Large Synteny Blocks Revealed Between Caenorhabditis elegans And Caenorhabditis briggsae Genomes Using OrthoCluster

Background: Accurate identification of synteny blocks is an important step in comparative genomics towards theunderstanding of genome architecture and expression. Most computer programs developed in the last decade foridentifying synteny blocks have limitations. To address these limitations, we recently developed a robust programcalled OrthoCluster, and an online database OrthoClusterDB. In this work, we have demonstrated the application ofOrthoCluster in identifying synteny blocks between the genomes of Caenorhabditis elegans and Caenorhabditisbriggsae, two closely related hermaphrodite nematodes.Results: Initial identification and analysis of synteny blocks using OrthoCluster enabled us to systematically improvethe genome annotation of C. elegans and C. briggsae, identifying 52 potential novel genes in C. elegans, 582 inC. 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. Thelargest 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%) ofthe C. elegans and C. briggsae genomes are covered by imperfect synteny blocks. The largest imperfect syntenyblock spans 6.14 Mb in Chromosome X of C. elegans and there are 11 synteny blocks that are larger than 1 Mb insize. 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 havefound that synteny blocks between C. elegans and C. briggsae are almost three-folds larger than previouslyidentified.