ArticleGenome research2004
Building genomic profiles for uncovering segmental homology in the twilight zone.
Article in Genome research, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Identification and analysis of lignin biosynthesis genes related to fruit ripening and stress response in banana (Frontiers in plant science · 2023Article
- Review
- Finding approximate gene clusters with Gecko 3.Nucleic acids research · 2016Article
- Genome-wide identification and characterization of R2R3MYB family in Solanum lycopersicum.Molecular genetics and genomics : MGG · 2014Article
- PhylDiag: identifying complex synteny blocks that include tandem duplications using phylogenetic gene trees.BMC bioinformatics · 2014Article
- SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes.PloS one · 2014Article
- Homoeologous chromosomes of Xenopus laevis are highly conserved after whole-genome duplication.Heredity · 2013Article
- Detecting long tandem duplications in genomic sequences.BMC bioinformatics · 2012Article
- i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets.Nucleic acids research · 2012Article
- Bacterial syntenies: an exact approach with gene quorum.BMC bioinformatics · 2011Article
- SyMAP v3.4: a turnkey synteny system with application to plant genomes.Nucleic acids research · 2011Article
- The Arabidopsis lyrata genome sequence and the basis of rapid genome size change.Nature genetics · 2011Article
- MicroSyn: a user friendly tool for detection of microsynteny in a gene family.BMC bioinformatics · 2011Article
- Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs.PLoS biology · 2010Article
- The hidden duplication past of the plant pathogen Phytophthora and its consequences for infection.BMC genomics · 2010Article
- Evidence and evolutionary analysis of ancient whole-genome duplication in barley predating the divergence from rice.BMC evolutionary biology · 2009Article
- Evolution of gene function and regulatory control after whole-genome duplication: comparative analyses in vertebrates.Genome research · 2009Article
- Gene cluster statistics with gene families.Molecular biology and evolution · 2009Article
- Génolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes.Nucleic acids research · 2009Article
- Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The identification of homologous regions within and between genomes is an essential prerequisite for studying genome structure and evolution. Different methods already exist that allow detecting homologous regions in an automated manner. These methods are based either on finding sequence similarities at the DNA level or on identifying chromosomal regions showing conservation of gene order and content. Especially the latter approach has proven useful for detecting homology between highly divergent chromosomal regions. However, until now, such map-based approaches required that candidate homologous regions show significant collinearity with other segments to be considered as being homologous. Here, we present a novel method that creates profiles combining the gene order and content information of multiple mutually homologous genomic segments. These profiles can be used to scan one or more genomes to detect segments that show significant collinearity with the entire profile but not necessarily with individual segments. When applying this new method to the combined genomes of Arabidopsis and rice, we find additional evidence for ancient duplication events in the rice genome.
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