Friday, 10 January 2014

Complete Genome of an Aurochs sequenced! Finally!

A paper presenting the fully-resolved nuclear genome of an aurochs individual from Britain is finally about to get published. They used an exceptionally well-preserved humerus from about 7.000 years BP.  Here you have the abstract: 


"The extinct wild Eurasian aurochs (Bos primigenius) was the progenitor of domestic taurine cattle (B. taurus). Although genetic and archaeological studies pinpoint the Near East as the centre of origin for Bos taurus, recent genetic evidence suggests that historical admixture may have occurred between domestic taurine cattle and wild aurochsen. Here, we present analyses of the first complete nuclear genome from an archaeologically-verified and exceptionally well-preserved aurochs humerus bone sample recovered from a cave site in Derbyshire, England and radiocarbon-dated to 6,738 ± 68 calibrated years before present (laboratory sample code: CPC98). Previous work in our laboratory has shown that this aurochs possessed a haplogroup P mitochondrial sequence, which predominates in Northern European aurochs samples examined to-date. For the present study, DNA extracts from the CPC98 humerus bone were prepared for Illumina® short read, high-throughput DNA sequencing. A consensus CPC98 B. primigenius nuclear genome was assembled, using the complete B. taurus genome. A mean read depth of 6.2× was generated from 470 million reads aligned to unique locations in the template genome, yielding a genome coverage of 2.37 Gb. Phylogenetic analyses using Illumina® BovineSNP50 BeadChip genotype data from modern B. taurus and B. indicus cattle place the CPC98 sample as an outgroup to all modern taurine cattle, consistent with common ancestry of taurine cattle from Near-Eastern aurochs. We have performed comparative analyses of coding sequences or candidate regulatory regions associated with genes using high-throughput DNA sequencing data from modern B. taurus and B. indicus cattle to identify over 300 genes in which CPC98 and indicine cattle share potentially functional SNP or indel alleles not seen in taurine cattle. Selection at these genes throughout the history of domestication and selective breeding may have played a key role in shaping the genome of modern taurine cattle."

Before you get too euphoric, this individual cannot be cloned yet. It is a reconstructed sequence, for cloning this aurochs you need a functioning set of chromosomes. One method to reconstruct this individual using the genome is to modify the genome of a domestic cattle step-by-step to achieve a 100% aurochs, but this is a long-term process. Another possibility is de novo synthesis of the chromosome set, which is technically not possible yet but might be in the near future. 
Nevertheless, this is more-ground braking than it sounds at first. The fact that it was possible to sequence the full genome from this early Holocene bone might indicate that this is possible with a large number of individuals - maybe close to 100, based on the large number of aurochs remains that we know. It might not only be possible to do that with the aurochs alone - it might be possible with the Holocene wild horses of Europe as well - and a whole set of other early Holocene and late Pleistocene extinct species. And if the gained genetic diversity to low, it can always be improved by crossing-in similar domestic counterparts. We know that these species serve a function in the european ecosystems and that they were exterminated by man, so the answer to the question "Should be do this?" is "yes, definitely we should". And even if the animals don't serve a function in modern ecosystems like saber-toothed cats, it's still a huge progress in studying these animals, so it is desirable in any case. The "ethical problems" related to genetic reconstructions provoked by people who have hardly an idea what they are talking about are quite a non-issue, so let's not concern us with that. 

Although technique is not ready yet, the possibility is good that we see several true aurochs in flesh again in a not too distant future!

7 comments:

  1. This comment has been removed by the author.

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  2. Another question would be how much use is the genome sequence to the current breeding back projects?

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    1. It could show which genes were present in this aurochs and which are not in cattle, and which cattle have genes in common with this aurochs that other cattle don't; the way I see it. I don't know if such studies will be conducted, and still nobody has a clue what role "genetics" (genetics is a wide field and in this context it can have several meanings) play in the Tauros Project. Probably not a large one, they cannot select for a good phenotype AND for certain haplotypes or whatever aurochs markers at the same time and expect to be done within this half of the century. My opinion.

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  3. Have other wild cattle been sequenced? How does it compare? How does this genome compare to domestic cattle?

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    1. Nothing is published yet, so we will still have to wait to get a better clue on that. BTW, I expect that the aurochs is at the base of the Bos genus, and therefore the sister species to the clade of Kouprey + Banteng + Gaur.

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    2. Well in that case it would merit the inclusion of those species in the effort to bring back primigenius. (I think Kouprey probably was a primigenius subspecies).

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    3. Not necessarily; it is indeed possible that other wild bovines have genes that were present in the aurochs but lost in domestic cattle, but that's only speculation by now. Domestic cattle are closer to the aurochs (phylogenetically, genetically, ecologically etc.) in any case.

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