| Summary: | <p>Abstract</p> <p>Background</p> <p>The HOX gene clusters are thought to be highly conserved amongst mammals and other vertebrates, but the long non-coding RNAs have only been studied in detail in human and mouse. The sequencing of the kangaroo genome provides an opportunity to use comparative analyses to compare the HOX clusters of a mammal with a distinct body plan to those of other mammals.</p> <p>Results</p> <p>Here we report a comparative analysis of <it>HOX</it> gene clusters between an Australian marsupial of the kangaroo family and the eutherians. There was a strikingly high level of conservation of <it>HOX</it> gene sequence and structure and non-protein coding genes including the microRNAs <it>miR-196a</it>, <it>miR-196b</it>, <it>miR-10a</it> and <it>miR-10b</it> and the long non-coding RNAs <it>HOTAIR</it>, <it>HOTAIRM1</it> and <it>HOX</it>A11AS that play critical roles in regulating gene expression and controlling development. By microRNA deep sequencing and comparative genomic analyses, two conserved microRNAs (<it>miR-10a</it> and <it>miR-10b</it>) were identified and one new candidate microRNA with typical hairpin precursor structure that is expressed in both fibroblasts and testes was found. The prediction of microRNA target analysis showed that several known microRNA targets, such as <it>miR-10</it>, <it>miR-414</it> and <it>miR-464</it>, were found in the tammar <it>HOX</it> clusters. In addition, several novel and putative miRNAs were identified that originated from elsewhere in the tammar genome and that target the tammar <it>HOXB</it> and <it>HOXD</it> clusters.</p> <p>Conclusions</p> <p>This study confirms that the emergence of known long non-coding RNAs in the HOX clusters clearly predate the marsupial-eutherian divergence 160 Ma ago. It also identified a new potentially functional microRNA as well as conserved miRNAs. These non-coding RNAs may participate in the regulation of <it>HOX</it> genes to influence the body plan of this marsupial.</p>
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