Articles
A MODEL PLANT GENOME RESOURCE AND COMPARATIVE GENOMICS
Article number
859_2
Pages
31 – 41
Language
English
Abstract
The goal of a novel model plant genomics resource database is to provide a community resource that allows researchers to build their research models by making use of data derived from one or more approaches, for example the forward and reverse genetics, comparative genomics, in silico predictions etc.
This resource can be built for a given plant species/genus or even for any plant taxonomic clade covering many species and tribes.
A database may house diverse types of data including annotated sequenced genomes of plant(s), individual sequence entries, markers, genetic maps, associated pathways, gene networks, phenotypes, quantitative trait loci (QTL) and the genetic diversity datasets that include genotype-phenotype associations.
To support queries across various data sets, as well as across other collaborative databases, a model plant genome database should strive to make extensive use of the five controlled vocabularies (ontologies): Trait Ontology (TO), Plant Ontology (PO), Environment Ontology (EO), Gene Ontology (GO), and the Taxonomy.
Users can query the database using various filters to find phenotypes, genes, QTLs, markers, maps, genomic landmarks, associated proteins, pathways and sequences.
Through such an effort, the database can foster discovery of candidate gene(s), regulatory elements, comparisons of genetic and genomic maps from plant models, phenotype features associated to mutant genes and mapped QTLs, gene functions and interating partners.
The ability to make connections across various data types presents a significant advance over the capabilities of previously existing resources.
With this view we will discuss the design and example queries using a well known plant genome database.
This resource can be built for a given plant species/genus or even for any plant taxonomic clade covering many species and tribes.
A database may house diverse types of data including annotated sequenced genomes of plant(s), individual sequence entries, markers, genetic maps, associated pathways, gene networks, phenotypes, quantitative trait loci (QTL) and the genetic diversity datasets that include genotype-phenotype associations.
To support queries across various data sets, as well as across other collaborative databases, a model plant genome database should strive to make extensive use of the five controlled vocabularies (ontologies): Trait Ontology (TO), Plant Ontology (PO), Environment Ontology (EO), Gene Ontology (GO), and the Taxonomy.
Users can query the database using various filters to find phenotypes, genes, QTLs, markers, maps, genomic landmarks, associated proteins, pathways and sequences.
Through such an effort, the database can foster discovery of candidate gene(s), regulatory elements, comparisons of genetic and genomic maps from plant models, phenotype features associated to mutant genes and mapped QTLs, gene functions and interating partners.
The ability to make connections across various data types presents a significant advance over the capabilities of previously existing resources.
With this view we will discuss the design and example queries using a well known plant genome database.
Authors
P. Jaiswal, P. Dharmawardhana, S. Naithani
Keywords
comparative genomics, plant genome, rice, Arabidopsis, apple, strawberry, QTL, pathway, ontology, comparative map
Online Articles (50)