Research Highlights -2010
Secretome analysis of P. capsici and R. similis was carried out. On exploring the ESTs of R. similis, 214 secretory proteins were identified and their functional annotation was carried out. About 45% of these secretory proteins showed similarity to nematodes. The mode of interaction of Glucanase Inhibitor Protein (GIP) from P. capsici with plant endo- β -1, 3-glucanases was studied through structural and docking studies.
New databases on ginger and turmeric germplasm accessions were developed and hosted on the Institute server. The scope of Phytolib, the literature database, was further widened to include articles on Ralstonia and Fusarium. PhytoPD, a repository of Polymerase Chain Reaction primer sets, useful for the identification and detection of Phytophthora species, was developed and uploaded. It includes all the universal primers and species-specific primers for more than 30 species of Phytophthora published in literature.
National consultative meet
Hortinformatics 2010, the National consultative meet on Bioinformatics in Horticulture was organized 11-12 October 2010. About 90 delegates from more than 30 research institutes and universities participated in the event. Sixteen invited talks and 23 posters were presented by various scientists in four technical sessions during the meet. Read More..
Research Highlights -2011
A new database, Phytophthora Genome Database (http://220.127.116.11/genomedb/) based on Phytophthora whole genome sequencing and annotation was developed. The database provides access to primary structure of the Phytophthora genome including genome sequence, number of genes, CDS, SNPs, inDels. nucleotide composition, intron-exon structure, start and stop codon, intron lengths, alternative splicing and untranslated regions (UTRs) to the research community. GenomeView, a nextgeneration stand-alone genome browser and editor developed at Broad Institute is used as the genome browser.
Another database on Radopholus genus called RADOBASE (http://www.spices.res.in/radobase) was developed and launched. This database contains comprehensive information on sequence and morphological details of 22 Radopholus species.
Research Highlights -2012
Phytophthora genome sequencing and
The complete genome of two Phytophthora
isolates (05-06 and 98-93) infecting black pepper
was sequenced using Illumina/Roche 454 platforms.
The cross-platform sequence data was de
novo assembled and annotated structurally and
functionally to curate all possible gene by gene
information. Whole genome alignment with the
reference genome revealed that 05-06 is 95.35%
similar while 98-93 is 87.90% similar to the reference
genome. Conserved domain search to identify
the protein families present in exonic regions
of whole genome sequences of the two different
isolates of Phytophthora sp. infecting black pepper
(05-06 and 98-93) has also been carried out
along with Blast2GO analysis.
Species and evolutionary tree estimation
of sequenced Phytophthora isolates
The evolutionary history of the Phytophthora
genomes sequenced was traced out using information from multilocus gene trees for four
mitochondrial and 10 nuclear markers from six
closely related species of Clade 2. The concatenation-
based multispecies coalescent approach
using Bayesian, maximum parsimony and maximum
likelihood methods was able to estimate
a moderately supported species tree showing a
close relationship among 05-06 with P. capsici
and 98-93 with P. tropicalis.
New databases developed
• Plant Virus Database: It provides a central
source of information about all the plant viruses
• Phytophthora Genome Database: Sequence
information of hybrid assemblies of two isolates
of Phytophthora infecting black pepper
was incorporated to the existing database
E-procurement module launched
An e-procurement module has been developed
and enabled after intensive testing making
the procurement of assets more transparent and
speedy. Vendor registration and online tender
submission have been initiated.