Sequence and analysis of rice chromosome 4

Nature. 2002 Nov 21;420(6913):316-20. doi: 10.1038/nature01183.


Rice is the principal food for over half of the population of the world. With its genome size of 430 megabase pairs (Mb), the cultivated rice species Oryza sativa is a model plant for genome research. Here we report the sequence analysis of chromosome 4 of O. sativa, one of the first two rice chromosomes to be sequenced completely. The finished sequence spans 34.6 Mb and represents 97.3% of the chromosome. In addition, we report the longest known sequence for a plant centromere, a completely sequenced contig of 1.16 Mb corresponding to the centromeric region of chromosome 4. We predict 4,658 protein coding genes and 70 transfer RNA genes. A total of 1,681 predicted genes match available unique rice expressed sequence tags. Transposable elements have a pronounced bias towards the euchromatic regions, indicating a close correlation of their distributions to genes along the chromosome. Comparative genome analysis between cultivated rice subspecies shows that there is an overall syntenic relationship between the chromosomes and divergence at the level of single-nucleotide polymorphisms and insertions and deletions. By contrast, there is little conservation in gene order between rice and Arabidopsis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics
  • Chromosomes, Plant / genetics*
  • Computational Biology
  • Contig Mapping
  • DNA Transposable Elements / genetics
  • Expressed Sequence Tags
  • Gene Order / genetics
  • Genes, Plant / genetics
  • Genetic Markers / genetics
  • Genome, Plant
  • Multigene Family / genetics
  • Mutation / genetics
  • Oryza / classification
  • Oryza / genetics*
  • Physical Chromosome Mapping*
  • Plant Proteins / classification
  • Plant Proteins / genetics
  • Polymorphism, Single Nucleotide / genetics
  • Repetitive Sequences, Nucleic Acid / genetics
  • Sensitivity and Specificity
  • Sequence Alignment
  • Sequence Analysis, DNA
  • Sequence Homology, Nucleic Acid
  • Species Specificity
  • Synteny / genetics


  • DNA Transposable Elements
  • Genetic Markers
  • Plant Proteins