TAILIEUCHUNG - Báo cáo khoa học: Detection of nucleolar organizer and mitochondrial DNA insertion regions based on the isochore map of Arabidopsis thaliana

Eukaryotic genomes are composed of isochores, . long sequences relat-ively homogeneous in GC content. In this paper, the isochore structure of Arabidopsis thalianagenome has been studied using a windowless technique based on theZcurve method and intuitive curves are drawn for all the five chromosomes. Using these curves, we can calculate the GC content at any resolution, even at the base level. | iFEBS Journal Detection of nucleolar organizer and mitochondrial DNA insertion regions based on the isochore map of Arabidopsis thaliana Ling-Ling Chen1 and Feng Gao2 1 Laboratory for ComputationalBiology Shandong ProvincialResearch Center for Bioinformatic Engineering and Techniques Shandong University of Technology Zibo China 2 Department of Physics Tianjin University China Keywords Arabidopsis thaliana GC content isochore mitochondrial insertion region nucleolar organizer Correspondence L-L Chen Laboratory for Computational Biology Shandong ProvincialResearch Center for Bioinformatic Engineering and Techniques Shandong University of Technology Zibo 255049 China Fax 86 5332780271 Tel 86 5332780271 E-mail llchen@ Received 7 January 2005 revised 23 April 2005 accepted 3 May 2005 doi Eukaryotic genomes are composed of isochores . long sequences relatively homogeneous in GC content. In this paper the isochore structure of Arabidopsis thaliana genome has been studied using a windowless technique based on the Z curve method and intuitive curves are drawn for all the five chromosomes. Using these curves we can calculate the GC content at any resolution even at the base level. It is observed that all the five chromosomes are composed of several GC-rich and AT-rich regions alternatively. Usually these regions named isochore-like regions have large fluctuations in the GC content. Five isochores with little fluctuations are also observed. Detailed analyses have been performed for these isochores. A GC-rich isochore-like region and a GC-isochore in chromosome II and IV respectively are the nucleolar organizer regions NORs and genes located in the two regions prefer to use GC-ending codons. Another GC-isochore located in chromosome II is a mitochondrial DNA insertion region the position and size of this region is precisely predicted by the current method. The amino acid usage and codon preference of genes in this .

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