- Bioinformatic approach to aid gene identification and characterisation in
- Evaluate and integrate the accuracy of Arabidopsis database
Arabidopsis thaliana is a model plant for research and has been used wisely to study many aspects of plant biology. There is significant amount of information about this plant in the database, such as fully sequenced and annotated genomic sequence, extensive expressional data and functional characterisation data. This project aims at using such information to aid gene identification.
The project will focus on a specific region (between AGIs 18,500,000 & 19,800,000) on Chromosome V, where a gene involved in root development has been mapped.
The project has three types of objectives they are:
1) To identify all possible genes in the region and most importantly to check whether there are genes mis- or incorrectly-annotated using sequence analyses
2) To establish the expression patterns and regulations of the genes using available microarray data.
3) And literature search of evidence for the functional properties of the genes of their homologues. The analyses will help to build an integrated picture which shows the genes in the region together with their expression profiles and functional properties. Such information can be used to guide our experimental strategy towards the identification of the interested gene and will provide a case-study for using bioinformatics approach to aid traditional genetic approach in gene identification.
Biological Background of Arabidopsis thaliana
Arabidopsis thaliana is a unique among plant model organisms due to its short life
Cycle (Heh and Bülow 2008 ) and in having a small genome, excellent physical and genetic maps, and some amount of repetitive DNA(Lin, Kaul et al. 1999).
Arabidopsis thaliana is the first plant for which the complete genome has been sequenced. The 120 megabase genome of Arabidopsis is formed into five chromosomes and consists of an approximate 20,000 genes(Sato, Kotani et al. 1997) . In this project we will focus on a specific region on chromosome V, where a gene involved in root development has been mapped.Chromosome V is 26 mega bases long and it also the second largest regions of genome(Tabata, Kaneko et al. 2000). The entire genome of chromosome 5, excluding the centromeric and telomeric regions, was covered up by two large contigs 11.6 Mb and 14.2 Mb long separated by the centromeric region(Kotani, Sato et al. 1997).The 5,874 genes encoded on chromosome 5 reveal several new functions in plant, and the patterns of gene organization provides insights into the mechanism and extent of genome evolution in plants(Tabata, Kaneko et al. 2000).
Arabidopsis thaliana is a member of the mustard family Cruciferae or Brassicaceae with a natural distribution all around Europe, Asia, and North. Many different ecotypes have been collected from natural...