Abstract
Hox genes encode transcription factors that regulate embryonic and post-embryonic developmental processes. The expression of Hox genes is regulated in part by the tight, spatial arrangement of conserved coding and non-coding sequences. The potential for evolutionary changes in Hox cluster structure is thought to be low among vertebrates; however, recent studies of a few non-mammalian taxa suggest greater variation than originally thought. Using next generation sequencing of large genomic fragments (>100 kb) from the red spotted newt (Notophthalamus viridescens), we found that the arrangement of Hox cluster genes was conserved relative to orthologous regions from other vertebrates, but the length of introns and intergenic regions varied. In particular, the distance between hoxd13 and hoxd11 is longer in newt than orthologous regions from vertebrate species with expanded Hox clusters and is predicted to exceed the length of the entire HoxD clusters (hoxd13–hoxd4) of humans, mice, and frogs. Many repetitive DNA sequences were identified for newt Hox clusters, including an enrichment of DNA transposon-like sequences relative to non-coding genomic fragments. Our results suggest that Hox cluster expansion and transposon accumulation are common features of non-mammalian tetrapod vertebrates.
Highlights
Bilaterian body plans are determined in part by DNA transcription factors called Hox genes [1,2,3,4]
BAC library screening, sequencing, assembly, and annotation A bacterial artificial clone (BAC) library of 41,472 clones was constructed for newt, and pools were screened by polymerase chain reaction (PCR) to identify clones that contained Hox genes
High sequence identity was observed for Hox genes, which is typical of transcription factors that function in highly conserved developmental pathways
Summary
Bilaterian body plans are determined in part by DNA transcription factors called Hox genes [1,2,3,4]. While some patterns of Hox expression in regenerating limbs recapitulate the expression pattern in developing limbs, spatial and temporal differences are observed [18,19,20,21] This raises the possibility that salamander Hox clusters may contain non-coding elements that uniquely regulate postembryonic, tissue regeneration; such elements may not be expected within Hox clusters of vertebrates incapable of limb regeneration. There is another reason to suspect that salamander Hox clusters may differ from other vertebrate taxa—salamanders as a group have extremely large genomes. This larger genome size is reflected in the structure of genes, as salamander introns are longer on average than orthologous introns in other vertebrates [23,24]
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