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Physical map of two tammar wallaby chromosomes: A strategy for mapping in non-model mammals

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Abstract

Marsupials are especially valuable for comparative genomic studies of mammals. Two distantly related model marsupials have been sequenced: the South American opossum (Monodelphis domestica) and the tammar wallaby (Macropus eugenii), which last shared a common ancestor about 70 Mya. The six-fold opossum genome sequence has been assembled and assigned to chromosomes with the help of a cytogenetic map. A good cytogenetic map will be even more essential for assembly and anchoring of the two-fold wallaby genome. As a start to generating a physical map of gene locations on wallaby chromosomes, we focused on two chromosomes sharing homology with the human X, wallaby chromosomes X and 5. We devised an efficient strategy for mapping large conserved synteny blocks in non-model mammals, and applied this to generate dense maps of the X and ‘neo-X’ regions and to determine the arrangement of large conserved synteny blocks on chromosome 5. Comparisons between the wallaby and opossum chromosome maps revealed many rearrangements, highlighting the need for comparative gene mapping between South American and Australian marsupials. Frequent rearrangement of the X, along with the absence of a marsupial XIST gene, suggests that inactivation of the marsupial X chromosome does not depend on a whole-chromosome repression by a control locus.

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Abbreviations

BAC:

bacterial artificial chromosome

BLASTN:

basic local alignment search tool nucleotide

bp:

base pair(s)

CCD:

charge-coupled device

cDNA:

complementary DNA

DAPI:

4′,6-diamidino-2-phenylindole dihydrochloride

dUTP:

2′-deoxyuridine 5′-triphosphate

FISH:

fluorescence in-situ hybridization

GGA:

Gallus gallus

HSA:

Homo sapiens

kb:

kilo base pairs

LB:

Luria broth

Mb:

mega base pairs

MDO:

Monodelphis domestica

MHC:

major histocompatibility complex

Mya:

million years ago

OR:

olfactory receptor

PCR:

polymerase chain reaction

RISH:

radioactive in-situ hybridization

SSC:

standard sodium citrate

XAR:

X added region

XCI:

X chromosome inactivation

XCR:

X conserved region

XIC:

X inactivation centre

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Acknowledgements

We thank Ke-Jun Wei for curation of the tammar wallaby BAC libraries, and Anthony Papenfuss and Kaighin McColl for bioinformatic tools used during this project. This project was funded by the Australian Research Council (to J.A.M.G. and M.B.R.).

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Correspondence to Janine E. Deakin.

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Deakin, J.E., Koina, E., Waters, P.D. et al. Physical map of two tammar wallaby chromosomes: A strategy for mapping in non-model mammals. Chromosome Res 16, 1159–1175 (2008). https://doi.org/10.1007/s10577-008-1266-y

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