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Solenodon Genome Supports Ancient Divergence Theory for Caribbean Mammal


NEW YORK (GenomeWeb) – An international team led by investigators in Puerto Rico, Ukraine, and Russia has produced and started analyzing a genome assembly for a venomous, shrew-like creature that's endemic to the Caribbean island of Hispaniola.

After comparing and contrasting several assembly methods, the researchers used low-coverage short read sequencing and string graph-based assembly strategies to tackle the homozygosity-rich Solenodon paradoxus genome, producing genome assemblies for S. paradoxus sub-species found in southern and northern regions of the Dominican Republic. 

"The resulting genome sequence data was sufficient for high-quality annotation of genes and functional elements, as well as for comparative genomics and population genetic analyses," senior author Taras Oleksyk, a biology researcher at the University of Puerto Rico at Mayagüez and head of its Caribbean Genome Center genomic diversity lab, and his co-authors wrote in a paper published today in GigaScience. "Prior to this study, the string graph assembler Fermi has been used only in studies for annotation, or as a complementary tool for de novo assemblies made with de Bruijm algorithms."

Through S. paradoxus genome annotation, comparative genomics, phylogenetics, and other analyses, the team got a glimpse at the genes involved in the solenodon's features such as its venom-tinged bite and unusually situated rear teats, as well as its relationship to other placental mammals. In particular, the results pointed to an ancient divergence between the solenodon lineage and the lineage leading to other mammals — placed at roughly 73.6 million years ago.

"We have confirmed the early speciation date for Solenodons, weighing on the ongoing debate on whether the solenodons have indeed survived the demise of dinosaurs after the asteroid impact in the Caribbean," Oleksyk said in a statement.

The Solenodon species S. paradoxus and S. cubanus have long histories on the islands of Hispaniola and Cuba, respectively. Even so, the team explained, the venomous creatures are currently endangered, prompting the investigators to pursue solenodon sequencing to inform future conservation genomics efforts.

"S. paradoxus survived in spectacular island isolation despite the devastating human impact to biodiversity in recent centuries," the authors wrote. "Nevertheless, survival of this species is now threatened by deforestation, increasing human activity, and predation by introduced dogs, cats, and mongooses."

In a 2016 paper appearing in Molecular Biology and Evolution, an international team assessed the genome of an extinct, insect-eating animal called Nesophontes that belonged to the same lineage as solenodon. That study put the divergence of Nesophontes, nicknamed the "Island Murderer," at nearly 73 million years ago.

For their new study, Oleksyk and his colleagues used Illumina HiSeq 2000 or MiSeq instruments to assess nuclear DNA from five wild representatives from a southern Dominican Republic S. paradoxus sub-species known as S. paradoxus woodi. They also sequenced one individual from the northern sub-species S. paradoxus paradoxus.

With the help of the string graph assembly method, the team demonstrated that it was possible to put together an informative genome assembly using relatively shallow sequencing, covering each S. paradoxus woodi genome to a depth of roughly five-fold, on average.

Combining the data produced an estimated depth of 26-fold average coverage, the researchers reported, owing in part to the low genetic diversity present in the solenodon sub-species. Once they compared a handful of genome assembly approaches and settled on the string graph assembly-based method, the investigators analyzed the sub-species genomes alone and in combination.

From the SNP sets distinguishing S. p. woodi and S. p. paradoxus individuals from a reference solenodon assembly, for example, the team estimated that the southern and northern S. paradoxus sub-species split some 300,000 years ago. The available sequence data also offered a look at historical population sizes for the sub-species, while highlighting potential trait-related genes and parts of the genome that appeared to have been subject to selection over solenodon's evolutionary history.

The team noted that a more refined look at the S. paradoxus species and sub-species may stem from the existing genome resources as well as future iterations of the solenodon genome that incorporate additional, long read sequence data.

"A more complete genome sequence may provide a better picture of its evolutionary history, possible signatures of selection, clues about the genetic basis of adaptive phenotypic features facilitating life on Caribbean islands, and contribute to a better insight into island evolution and possible responses to current and future climate change," the authors concluded.