Published today, in the open-access journal GigaScience, is an article that presents a draft genome of a small shrew-like animal, the venomous Hispaniolan solenodon (Solenodon paradoxus). This species is unusual not only because it is one of the very few venomous mammals, it is also the sole remaining branch of mammals that split from other insectivores at the time of the dinosaurs. The genome sequencing and analysis of this endangered animal was carried out by an international team lead by Dr. Taras K. Oleksyk from the University of Puerto Rico at Mayagüez. The availability of the solenodon genome sequence allowed the researchers to answer several evolutionary questions, particularly whether the solenodon species indeed survived the meteor impact that laid waste to the dinosaurs.
As one of the only extant mammals that are venomous, the Solenodon's venomous saliva flows from modified salivary glands through grooves on their sharp incisors ("solenodon" derives from the Greek for "grooved tooth"). They also have several other primitive and very unusual characteristics for a mammal: very large claws, a flexible snout with a ball-and-socket joint, and oddly positioned teats, which are on their rear. While the mammalian tree of life has been heavily researched, this is the most distantly related branch to be added to the 'genome club'. It has particular importance and implications for conservation because morphometric studies have suggested that southern and northern Hispaniolan solenodons may be subspecies rather than separate species.
Solenodon is not just genetically but also geographically isolated. Highly endangered, they remain only in a few remote corners of the Caribbean islands of Cuba and Hispaniola. Its nocturnal lifestyle makes it even more elusive and therefore less studied. Thus, it was crucial for the researchers to work with local experts at the Instituto Tecnológico de Santo Domingo and Universidad Autónoma de Santo Domingo and with local guides who helped them track and ambush passing solenodons at night.
One of the lead authors, Dr Juan Carlos Martinez-Cruzado, noted that "local resources are absolutely necessary for this kind of work; only they truly know their animal's behavior." He added, "this project may open doors to many others to come, and we always assumed this to be one of many projects that will help research, education and conservation efforts in the Dominican Republic."
For this project, there was more than just the challenge of obtaining the organisms for blood samples, the solenodon genome proved particularly difficult to sequence. Carrying out genomics research in remote parts of the Caribbean provided a challenge, particularly in transporting high quality DNA to the lab. Due to the constraints of poor quality DNA as well as a limited budget, the commercial lab used to carry out the sequencing turned out a very low coverage per individual.
Having already ventured into the jungle, the researchers embraced this new challenge by coming up with novel approaches to assemble the genome. First, the researchers reasoned that because the species has existed for tens of millions of years in isolation, it was extremely inbred and had a very homozygous genome. This lead to a potential work-around, because the five collected sets of genomic data could be pooled to increase the coverage. Despite initial doubts, this worked better than expected especially when that strategy was combined with using a string graph approach rather than the more standard de Brujn graph assembly method. String graphs incorporate more of the sequencing data than de Brujn graphs. Based on the results here, this new technique provides a low budget alternative for genome assembly, particularly in the highly homozygous genomes of endangered species.
The first author of the paper, Kirill Grigorev elaborates: "For me, perhaps the most interesting part of this research was the challenge of delivering a de novo genome assembly that was suitable for comparative genomics, using an amount of sequencing data much smaller than in other similar projects".
After carrying out their assembly, the researchers had data of sufficient quality for answering many scientific questions on solenodon evolution. With regard to conservation plans, the data supports that there was a subspecies split within the Hispaniolan solenodon at least 300,000 years ago, meaning the northern and southern populations should be treated as two separate conservation units and may therefore need independent breeding strategies.
These data also shed light on the initial speciation event for this branch, and showed that solenodons likely diverged from other extant mammals 73.6 million years ago. Dr. Oleksyk said: "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."
This research was the inaugural winner of the GigaScience prize at the International Conference on Genomics in Shenzhen on the 30st October 2017. Presenting in the prize track, the international panel of judges voted the paper the winner of the $1000 prize and trophy. The GigaScience prize track will run again at ICG-13, and the journal will begin taking papers for it next month. Follow GigaScience on social media for more information.
In keeping with the journal's goals of making the data underlying the analyses used in published research fully and freely available, all data from this project are available under a CC0 waiver in the GigaScience database, GigaDB, in a citable format as follows: Grigorev, K et al. (2018): Supporting data for "Innovative assembly strategy contributes to understanding the evolution and conservation genetics of the endangered Solenodon paradoxus from the island of Hispaniola" GigaScience Database. http://dx.doi.org/10.5524/100422
Grigorev, K et al. (2018): Innovative assembly strategy contributes to understanding the evolution and conservation genetics of the endangered Solenodon paradoxus from the island of Hispaniola. GigaScience. doi: 10.1093/gigascience/giy025
A video of the researchers presenting the award winning work at the ICG12 GigaScience prize track is here: https://youtu.be/R1U6LOxVKPc
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GigaScience is co-published by BGI and Oxford University Press. Winner of the 2018 PROSE award for Innovation in Journal Publishing (Multidisciplinary), the journal covers research that uses or produces 'big data' from the full spectrum of the life sciences. It also serves as a forum for discussing the difficulties of and unique needs for handling large-scale data from all areas of the life sciences. The journal has a completely novel publication format -- one that integrates manuscript publication with complete data hosting, and analyses tool incorporation. To encourage transparent reporting of scientific research as well as enable future access and analyses, it is a requirement of manuscript submission to GigaScience that all supporting data and source code be made available in the GigaScience database, GigaDB, as well as in publicly available repositories. GigaScience will provide users access to associated online tools and workflows, and has integrated a data analysis platform, maximizing the potential utility and re-use of data.