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Background  Accurate identification of synteny blocks is an important step in comparative genomics towards the understanding of genome architecture and expression. Most computer programs developed in the last decade for identifying synteny blocks have limitations. To address these limitations, we recently developed a robust program called OrthoCluster, and an online database OrthoClusterDB. In this work, we have demonstrated the application of OrthoCluster in identifying synteny blocks between the genomes of  Caenorhabditis elegans  and  Caenorhabditis briggsae , two closely related hermaphrodite nematodes.    Results  Initial identification and analysis of synteny blocks using OrthoCluster enabled us to systematically improve the genome annotation of  C. elegans  and  C. briggsae , identifying 52 potential novel genes in  C. elegans , 582 in  C. briggsae , and 949 novel orthologous relationships between these two species. Using the improved annotation, we have detected 3,058 perfect synteny blocks that contain no mismatches between  C. elegans  and  C. briggsae . Among these synteny blocks, the majority are mapped to homologous chromosomes, as previously reported. The largest perfect synteny block contains 42 genes, which spans 201.2 kb in Chromosome V of  C. elegans . On average, perfect synteny blocks span 18.8 kb in length. When some mismatches (interruptions) are allowed, synteny blocks ("imperfect synteny blocks") that are much larger in size are identified. We have shown that the majority (80%) of the  C. elegans  and  C. briggsae  genomes are covered by imperfect synteny blocks. The largest imperfect synteny block spans 6.14 Mb in Chromosome X of  C. elegans  and there are 11 synteny blocks that are larger than 1 Mb in size. On average, imperfect synteny blocks span 63.6 kb in length, larger than previously reported.    Conclusions  We have demonstrated that OrthoCluster can be used to accurately identify synteny blocks and have found that synteny blocks between  C. elegans  and  C. briggsae  are almost three-folds larger than previously identified.

Large synteny blocks revealed between Caenorhabditis elegans and Caenorhabditis briggsae genomes using OrthoCluster