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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.

Phytophthora Genome Sequencing: Summary Table

05-06 Isolate 98-93 Isolate
Total number of base pairs 63.8 Mb 46.1 Mb
Total number of reads Illumina Platform
20287313 reads *101 = 2049018613 bp each
Illumina Platform
20965441 reads * 101 = 2117509541 bp each
GS FLX+ Platform:
373988587 bp & 161526737 bp
GS FLX+ Platform:
331426471 bp & 194705193 bp
GC % 54%
Total number of Contigs (Hybrid Assembly) 32044
Total number of Bases 47280344
41183427 bp
Largest Contig Length 42775 bp
180159 bp
Smallest Contig Length 200 bp
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