At the latest Biology of Genomes meeting the University of Oxford's Hilary Martin described how she and her colleagues endeavored to improve the draft platypus genome, while also seeking to better understand how biological processes like recombination and how multiple sex chromosomes have evolved in the platypus, which diverged from other mammals some 166 million years ago.
A draft platypus genome was published in Nature in 2008, but Martin noted that it is incomplete because only a small portion of scaffolds were able to be assigned to the platypus' 21 autosome pairs, as much of the genome is marked by repetitive sequences.
To improve on that assembly, she and her colleagues sequenced 61 platypuses from 14 rivers in eastern Australia and Tasmania using a combination of approaches, including long mate-pair reads, BACs, and fosmids, as well as Illumina Moleculo and optical mapping-derived reads.
At this point, Martin said that she and her colleagues have been able to reduce the errors and fill in about a third of the gaps.
She also noted that they took a stringent approach to SNP calling and only called ones that were flagged by both GATK and CORTEX, generating some 2.4 million SNPs.
There are numerous lines of evidence, Martin said, suggesting that the platypus lacks any PRDM9 genes, the product of which are responsible in mammals for determining where genomic hotspots of recombination are located.
Still, she said that their examination of multiple platypus genomes indicated that there are regions of the genome that are indeed recombination hotspots. Platypuses from rivers 400 kilometers apart had both overlapping and unique genomic regions where recombination occurred. She added that at a finer scale there are differences in recombination rates between platypus populations.
This, Martin said, suggests that there may either be undetected PRDM9 genes in the platypus genome or a new mechanism that is acting to mark recombination hotspots in the platypus.
Rather than relying on one pair of sex chromosomes, the platypus genome has five — a male platypus has five X and five Y chromosomes, all of which are linked together in a chain through nine pseudoautosomal regions during cell division. Martin noted that the chain is thought to have evolved starting from the X5Y5 end down on to the X1Y1 end through serial translocations, and the different XY pairs have different ages.
The reference platypus genome was a derived from a female animal, so Martin and her colleagues had to determine the Y sequence by assembling male-specific reads, mapping them to the female reference, and seeing where they diverged. They noted that Y-specific sequences, especially ones near the PAR boundaries, are similar to the X-chromosome versions, and that there appeared to be some variation based on which river the platypus hailed from.
One male sample, she noted, had a PAR boundary that was shifted with respect to what many of his fellow males had, though a few others from his river had the polymorphism. This, Martin said, suggests that a rather recent recombination event has taken place between the Y and the X chromosome. The event, she added, could either have been due to meiotic recombination or non-allelic homologous recombination.