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Team:Cambridge-JIC/Marchantia/Codon
From 2014.igem.org
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<h1>Codon Optimisation</h1> | <h1>Codon Optimisation</h1> | ||
| - | <font color="black" style="BACKGROUND-COLOR: #E6E6E6">A | + | <font color="black" style="BACKGROUND-COLOR: #E6E6E6">A codon table for <Em>Marchantia polymorpha</Em> |
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<h2 class="section-heading">Method</h2> | <h2 class="section-heading">Method</h2> | ||
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<p> | <p> | ||
| - | Our dataset was made of large gap read mapping transcripts obtained by mRNA sequencing conducted by the Haseloff Lab on the | + | Our dataset was made of large gap read mapping transcripts obtained by mRNA sequencing conducted by the Haseloff Lab on the <em>M. polymorpha</em> Cam strain. Open Reading Frame (ORF) and Coding Sequence (CDS) predictions were made using the CLC bio Transcript Discovery plugin<a href="#Footnote1">[1]</a>. |
</p> | </p> | ||
<p> | <p> | ||
| - | We used ran blastx on our data <a href="#Footnote2">[2]</a> to verify the validity of the predicted ORFs and to compare the sequences with the proteins present in | + | We used ran blastx on our data <a href="#Footnote2">[2]</a> to verify the validity of the predicted ORFs and to compare the sequences with the proteins present in <em>Arabidopsis</em>. A list of candidate genes was compiled from the results and this list was used to calculate a frequency table of codon usage for <em>M. polymorpha</em>. |
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<h2 class="section-heading">Results and Discussion</h2> | <h2 class="section-heading">Results and Discussion</h2> | ||
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| - | <p>The number of Open Reading Frames (ORFs) resulting from our initial predictions totalled 99 000, which seemed too large to be realistic, and half of these were only 100 amino acids (100 aa) long. By filtering the dataset using a threshold of 300 aa for candidate genes we obtained a | + | <p>The number of Open Reading Frames (ORFs) resulting from our initial predictions totalled 99 000, which seemed too large to be realistic, and half of these were only 100 amino acids (100 aa) long. By filtering the dataset using a threshold of 300 aa for candidate genes we obtained a distribution of lengths that seemed reasonable. |
| - | + | <figure> | |
| + | <img src="https://static.igem.org/mediawiki/2014/9/93/Cambridge-JIC_Gene_Lengths.png" width = "550px"> | ||
| + | <figcaption>Figure 2: A histogram of the lengths of predicted genes in <i>m. polymorpha</i></figcaption> | ||
| + | </figure> | ||
| + | <br> | ||
</p> | </p> | ||
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| - | In the blastx output, the longest complete sequence match was 40%. This is small as expected given the phylogenetic distance between </i> | + | In the blastx output, the longest complete sequence match was 40%. This is small as expected given the phylogenetic distance between </i>M.polymorpha</i> and <i>A. thaliana</i> <a href="#Footnote3">[3]</a><a href="#Footnote4">[4]</a>. |
</p> | </p> | ||
<p> | <p> | ||
| - | The Codon Usage table we obtained for <i> | + | The Codon Usage table we obtained for <i> M. polymorpha</i> is not strikingly similar to that of <i>A. thaliana</i>, as expected from the 400 million years of evolutionary divergence between them <a href="#Footnote5">[5]</a>. |
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<h4>References</h4> | <h4>References</h4> | ||
