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Tarsier Genome Assembly Helps Explain Evolutionary History of Primates

NEW YORK (GenomeWeb) – A new tarsier genome assembly places the Southeast Asian primate within the anthropoidea lineage, which also includes monkeys, apes, and humans.

The nocturnal, carnivorous, and arboreal primate is small, with long fingers and legs as well as bulging eyes. It sits at a key node of primate phylogeny and shares certain features, like an unfused lower jaw, with one branch of primates and the lack of a wet nose with another.

After sequencing and assembling the tarsier genome, researchers from the US and Germany examined the animal's spot in the primate lineage, reporting their findings today in Nature Communications. They also uncovered a number of interspersed elements within the tarsier genome, a mitochondrial genome insertion, and several regions under positive selection.

"We sequenced the tarsier not only to determine where they fit in primate evolution, but because their physiology, anatomy, and feeding behavior are very unique," senior author Wesley Warren from Washington University School of Medicine in St. Louis said in a statement.

Warren and his colleagues sequenced the genome of a female tarsier, Tarsius syrichta, from the Philippines to 44X coverage using a combination of Sanger ABI 3730 and Illumina sequencing. From the assembly, they predicted the tarsier genome to include 20,820 protein-coding genes and detected 223 snoRNAs.

Using a three-pronged approach, the researchers then examined transposable elements within the tarsier genome to gauge when various families of transposons were active within the primate lineage. They uncovered some 740 families of repeats within the tarsier genome, including long interspersed elements, long terminal repeats, and short interspersed elements.

Alu elements, they reported, were active in all primate lineages, though younger tarsier Alu sequences were more commonly found within AT-rich sequences, while older ones were in GC-rich regions. They also uncovered three families of repetitive elements specific to the tarsier genome, or TINEs.

Tarsiers, they found, share more recent transposon families with the squirrel monkey and humans, and only the oldest with bushbabies, suggesting that they belong to the same lineage as monkeys, apes, and humans.

The tarsier nuclear genome also harbors a complete insertion of a mitochondrial genome, the first time that has been identified in a mammal, the researchers said. They confirmed the insertion using PCR followed by sequencings and by Southern blot analysis. It is likely the result of recombination between existing transfers of mitochondrial DNA into nuclear DNA, the researchers said, and it suggests that random mitochondrial fragments have been continuously inserted and accumulated throughout primate evolution.

The researchers uncovered 192 genes within the tarsier genome that are under positive selection. When they tested them for disease or pathway associations, they found that eight of the genes have been linked to eye development and visual issues. This, the researchers noted, might reflect tarsiers' adaptations for seeing at night and catching prey.

At the same time, other regions under selection in the tarsier genome have been lined to musculoskeletal disorders in people, including mutations in the TCAP protein, which are linked to calf hypertrophy and proximal atrophy in the upper limbs and distal atrophy in the lower limbs.

"The tarsier genes that display unique alterations can give us a clue into human diseases involving the same genes," Warren said. "If an amino acid has been uniquely changed and it is putatively associated with the tarsier's novel musculature, maybe it's an important part of the protein and worthy of a closer look when linked to human disease."

Tarsiers' effective population size has been falling, the researchers reported. "We think the population size is declining and not rebounding," Warren said. "Most of the decline is due to loss of habitat, but the pet trade also is contributing. … It's possible that some tarsier species will go extinct if we don't change these trajectories."