BACKGROUND: 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.
RESULTS: Here we report a comparative analysis of HOX gene clusters between an 
Australian marsupial of the kangaroo family and the eutherians. There was a 
strikingly high level of conservation of HOX gene sequence and structure and 
non-protein coding genes including the microRNAs miR-196a, miR-196b, miR-10a and 
miR-10b and the long non-coding RNAs HOTAIR, HOTAIRM1 and HOXA11AS that play 
critical roles in regulating gene expression and controlling development. By 
microRNA deep sequencing and comparative genomic analyses, two conserved 
microRNAs (miR-10a and miR-10b) 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 miR-10, miR-414 and miR-464, were found 
in the tammar HOX clusters. In addition, several novel and putative miRNAs were 
identified that originated from elsewhere in the tammar genome and that target 
the tammar HOXB and HOXD clusters.
CONCLUSIONS: 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 HOX 
genes to influence the body plan of this marsupial.