title: Comparing the whole-genome-shotgun and map-based sequences of the rice genome.
abstract: The rice genome has now been sequenced using whole-genome-shotgun and map-based methods. The relative merits of the two methods are the subject of debate, as they were in the human genome project. In this Opinion article, we will show that the serious discrepancies between the resultant sequences are mostly found in the large transposable elements such as copia and gypsy that populate the intergenic regions of plant genomes. Differences in published gene counts and polymorphism rates are similarly resolved by considering how transposable elements affect the sequence analysis.
authors.affiliation: Beijing Institute of Genomics of Chinese Academy of Sciences, Beijing 101300, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
authors.forename: Peixiang
authors.initials: P
authors.lastname: Ni
authors.forename: Gane Ka-Shu
authors.initials: GK
authors.lastname: Wong
mesh_terms: D032461:Chromosomes, Plant; D003362:Cost-Benefit Analysis; D018744:DNA, Plant; D015894:Genome, Human; D018745:Genome, Plant; D006801:Humans; D012275:Oryza / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA / Q000191:economics / Q000379:methods*
chemical_list: D018744:DNA, Plant