EumicrobeDB : Oomycetes Genomics

DatabaseArup Ghosh

NP- 02Working under the supervision of Dr. Sucheta Tripathy

Computational Genomics Lab, IICB

ContentsIntroductionLife cycleObjectiveEumicrobeDBTools DevelopedFuture WorkSummaryReference

Introduction

Oömycetes ("commonly known as water molds") is a group of organisms related to diatoms and brown algae. Many are important pathogens of plants, causing several billions of dollars in crop loss each year.The oomycetes are also often referred to as water molds, although the water-preferring nature which led to that name is not true of most species, which are terrestrial pathogens. Recently, the complete genome sequence has been determined for several members of this group and their relatives.

Photos of Oomycetes

Objective of Oomycete Genome Study

Oomycetes evolved the ability to infect plants and animals independently of other eukaryotic microbes, and they have probably developed unique mechanisms of pathogenicity. With the availability of a respectable molecular toolbox and a multitude of gene sequences, significant progress has been made in understanding the molecular basis of infection by oomycetes. With the advancement in genomics study of Oomycetes we can determine the cause of pathogenesis and reduce the damage caused by this organisms.

Global Crop Loss Statistics

EumicrobeDB

EumicrobeDB integrates whole genome sequence and annotation and also includes experimental and environmental isolate sequence data. The database includes comparative genomics, analysis of gene expression, and supplemental bioinformatics analyses and a web interface for data-mining.The web interface also allows users to upload and visualize genome feature files.

Genome Browser Page

Synteny Viewer• The term ‘Synteny’ (or syntenic) refers to gene loci on the same

chromosome regardless of whether or not they are genetically linked by classic linkage analysis.

• ‘Synteny’ means ‘same thread’ (or ribbon), a state of being together in location, as synchrony would be together in time.

• Nowadays the term ‘Synteny’ is often used to refer to gene loci in different organisms located on a chromosomal region of common evolutionary ancestry.

Continued..

Synetny between P.sojae V1 scaffold_1 and P.sojae V5 Scaffold_1

Synetny between P.sojae V4 scaffold_1 and P.sojae V5 Scaffold_1

Query Page

1. Go to query page.

3. Select Organism name from the drop down box. Default - Albugo laibachii Nc14

2.

4. Type annotation in the text box.

5. Click Search.

Query search example with Annotation

Search Results

Future Work

As new genome sequences of organisms belonging to this group are getting available, we are including them in EumicrobeDB database for comparative genomics analysis.We are also focused on improving the platform with new comparative genomics tools, algorithms to provide better visualization of genome data.

Conclusion

With the advancement of plant pathogen genome study we can solve crop loss in developing countries like India without much investment on harmful pesticides. Furthermore comparative genomics can provide us information about commercially important secondary metabolites from different organisms.

Reference

• Molecular Genetics of Pathogenic Oomycetes, Sophien Kamoun, Eukaryotic Cell April 2003 vol. 2 no. 2 191-199.

• Dynamics and Innovations within Oomycete Genomes, Howard S. Judelson, Eukaryotic Cell November 2012 vol. 11 no. 11 1304-1312.

• Insights from Sequencing Fungal and Oomycete Genomes, Darren M. Soanes, Plant Cell. 2007 Nov; 19(11): 3318–3326.

• Oomycete Transcriptomics Database, Tripathy et al. BMC Genomics2012,13:303.

• Common infection strategies of pathogenic eukaryotes, Kasturi Haldar, Sophien Kamoun,Nature Publishing Group, DECEMBER 2006 , VOLUME 4.