PeanutMap: an online genome database for comparative molecular maps of peanut
Arun M Jesubatham1, Mark D Burow
1Department of Computer Science, Texas Tech University, Lubbock, TX 79409, USA. arunmoses99@yahoo.com
BMC Bioinformatics
|August 15, 2006
Summary
A new database, PeanutMap, centralizes peanut genetic linkage maps for improved varietal development and comparative genomics. This resource facilitates cross-species comparisons, aiding legume research.
Area of Science:
- Genomics
- Bioinformatics
- Plant Science
Background:
- Molecular maps are crucial for plant varietal development and comparative genomics.
- Databases for linkage map data are lacking for many species, including peanut.
- Cultivated peanut is a disomic tetraploid, necessitating specialized comparative mapping tools.
Purpose of the Study:
- To develop a centralized, web-based database for peanut genetic linkage maps.
- To facilitate the comparison of multiple peanut maps and linkage groups.
- To enable cross-species comparisons within the Legume Information System.
Main Methods:
- Developed PeanutMap, a web-based interface for visualizing and comparing peanut linkage maps.
- Integrated data from existing peanut genome and phenotypic trait map sets.
- Incorporated PeanutMap data into the Legume Information System for broader accessibility.
Main Results:
- PeanutMap allows viewing and comparison of multiple linkage maps based on marker or trait correspondences.
- The database enables comparison of linkage groups across different map sets and research projects.
- Peanut map data is now available for cross-species comparisons within the Legume Information System.
Conclusions:
- PeanutMap enhances the utility of existing peanut genetic data.
- The database is expected to grow with ongoing SSR-based map development and legume comparative mapping efforts.
- Development of comparative analysis tools will further optimize the use of this valuable resource.
More Related Videos
Related Concept Videos
02:54Evolutionary Relationships through Genome Comparisons
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
02:16Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
02:47Protein Families
Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key locations, protein...
03:36Genome Annotation and Assembly
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.