ArticleBMC genomics2009
Comparative genomics and evolution of conserved noncoding elements (CNE) in rainbow trout.
Article in BMC genomics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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4 citing papers in PubMed, 13 citations in OpenAlex.
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- Clock genes and their genomic distributions in three species of salmonid fishes: Associations with genes regulating sexual maturation and cell cycling.BMC research notes · 2010Article
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Authors and funding
3 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundRecent advances in the accumulation of genetic mapping and DNA sequence information from several salmonid species support the long standing view of an autopolyploid origin of these fishes (i.e., 4R). However, the paralogy relationships of the chromosomal segments descendent from earlier polyploidization events (i.e., 2R/3R) largely remain unknown, mainly due to an unbalanced pseudogenization of paralogous genes that were once resident on the ancient duplicated segments. Inter-specific conserved noncoding elements (CNE) might hold the key in identifying these regions, if they are associated with arrays of genes that have been highly conserved in syntenic blocks through evolution. To test this hypothesis, we investigated the chromosomal positions of subset of CNE in the rainbow trout genome using a comparative genomic framework.
resultsThrough a genome wide analysis, we selected 41 pairs of adjacent CNE located on various chromosomes in zebrafish and obtained their intervening, less conserved, sequence information from rainbow trout. We identified 56 distinct fragments corresponding to about 150 Kbp of sequence data that were localized to 67 different chromosomal regions in the rainbow trout genome. The genomic positions of many duplicated CNE provided additional support for some previously suggested homeologies in this species. Additionally, we now propose 40 new potential paralogous affinities by analyzing the variation in the segregation patterns of some multi-copy CNE along with the synteny association comparison using several model vertebrates. Some of these regions appear to carry signatures of the 1R, 2R or 3R duplications. A subset of these CNE markers also demonstrated high utility in identifying homologous chromosomal segments in the genomes of Atlantic salmon and Arctic charr.
conclusionCNE seem to be more efficacious than coding sequences in providing insights into the ancient paralogous affinities within the vertebrate genomes. Such a feature makes these elements extremely attractive for comparative genomics studies, as they can be treated as 'anchor' markers to investigate the association of distally located candidate genes on the homologous genomic segments of closely or distantly related organisms.
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