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Review
. 2003 Feb;4(2):143-7.
doi: 10.1038/sj.embor.embor739.

The kangaroo genome. Leaps and bounds in comparative genomics

Matthew J Wakefield  1 , Jennifer A Marshall Graves
Affiliations
Review

The kangaroo genome. Leaps and bounds in comparative genomics

Matthew J Wakefield et al. EMBO Rep. 2003 Feb.

Abstract

The kangaroo genome is a rich and unique resource for comparative genomics. Marsupial genetics and cytology have made significant contributions to the understanding of gene function and evolution, and increasing the availability of kangaroo DNA sequence information would provide these benefits on a genomic scale. Here we summarize the contributions from cytogenetic and genetic studies of marsupials, describe the genomic resources currently available and those being developed, and explore the benefits of a kangaroo genome project.

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Figures

Figure 1
Figure 1
The kangaroo fills a large gap in the vertebrate phylogeny and provides a middle ground between birds and eutherian mammals. Most eutherian mammals diverged less than 80 million years ago, whereas birds diverged about 350 million years ago (Benton, 1990; Murphy et al., 2001). The short divergence time to the mouse results in large amounts of background noise owing to the chance conservation of sequence, whereas avian sequences are difficult to align unambiguously outside highly conserved coding regions, often resulting in comparisons being made with non-homologous sequences. Marsupials, which diverged from eutherian mammals 130–180 million years ago, are the middle ground with more readily aligned sequence, and clear phylogenetic signals with low background noise.
Figure 2
Figure 2
Phylogenetic footprinting of the 3′ untranslated region of the SLC16A2 (XPCT) gene from human, mouse and tammar wallaby. Human, mouse and tammar wallaby were compared with VISTA (Dubchak et al., 2000). The human/mouse comparison indicates sequence similarity across the entire untranslated region, masking any localized regions of high functional constraint. In tammar/human and tammar/mouse comparisons the background level of conservation is lower, permitting the observation of localized regions of functional constraint. Similar results were obtained with the alternative phylogenetic footprinting program PipMaker2 (data not shown). bp, base pairs.
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