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.

This study discusses three software tools, the first two aid in integrating sequence with an FPC physical map and the third automatically selects a minimal tiling path given genomic draft sequence and BAC end sequences. The first tool, FSD (FPC Simulated Digest), takes a sequenced clone and adds it back to the map based on a fingerprint generated by an in silico digest of the clone. This allows verification of sequenced clone positions and the integration of sequenced clones that were not originally part of the FPC map. The second tool, BSS (Blast Some Sequence), takes a query sequence and positions it on the map based on sequence associated with the clones in the map. BSS has multiple uses as follows: (1) When the query is a file of marker sequences, they can be added as electronic markers.(2) When the query is draft sequence, the results of BSS can be used to close gaps in a sequenced clone or the physical map. (3) When the query is a sequenced clone and the target is BAC end sequences, one may select the next clone for sequencing using both sequence comparison results and map location. (4) When the query is whole-genome draft sequence and the target is BAC end sequences, the results can be used to select many clones for a minimal tiling path at once. The third tool, pickMTP, automates the majority of this last usage of BSS. Results are presented using the rice FPC map, BAC end sequences, and whole-genome shotgun from Syngenta.

Many clone-based physical maps have been built with the FingerPrinted Contig (FPC) software, which is written in C and runs locally for fast and flexible analysis. If the maps were viewable only from FPC, they would not be as useful to the whole community since FPC must be installed on the user machine and the database downloaded. Hence, we have created a set of Web tools so users can easily view the FPC data and perform salient queries with standard browsers. This set includes the following four programs: WebFPC, a view of the contigs; WebChrom, the location of the contigs and genetic markers along the chromosome; WebBSS, locating user-supplied sequence on the map; and WebFCmp, comparing fingerprints. For additional FPC support, we have developed an FPC module for BioPerl and an FPC browser using the Generic Model Organism Project (GMOD) genome browser (GBrowse), where the FPC BioPerl module generates the data files for input into GBrowse. This provides an alternative to the WebChrom/WebFPC view. These tools are available to download along with documentation. The tools have been implemented for both the rice (Oryza sativa) and maize (Zea mays) FPC maps, which both contain the locations of clones, markers, genetic markers, and sequenced clone (along with links to sites that contain additional information).

Rice is the world's most important food crop and a model for cereal research. At 430 megabases in size, its genome is the most compact of the cereals. We report the sequence of chromosome 10, the smallest of the 12 rice chromosomes (22.4 megabases), which contains 3471 genes. Chromosome 10 contains considerable heterochromatin with an enrichment of repetitive elements on 10S and an enrichment of expressed genes on 10L. Multiple insertions from organellar genomes were detected. Collinearity was apparent between rice chromosome 10 and sorghum and maize. Comparison between the draft and finished sequence demonstrates the importance of finished sequence.