Presented at ICG12

Included in genome_assembly theme

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

Created on 18th July 2017

This paper has been published in GigaScience.

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; David Hernández-Martich; Audrey J Majeske; Agostinho Antunes; Alfred L Roca; Stephen J O'Brien; Juan Carlos Martinez-Cruzado; Taras K Oleksyk;

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.

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