PT  - JOURNAL ARTICLE
AU  - Kirill Grigorev
AU  - Sergey Kliver
AU  - Pavel Dobrynin
AU  - Aleksey Komissarov
AU  - Walter Wolfsberger
AU  - Ksenia Krasheninnikova
AU  - Yashira M. Afanador-Hernández
AU  - Liz A. Paulino
AU  - Rosanna Carreras
AU  - Luis E. Rodríguez
AU  - Adrell Núñez
AU  - Filipe Silva
AU  - J. David Hernández-Martich
AU  - Audrey J. Majeske
AU  - Agostinho Antunes
AU  - Alfred L. Roca
AU  - Stephen J. O’Brien
AU  - Juan Carlos Martinez-Cruzado
AU  - Taras K. Oleksyk
TI  - Innovative assembly strategy contributes to the understanding of evolution and conservation genetics of the critically endangered <em>Solenodon paradoxus</em> from the island of Hispaniola
AID  - 10.1101/164574
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 164574
4099  - http://biorxiv.org/content/early/2017/07/18/164574.short
4100  - http://biorxiv.org/content/early/2017/07/18/164574.full
AB  - 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. 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) and one sequence of the northern subspecies (S. p. paradoxus) 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.