Articles
DATA MINING OF CITRUS EXPRESSION SEQUENCE DATA SETS AND APPLICATION FOR FUNCTIONAL GENOMIC STUDY
Article number
892_2
Pages
29 – 36
Language
English
Abstract
The advent of genome era on citrus is expected to open the door to solve a variety of complex genetic problems.
Sequences obtained from expressed genes give not only a direct insight into understanding the gene function but also provide valuable information for molecular analysis.
Sequence assembly to reduce redundancy among EST sequences estimated 98,869 contigs and singletons from a total of 564,887 EST sequences obtained from more than 10 citrus cultivars.
A survey identified 143,660 repeat sequence regions that ranged from 2 to 477 bp in motif length.
Alignment analysis of the contigs against all of the EST sequences identified regions exhibiting indels or nucleotide mismatches.
Functional evaluation classified the gene ontology of 54.5-65.6% of the contigs and the biological pathway from the KEGG database for 16.4% of the contigs.
A comparison of homology against cDNA sequences from Arabidopsis classified 22.1% of the contigs to a gene family, and 4.4% of the genes to a transcriptional factor gene.
From these observations, we designed an oligonucleotide microarray for gene expression analysis using a set of 43,798 non-redundant probes.
All resources accumulated in this study were collated in a comprehensive database system.
The microarray system in conjunction with the database will help to facilitate functional genomic study of citrus through transcriptome analysis.
Sequences obtained from expressed genes give not only a direct insight into understanding the gene function but also provide valuable information for molecular analysis.
Sequence assembly to reduce redundancy among EST sequences estimated 98,869 contigs and singletons from a total of 564,887 EST sequences obtained from more than 10 citrus cultivars.
A survey identified 143,660 repeat sequence regions that ranged from 2 to 477 bp in motif length.
Alignment analysis of the contigs against all of the EST sequences identified regions exhibiting indels or nucleotide mismatches.
Functional evaluation classified the gene ontology of 54.5-65.6% of the contigs and the biological pathway from the KEGG database for 16.4% of the contigs.
A comparison of homology against cDNA sequences from Arabidopsis classified 22.1% of the contigs to a gene family, and 4.4% of the genes to a transcriptional factor gene.
From these observations, we designed an oligonucleotide microarray for gene expression analysis using a set of 43,798 non-redundant probes.
All resources accumulated in this study were collated in a comprehensive database system.
The microarray system in conjunction with the database will help to facilitate functional genomic study of citrus through transcriptome analysis.
Authors
T. Shimizu, H. Fujii, N. Kotoda, K. Yano, T. Endo
Keywords
Expressed Sequence Tag (EST), annotation, polymorphism, microarray, data mining, SSR, SNP, gene ontology, database
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