Grigorev, Kirill

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    Novel assembly of homozygous genomes indicates ancient divergence times and suggests new conservation strategies for the critically endangered Solenodon paradoxus
    (2017) Grigorev, Kirill; Oleksyk, Taras K.; College of Arts and Sciences - Sciences; Martínez-Cruzado, Juan C.; Majeske, Audrey; Department of Biology; Hudgins, Thomas R.
    Solenodons are ancient insectivores living on the Caribbean islands Hispaniola and Cuba, with no other surviving relatives found elsewhere. The genus is estimated to have diverged from the rest of the mammalian order circa 78 Mya (Brandt et al. 2016), and occupies a unique evolutionary position representing the most ancient isolated branch of the placental tree. Of additional interest is the conservation status of the Hispaniolan species (Solenodon paradoxus) because it appears to be subdivided in two separate subspecies (Ottenwalder 2001). The origins, the unique biology and adaptations of these enigmatic venomous species, coupled with their endangered status, can be greatly advanced given the availability of genome data. This study corroborates previous estimates of ancient vicariant origins of the Solenodon lineage based on mitochondrial DNA. A whole genome assembly for either of the species has never been previously performed, partially due to the difficulty in obtaining high quality genome grade DNA samples from the field. We hypothesized that the span of millions of years of island isolation resulted in extreme homozygosity in S. paradoxus genomes. Thus, after generating short paired end sequence libraries from multiple individuals, we employed several assembly strategies with the assumption that there was low genetic diversity between samples. Results indicated that the string-graph based assembly strategy with Fermi software package (Li 2012) had the best results compared to the standard de Bruijn approach with SOAPdenovo2 (Luo et al. 2012), yet two other Fermi-based pipelines yielded high quality contig assemblies, as evidenced by high N50, conserved gene content and favorable REAPR (Hunt et al. 2013) scores. An optimized Fermi-based pipeline surpassed the rest in gene annotation quality, providing the closest representation of the genome. This provides an argument that string-graph-model assembly methods may be the better choice for the homozygous genomes, which is often a hallmark of endemic or endangered species. Once the consensus reference genome was assembled, the genome variants were collected by comparing the five individual sequences from the southern subspecies (S. p. woodi) plus one sequence of the northern subspecies (S. p. paradoxus). This allowed to infer the demographic histories of the two subspecies, which indicated a split at at least 300 Kya or more, suggesting that separate conservation units be applied to each subspecies. New genomic signatures of the Solenodon genome were characterized and annotated, with a specific emphasis on the venomous genes, wherein results indicate several unusual sequence insertions as well as phylogenetic proximity to the reptilians. Also, the phylogenetic positioning of the species S. paradoxus was inferred based on 4,416 monoorthologs from 10 other mammalian species.