A Comparative Map of the Zebrafish Genome

Abstract

Zebrafish mutations define the functions of hundreds of essential genes in the vertebrate genome. To accelerate the molecular analysis of zebrafish mutations and to facilitate comparisons among the genomes of zebrafish and other vertebrates, we used a homozygous diploid meiotic mapping panel to localize polymorphisms in 691 previously unmapped genes and expressed sequence tags (ESTs). Together with earlier efforts, this work raises the total number of markers scored in the mapping panel to 2119, including 1503 genes and ESTs and 616 previously characterized simple-sequence length polymorphisms. Sequence analysis of zebrafish genes mapped in this study and in prior work identified putative human orthologs for 804 zebrafish genes and ESTs. Map comparisons revealed 139 new conserved syntenies, in which two or more genes are on the same chromosome in zebrafish and human. Although some conserved syntenies are quite large, there were changes in gene order within conserved groups, apparently reflecting the relatively frequent occurrence of inversions and other intrachromosomal rearrangements since the divergence of teleost and tetrapod ancestors. Comparative mapping also shows that there is not a one-to-one correspondence between zebrafish and human chromosomes. Mapping of duplicate gene pairs identified segments of 20 linkage groups that may have arisen during a genome duplication that occurred early in the evolution of teleosts after the divergence of teleost and mammalian ancestors. This comparative map will accelerate the molecular analysis of zebrafish mutations and enhance the understanding of the evolution of the vertebrate genome.

Partitioning of Tissue Expression Accompanies Multiple Duplications of the Na+/K+ ATPase α Subunit Gene

“…The two ␣3 paralogs map to LG 16 and LG 19, linked to the duplicated Hoxa clusters Gates et al 1999;, and the duplication occurred prior to divergence of the lineage leading to Tilapia. Similarly, the ␣1B paralogs map to LG 1 and LG 9, which have been suggested to contain paralogous regions, as teleost-specific members of other gene families, such as distalless and engrailed, map to these chromosomes Woods et al 2000). Here too, the phylogenetic position of the duplications is consistent with the large-scale duplication.…”

“…For example, seven Hox clusters are found in zebrafish resulting from a duplication of the four Hox clusters found in most other higher vertebrates Prince et al 1998). As would be predicted from a ploidy duplication, genes linked to the seven Hox clusters are also duplicated with syntenic conservation to the corresponding cluster in mammals Woods et al 2000). Other syntenic regions between human and zebrafish chromosomes lend further support to this model .…”

Timing and mechanism of ancient vertebrate genome duplications – the adventure of a hypothesis

“…The mapping of Hox clusters and many duplicated genes in zebrafish [49,50], pufferfish [51] and medaka [52] suggested an extra WGD in ray-finned fish. The analysis of the Fugu genome revealed 159 statistically significant paralogons that contained 544 paralogous gene pairs (3.4 anchor points per block) [32].…”

Mycobacterium marinum produces long-term chronic infections in medaka: A new animal model for studying human tuberculosis

“…The zebrafish model offers numerous mutant lines (Amsterdam et. al., 1999), a completed genome sequence, the ability to make transgenic strains, and a large research community (Woods et. al., 2000).…”