-collapse: collapse; empty-cells: show; border-spacing: 0px; border-style: solid; border-color: rgb(204, 204, 204); min-width: 50%; color: rgb(51, 51, 51); font-family: Arial, sans-serif; font-size: 14px; line-height: 17.8181819915772px; background-color: rgb(255, 255, 255);">
<thead>
<tr class="row0"><th class="col0 centeralign" style="margin: 0px; vertical-align: top; border-top-style: solid; border-right-style: solid; border-left-style: solid; border-color: rgb(204, 204, 204); text-align: center; background-color: rgb(238, 238, 238);">Segment</th><th class="col1 centeralign" style="margin: 0px; vertical-align: top; border-top-style: solid; border-right-style: solid; border-left-style: solid; border-color: rgb(204, 204, 204); text-align: center; background-color: rgb(238, 238, 238);">Individual</th><th class="col3 centeralign" style="margin: 0px; vertical-align: top; border-top-style: solid; border-right-style: solid; border-left-style: solid; border-color: rgb(204, 204, 204); text-align: center; background-color: rgb(238, 238, 238);">Quality trimmed reads</th><th class="col5 centeralign" style="margin: 0px; vertical-align: top; border-top-style: solid; border-right-style: solid; border-left-style: solid; border-color: rgb(204, 204, 204); text-align: center; background-color: rgb(238, 238, 238);">rRNA</th><th class="col6 centeralign" style="margin: 0px; vertical-align: top; border-top-style: solid; border-right-style: solid; border-left-style: solid; border-color: rgb(204, 204, 204); text-align: center; background-color: rgb(238, 238, 238);">Plastid</th><th class="col7 rightalign" style="margin: 0px; vertical-align: top; border-top-style: solid; border-right-style: solid; border-left-style: solid; border-color: rgb(204, 204, 204); text-align: right; background-color: rgb(238, 238, 238);">Mitochondria</th><th class="col8" style="margin: 0px; vertical-align: top; border-top-style: solid; border-right-style: solid; border-left-style: solid; border-color: rgb(204, 204, 204); background-color: rgb(238, 238, 238);">Remaining paired-end reads</th></tr></thead>
<tbody>
<tr class="row1"><td class="col0" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">Bo</td>
<td class="col1" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">235Bo</td>
<td class="col3" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">55.209.307</td>
<td class="col5" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">32.42%</td>
<td class="col6" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">0,90%</td>
<td class="col7" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">0,11%</td>
<td class="col8" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">37.042.139</td></tr>
<tr class="row2"><td class="col0" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">M</td>
<td class="col1" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">235M</td>
<td class="col3" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">22.796.562</td>
<td class="col5" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">37.26%</td>
<td class="col6" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">1,30%</td>
<td class="col7" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">0,13%</td>
<td class="col8" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">14.146.578</td></tr>
<tr class="row3"><td class="col0" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">T</td>
<td class="col1" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">235P</td>
<td class="col3" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">30.003.751</td>
<td class="col5" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">16,78%</td>
<td class="col6" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">1,11%</td>
<td class="col7" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">0,05%</td>
<td class="col8" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">24.722.651</td></tr>
<tr class="row5"><td class="col0" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">Bo</td>
<td class="col1" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">234Bo</td>
<td class="col3" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">19.764.755</td>
<td class="col5" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">35,28%</td>
<td class="col6 leftalign" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">0,46%</td>
<td class="col7" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">0,06%</td>
<td class="col8" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">12.779.105</td></tr>
<tr class="row6"><td class="col0" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">M</td>
<td class="col1" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">234M</td>
<td class="col3" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">49.018.540</td>
<td class="col5" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">12,72%</td>
<td class="col6" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">0,25%</td>
<td class="col7" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">0,02%</td>
<td class="col8" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">42.721.041</td></tr><tr class="row7"><td class="col0" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">T</td>
<td class="col1" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">234P</td>
<td class="col3 leftalign" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">34.074.014</td>
<td class="col5" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">19,30%</td>
<td class="col6" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">0,41%</td>
<td class="col7" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">0,04%</td>
<td class="col8" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">27.316.488</td></tr><tr class="row8"><td class="col0" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">B</td>
<td class="col1" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">138B</td>
<td class="col3" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">18.689.034</td>
<td class="col5" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">6,72%</td>
<td class="col6" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">0,11%</td>
<td class="col7" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">0,01%</td>
<td class="col8" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">16.543.744</td></tr><tr class="row9"><td class="col0" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">Bo</td>
<td class="col1" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">138Bo</td>
<td class="col3" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">29.404.833</td>
<td class="col5" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">11,78%</td>
<td class="col6" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">0,16%</td>
<td class="col7" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">0,02%</td>
<td class="col8" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">25.928.715</td></tr><tr class="row10"><td class="col0" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">M</td>
<td class="col1" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">138M</td>
<td class="col3" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">36.072.049</td>
<td class="col5" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">13,14%</td>
<td class="col6" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">0,37%</td>
