Use of the Japanese Pufferfish (Fugu rubripes) in Comparative Genomics

Abstract

With the draft sequence of the human genome available and an increasing number of organisms being sequenced, attention is becoming focused on sequence interpretation and functional analysis. Comparative genomics will play an important role in evaluating these data. At the molecular level, roles for uncharacterized proteins can be hypothesized by identifying conserved protein domains and putative noncoding regulatory elements can be defined from direct sequence comparisons of evolutionarily distant organisms. At a higher level, questions, such as the importance of gene order positioning, conservation of linkage, and genome evolution, can begin to be answered by collecting map data from different organisms. This minireview, centering on Fugu regions sharing synteny with human chromosomes 11p, 20q, and 6p21.3, details some of the ways in which the Japanese pufferfish can contribute to the study of comparative genomics and evaluation of sequence data from the genome programs.

The Genetic Map ofXiphophorusFishes Represented by 24 Multipoint Linkage Groups

“…All of these fish taxa have genome sizes substantially smaller than that of mammals, including human, and the tetraodontiform fishes, including Fugu particularly, has been exploited for the study of comparative genomics. 53 The linkage map derived from X. maculatus/X. helleri hybrids shows several peculiar characteristics.…”

Isolation of seven IL-17 family genes from the Japanese pufferfish Takifugu rubripes

“…The Fugu genome [20] database was searched using BLAST analysis [21] and the amino acid sequences of the human and zebrafish IL-17 family genes. The Fugu homologues for these molecules were identified within various DNA contigs (Scaffold_1, _38, _143, _264 and _430) in the database.…”

Discovery of a new class of immunoglobulin heavy chain from fugu

“…Simultaneously, we were working on the fugu IgH locus in order to identify new Ig H-chain genes. Fugu is a good model for the comparative genomic study because of its compact genome [18]. Using fugu genome sequence information [19], we could identify a new Ig H-chain class present on the IgH locus, upstream of l and d regions.…”