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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

Examples of FISH determining the orientation of adjacent BAC clones on tammar wallaby metaphase chromosomes. Orientation of (A)SERPINA1 labelled green and NUDC2 in red on chromosome 1; (B)RUNX2 in red and MRPS10 in green on chromosome 2 and (C)CORTBP2 in green and p100 in red on chromosome 3. Chromosomes have been counterstained with DAPI. Scale bar represents 10 μm.
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Figure 1: Examples of FISH determining the orientation of adjacent BAC clones on tammar wallaby metaphase chromosomes. Orientation of (A)SERPINA1 labelled green and NUDC2 in red on chromosome 1; (B)RUNX2 in red and MRPS10 in green on chromosome 2 and (C)CORTBP2 in green and p100 in red on chromosome 3. Chromosomes have been counterstained with DAPI. Scale bar represents 10 μm.

Mentions: Given the resolution limitations of FISH on condensed metaphase chromosomes to regions separated by more than 1 Mb [33], we targeted genes at both ends of large conserved blocks (>3 Mb) and one gene within a smaller block (<3 Mb). Wallaby-specific overgo probes were designed for these genes using wallaby genome sequence, and used to screen the wallaby BAC library. BACs containing these genes were mapped using fluorescence in situ hybridisation (FISH). The relative order of genes on the same chromosome was determined by labelling adjacent BACs with different fluorochromes (see Figure 1 for examples). We mapped 242 genes to wallaby chromosomes in this study and combined this with previously obtained physical mapping data (Table 2) to bring the total number of genes assigned to chromosomes in the wallaby to 554 (Figures 2, 3 and 4). The genes mapped and their corresponding BACs are listed in Additional file 1.


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)

Examples of FISH determining the orientation of adjacent BAC clones on tammar wallaby metaphase chromosomes. Orientation of (A)SERPINA1 labelled green and NUDC2 in red on chromosome 1; (B)RUNX2 in red and MRPS10 in green on chromosome 2 and (C)CORTBP2 in green and p100 in red on chromosome 3. Chromosomes have been counterstained with DAPI. Scale bar represents 10 μm.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Examples of FISH determining the orientation of adjacent BAC clones on tammar wallaby metaphase chromosomes. Orientation of (A)SERPINA1 labelled green and NUDC2 in red on chromosome 1; (B)RUNX2 in red and MRPS10 in green on chromosome 2 and (C)CORTBP2 in green and p100 in red on chromosome 3. Chromosomes have been counterstained with DAPI. Scale bar represents 10 μm.
Mentions: Given the resolution limitations of FISH on condensed metaphase chromosomes to regions separated by more than 1 Mb [33], we targeted genes at both ends of large conserved blocks (>3 Mb) and one gene within a smaller block (<3 Mb). Wallaby-specific overgo probes were designed for these genes using wallaby genome sequence, and used to screen the wallaby BAC library. BACs containing these genes were mapped using fluorescence in situ hybridisation (FISH). The relative order of genes on the same chromosome was determined by labelling adjacent BACs with different fluorochromes (see Figure 1 for examples). We mapped 242 genes to wallaby chromosomes in this study and combined this with previously obtained physical mapping data (Table 2) to bring the total number of genes assigned to chromosomes in the wallaby to 554 (Figures 2, 3 and 4). The genes mapped and their corresponding BACs are listed in Additional file 1.

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