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Open Access Research article

A first-generation integrated tammar wallaby map and its use in creating a tammar wallaby first-generation virtual genome map

Chenwei Wang12, Janine E Deakin13*, Willem Rens4, Kyall R Zenger15, Katherine Belov12, Jennifer A Marshall Graves13 and Frank W Nicholas2

Author affiliations

1 Australian Research Council (ARC) Centre of Excellence for Kangaroo Genomics

2 Faculty of Veterinary Science, University of Sydney, NSW 2006, Australia

3 Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia

4 Department of Veterinary Medicine, University of Cambridge, UK

5 School of Marine & Tropical Biology, James Cook University, Townsville, QLD 4811, Australia

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Citation and License

BMC Genomics 2011, 12:422  doi:10.1186/1471-2164-12-422

Published: 19 August 2011

Abstract

Background

The limited (2X) coverage of the tammar wallaby (Macropus eugenii) genome sequence dataset currently presents a challenge for assembly and anchoring onto chromosomes. To provide a framework for this assembly, it would be a great advantage to have a dense map of the tammar wallaby genome. However, only limited mapping data are available for this non-model species, comprising a physical map and a linkage map.

Results

We combined all available tammar wallaby mapping data to create a tammar wallaby integrated map, using the Location DataBase (LDB) strategy. This first-generation integrated map combines all available information from the second-generation tammar wallaby linkage map with 148 loci, and extensive FISH mapping data for 492 loci, especially for genes likely to be located at the ends of wallaby chromosomes or at evolutionary breakpoints inferred from comparative information. For loci whose positions are only approximately known, their location in the integrated map was refined on the basis of comparative information from opossum (Monodelphis domestica) and human. Interpolation of segments from the opossum and human assemblies into the integrated map enabled the subsequent construction of a tammar wallaby first-generation virtual genome map, which comprises 14336 markers, including 13783 genes recruited from opossum and human assemblies. Both maps are freely available at http://compldb.angis.org.au webcite.

Conclusions

The first-generation integrated map and the first-generation virtual genome map provide a backbone for the chromosome assembly of the tammar wallaby genome sequence. For example, 78% of the 10257 gene-scaffolds in the Ensembl annotation of the tammar wallaby genome sequence (including 10522 protein-coding genes) can now be given a chromosome location in the tammar wallaby virtual genome map.