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Open Access Research article

Reconstruction of the ancestral marsupial karyotype from comparative gene maps

Janine E Deakin123*, Margaret L Delbridge12, Edda Koina124, Nerida Harley125, Amber E Alsop126, Chenwei Wang17, Vidushi S Patel12 and Jennifer A Marshall Graves128

Author Affiliations

1 ARC Centre of Excellence for Kangaroo Genomics, Canberra, Australia

2 Evolution, Ecology and Genetics; Research School of Biology, The Australian National University, Canberra ACT 0200, Australia

3 Institute of Applied Ecology, University of Canberra, Canberra ACT 2601, Australia

4 Current Address: Cytogenetics Department, ACT Pathology, The Canberra Hospital, Yamba Drive, Canberra 2605, Australia

5 Current Address: Surgery, The University of Western Australia, 35 Stirling Highway, Crawley WA 6009, Australia

6 Current Address: Walter & Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Victoria 3052, Australia

7 Australian Prostate Cancer Research Centre-Queensland, Queensland University of Technology, 199 Ipswich Rd, Brisbane, QLD 4102, Australia

8 La Trobe Institute of Molecular Sciences, La Trobe University, Melbourne, Victoria 3086, Australia

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BMC Evolutionary Biology 2013, 13:258  doi:10.1186/1471-2148-13-258

Published: 21 November 2013

Abstract

Background

The increasing number of assembled mammalian genomes makes it possible to compare genome organisation across mammalian lineages and reconstruct chromosomes of the ancestral marsupial and therian (marsupial and eutherian) mammals. However, the reconstruction of ancestral genomes requires genome assemblies to be anchored to chromosomes. The recently sequenced tammar wallaby (Macropus eugenii) genome was assembled into over 300,000 contigs. We previously devised an efficient strategy for mapping large evolutionarily conserved blocks in non-model mammals, and applied this to determine the arrangement of conserved blocks on all wallaby chromosomes, thereby permitting comparative maps to be constructed and resolve the long debated issue between a 2n = 14 and 2n = 22 ancestral marsupial karyotype.

Results

We identified large blocks of genes conserved between human and opossum, and mapped genes corresponding to the ends of these blocks by fluorescence in situ hybridization (FISH). A total of 242 genes was assigned to wallaby chromosomes in the present study, bringing the total number of genes mapped to 554 and making it the most densely cytogenetically mapped marsupial genome. We used these gene assignments to construct comparative maps between wallaby and opossum, which uncovered many intrachromosomal rearrangements, particularly for genes found on wallaby chromosomes X and 3. Expanding comparisons to include chicken and human permitted the putative ancestral marsupial (2n = 14) and therian mammal (2n = 19) karyotypes to be reconstructed.

Conclusions

Our physical mapping data for the tammar wallaby has uncovered the events shaping marsupial genomes and enabled us to predict the ancestral marsupial karyotype, supporting a 2n = 14 ancestor. Futhermore, our predicted therian ancestral karyotype has helped to understand the evolution of the ancestral eutherian genome.

Keywords:
Comparative genomics; Comparative mapping; Physical map; Marsupial; Ancestral karyotype