Bioinformatics Support

Tomato Mitochondrial Genome

We built a result analysis pipeline and website to track the progress of the sequencing of the DNA of the tomato mitochondrion. This was done for the Argentinian National Agricultural Technology Institute (INTA), that was part of the The international sequence project of tomato genome (Solanum lycopersicum).

Goal

The mitochondrion is the organelle within the eukaryotic cell that is primarily concerned with the synthesis of ATP. Full comprehension of the mitochondrial genome structure is of fundamental importance to understanding genetics, evolutionary and biochemical processes that take place into this organelle in crop model species. In the international effort made to sequence the DNA of tomato (Solanum lycopersicum), the DNA of the mitochondrion was assigned to INTA (Argentinian National Agricultural Technology Institute) and they had to build a result analysis pipeline and create a website to track the progress of the project.

Solution

Several custom made Python and Bash scripts were developed to process data coming from the DNA sequencers (AB3730 and Solexa GA2x). The scripts handled from cleaning up reads up to contig assembling for submission to Genbank.

    Availability

    Tomato mitochondrial genome was published on mitochondrialgenome.org website and resulting sequences are available on NCBI.

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