Team:Evry/Biology/CellCharacterization/GenomeAssembly

From 2014.igem.org

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<h3>DNA extraction</h3>
<h3>DNA extraction</h3>
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<h3>Assembly Strategy</h3>
<h3>Assembly Strategy</h3>
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<h4>software used</h4>
<h4>software used</h4>
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<h4>Velvet for de novo Assembly</h4>
<h4>Velvet for de novo Assembly</h4>
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best with kmer length 97contigs: 275
best with kmer length 97contigs: 275
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<h4>Contigs quality</h4>
<h4>Contigs quality</h4>
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<h3>Annotation</h3>
<h3>Annotation</h3>
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<h4>Prokka tools for annotation</h4>
<h4>Prokka tools for annotation</h4>
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organism: Pseudovibrio species strain  
organism: Pseudovibrio species strain  
contigs: 275
contigs: 275
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tmRNA: 1
tmRNA: 1
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<h4>Proteome Comparisons with FOBEG1</h4>
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<h4>Annotation</h4>
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<h4>Annotation</h4>
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<h4>Annotation</h4>
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Revision as of 15:09, 14 October 2014

De novo Genome assembly




DNA extraction


Assembly Strategy


software used


Velvet for de novo Assembly


best with kmer length 97contigs: 275

Contigs quality


Annotation


Prokka tools for annotation


organism: Pseudovibrio species strain contigs: 275 bases: 6103562 CDS: 5427 tRNA: 62 tmRNA: 1 talk about output

Proteome Comparisons with FOBEG1


Annotation


Annotation


Annotation


With the help of the 'Molecules of defence and communication in the microbial ecosystems' team of the National museum of natural history of Paris (their web page here), we succeed to cultivate our bacteria Pseudovibrio denitrificans in two medium, the marine broth (MB) and the minimal medium M9 added by 3% of NaCl.

Table1: Composition of used media, marine broth and M9+3% NaCl.
text to print if image not found

Because of the opaqueness of the marine broth, it's impossible to obtain reliable data of the growth of the bacteria. Thus, the growth curve that we have made, has been made in M9+3%NaCl 1X, with the TECAN infiniteM200.

Curve TECAN
Figure1: Curve of growth in liquid M9+3%NaCl 1X.

The marine broth is more complete than the M9+3%NaCl, even if we have adjusted the salinity. As we can see in the Table2, Pseudovibrio denitrificans grows better on MB media. The number of colony is higher, and they are significantly bigger (Figure2). Moreover, the growth is faster.

Table+Photos of MB 1X and M9+3%NaCl 1X plates
Figure2: Number of CFU and photos of MB 1X and M9+3%NaCl 1X plates.

In the aim to know if we can transfer Pseudovibrio denitrificans from a media, to the other one, we have made some tests and calculate a ratio of survivability. We have made two pre-cultures of Pseudovibrio denitrificans in MB 1X and M9+3%NaCl 1X, and after a culture overnight, we sowed them on plates of MB 1X and M9+3%NaCl 1X (Figure3).

Table+Photos of ratio of survivability
Figure3: Tests of survivability, table of ratio and photos.

Pseudovibrio denitrificans can survive even if we tranfer them from a media to the other one. But we can see that even cells come from a pre-culture of M9+3%NaCl, they grow better and faster on MB plates. Moreover, even if they come from a MB pre-culture, they don't grow very well on M9+3%NaCl plates.