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Reconstruction of the ancestral marsupial karyotype from comparative gene maps.

Deakin JE, Delbridge ML, Koina E, Harley N, Alsop AE, Wang C, Patel VS, Graves JA - BMC Evol. Biol. (2013)

Bottom Line: Expanding comparisons to include chicken and human permitted the putative ancestral marsupial (2n = 14) and therian mammal (2n = 19) karyotypes to be reconstructed.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: ARC Centre of Excellence for Kangaroo Genomics, Canberra, Australia. janine.deakin@canberra.edu.au.

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.

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Related in: MedlinePlus

Mapping of genes to the short arm of wallaby chromosome 2. FISH mapping of BET1L (green) and AIP (red) indicates homology to human 11p. Scale bar represents 1 ╬╝m.
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Figure 5: Mapping of genes to the short arm of wallaby chromosome 2. FISH mapping of BET1L (green) and AIP (red) indicates homology to human 11p. Scale bar represents 1 ╬╝m.

Mentions: Gene mapping also resolved previous blank spots on the map where homology between species was not previously identified by chromosome painting and unassigned genes in the opossum genome assembly. For instance, chromosome painting failed to identify the opossum region homologous to wallaby 2p [6]. Several human chromosome 11p15.5 genes (IGF2, MRPL23, CD81) had been assigned to wallaby 2p as part of studies into the location of imprinted gene clusters in the wallaby [34,35]. These genes have no chromosomal assignment in the opossum genome assembly [24]. However, IGF2 has been localised by FISH to opossum 5q3 [36], suggesting that wallaby 2p is homologous to a small region on opossum 5q3. We mapped two other genes (BET1L, TSSC4) from human 11p15.5 in the wallaby to 2p, providing more support for this claim. An additional gene (AIP from a different region of human chromosome 11q13.3), expected from its opossum location to map to wallaby chromosome 3, also localised to wallaby 2p (Figure 5). This suggests either that a transposition event occurred or there is an error in the opossum genome assembly.


Reconstruction of the ancestral marsupial karyotype from comparative gene maps.

Deakin JE, Delbridge ML, Koina E, Harley N, Alsop AE, Wang C, Patel VS, Graves JA - BMC Evol. Biol. (2013)

Mapping of genes to the short arm of wallaby chromosome 2. FISH mapping of BET1L (green) and AIP (red) indicates homology to human 11p. Scale bar represents 1 ╬╝m.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4222502&req=5

Figure 5: Mapping of genes to the short arm of wallaby chromosome 2. FISH mapping of BET1L (green) and AIP (red) indicates homology to human 11p. Scale bar represents 1 ╬╝m.
Mentions: Gene mapping also resolved previous blank spots on the map where homology between species was not previously identified by chromosome painting and unassigned genes in the opossum genome assembly. For instance, chromosome painting failed to identify the opossum region homologous to wallaby 2p [6]. Several human chromosome 11p15.5 genes (IGF2, MRPL23, CD81) had been assigned to wallaby 2p as part of studies into the location of imprinted gene clusters in the wallaby [34,35]. These genes have no chromosomal assignment in the opossum genome assembly [24]. However, IGF2 has been localised by FISH to opossum 5q3 [36], suggesting that wallaby 2p is homologous to a small region on opossum 5q3. We mapped two other genes (BET1L, TSSC4) from human 11p15.5 in the wallaby to 2p, providing more support for this claim. An additional gene (AIP from a different region of human chromosome 11q13.3), expected from its opossum location to map to wallaby chromosome 3, also localised to wallaby 2p (Figure 5). This suggests either that a transposition event occurred or there is an error in the opossum genome assembly.

Bottom Line: Expanding comparisons to include chicken and human permitted the putative ancestral marsupial (2n = 14) and therian mammal (2n = 19) karyotypes to be reconstructed.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: ARC Centre of Excellence for Kangaroo Genomics, Canberra, Australia. janine.deakin@canberra.edu.au.

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.

Show MeSH
Related in: MedlinePlus