Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Analysis Of Expressed Sequence Tags Of Brassica rapa

Myung-Ho Lim¹ , Yoonkang Hur² , Jin-A Kim¹ , Ji-Young Lee¹ , Yang-Sun Park¹ , Beom-Soon Choi¹ , Young-Joo Seol¹ , Jungsun Kim¹ , Mina Jin¹ , Ki-Byung Lim¹ , Tae-Jin Yang¹ , Ho-Il Kim¹ , Chae Oh Lim³ , Young-Yoon Chung⁴ , Baek-Hie Nahm⁵ , Beom-Seok Park¹

¹  Brassica Genomics Team, National Institute of Agricultural Biotechnology (NIAB), Suwon 441-707, Korea

²  Genome Research Center, Chungnam National University, Daejon 305-764, Korea

³  Environmental Biotechnology National Core Research Center, Gyeongsang University, Jinju, Korea

⁴  School of life Science & Biotechnology, Korea University, Seoul 136-701, Korea

⁵  GreenGene Bio Tech Inc., Myungji University, Youngin 449-728, Korea

A set of 100,000 EST sequences was analyzed from 20 different cDNA libraries of B. rapa (ssp. peckinensis) cv. Chiifu. Tissues and organs in diverse developmental stages, tissues treated with NaCl, and cold, and developing calli on the regeneration medium were used for the cDNA library constructions. These ESTs were clustered and assembled using megablast-Cap3 and produced a set of 12,298 tentative contigs and 11,576 singleton sequences. This set of 23,874 unigenes have an un-biased collection of ~50% of Brassica genes (ca. 45,000 genes) and covers ~75% of the CDS of Arabidopsis genomes. About 90% and 82% of Brassica unigenes have matching counter-part with Arabidopsis and rice, respectively in the criteria of E-30 (blastx). From the blastn (E-08) analysis, genes of B. rapa showed ~84%, ~93% and ~95% sequence identity with Arabidopsis, B. oleracea and B. napus, respectively. In-silico localization of Brassica unigenes onto the Arabidopsis chromosomes resulted in 23.3%, 13.1%, 18.4%, 13.9%, and 20.1% of localized genes onto the chr1, 2, 3, 4, and 5 of Arabidopsis, respectively. When ESTs from five different tissues were comparatively allocated onto the chromosomes of Arabidopsis, there were significant numbers of locations on the chromosome that shows high-level expression of genes with tissue(s)-specificity though this should be confirmed by the in-vitro experiment. In this talk, we'll present results of EST analysis and expressions profiles of the microarray analysis. All the data and information of EST analysis along with microarray data will be presented at www.brassica-rapa.org.