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Rhinoceros Genome Developments Debut at PAG Conference

SAN DIEGO (GenomeWeb) – Researchers are completing rhinoceros genome assemblies and other tools for deciphering Rhinocerotidae evolutionary relationships and biology — resources that may boost strategies to stop the remaining rhino species from sliding into extinction.

At a rhinoceros-focused session at the Plant and Animal Genomes meeting yesterday, the Swedish Museum of Natural History's Love Dalén described efforts to establish reference genomes for three rhino species: the black rhino (Diceros bicornis), Sumatran rhino (Dicerorhinus sumatrensis), and the extinct woolly rhino (Coelodonta antiquitatis).

There are five living species in the Rhinocerotidae family, which originated roughly 30 million to 40 million years ago, Dalén explained. Three other species became extinct in relatively recent evolutionary time, while several current species and sub-species are creeping closer to the brink.

Just three individuals remain from the northern white rhino (Ceratotherium simum cottoni) sub-species in Africa, for example, and all of them live in captivity. Southern white rhinos (C. simum simum) have fared somewhat better due to concentrated conservation efforts.

For their black rhino sequencing project, Dalén and his colleagues generated Illumina HiSeq X and HiSeq 2500 reads, which were assembled de novo using several different strategies. After continuing to improve that genome, they plan to resequence around 20 more black rhino genomes en route to a more refined view of black rhino diversity, population divergence, local adaptations, and the like.

In 2015, a University of Washington-led team crowd-funded a project to sequence their own black rhino, a female named Ntombi. As of August 2016, that group was working to obtain "an appropriate biological sample," according to the project's website.

Compared with the white rhino, the black rhino differs in size, lip shape, herbivory behavior, and distribution, presenter Yoshan Moodley, a genetics and evolutionary biology researcher at the University of Venda in South Africa, explained during his presentation on black and white rhino population histories and genetic diversity.

Though the black rhino has bounced back to some extent over the past few decades, Moodley called its story a "very woeful tale," considering the pan-African collapse the species experienced in the 20th century — dipping from more than 100,000 in the mid-1950s to fewer than 2,500 individuals in the early 1990s.

The small number of the Sumatran rhino, which is represented by 50 to 100 individuals, is also cause for concern. In collaboration with other groups, Dalén's team sequenced genomic DNA from a male Sumatran rhino with the Illumina HiSeq 2500, using three methods to produce genome assemblies from the data.

The researchers have started some preliminary population analyses with that rhino genome, he explained. They plan to resequence 20 modern Sumatran rhino genomes and about as many historical samples in order to tease apart changes in genetic variation that might inform future conservation efforts.

To prepare for what's ahead for the current rhino species, Dalén and his team also took a look into the past, sequencing the genome of a 28,500-year-old woolly rhino to around 3-fold average coverage. Prior studies suggested that the Sumatran rhino is the woolly rhino's closest living relative. With the woolly rhino genome in hand, though, it should be possible to get a better look at the divergence time for extinct and existing rhino species.

In the same session, Tate Tunstall from the San Diego Zoo Institute for Conservation Research outlined work being done at his institution to sequence the genomes of nine northern white rhinos and four southern white rhinos with DNA tucked away in the San Diego Frozen Zoo. Two more rhino species — the Javan and Indian rhino — are yet to be sequenced to round out the reference genome set.

Even as the existing genome assemblies are completed and improved, though, other teams are developing genetic markers for tracking and managing rhino populations, while laying the foundation for future resequencing efforts on already-sequenced species.

"Generating complete genome sequences from all rhinoceros species is a prerequisite for exploring the comparative genomics and evolutionary relationships within the Rhinocerotidae," Dalén and his co-authors noted in the abstract accompanying Tuesday's PAG presentation.

"In addition, providing access to reference genome assemblies will enable future projects aimed at developing markers for genetic monitoring, assessing population genomic structure, and local adaptations," they added, "as well as to quantify the extent to which demographic declines have affected genome-wide diversity, inbreeding, and genetic load within each species."