<p id="Footnote1">1. Qiagen, CLC bio Transcript Discovery ®, <a href="http://www.clcbio.com/clc-plugin/transcript-discovery/#description">http://www.clcbio.com/clc-plugin/transcript-discovery/#description</a> <a href="#">back to top</a></p> | <p id="Footnote1">1. Qiagen, CLC bio Transcript Discovery ®, <a href="http://www.clcbio.com/clc-plugin/transcript-discovery/#description">http://www.clcbio.com/clc-plugin/transcript-discovery/#description</a> <a href="#">back to top</a></p> | ||
| - | <p id="Footnote2">2. Turmel M, Otis C and Lemieux C. 2003. <i>The Mitochondrial Genome of Chara vulgaris: Insights into the Mitochondrial DNA Architecture of the Last Common Ancestor of Green Algae and Land Plants.</i> The Plant Cell 15(8), pp. 1888-1903. <a href="#">back to top</a></p> | + | <p id="Footnote2">2. NCBI Blast ®, http://blast.ncbi.nlm.nih.gov/Blast.cgi <a href="#">back to top</a></p> |
| - | <p id=" | + | <p id="Footnote3">3. Turmel M, Otis C and Lemieux C. 2003. <i>The Mitochondrial Genome of Chara vulgaris: Insights into the Mitochondrial DNA Architecture of the Last Common Ancestor of Green Algae and Land Plants.</i> The Plant Cell 15(8), pp. 1888-1903. <a href="#">back to top</a></p> |
| - | + | <p id="Footnote4">4. Cantarel BL, Morrison HG, Pearson W. 2006. Exploring the Relationship between Sequence Similarity and Accurate Phylogenetic Trees. Molecular Biology and Evolution 23(11), pp. 2090-2100. <a href="#">back to top</a></p> | |
<p id="Footnote5">5. Wellman CH, Osterloff PL, Mohiuddin U. 2003. <i>Fragments of the earliest land plants.</i> Nature 425, pp. 282-285. <a href="#">back to top</a></p> | <p id="Footnote5">5. Wellman CH, Osterloff PL, Mohiuddin U. 2003. <i>Fragments of the earliest land plants.</i> Nature 425, pp. 282-285. <a href="#">back to top</a></p> | ||
Latest revision as of 01:23, 18 October 2014
Method
Our dataset was made of large gap read mapping transcripts obtained by mRNA sequencing conducted by the Haseloff Lab on the M. polymorpha Cam strain. Open Reading Frame (ORF) and Coding Sequence (CDS) predictions were made using the CLC bio Transcript Discovery plugin[1].
We used ran blastx on our data [2] to verify the validity of the predicted ORFs and to compare the sequences with the proteins present in Arabidopsis. A list of candidate genes was compiled from the results and this list was used to calculate a frequency table of codon usage for M. polymorpha.
Results and Discussion
The number of Open Reading Frames (ORFs) resulting from our initial predictions totalled 99 000, which seemed too large to be realistic, and half of these were only 100 amino acids (100 aa) long. By filtering the dataset using a threshold of 300 aa for candidate genes we obtained a distribution of lengths that seemed reasonable.
In the blastx output, the longest complete sequence match was 40%. This is small as expected given the phylogenetic distance between M.polymorpha and A. thaliana [3][4].
The Codon Usage table we obtained for M. polymorpha is not strikingly similar to that of A. thaliana, as expected from the 400 million years of evolutionary divergence between them [5].
However, there is a similarity in the slight preference for C over other bases at the end of codons and that for G-p-C sites, as can be seen in the codon table.
References
1. Qiagen, CLC bio Transcript Discovery ®, http://www.clcbio.com/clc-plugin/transcript-discovery/#description back to top
2. NCBI Blast ®, http://blast.ncbi.nlm.nih.gov/Blast.cgi back to top
3. Turmel M, Otis C and Lemieux C. 2003. The Mitochondrial Genome of Chara vulgaris: Insights into the Mitochondrial DNA Architecture of the Last Common Ancestor of Green Algae and Land Plants. The Plant Cell 15(8), pp. 1888-1903. back to top
4. Cantarel BL, Morrison HG, Pearson W. 2006. Exploring the Relationship between Sequence Similarity and Accurate Phylogenetic Trees. Molecular Biology and Evolution 23(11), pp. 2090-2100. back to top
5. Wellman CH, Osterloff PL, Mohiuddin U. 2003. Fragments of the earliest land plants. Nature 425, pp. 282-285. back to top
