The tarsier's nuclear genome comes with a bonus mitochodrial genome

A tarsier, looking as shocked as we are.(Fickr: Keren Tan)

A tarsier, looking as shocked as we are. (Fickr: Keren Tan)

This week Nature Communications published a paper presenting a new genome assembly for Tarsius syrichta, the Phillipine tarsier. Tarsiers are the subject of one of the best of Ze Frank’s “True Facts” videos, and they occupy an interesting place in the family tree of primates — their common ancestor with humans pre-dates the common ancestor of monkeys and apes, but post-dates the divergence of the group that includes lemurs and lorises, the Strepsirrhini. This phylogenetic position doesn’t mean that tarsiers are a transitional form between (say) lemurs and gorillas, they do have traits that are considered distinctive to both groups, and a tarsier genome sequence helps to understand evolutionary change across the primates.
The genome turns out to have a lot of what we casually call junk. Long and short interspersed elements (LINEs and SINEs) account for over 31% of the new genome assembly, and the paper’s authors invent the term “tarsier intersperesed elements” (TINEs) for repetive sequence elements unique to the tarsier genome. They also found sequences that were likely transferred from the mitochondrial genome, the set of genetic code inside the mitochondria of every cell. This is a common enough phenomenon in eukaryotes — but one of the ones in the tarsier genome comprises the entire, contiguous mitochondrial genome sequence.
(Schmitz et al. 2016: Figure 4)

Alignment of a 17,866bp-long region of tarsier nuclear DNA sequence against the nuclear genome, with Southern blog images inset. (Schmitz et al. 2016: Figure 4)

The authors suggest that some ancestral tarsier’s nucleus didn’t swallow the mitochondrial genome in one gulp, so to speak, but that this represents a sort of assembly over time — mutiple fragments transferred separately, then brought together by recombination. (It is not clear to me that the former is more parsimonious than the latter.) Although they go to some additional effort to validate the whole-mitochondrial-genome sequence with a Southern blot, the authors do not evaluate whether any of it is expressed — that’s probably a whole different paper. They do point out that the duplication provides a kind of interesting experiment in molecular evolution:

We contend that this unique tarsier event offers a new perspective in comparing the evolutionary changes between the rapidly changing mitochondrial DNA and slowly changing nuclear sequences, both originating from the same source but evolving under very different selective constraints.

All in all, there’s every reason to think this reference genome has laid the groundwork for some very cool science yet to come. Maybe Ze Frank can do a sequel?

Perelman P, Johnson WE, Roos C, Seuanez HN, Horvath JE, et al. 2011. A molecular phylogeny of living primates. PLOS Genetics 7(3): e1001342. doi: 10.1371/journal.pgen.1001342
Richly, E. and D. Leister. 2004. NUMTs in sequenced eukaryotic genomes. Molecular Biology and Evolution 21: 1081-1084. doi: 10.1093/molbev/msh110
Schmitz, J. et al. 2016. Genome sequence of the basal haplorrhine primate Tarsius syrichta reveals unusual insertions. Nature Communications 7: 12997 doi: 10.1038/ncomms12997

About Jeremy Yoder

Jeremy B. Yoder is an Associate Professor of Biology at California State University Northridge, studying the evolution and coevolution of interacting species, especially mutualists. He is a collaborator with the Joshua Tree Genome Project and the Queer in STEM study of LGBTQ experiences in scientific careers. He has written for the website of Scientific American, the LA Review of Books, the Chronicle of Higher Education, The Awl, and Slate.
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