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They form an isolated branch in the tree of placental mammals that are highly divergent from other eulipothyplan insectivores The history, unique biology, and adaptations of these enigmatic venomous species could be illuminated by the availability of genome data. However, a whole genome assembly for solenodons has not been previously performed, partially due to the difficulty in obtaining samples from the field. Island isolation and reduced numbers have likely resulted in high homozygosity within the Hispaniolan solenodon (Solenodon paradoxus). Thus, we tested the performance of several assembly strategies on the genome of this genetically impoverished species. The string graph\u2013based assembly strategy seemed a better choice compared to the conventional de Bruijn graph approach due to the high levels of homozygosity, which is often a hallmark of endemic or endangered species. A consensus reference genome was assembled from sequences of 5 individuals from the southern subspecies (S. p. woodi). In addition, we obtained an additional sequence from 1 sample of the northern subspecies (S. p. paradoxus). The resulting genome assemblies were compared to each other and annotated for genes, with an emphasis on venom genes, repeats, variable microsatellite loci, and other genomic variants. Phylogenetic positioning and selection signatures were inferred based on 4,416 single-copy orthologs from 10 other mammals. We estimated that solenodons diverged from other extant mammals 73.6 million years ago. Patterns of single-nucleotide polymorphism variation allowed us to infer population demography, which supported a subspecies split within the Hispaniolan solenodon at least 300 thousand years ago.<\/jats:p>","DOI":"10.1093\/gigascience\/giy025","type":"journal-article","created":{"date-parts":[[2018,3,16]],"date-time":"2018-03-16T14:05:29Z","timestamp":1521209129000},"source":"Crossref","is-referenced-by-count":18,"title":["Innovative assembly strategy contributes to understanding the evolution and conservation genetics of the endangered <i>Solenodon paradoxus<\/i> from the island of Hispaniola"],"prefix":"10.1093","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3628-0123","authenticated-orcid":false,"given":"Kirill","family":"Grigorev","sequence":"first","affiliation":[{"name":"Department of Biology, University of Puerto Rico at Mayag\u00fcez, Mayag\u00fcez, Puerto Rico"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2965-3617","authenticated-orcid":false,"given":"Sergey","family":"Kliver","sequence":"additional","affiliation":[{"name":"Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia"}]},{"given":"Pavel","family":"Dobrynin","sequence":"additional","affiliation":[{"name":"Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia"}]},{"given":"Aleksey","family":"Komissarov","sequence":"additional","affiliation":[{"name":"Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia"}]},{"given":"Walter","family":"Wolfsberger","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Puerto Rico at Mayag\u00fcez, Mayag\u00fcez, Puerto Rico"},{"name":"Biology Department, Uzhhorod National University, Uzhhorod, Ukraine"}]},{"given":"Ksenia","family":"Krasheninnikova","sequence":"additional","affiliation":[{"name":"Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia"}]},{"given":"Yashira M","family":"Afanador-Hern\u00e1ndez","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Puerto Rico at Mayag\u00fcez, Mayag\u00fcez, Puerto Rico"}]},{"given":"Adam L","family":"Brandt","sequence":"additional","affiliation":[{"name":"Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA"},{"name":"Division of Natural Sciences, St. Norbert College, De Pere, Wisconsin, USA"}]},{"given":"Liz A","family":"Paulino","sequence":"additional","affiliation":[{"name":"Instituto Tecnol\u00f3gico de Santo Domingo (INTEC), Santo Domingo, Dominican Republic"}]},{"given":"Rosanna","family":"Carreras","sequence":"additional","affiliation":[{"name":"Instituto Tecnol\u00f3gico de Santo Domingo (INTEC), Santo Domingo, Dominican Republic"}]},{"given":"Luis E","family":"Rodr\u00edguez","sequence":"additional","affiliation":[{"name":"Instituto Tecnol\u00f3gico de Santo Domingo (INTEC), Santo Domingo, Dominican Republic"}]},{"given":"Adrell","family":"N\u00fa\u00f1ez","sequence":"additional","affiliation":[{"name":"Department of Conservation and Science, Parque Zoologico Nacional (ZOODOM), Santo Domingo, Dominican Republic"}]},{"given":"Jessica R","family":"Brandt","sequence":"additional","affiliation":[{"name":"Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA"},{"name":"Department of Biology, Marian University, Fond du Lac, Wisconsin, USA"}]},{"given":"Filipe","family":"Silva","sequence":"additional","affiliation":[{"name":"CIIMAR\/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Av. General Norton de Matos, s\/n, 4450\u2013208 Porto, Portugal"},{"name":"Department of Biology, Faculty of Sciences, University of Porto. Rua do Campo Alegre, 4169-007 Porto, Portugal"}]},{"given":"J David","family":"Hern\u00e1ndez-Martich","sequence":"additional","affiliation":[{"name":"Instituto de Investigaciones Bot\u00e1nicas y Zool\u00f3gicas, Universidad Aut\u00f3noma de Santo Domingo, Santo Domingo, Dominican Republic"}]},{"given":"Audrey J","family":"Majeske","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Puerto Rico at Mayag\u00fcez, Mayag\u00fcez, Puerto Rico"}]},{"given":"Agostinho","family":"Antunes","sequence":"additional","affiliation":[{"name":"CIIMAR\/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leix\u00f5es, Av. General Norton de Matos, s\/n, 4450\u2013208 Porto, Portugal"},{"name":"Department of Biology, Faculty of Sciences, University of Porto. Rua do Campo Alegre, 4169-007 Porto, Portugal"}]},{"given":"Alfred L","family":"Roca","sequence":"additional","affiliation":[{"name":"Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA"},{"name":"Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA"}]},{"given":"Stephen J","family":"O'Brien","sequence":"additional","affiliation":[{"name":"Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia"},{"name":"Oceanographic Center, Nova Southeastern University, Fort Lauderdale, Florida, USA"}]},{"given":"Juan Carlos","family":"Mart\u00ednez-Cruzado","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Puerto Rico at Mayag\u00fcez, Mayag\u00fcez, Puerto Rico"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8148-3918","authenticated-orcid":false,"given":"Taras K","family":"Oleksyk","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Puerto Rico at Mayag\u00fcez, Mayag\u00fcez, Puerto Rico"},{"name":"Biology Department, Uzhhorod National University, Uzhhorod, Ukraine"}]}],"member":"286","published-online":{"date-parts":[[2018,3,16]]},"reference":[{"key":"2024111706490769100_bib1","article-title":"\u201cLast occurrence\u201d of the Antillean insectivoran Nesophontes: new radiometric dates and their interpretation","volume-title":"American Museum novitates","author":"MacPhee","year":"1999"},{"key":"2024111706490769100_bib2","first-page":"253","article-title":"Systematics and biogeography of the West Indian genus Solenodon","volume-title":"Biogeogr. 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