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Genome Sequencing Offers Look at Leaf, Seed Consumption in Snub-Nosed Monkeys

NEW YORK (GenomeWeb News) – Researchers from China, the US, and Germany have produced a draft genome for the golden snub-nosed monkey, Rhinopithecus roxellana, and re-sequenced three related species in an effort to understand a group of leaf- and seed-eating Old World monkeys called colobines.

Reporting in Nature Genetics this weekend, the team described features of the golden snub-nosed monkey assembly and genome sequences from three other Asian colobine monkeys: the black-white snub-nosed monkey (R. bieti), found in China and on the Tibetan plateau, the gray snub-nosed monkey (R. brelichi), which is native to China, and the Myanmar snub-nosed monkey (R. strykeri).

By comparing these sequences to one another and to the genomes of other animals, the researchers untangled relationships between colobine monkeys and dredged up new clues about their dietary adaptations and evolutionary history.

Meanwhile, complementary gut microbiome experiments suggest that cellulose-processing gut bugs help the colobine monkeys digest plant products that other primates can't easily break down.

From this data, the study's authors described the "phylogenetic status, evolution of gene families, stomach metagenomics, and climate-shaped demographic histories" for snub-nosed monkeys — features that they said will "provide a key database and framework for understanding the evolution and functional adaptive patterns of colobines and for developing a program of conservation to promote the survival of these endangered species."

Most Old World monkeys consume fruits and insects, prompting interest in colobines' taste for leaves and seeds, a dietary adaptation known as folivory, the researchers explained. The monkeys digest plant material using a compartmentalized stomach that ferments and digests plant material in a manner that resembles that found in cattle, deer, pigs, goats, and other animals.

In an effort to understand the genetics of this dietary adaptation and gain more general clues to conserving endangered snub-nosed species, the team started by using an Illumina HiSeq 2000 instrument to sequence DNA from a male golden snub-nosed monkey at the Beijing Wildlife Park.

The researchers used these reads to put together a 3.05-billion-base de novo genome assembly, covered to an average depth of around 146-fold. They also did transcriptome sequencing on tissue samples collected from a deceased female golden snub-nosed monkey at the Beijing zoo, including RNA sequencing on stomach tissue.

The team's analysis of the genome uncovered 21,813 apparent protein-coding genes — an annotation supported by transcriptome sequences that verified nearly 90 percent of the predicted genes. It also identified sequences stemming from mobile elements, which made up roughly half of the golden snub-nosed monkey genome.

Through comparisons with sequences from primates such as humans, chimpanzees, and rhesus macaques and from other mammals, the researchers saw gene family expansions in the golden snub-nosed monkey genome that are expected to make the animals more adept at breaking down potentially toxic compounds such as secondary metabolites found in some leaves.

Among genes showing signs of positive selection, meanwhile, were those that appear to help in producing and using energy found in fatty acids and in other metabolic processes needed to subsist on high-fiber, nutrient-poor, low-energy food sources. Many of the same genes seem to be changing rapidly in cattle, too, the researchers noted, consistent with parallel evolution between plant-consuming creatures from each lineage.

Likewise, the snub-nosed monkey genome analysis revealed duplications in an enzyme-coding gene called RNASE1, which has been linked to bacterial RNA digestion in ruminant animals.

To further explore the snub-nosed monkey's digestive capabilities, the team used 16S ribosomal RNA gene sequencing to identify members of the monkey's gut bacterial communities that help break down difficult-to-digest materials.

While the monkeys' gut microbiomes shared some features with those described in humans, for instance, the bacterial genera tended to be even more closely comparable to those found in the cattle gut microbiome, including fermentation-related microbes.

Finally, by re-sequencing a black-white snub-nosed monkey from a nature reserve in China's Yunnan province, a gray snub-nosed monkey from the Beijing zoo, and a Myanmar sub-nosed monkey from another Yunnan nature reserve near the border with Myanmar, the investigators fleshed out relationships between four of the five known Rhinopithecus species and discerned new details about their evolutionary histories.

For instance, the analysis suggests that the black-white snub-nosed monkey and Myanmar snub-nosed monkey split from the species found in more northern sites at around the time the Tibetan plateau and Himalayan mountains arose, with climatic shifts and habitat changes impacting snub-nosed species since then.