Abstract
BackgroundThe 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.ResultsWe 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.ConclusionsThe 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.
Highlights
The limited (2X) coverage of the tammar wallaby (Macropus eugenii) genome sequence dataset currently presents a challenge for assembly and anchoring onto chromosomes
The integrated and virtual maps of the tammar wallaby genome were created from the second-generation linkage map, comprising 148 loci [22], together with fluorescent in situ hybridisation (FISH)-mapping data for 492 loci (Deakin et al, unpublished data), using the strategy described by Liao et al [20]
We identified blocks of conserved synteny between tammar wallaby and opossum, and identified breakpoints between them
Summary
The limited (2X) coverage of the tammar wallaby (Macropus eugenii) genome sequence dataset currently presents a challenge for assembly and anchoring onto chromosomes. Marsupials are a interesting lineage of mammals, being only distantly related to eutherian (placental) mammals such as human and mouse. They have many major features common to all mammals, such as bearing. The first version (Meug_1.0) of the tammar wallaby assembly, released in December 2008, comprised relatively small contigs (N50 = 2.5 kb) and scaffolds (14.5 kb), consistent with the relatively low coverage. In July 2009, Ensembl released its annotation of these segments [13], but there remains insufficient genome structure information to enable any of these sequence segments to be assembled onto M. eugenii chromosomes
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