<td class="col7" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">0,03%</td>
<td class="col8" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">31.261.141</td></tr><tr class="row11"><td class="col0" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">T</td>
<td class="col1" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">138P</td>
<td class="col3" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">58.826.816</td>
<td class="col5" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">34,52%</td>
<td class="col6" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">0,24%</td>
<td class="col7" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">0,02%</td>
<td class="col8" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">50.767.882</td></tr><tr class="row12"><td class="col0" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">B</td>
<td class="col1" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">163B</td>
<td class="col3" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">10.170.698</td>
<td class="col5" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">34,52%</td>
<td class="col6" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">0,42%</td>
<td class="col7" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">0,05%</td>
<td class="col8" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">6.659.348</td></tr><tr class="row13"><td class="col0" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">M</td>
<td class="col1" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">163M</td>
<td class="col3" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">21.348.210</td>
<td class="col5" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">27,48%</td>
<td class="col6" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">0,28%</td>
<td class="col7" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">0,04%</td>
<td class="col8" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">15.476.837</td></tr><tr class="row14"><td class="col0" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">T</td>
<td class="col1" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">163P</td>
<td class="col3" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">39.844.966</td>
<td class="col5" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">16,47%</td>
<td class="col6" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">0,25%</td>
<td class="col7" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">0,03%</td>
<td class="col8" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">33.233.302</td></tr><tr class="row15"><td class="col0" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">B</td>
<td class="col1" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">234B</td>
<td class="col3" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">48.065.788</td>
<td class="col5" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">12,79%</td>
<td class="col6" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">0,18%</td>
<td class="col7" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">0,02%</td>
<td class="col8" style="margin: 0px; vertical-align: top; border-style: solid; border-color: rgb(204, 204, 204);">41.882.487</td></tr></tbody></table><div>rRNA was detected using <a href="http://bioinfo.lifl.fr/RNA/sortmerna/">SortMeRNA</a>. Mitochondrial and plastid reads were identifiedy by mapping them to the Sorghum mitrocondrial genome (<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_008360">NC_008360.1</a>) and the sugarcane chloroplast genome (<a href="http://www.ncbi.nlm.nih.gov/nuccore/NC_005878">NC_005878.2</a>).</div><div> </div><div>In order to increase coverage of the gene space of Sugarcane, we decided to include a sample that resulted from pooling the whole leaf+1 from plants at one and two months of age, as well as the stalk and roots of the same plants. For this sample (DP3) we have 15.513.277 high quality, strand-specific, paired-end sequenced fragments.</div><div> </div><div>High quality reads were de novo assembled using <a href="https://github.com/trinityrnaseq/trinityrnaseq/wiki">Trinity</a> (Excep for reads coming from the individual 235, which has not been sequenced at that time). We mapped this preliminary assembly to the NCBI's nucleotide database, and analysed the result using <a href="http://ab.inf.uni-tuebingen.de/software/megan5/">MEGAN5</a>, which allowed us to detect some contaminants. In order to remove the contamination we mapped all reads (this time including individual 235) against the contaminants and excluded them. The unmmaped reads were used to make a new de novo Trinity assembly. The resulting 250.035 assembled transcripts were annotated with <a href="https://trinotate.github.io/">Trinotate</a>.</div><div> </div><div>The raw reads can be obtained from the SRA with accession numbers <a href="http://www.ncbi.nlm.nih.gov/bioproject/PRJNA244522">SRR1979656 to SRR1979669 and SRR1974519</a>. The assembled transcriptome was submitted to NCBI's TSA under accession number: <a href="http://www.ncbi.nlm.nih.gov/nuccore/GCZX00000000">GCZX00000000</a>.</div><div> </div><div>We have a public <a href="http://bce.bioetanol.cnpem.br/ctbeblast">BLAST server</a>, where you can search for your favorite genes against our sugarcane transcriptome.</div><div> </div><div>Below you can find our transcript assembly and annotation. Remember this is a strand-specific assembly, thus all trancripts are in the correct orientation. If you use this resourse, please do cite our paper <a href="http://www.ncbi.nlm.nih.gov/pubmed/26714767">Mattiello <em>et al.</em>, 2015</a>.</div><div> </div><h3><strong>Downloads</strong></h3><p>
</p>
<ol>
<li><a href="http://bce.bioetanol.cnpem.br/exchange/sugarcane/transcriptome/leaf_plus_one/SP803280_Transcriptome.fasta.bz2">Strand-specific transcript assembly</a></li>
<li><a href="http://bce.bioetanol.cnpem.br/exchange/sugarcane/transcriptome/leaf_plus_one/SP803280_Transcriptome.annotation.txt.bz2">Transcript annotation</a></li>
<li><a href="http://bce.bioetanol.cnpem.br/exchange/sugarcane/transcriptome/leaf_plus_one/SP803280_DeducedProteome.fasta.bz2">Deduced proteins</a></li>
<li><a href="http://bce.bioetanol.cnpem.br/exchange/sugarcane/transcriptome/leaf_plus_one/SP803280_Transcriptome.TAPs.txt.bz2">Identified Transcription Associated Proteins</a> (Transcription factors and other transcriptional regulator using the methods described in <a href="http://www.ncbi.nlm.nih.gov/pubmed/19858103">Perez-Rodriguez, et al., 2010</a>)</li>
<li><a href="http://bce.bioetanol.cnpem.br/exchange/sugarcane/transcriptome/leaf_plus_one/SP803280_Transcriptome.KEGG.txt.bz2">Identified KEEG metabolic pathways</a></li>
<li><a href="http://bce.bioetanol.cnpem.br/exchange/sugarcane/transcriptome/leaf_plus_one/OrthoMCL_Groups_LeafDev_mcl15.tbl.bz2">Orthologous gene groups</a> identified using OrthoMCL and an inflation value of 1.5 (SACC= <em>Saccharum</em> hybrid cultivar SP80-3280, OSAT= <em>Orysa sativa</em>, SBIC= <em>Sorghum bicolor</em>, SITA= <em>Setaria italica</em>, ZMAY= <em>Zea mays</em>)</li>
<li><a href="http://bce.bioetanol.cnpem.br/exchange/sugarcane/transcriptome/leaf_plus_one/AccessionNumbers.txt.bz2">Accession numbers for transcripts at NCBI</a></li>
</ol>
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