PUBLICATION
Analyses of the extent of shared synteny and conserved gene orders between the genome of Fugu rubripes and human 20q
- Authors
- Smith, S.F., Snell, P., Gruetzner, F., Bench, A.J., Haaf, T., Metcalfe, J.A., Green, A.R., and Elgar, G.
- ID
- ZDB-PUB-020701-5
- Date
- 2002
- Source
- Genome research 12(5): 776-784 (Other)
- Registered Authors
- Elgar, Greg
- Keywords
- none
- MeSH Terms
-
- Animals
- Cell Line
- Chromosomes, Human, Pair 20/genetics*
- Conserved Sequence/genetics*
- Contig Mapping/methods
- Cosmids/genetics
- Gene Duplication
- Gene Order/genetics*
- Genome*
- Genome, Human
- Humans
- Microscopy, Fluorescence
- Sequence Tagged Sites
- Synteny/genetics*
- Takifugu/genetics*
- Zebrafish/genetics
- PubMed
- 11997344 Full text @ Genome Res.
Citation
Smith, S.F., Snell, P., Gruetzner, F., Bench, A.J., Haaf, T., Metcalfe, J.A., Green, A.R., and Elgar, G. (2002) Analyses of the extent of shared synteny and conserved gene orders between the genome of Fugu rubripes and human 20q. Genome research. 12(5):776-784.
Abstract
Cosmid and BAC contig maps have been constructed across two Fugu genomic regions containing the orthologs of human genes mapping to human chromosome 20q. Contig gene contents have been assessed by sample sequencing and comparative database analyses. Contigs are centered around two Fugu topoisomerase1 (top1) genes that were initially identified by sequence similarity to human TOP1 (20q12). Two other genes (SNAI1 and KRML) mapping to human chromosome 20 are also duplicated in Fugu. The two contigs have been mapped to separate Fugu chromosomes. Our data indicate that these linkage groups result from the duplication of an ancestral chromosome segment containing at least 40 genes that now map to the long arm of human chromosome 20. Although there is considerable conservation of synteny, gene orders are not well conserved between Fugu and human, with only very short sections of two to three adjacent genes being maintained in both organisms. Comparative analyses have allowed this duplication event to be dated before the separation of Fugu and zebrafish. Our data (which are best explained by regional duplication, followed by substantial gene loss) support the hypothesis that there have been a large number of gene and regional duplications (and corresponding gene loss) in the fish lineage, possibly resulting from a single whole genome duplication event.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping