Supporting data for "The draft genome sequence of the spider Dysdera silvatica (Araneae, Dysderidae): A valuable resource for functional and evolutionary genomic studies in chelicerates"

Dataset type: Genomic, Transcriptomic
Data released on July 12, 2019

Sanchez-Herrero JF; Frías-López C; Escuer P; Hinojosa-Alvarez S; Arnedo MA; Sánchez-Gracia A; Rozas J (2019): Supporting data for "The draft genome sequence of the spider Dysdera silvatica (Araneae, Dysderidae): A valuable resource for functional and evolutionary genomic studies in chelicerates" GigaScience Database. http://dx.doi.org/10.5524/100628

DOI10.5524/100628

We present the draft genome sequence of Dysdera silvatica, a nocturnal ground dwelling spider from a genus that undergone a remarkable adaptive radiation in the Canary Islands. The draft assembly was obtained using short (illumina) and long (PacBio and Nanopore) sequencing reads. Our de novo assembly (1.36 Gb), that represents the 80% of the genome size estimated by flow-cytometry (1.7 Gb), is constituted by a high fraction of interspersed repetitive elements (53.8%). The assembly completeness, using BUSCO (benchmarking universal single-copy orthologs) and CEG (Core Eukaryotic genes), ranges from 90% to 96%. Functional annotations based on both ab initio and evidence-based information (including D. silvatica RNA-seq) yielded a total of 48 619 protein-coding sequences, of which 36 398 (74.9%) have the molecular hallmark of known protein domains, or sequence similarity with swissprot sequences. The D. silvatica assembly is the first representative of the superfamily Dysderoidea, and just the second available genome of Synspermiata, one of the major evolutionary lineages of the “true spiders” (Araneomorphae). Dysderoids, which are known for their numerous instances of adaptation to underground environments, include some of the few examples of trophic specialization within spiders and are excellent models for the study of cryptic female choice. This resource, will be therefore very useful as an starting point to study fundamental evolutionary and functional questions, including the molecular bases of the adaptation to extreme environments and ecological shifts, as well of the origin and evolution of relevant spider traits, such as the venom and silk.

Additional details

Read the peer-reviewed publication(s):

(PubMed: 31430368)

Github links:

https://github.com/molevol-ub/Dysdera_silvatica_genome

Accessions (data generated as part of this study):

BioProject: PRJNA475203





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
Dsil_NMH25907477319  Dysdera silvatica Description:DNA isolate from the whole body of an ...
Alternative accession-BioSample:SAMN09381545
Alternative accession-BioProject:PRJNA475203
...
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Dsil_NMH2605477319  Dysdera silvatica Description:DNA isolate from the whole body of an ...
Alternative accession-BioSample:SAMN09381544
Alternative accession-BioProject:PRJNA475203
...
+
Dysdera silvatica ONT_1-3 gDNA477319  Dysdera silvatica Description:DNA isolate from the whole body of an ...
Alternative accession-BioSample:SAMN11609372
Alternative accession-BioProject:PRJNA475203
...
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Dysdera silvatica ONT_4-5 gDNA477319  Dysdera silvatica Description:DNA isolate from the whole body of an ...
Alternative accession-BioSample:SAMN11609373
Alternative accession-BioProject:PRJNA475203
...
+
Dysdera silvatica pacbio gDNA 477319  Dysdera silvatica Description:DNA isolate from the whole body of an ...
Alternative accession-BioSample:SAMN09389329
Alternative accession-BioProject:PRJNA475203
...
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Displaying 1-5 of 5 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
AnnotationTAR345.16 MB2019-07-08
Protein sequenceFASTA13.81 MB2019-07-08
Coding sequenceFASTA40.4 MB2019-07-08
Transcriptome sequenceFASTA208.52 MB2019-07-08
Repeat sequenceTAR56.9 MB2019-07-08
Repeat sequenceFASTA1.77 MB2019-07-08
Mixed archivezip621.3 KB2019-07-16
ReadmeTEXT3.47 KB2019-07-12
TextTEXT0.34 KB2019-07-08
Displaying 1-9 of 9 File(s).
Funding body Awardee Award ID Comments
Ministerio de Economía y Competitividad J Rozas CGL2013-45211
Comissió Interdepartamental de Recerca i Innovació Tecnològica J Rozas 2014SGR-1055
Comissió Interdepartamental de Recerca i Innovació Tecnològica J Rozas 2017 SGR 1287
Comissió Interdepartamental de Recerca i Innovació Tecnològica M A Arnedo 2014SGR-1604
Comissió Interdepartamental de Recerca i Innovació Tecnològica M A Arnedo 2017 SGR 83
Ministerio de Economía y Competitividad M A Arnedo CGL2012-36863
Ministerio de Economía y Competitividad J Rozas CGL2016-75255
Date Action
July 12, 2019 Dataset publish
August 7, 2019 Manuscript Link added : 10.1093/gigascience/giz099
October 14, 2022 Manuscript Link updated : 10.1093/gigascience/giz099