Rice, one of the world's most important food plants, has important syntenic relationships with the other cereal species and is a model plant for the grasses. Here we present a map-based, finished quality sequence that covers 95% of the 389 Mb genome, including virtually all of the euchromatin and two complete centromeres. A total of 37,544 nontransposable-element-related protein-coding genes were identified, of which 71% had a putative homologue in Arabidopsis. In a reciprocal analysis, 90% of the Arabidopsis proteins had a putative homologue in the predicted rice proteome. Twenty-nine per cent of the 37,544 predicted genes appear in clustered gene families. The number and classes of transposable elements found in the rice genome are consistent with the expansion of syntenic regions in the maize and sorghum genomes. We find evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes. The map-based sequence has proven useful for the identification of genes underlying agronomic traits. The additional single-nucleotide polymorphisms and simple sequence repeats identified in our study should accelerate improvements in rice production.

Two methods for increasing the length of DNA sequence data that can be read off a polyacrylamide gel are described. We have developed a rapid way to pour a buffer concentration gradient gel that, by altering the vertical band separation on an autoradiograph, allows more sequence to be obtained from a gel. We also show that the use of deoxyadenosine 5'-(a-[3S]thio)triphosphate as the label incorporated in dideoxynucleotide sequence reactions increases the sharpness of the bands on an autoradiograph and so increases the resolution achieved.Both major rapid DNA sequence determination methods (1, 2) rely on thin denaturing polyacrylamide gels (3) to fractionate single-stranded DNA reaction products. To determine a sufficient length of sequence data from an experiment, it is usual to load aliquots from a reaction onto two or more gels run for various times. It would be advantageous to be able to obtain more sequence from each gel because this would allow either more total sequence to be obtained or fewer gels to be run per reaction. We describe two methods for increasing the amount of readable sequence per gel and demonstrate their effectiveness with the dideoxy sequence analysis technique.One of the main limits on the length of sequence obtainable from an autoradiograph is the progressively poor separation of the bands corresponding to longer DNA molecules. Yet the spacing between the shorter DNA molecules is wider than is required for correct interpretation of the sequence pattern. It is possible, by use of a suitable gradient positioned only in the lower (anode) end of a gel, to selectively reduce the spacing between these shorter DNA molecules. By virtue of having traveled through a greater length of polyacrylamide gel, the higher molecular weight DNA molecules, lying above the gradient, will have an increased separation. We have found that an effective gradient consists of an increase in Tris/borate/EDTA (TBE) buffer concentration towards the bottom of the gel. A limit on the use of gradient gels has been the inconvenience and length of time needed for pouring such gels. We present a rapid technique, using simple apparatus, for pouring gradient gels, making their routine use for DNA sequence analysis realistic.The principle by which a buffer gradient can be used to reduce the vertical band spacing on a polyacrylamide sequencing gel is that, as the buffer concentration increases progressively in the lower 10-15 cm of the gel, electrical resistance per cm down the gel decreases. This is because the buffer is the major charge carrier in the gel. Because the current is constant throughout the length of the gel, by Ohm's law the voltage drop per unit length will also decrease towards the anode. It is the potential difference across the gel that drives the polynucleotide migration, and so a fall in voltage drop per cm will cause a reduction in band migration rate. Thus the spacing between DNA molecules of n and n + 1 nucleotide residues can be reduced as they enter a gradient of increasing buffer concentratio...

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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.

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