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Innovative assembly strategy contributes to the understanding of evolution and conservation genetics of the critically endangered Solenodon paradoxus from the island of Hispaniola

Kirill Grigorev, Sergey Kliver, Pavel Dobrynin, Aleksey Komissarov, Walter Wolfsberger, Ksenia Krasheninnikova, Yashira M. Afanador-Hernández, Liz A. Paulino, Rosanna Carreras, Luis E. Rodríguez, Adrell Núñez, Filipe Silva, J. David Hernández-Martich, Audrey J. Majeske, Agostinho Antunes, Alfred L. Roca, Stephen J. O’Brien, Juan Carlos Martinez-Cruzado, Taras K. Oleksyk
doi: https://doi.org/10.1101/164574
Kirill Grigorev
aDepartment of Biology, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico
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Sergey Kliver
bTheodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
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Pavel Dobrynin
bTheodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
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Aleksey Komissarov
bTheodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
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Walter Wolfsberger
aDepartment of Biology, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico
cBiology Department, Uzhhorod National University, Uzhhorod, Ukraine
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Ksenia Krasheninnikova
bTheodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
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Yashira M. Afanador-Hernández
aDepartment of Biology, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico
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Liz A. Paulino
dInstituto Tecnologico de Santo Domingo (INTEC), Santo Domingo, Dominican Republic
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Rosanna Carreras
dInstituto Tecnologico de Santo Domingo (INTEC), Santo Domingo, Dominican Republic
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Luis E. Rodríguez
dInstituto Tecnologico de Santo Domingo (INTEC), Santo Domingo, Dominican Republic
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Adrell Núñez
eDepartment of Conservation and Science, Parque Zoologico Nacional (ZOODOM), Santo Domingo, Dominican Republic
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Filipe Silva
fCIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal
gDepartment of Biology, Faculty of Sciences, University of Porto. Rua do Campo Alegre, 4169-007 Porto, Portugal
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J. David Hernández-Martich
hInstituto de Investigaciones Botanicas y Zoologicas, Universidad Autonoma de Santo Domingo, Santo Domingo, Dominican Republic;
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Audrey J. Majeske
aDepartment of Biology, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico
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Agostinho Antunes
fCIIMAR/CIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos, s/n, 4450–208 Porto, Portugal
gDepartment of Biology, Faculty of Sciences, University of Porto. Rua do Campo Alegre, 4169-007 Porto, Portugal
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Alfred L. Roca
iDepartment of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
jCarl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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Stephen J. O’Brien
bTheodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
kOceanographic Center, Nova Southeastern University, Fort Lauderdale, Florida, USA
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Juan Carlos Martinez-Cruzado
aDepartment of Biology, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico
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Taras K. Oleksyk
aDepartment of Biology, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico
cBiology Department, Uzhhorod National University, Uzhhorod, Ukraine
kOceanographic Center, Nova Southeastern University, Fort Lauderdale, Florida, USA
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  • For correspondence: taras.oleksyk@upr.edu
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Abstract

Solenodons are insectivores living on the Caribbean islands, with few surviving related taxa. The genus occupies one of the most ancient branches among the placental mammals. The history, unique biology and adaptations of these enigmatic venomous species, can be greatly advanced given the availability of genome data, but the whole genome assembly for solenodons has never been previously performed, partially due to the difficulty in obtaining samples from the field. Island isolation has likely resulted in extreme homozygosity within the Hispaniolan solenodon (Solenodon paradoxus), thus we tested the performance of several assembly strategies for performance with genetically impoverished species’ genomes. The string-graph based assembly strategy seems a better choice compared to the conventional de Brujn 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 five individuals from the southern subspecies (S. p. woodi). In addition, we obtained one additional sequence of the northern subspecies (S. p. paradoxus). The resulting genome assemblies were compared to each other, and annotated for genes, with a specific emphasis on the venomous 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. Patterns of SNP variation allowed us to infer population demography, which indicated a subspecies split within the Hispaniolan solenodon at least 300 Kya.

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Innovative assembly strategy contributes to the understanding of evolution and conservation genetics of the critically endangered Solenodon paradoxus from the island of Hispaniola
Kirill Grigorev, Sergey Kliver, Pavel Dobrynin, Aleksey Komissarov, Walter Wolfsberger, Ksenia Krasheninnikova, Yashira M. Afanador-Hernández, Liz A. Paulino, Rosanna Carreras, Luis E. Rodríguez, Adrell Núñez, Filipe Silva, J. David Hernández-Martich, Audrey J. Majeske, Agostinho Antunes, Alfred L. Roca, Stephen J. O’Brien, Juan Carlos Martinez-Cruzado, Taras K. Oleksyk
bioRxiv 164574; doi: https://doi.org/10.1101/164574
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Innovative assembly strategy contributes to the understanding of evolution and conservation genetics of the critically endangered Solenodon paradoxus from the island of Hispaniola
Kirill Grigorev, Sergey Kliver, Pavel Dobrynin, Aleksey Komissarov, Walter Wolfsberger, Ksenia Krasheninnikova, Yashira M. Afanador-Hernández, Liz A. Paulino, Rosanna Carreras, Luis E. Rodríguez, Adrell Núñez, Filipe Silva, J. David Hernández-Martich, Audrey J. Majeske, Agostinho Antunes, Alfred L. Roca, Stephen J. O’Brien, Juan Carlos Martinez-Cruzado, Taras K. Oleksyk
bioRxiv 164574; doi: https://doi.org/10.1101/164574

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