ArticleBMC genomics2010
Large synteny blocks revealed between Caenorhabditis elegans and Caenorhabditis briggsae genomes using OrthoCluster.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 24 citations in OpenAlex.
- ntSynt: multi-genome synteny detection using minimizer graph mappings.BMC biology · 2025Article
- Visualizing genomic evolution in Caenorhabditis through WormSynteny.BMC genomics · 2024Article
- High-qualityFrontiers in plant science · 2023Article
- Comparative Genomic Characterization of Relaxin Peptide Family in Cattle and Buffalo.BioMed research international · 2022Article
- Comparative Genomic Characterization of Insulin-Like Growth Factor Binding Proteins in Cattle and Buffalo.BioMed research international · 2022Article
- Early experiences mediate distinct adult gene expression and reproductive programs in Caenorhabditis elegans.PLoS genetics · 2018Article
- Inferring synteny between genome assemblies: a systematic evaluation.BMC bioinformatics · 2018Article
- SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand.Genome biology and evolution · 2015Article
- Genome sequence and transcriptome analyses of the thermophilic zygomycete fungus Rhizomucor miehei.BMC genomics · 2014Article
- Genome-wide variations in a natural isolate of the nematode Caenorhabditis elegans.BMC genomics · 2014Article
- Cell- and subunit-specific mechanisms of CNG channel ciliary trafficking and localization in C. elegans.Journal of cell science · 2013Article
- RNA-seq analysis of the C. briggsae transcriptome.Genome research · 2012Article
- MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity.Nucleic acids research · 2012Article
- A method for rapid and simultaneous mapping of genetic loci and introgression sizes in nematode species.PloS one · 2012Article
- Family size and turnover rates among several classes of small non-protein-coding RNA genes in Caenorhabditis nematodes.Genome biology and evolution · 2012Article
- Schistosoma comparative genomics: integrating genome structure, parasite biology and anthelmintic discovery.Trends in parasitology · 2011Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
backgroundAccurate 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.
resultsInitial 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.
conclusionsWe 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.
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