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

Miquel A Arnedo,Julio Rozas,Paula Escuer,Cristina Frías-López,Jose Francisco Sánchez-Herrero,Silvia Hinojosa-Alvarez,Alejandro Sánchez-Gracia

doi:10.1093/gigascience/giz099

Abstract

BackgroundWe present the draft genome sequence of Dysdera silvatica, a nocturnal ground-dwelling spider from a genus that has undergone a remarkable adaptive radiation in the Canary Islands.ResultsThe draft assembly was obtained using short (Illumina) and long (PaciBio and Nanopore) sequencing reads. Our de novo assembly (1.36 Gb), which represents 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 and core eukaryotic genes, ranges from 90% to 96%. Functional annotations based on both ab initio and evidence-based information (including D. silvatica RNA sequencing) 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 Swiss-Prot 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).ConclusionsDysderoids, 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 useful as a 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.

Highlights

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
We found that the 10 most abundant repeat families among the 2,604 identi ed in D. silvatica account for ~7% of the genome and encode 5 unknown, 3 Short Interspersed Nuclear Element (SINE) and 2 Long Interspersed Nuclear Element (LINE), with an average length of ~193 bp, ~161 bp and ~1040 bp, respectively (Supplementary Table S1-9b)
We extended the search for D. silvatica homologs to a broader taxonomic range (Figure 2; Supplementary Table S1-11) by including other metazoan lineages and performing a series of local BLASTP searches (E-value cuto < 10-3; >30% aligna)

Summary

Introduction

We chose for each software the parameter values that generated the best assembly (Supplementary Table S1-7) in terms of, i) continuity and contig size statistics, such as the N50, L50, and the total number of sequences and bases assembled, and ii) completeness measures, obtained as the fraction (and length) of a series of highly conserved proteins present in the draft genome.

Results

Conclusion