**6. References**

14 Bacterial Artificial Chromosomes

genome assembly made it more difficult to anchor each scaffold but FISH-mapping of BACs assigned 198 scaffolds, corresponding to approximately 20% of the genome, to

Anchoring of the even more fragmented wallaby and devil genome assemblies required a different approach. A novel approach was developed to anchor the low-coverage wallaby genome sequence to chromosomes. A cytogenetic map of the genome was constructed by mapping BACs containing genes from the ends of human-opossum conserved gene blocks. This strategy was first trialed on tammar wallaby chromosome 5 (Deakin et al., 2008b) and later applied to the entire genome (Renfree et al., 2011). A virtual map of the wallaby genome was made by extrapolating from the content of these mapped conserved blocks from the opossum genome assembly, thereby allowing the location of each gene on tammar wallaby chromosomes to be predicted (Wang et al., 2011a). A similar approach is being used to construct a map of the devil genome, which has been sequenced entirely by next

Linkage (genetic) maps are a useful resource as they provide information not only on the order of genetic markers on a chromosome but on the location and frequencies of crossover events. Such maps are even more valuable if the maps are anchored to chromosomes and integrated with available genome assembly and/or cytogenetic mapping data. Linkage maps have been constructed for two marsupial species, opossum (Samollow et al., 2007) and the wallaby (Wang et al., 2011b). BACs containing markers at the ends of linkage groups have been used to cytogenetically assign these groups to chromosomes and determine the genome coverage of the linkage maps (Samollow et al., 2007; Wang et al., 2011b). The opossum linkage map was integrated with the genome assembly and cytogenetic map by FISH-mapping 34 BAC clones from the ends of linkage groups (Duke et al., 2007; Samollow et al., 2007). A sophisticated approach was used in the marker selection for construction of the wallaby linkage map to facilitate the integration of cytogenetic and linkage map data. Three strategies were developed to fill gaps in the 1st generation linkage map (Zenger et al., 2002) using information from BACs. The first strategy involved identifying microsatellites in BACs that had been previously assigned to chromosomes by FISH. The second strategy identified microsatellites within BAC end sequences and the third used the wallaby genome sequence to identify microsatellite markers near BACs that had been mapped by FISH. This resulted in a linkage map that could easily be incorporated with the physical map data to generate an integrated map (Wang et al., 2011a, 2011b). Information from the integrated map has been used to

improve and anchor the tammar wallaby genome assembly (Renfree et al., 2011).

Our understanding of marsupial and monotreme genomes has been greatly advanced due in large part to the availability of BAC libraries for several key species. With the emergence of Devil Facial Tumour Disease (DFTD), a transmissible cancer threatening the extinction of this species in the wild within the next 25 years (McCallum et al., 2007), many marsupial researchers are are focusing their efforts on characterization of this devastating disease. BAC libraries are playing a play a major role in this work, building on the strategies developed

chromosomes (Warren et al., 2008).

generation sequencing (Miller et al., 2011).

**4. BACs and marsupial linkage maps** 

**5. Conclusions** 


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