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EumicrobeDB : Oomycetes
Genomics Database
Arup Ghosh
NP- 02
Working under the supervision of Dr. Sucheta Tripathy
Computational Genomics Lab, IICB
Contents
Introduction
Life cycle
Objective
EumicrobeDB
Tools Developed
Future Work
Summary
Reference
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.
Eumicrobedb - Oomycetes Genomics Database

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Eumicrobedb - Oomycetes Genomics Database

  • 1. EumicrobeDB : Oomycetes Genomics Database Arup Ghosh NP- 02 Working under the supervision of Dr. Sucheta Tripathy Computational Genomics Lab, IICB
  • 3. 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.
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  • 6. 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.
  • 7. Global Crop Loss Statistics
  • 8. 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.
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  • 11. 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..
  • 12. 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
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  • 15. 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
  • 17. 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.
  • 18. 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.
  • 19. 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.