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Briefings in Bioinformatics Advance Access originally published online on August 31, 2009
Briefings in Bioinformatics 2009 10(6):619-630; doi:10.1093/bib/bbp037
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© The Author 2009. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

This article appears in the following Briefings in Bioinformatics issue: Special Issue: Plant Genomics [View the issue table of contents]

Improved criteria and comparative genomics tool provide new insights into grass paleogenomics

Jerome Salse, Michael Abrouk, Florent Murat, Umar Masood Quraishi and Catherine Feuillet

Corresponding author. Jerome Salse, INRA/Université Blaise Pascal UMR 1095, Génétique, Diversité et Ecophysiologie des Céréales, Domaine de Crouelle, 234 avenue du Brézet, 63100 Clermont-Ferrand, France. Tel: +33-4-73-62-43-80; Fax: +33-4-73-62-44-53; E-mail: jsalse{at}clermont.inra.fr

In the past decade, a number of bioinformatics tools have been developed to perform comparative genomics studies in plants and animals. However, most of the publicly available and user friendly tools lack common standards for the identification of robust orthologous relationships between genomes leading non-specialists to often over interpret the results of large scale comparative sequence analyses. Recently, we have established a number of improved parameters and tools to define significant relationships between genomes as a basis to develop paleogenomics studies in grasses. Here, we describe our approaches and propose the development of community-based standards that can be used in comparative genomic studies to (i) identify robust sets of orthologous gene pairs, (ii) derive complete sets of chromosome to chromosome relationships within and between genomes and (iii) model common paleo-ancestor genome structures. The rice and sorghum genome sequences are used to exemplify step-by-step a methodology that should allow users to perform accurate comparative genome analyses in their favourite species. Finally, we describe two applications for accurate gene annotation and synteny-based cloning of agronomically important traits.

Keywords: cereals, synteny, paleogenomics, evolution

Submitted: May 24, 2009. Received (in revised form): July 31, 2009.


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