Analyses of the extent of shared synteny and conserved gene orders between the genome of Fugu rubripes and human 20q - PubMed (original) (raw)

Comparative Study

Analyses of the extent of shared synteny and conserved gene orders between the genome of Fugu rubripes and human 20q

Sarah F Smith et al. Genome Res. 2002 May.

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.

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Figures

Figure 1

Figure 1

Tiling paths for scanned BACs in the two Fugu contigs. An additional 14 cosmids have been scanned to generate data for Fugu contig 1 and a further 13 cosmids for Fugu contig 2. In total, 64 BACs and 77 BACs were used in the STS mapping of the genes on contig 1, whereas 43 BACs and 25 cosmids were used to create the contig 2 gene map.

Figure 2

Figure 2

Gene content on the two Fugu contigs. Genes are named according to the nomenclature for the orthologous human gene. Human mapping locations are shown in italics after the gene name. For genes mapping to Hsa20, locations are shown as positions on bacterial clones in the Hsa20 contig map. In contig 1 there is a clear break in shared synteny with human 20q, whereas in contig 2 synteny with 20q is conserved along the entire contig length. If a gene is duplicated in Fugu, or the Fugu gene has already been named elsewhere, the corresponding Fugu gene name is shown in italics. The relative positions of the duplicated Fugu genes are indicated by arrows.

Figure 3

Figure 3

(A) FISH mapping of nonsyntenic BACs B294L23 (contig 1) and B299O09 (contig 2) to Fugu metaphase chromosomes. The two Fugu contigs are therefore not linked in the Fugu genome. (B) FISH mapping of syntenic BACs B234K08 and B294L23 (both contig 1) to Fugu metaphase chromosomes. These BACs, which span the breakpoint in shared synteny between contig 1 and human 20q, show no evidence of chimerism.

Figure 4

Figure 4

Fugu/Human 20q comparative gene maps. The positions of the human 20q orthologs of genes identified on the two Fugu contigs are shown on an ideogram of human chromosome 20. Mapping locations for the human genes span the whole of human 20q. Genes are named according to the nomenclature for the orthologous human gene. If a gene is duplicated in Fugu, the corresponding Fugu gene name is shown in italics. The positions of the Fugu and human orthologs are linked by black lines. Genes that have been identified as being present in two copies in Fugu are linked to the mapping position of the corresponding human gene by dashed lines. Although Fugu contig 1 has been inverted in this diagram to reduce the number of crossover events, the number of changes in gene orders between the Fugu contigs and human 20q remains high. This indicates that gene orders in the two lineages have been disrupted by a number of localized rearrangements.

Figure 5

Figure 5

Fugu/human 20q11.2–12 comparative gene map. This ideogram provides a more detailed comparison between the two Fugu contigs and a 7-Mb section of human 20q (a section that contains the human orthologs of two of the genes, KRML and TOP1, known to be duplicated in Fugu). The orthologs of ∼25% of the genes mapping to this region are represented on one or another of the two Fugu contigs. The distribution of the genes between the two Fugu contigs, however, appears to be random, indicating a pattern of duplication in the Fugu lineage followed by the loss (in the majority of cases) of one of the additional gene copies.

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