Chromosome Research

, Volume 16, Issue 8, pp 1159–1175 | Cite as

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

  • Janine E. Deakin
  • Edda Koina
  • Paul D. Waters
  • Ruth Doherty
  • Vidushi S. Patel
  • Margaret L. Delbridge
  • Bianca Dobson
  • James Fong
  • Yanqiu Hu
  • Cecilia van den Hurk
  • Andrew J. Pask
  • Geoff Shaw
  • Carly Smith
  • Katherine Thompson
  • Matthew J. Wakefield
  • Hongshi Yu
  • Marilyn B. Renfree
  • Jennifer A. Marshall Graves
Article

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.

Key words

comparative mapping genomics marsupial X chromosome evolution 

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

Supplementary material

10577_2008_1266_MOESM1_ESM.doc (146 kb)
(DOC 146 KB)
10577_2008_1266_MOESM2_ESM.xls (250 kb)
(XLS 249 KB)

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Copyright information

© Springer Science+Business Media B.V. 2008

Authors and Affiliations

  • Janine E. Deakin
    • 1
  • Edda Koina
    • 1
  • Paul D. Waters
    • 1
  • Ruth Doherty
    • 1
  • Vidushi S. Patel
    • 1
  • Margaret L. Delbridge
    • 1
  • Bianca Dobson
    • 1
  • James Fong
    • 1
  • Yanqiu Hu
    • 2
  • Cecilia van den Hurk
    • 1
  • Andrew J. Pask
    • 2
  • Geoff Shaw
    • 2
  • Carly Smith
    • 1
  • Katherine Thompson
    • 1
  • Matthew J. Wakefield
    • 3
  • Hongshi Yu
    • 2
  • Marilyn B. Renfree
    • 2
  • Jennifer A. Marshall Graves
    • 1
  1. 1.ARC Centre of Excellence for Kangaroo Genomics, Research School of Biological SciencesThe Australian National UniversityCanberraAustralia
  2. 2.ARC Centre of Excellence for Kangaroo Genomics, Department of ZoologyUniversity of MelbourneVictoriaAustralia
  3. 3.The Walter and Eliza Hall InstituteVictoriaAustralia

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