What is Phytophthora?
Phytophthora is an oomycete plant pathogen infecting a wide range of hosts such as eggplant, cucumber, watermelon, pumpkin, squash, cocoa, coconut, arecanut, cardamom, black pepper, rubber etc. Oomycetes are a group of organisms related to diatoms and brown algae. These plant pathogens cause crop loss to the tune of several crores of rupees every year. Whole genome sequencing helps in understanding of the molecular basis of pathogenicity and host specificity by assisting the isolation of novel virulence and avirulence genes, as well as by helping to identify targets for chemical control.
About sequencing the project
The study of oomycetes has reached new height with the completion of the genome sequence drafts of three Phytophthora species viz. P. infestans, P. ramorum and P. sojae has now been completed and is in progress for five more species such as P. andina, P. capsici, P. ipomoeae, P. mirabilis, and P. phaseoli. The Indian initiative of sequencing Phytophthora was taken up as part of the Outreach Project on Phytophthora, Fusarium, and Ralstonia, funded by Indian Council of Agricultural Research (ICAR). For this, a native isolate of Phytophthora, (Is. No. 98-93) infecting black pepper was completely sequenced at The centre for Genomic Application(TCGA) using next generation sequencing platform, Illumina - Solexa GA II. The sequence data was assembled by taking Joint Genome Institute’s P. capsici as reference genome with ~ 87.53 % coverage. A summary of results obtained is given in the table.
| Total number of base pairs | 63.8 Mb |
| Total number of reads | Illumina Platform 20287313 reads *101 = 2049018613 bp each |
| GS FLX+ Platform: 373988587 bp & 161526737 bp |
|
| GC % | 54% |
| Total number of Contigs (Hybrid Assembly) | 32044 |
| Total number of Bases | 47280344 |
| Largest Contig Length | 42775 bp |
| Smallest Contig Length | 200 bp |
| Average Contig Length | 1475.42 |
| Total number of SSRs | 1344 |
| Total number of SSR containg Sequence | 1214 |
| Total number of Gene count | 16356 |
| Total number of exon | 38947 |
| Total number of CDS | 16356 |
| Predicted proteins | 7154 |
98-93 Isolate Summary
| Total number of base pairs | 46.1 Mb |
| Total number of reads | Illumina Platform 20965441 reads * 101 = 2117509541 bp each |
| GS FLX+ Platform: 331426471 bp & 194705193 bp |
|
| GC % | 52% |
| Total number of Contigs (Hybrid Assembly) | 9831 |
| Total number of Bases | 41183427 bp |
| Largest Contig Length | 180159 bp |
| Smallest Contig Length | 200 bp |
| Average Contig Length | 2407.402 |
| Total number of SSRs | 2496 |
| Total number of SSR containg Sequence | 2401 |
| Total number of Gene count | 13068 |
| Total number of exon | 33813 |
| Total number of CDS | 13068 |
| Predicted proteins | 9344 |
The sequence data are archived in this database. 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 research community. GenomeView, a next-generation stand-alone genome browser and editor developed at Broad Institute is used as the genome browser.
Future
The next challenge is to annotate the genome to assign putative functions to the genes. It provides interactive visualization of sequences, annotation, multiple alignments, syntenic mappings, short read alignments and more. Structural annotation of Phytophthora genome is completed with an approximate of 19805 genes. Functional annotation is being carried out, which requires additional financial and human resources. We aim to provide a genome database to access primary structure of the Phytophthora genome including genome sequence, number of genes, CDS, SNP’s, InDels, Nucleotide composition, intron-exon structure, start and stop codon, intron lengths, alternative splicing and untranslated regions (UTRs) to research community.