Tandemly Arrayed Genes in Vertebrate Genomes

Abstract

Tandemly arrayed genes (TAGs) are duplicated genes that are linked as neighbors on a chromosome, many of which have important physiological and biochemical functions. Here we performed a survey of these genes in 11 available vertebrate genomes. TAGs account for an average of about 14% of all genes in these vertebrate genomes, and about 25% of all duplications. The majority of TAGs (72–94%) have parallel transcription orientation (i.e., they are encoded on the same strand) in contrast to the genome, which has about 50% of its genes in parallel transcription orientation. The majority of tandem arrays have only two members. In all species, the proportion of genes that belong to TAGs tends to be higher in large gene families than in small ones; together with our recent finding that tandem duplication played a more important role than retroposition in large families, this fact suggests that among all types of duplication mechanisms, tandem duplication is the predominant mechanism of duplication, especially in large families. Finally, several species have a higher proportion of large tandem arrays that are species-specific than random expectation.

Origins and Evolution of tetherin , an Orphan Antiviral Gene

“…Because duplicated genes are often positioned adjacent to each other in genomes (Pan and Zhang, 2008), we inspected the organization of genes proximal to tetherin in human and mouse genomes. Strikingly, two genes whose protein product had a TM-CC configuration were positioned proximally to tetherin in human and mouse genomes (Figure 1A).…”

“…Among the 211 and 175 TM-CC-encoding genes in the human and mouse genomes respectively, 10 (human) and 6 (mouse) gene pairs were found adjacent to each other and in the same orientation. Most duplicated genes (72–94%) remain adjacent to each other and in the same orientation (Pan and Zhang, 2008). We observed that most of the few adjacent TM-CC gene pairs (7 of 10 human and 5 of 6 mouse) share clear sequence similarity, usually belong to obvious gene families (e.g.…”

Genome-wide Analysis of WD40 Protein Family in Human

“…The hyper-geometric distribution test was used to detect the chromosomes with biased WD40 abundance. Among the WD40 genes with highly similar domains, we also defined two WD40 genes adjacent to each other on the same chromosome with at most one spacer gene as tandemly arrayed genes (TAGs)48.…”

Functional analyses of PAU genes in Saccharomyces cerevisiae

“…DUP gene duplication is thought to have occurred through non-reciprocal translocation, tandem duplication and transposon Tyassociated duplication (Despons et al, 2006). Gene duplication has long been considered a major force driving evolution (Ohno, 1970), and may occur via three mechanisms: chromosomal or segmental duplication, retroposition and tandem duplication (Zhang, 2003;Kong et al, 2007;Pan & Zhang, 2008). The duplicated genes may either be lost or gain novel functions to retain their existence through divergence of sequence and expression during evolution (Taylor & Raes, 2004;Lynch & Conery, 2000).…”