title: A microarray analysis of the rice transcriptome and its comparison to Arabidopsis.
abstract: Arabidopsis and rice are the only two model plants whose finished phase genome sequence has been completed. Here we report the construction of an oligomer microarray based on the presently known and predicted gene models in the rice genome. This microarray was used to analyze the transcriptional activity of the gene models in representative rice organ types. Expression of 86% of the 41,754 known and predicted gene models was detected. A significant fraction of these expressed gene models are organized into chromosomal regions, about 100 kb in length, that exhibit a coexpression pattern. Compared with similar genome-wide surveys of the Arabidopsis transcriptome, our results indicate that similar proportions of the two genomes are expressed in their corresponding organ types. A large percentage of the rice gene models that lack significant Arabidopsis homologs are expressed. Furthermore, the expression patterns of rice and Arabidopsis best-matched homologous genes in distinct functional groups indicate dramatic differences in their degree of conservation between the two species. Thus, this initial comparative analysis reveals some basic similarities and differences between the Arabidopsis and rice transcriptomes.
authors.affiliation: Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871.
authors.forename: Ligeng
authors.initials: L
authors.lastname: Ma
authors.forename: Chen
authors.initials: C
authors.lastname: Chen
authors.forename: Xigang
authors.initials: X
authors.lastname: Liu
authors.forename: Yuling
authors.initials: Y
authors.lastname: Jiao
authors.forename: Ning
authors.initials: N
authors.lastname: Su
authors.forename: Lin
authors.initials: L
authors.lastname: Li
authors.forename: Xiangfeng
authors.initials: X
authors.lastname: Wang
authors.forename: Mengliang
authors.initials: M
authors.lastname: Cao
authors.forename: Ning
authors.initials: N
authors.lastname: Sun
authors.forename: Xiuqing
authors.initials: X
authors.lastname: Zhang
authors.forename: Jingyue
authors.initials: J
authors.lastname: Bao
authors.forename: Jian
authors.initials: J
authors.lastname: Li
authors.forename: Soren
authors.initials: S
authors.lastname: Pedersen
authors.forename: Lars
authors.initials: L
authors.lastname: Bolund
authors.forename: Hongyu
authors.initials: H
authors.lastname: Zhao
authors.forename: Longping
authors.initials: L
authors.lastname: Yuan
authors.forename: Gane Ka-Shu
authors.initials: GK
authors.lastname: Wong
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Xing Wang
authors.initials: XW
authors.lastname: Deng
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D020869:Gene Expression Profiling; D018745:Genome, Plant; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D009928:Organ Specificity; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D046988:Proteasome Endopeptidase Complex / Q000378:metabolism; D013045:Species Specificity; D014158:Transcription, Genetic; D025801:Ubiquitin / Q000378:metabolism
chemical_list: D025801:Ubiquitin; D046988:Proteasome Endopeptidase Complex