Genomic structure and evolutionary context of the human feline leukemia virus subgroup C receptor ( hFLVCR) gene: evidence for block duplications and de novo gene formation within duplicons of the hFLVCR locus

Abstract

In this paper we sought to analyze the genomic structure and context of human feline leukemia virus subgroup C receptor ( hFLVCR), a human glucarate transporter-like gene at chromosome 1q31, and compare it to that of a paralog ( FLVCR14q) at chromosome 14q24. Splicing, polyadenylation, and expression patterns, as estimated by in silico analysis, differed between the two FLVCR genes despite their similar genomic structures, suggesting active and independent evolution of transcriptional and messenger RNA processing patterns after gene duplication. Promoter activity was bi-directional for hFLVCR, but not for its 14q paralog. The upstream 1q transcribed sequences were determined to comprise a novel gene of unknown function, LQK1. Annotation of contigs centered at hFLVCR and FLVCRL14q also revealed highly conserved gene clusters on chromosomes 1 and 14, inferred to result from a duplication. The clusters contained members of the FLVCR, Angel ( KIAA0759), JDP, p21SNFT, and TGF-β families, as well as two uncharacterized families. The genome-wide locations of both previously recognized and four de novo in silico predicted genes belonging to these seven families were determined. Phylogenetic analyses of these families were consistent with the hypothesis that the 1q/14q duplication occurred early within, or immediately prior to the vertebrate divergence, after the protostome–deuterostome divergence but before the amniote–amphibian divergence.