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Genomics

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

Genome-wide Association Studies-GWAS

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...

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Updated: May 27, 2026

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

The Comprehensive Phytopathogen Genomics Resource: a web-based resource for data-mining plant pathogen genomes.

John P Hamilton¹, Eric C Neeno-Eckwall, Bishwo N Adhikari

¹Department of Plant Biology, 178 Wilson Lane, Michigan State University, East Lansing, MI 48824, USA.

Database : the Journal of Biological Databases and Curation

|November 29, 2011

Summary

The Comprehensive Phytopathogen Genomics Resource (CPGR) offers a web portal with genomic and transcriptomic data for 806 plant pathogens. This resource aids plant pathologists and diagnosticians in analyzing pathogen genomes and developing diagnostic markers.

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Area of Science:

Plant Pathology
Genomics
Bioinformatics

Background:

Plant pathogens pose significant threats to global food security.
Genomic and transcriptomic data are crucial for understanding pathogen biology and developing control strategies.
Existing resources for accessing and analyzing phytopathogen data are fragmented.

Purpose of the Study:

To develop a centralized, web-based resource for accessing and analyzing phytopathogen genomic and transcriptomic data.
To provide tools for searching, analyzing, and mining pathogen genome sequences.
To facilitate the development of diagnostic markers for plant pathogens.

Main Methods:

Integrated data from GenBank and the A Systematic Annotation Package (ASAP) database.
Annotated genome sequences for 74 bacterial, fungal, and oomycete pathogens.
Assembled and annotated transcriptomes from 82 eukaryotic pathogens using EST data.
Compiled a Plant Pathogen Ribosomal DNA (rDNA) database with over 131,000 sequences.

Main Results:

The Comprehensive Phytopathogen Genomics Resource (CPGR) provides access to genome and transcriptome data for 806 plant pathogens.
Includes tools for searching and analyzing annotated genomes of 74 pathogens.
Offers curated gene lists for bacterial pathogenicity and avirulence.
Provides tools for data mining and candidate diagnostic marker development.

Conclusions:

CPGR serves as a valuable, integrated resource for plant pathologists and diagnosticians.
The resource enhances the study of phytopathogen genomics and transcriptomics.
CPGR supports the development of novel diagnostic tools for plant disease management.