Supporting data for "Innovative assembly strategy contributes to understanding the evolution and conservation genetics of the endangered Solenodon paradoxus from the island of Hispaniola"

Dataset type: Genomic
Data released on March 09, 2018

Grigorev K; Kliver S; Dobrynin P; Komissarov A; Wolfsberger W; Krasheninnikova K; Afanador-Hernández YM; Brandt AL; Paulino LA; Carreras R; Rodríguez LE; Núñez A; Brandt JR; Silva F; Hernández-Martich JD; Majeske AJ; Antunes A; Roca AL; O’Brien SJ; Martínez-Cruzado JC; Oleksyk TK (2018): Supporting data for "Innovative assembly strategy contributes to understanding the evolution and conservation genetics of the endangered Solenodon paradoxus from the island of Hispaniola" GigaScience Database. http://dx.doi.org/10.5524/100422

DOI10.5524/100422

Solenodons are insectivores living in Hispaniola and Cuba that form an isolated branch in the tree of placental mammals 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, but 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 based 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 five individuals from the southern subspecies (S. p. woodi). In addition, we obtained additional sequence from one sample 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 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 Mya. Patterns of SNP variation allowed us to infer population demography, which supported a subspecies split within the Hispaniolan solenodon at least 300 Kya.

Keywords:

Additional details

Read the peer-reviewed publication(s):

Grigorev, K., Kliver, S., Dobrynin, P., Komissarov, A., Wolfsberger, W., Krasheninnikova, K., … Oleksyk, T. K. (2018). Innovative assembly strategy contributes to understanding the evolution and conservation genetics of the endangered Solenodon paradoxus from the island of Hispaniola. GigaScience, 7(6). doi:10.1093/gigascience/giy025

Additional information:

http://doi.org/10.5281/zenodo.1185377

Accessions (data included in GigaDB):

ENA: NKTL01000000
PROJECT: PRJNA368679





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
SAMN072649791906352  Solenodon paradoxus paradoxus Description:Genomic DNA isolated from the blood of...
Isolate:1
Life stage:adult
...
+
SAMN073141781906352  Solenodon paradoxus paradoxus Description:Genomic DNA isolated from the blood of...
Isolate:south
Life stage:adult
...
+
SAMN072649761906353  Solenodon paradoxus woodi Description:Genomic DNA isolated from the blood of...
Isolate:M
Life stage:adult
...
+
SAMN072649741906353  Solenodon paradoxus woodi Description:Genomic DNA isolated from the blood of...
Isolate:K
Life stage:adult
...
+
SAMN072649781906353  Solenodon paradoxus woodi Description:Genomic DNA isolated from the blood of...
Isolate:O
Life stage:adult
...
+
SAMN072649771906353  Solenodon paradoxus woodi Description:Genomic DNA isolated from the blood of...
Isolate:N
Life stage:adult
...
+
SAMN072649751906353  Solenodon paradoxus woodi Description:Genomic DNA isolated from the blood of...
Isolate:L
Life stage:adult
...
+
Displaying 1-7 of 7 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
Sequence variantsVCF2.94 MB2018-03-06
Sequence variantsVCF512 KB2018-03-06
Sequence variantsVCF1.44 MB2018-03-06
Sequence variantsVCF712.74 KB2018-03-06
Sequence variantsVCF710.24 KB2018-03-06
Phylogenetic treeUNKNOWN0.24 KB2018-03-06
Phylogenetic treeUNKNOWN0.41 KB2018-03-06
Sequence variantsEXCEL233.36 KB2018-03-06
annotationFASTA61.7 KB2018-03-06
Displaying 21-29 of 29 File(s).
Funding body Awardee Award ID Comments
National Science Foundation Taras K Oleksyk 1432092
Ministry of Education and Science of the Russian Federation Stephen J O'Brien Mega-grant 11.G34.31.0068
Saint Petersburg State University Stephen J O'Brien 1.50.1623.2013
Date Action
March 9, 2018 Dataset publish
July 4, 2018 Manuscript Link added : 10.1093/gigascience/giy025