Reconstruction of the ancestral marsupial karyotype from comparative gene maps

Abstract

BackgroundThe 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.ResultsWe 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.ConclusionsOur 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.

Identification of candidate genes for devil facial tumour disease tumourigenesis

“…The devil genome project, which sequenced flow sorted chromosomes, allowed genes to be assigned to normal devil chromosomes but their precise location on the chromosome was unknown 15 . We isolated BAC clones for mapping corresponding to genes previously mapped to tammar wallaby chromosomes 21 (to permit a direct comparison of gene arrangement between marsupials if needed), or the ends of large (>3 Mbp) sequence scaffolds in the devil genome assembly (version 7.0). The genome coordinates of most BAC clones within the devil genome assembly were determined by sequencing the ends of each BAC clone (Supplementary Dataset 1A ).…”

“…Overgo probes for (i) genes mapped in the tammar wallaby and located near the ends of human-opossum evolutionary conserved blocks 21 , (ii) sequences located near the ends of large sequence scaffolds in the devil genome assembly 15 or (iii) for genes involved in human cancer. Devil genomic sequence for the genes or regions of interest were obtained from Ensembl (genome assembly Devil_ref7.0) and used as input sequence for the Overgo Maker program developed by The Genome Institute at Washington University.…”

Anchoring genome sequence to chromosomes of the central bearded dragon (Pogona vitticeps) enables reconstruction of ancestral squamate macrochromosomes and identifies sequence content of the Z chromosome

“…Our initial approach was to isolate BAC clones containing a gene located at the end of either anole-chicken or chicken-human homologous synteny blocks (HSBs) with the intention that, by mapping a gene from each block, we would be able to extrapolate and assign a virtual location for all genes within the block to the chromosome from which the BAC mapped. A similar approach was successfully used to anchor the tammar wallaby genome to chromosomes, where conserved gene blocks ranged in size from 30 kb to 218 Mb [ 4 , 37 , 38 ]. We chose 40 of the larger 256 anole-chicken HSBs representing 18 chicken chromosomes as well as the six anole macrochromosomes and four anole linkage groups (Additional file 1 ).…”

“…Ancestral karyotype reconstructions over greater evolutionary distances are possible when chromosome painting data are combined with gene mapping and whole genome sequence data. For instance, a comparison of gene mapping data for the tammar wallaby ( Macropus eugenii ) genome compared with anchored genome assemblies for the grey short-tailed opossum ( Monodelphis domestica ), chicken ( Gallus gallus ) and human permitted the first prediction of the ancestral therian (marsupial and eutherian) mammal karyotype [ 4 ]. Similarly, a comparison of gene mapping data for species of turtle, crocodile, frog, salamander and snake compared with genome assemblies for chicken and human enabled the ancestral karyotype of amniotes to be predicted [ 5 ].…”

Tracing the evolution of amniote chromosomes

“…The arrangement of the conserved segments in the 2 n  = 14 species was observed to be more ancestral than that predicted for the 2 n  = 22 species. The chromosome arrangements of other species could be easily derived, mainly by fissions and inversions, from a 2 n  = 14 karyotype (Deakin et al 2013). …”