The annotation software will be based on the one being used in the Xanthomonas axonopodis project. Whose bioinformatics is also carried partially by LBI. The annotation environment was developed internally by LBI and is composed basically of software that interfaces typical annotation oriented programs (e.g. BLAST). The annotation Web interface was also developed by LBI. All annotation data are managed by MySQL, a relational database manager system (DBMS).
Many different shotgun libraries were prepared and distributed for sequencing. About 690 plates of 96 clones each have been distributed to the Sls and Sus for DNA preparation and sequencing. A cosmid library was constructed and a total of 2,717 cosmid ends were sequenced.
The submitted shotgun sequences are only accepted as 96 sample plates, with at least 65%of the sequences with 400 bases with phred quality above 20. When the plates did not meet this criterion they were sequenced again.
Accepted reads deposited (28/02/01): We have a total of 84,167 accepted reads covering about 19 fold of the genome.
We have achieved around 19-fold coverage of the genome with the shotgun sequences alone. The cosmid library end sequencing was done to help in the assembly of the genome. At this point we have identified 17 gaps of which 14 should be closed by cosmid sequencing. We are going to use the PCR strategy to address the other three gaps. The cosmids to close the gaps were distributed in the last week of February to the SLs interested.
The genome assembly, as mentioned above, is done using Phil Green’s phrap. At this point of the project, assemblies are done only to solve genome closure problems (varying stringency and including complete cosmid and plasmid sequences). Scaffolding is done by a program developed at LBI. Genome closure is done based on cosmid and plasmid ends anchoring and ORF colinearity with Xylella fastidiosa-CVC genes when it applied.
While the sequencing to close the gaps is going on, the genome annotation interface is being built in order to undertake detailed comparison to the CVC strain.