ArticleYeast (Chichester, England)2000
Estimation of synteny conservation and genome compaction between pufferfish (Fugu) and human.
Article in Yeast (Chichester, England), 2000. 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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29 citing papers in PubMed, 79 citations in OpenAlex.
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- A guided tour of large genome size in animals: what we know and where we are heading.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2011Review
- A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi.Genome biology · 2011Article
- Integration of the genetic map and genome assembly of fugu facilitates insights into distinct features of genome evolution in teleosts and mammals.Genome biology and evolution · 2011Article
- Genome size evolution in pufferfish: an insight from BAC clone-based Diodon holocanthus genome sequencing.BMC genomics · 2010Article
- Simultaneous Bayesian gene tree reconstruction and reconciliation analysis.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- CONDOR: a database resource of developmentally associated conserved non-coding elements.BMC developmental biology · 2007Article
- Comparative genomics using Fugu reveals insights into regulatory subfunctionalization.Genome biology · 2007Article
- Comparative genomic analysis links karyotypic evolution with genomic evolution in the Indian muntjac (Muntiacus muntjak vaginalis).Chromosoma · 2006Article
- Ancient duplicated conserved noncoding elements in vertebrates: a genomic and functional analysis.Genome research · 2006Article
- Characterisation and expression analysis of interleukin 2 (IL-2) and IL-21 homologues in the Japanese pufferfish, Fugu rubripes, following their discovery by synteny.Immunogenetics · 2005Article
- Size of the protein-coding genome and rate of molecular evolution.Journal of human genetics · 2005Article
- Incongruent patterns of local and global genome size evolution in cotton.Genome research · 2004Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundKnowledge of the amount of gene order and synteny conservation between two species gives insights to the extent and mechanisms of divergence. The vertebrate Fugu rubripes (pufferfish) has a small genome with little repetitive sequence which makes it attractive as a model genome. Genome compaction and synteny conservation between human and Fugu were studied using data from public databases.
methodsIntron length and map positions of human and Fugu orthologues were compared to analyse relative genome compaction and synteny conservation respectively. The divergence of these two genomes by genome rearrangement was simulated and the results were compared to the real data.
resultsAnalysis of 199 introns in 22 orthologous genes showed an eight-fold average size reduction in Fugu, consistent with the ratio of total genome sizes. There was no consistent pattern relating the size reduction in individual introns or genes to gene base composition in either species. For genes that are neighbours in Fugu (genes from the same cosmid or GenBank entry), 40-50% have conserved synteny with a human chromosome. This figure may be underestimated by as much as two-fold, due to problems caused by incomplete human genome sequence data and the existence of dispersed gene families. Some genes that are neighbours in Fugu have human orthologues that are several megabases and tens of genes apart. This is probably caused by small inversions or other intrachromosomal rearrangements.
conclusionsComparison of observed data to computer simulations suggests that 4000-16 000 chromosomal rearrangements have occurred since Fugu and human shared a common ancestor, implying a faster rate of rearrangement than seen in human/mouse comparisons.
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10797599PMC2447035W2021620549What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.