Chromosome-level reference genome of the European wasp spiderArgiope bruennichi: a resource for studies on range expansion and evolutionary adaptation

Abstract

Background Argiope bruennichi, the European wasp spider, has been investigated intensively as a focal species for studies on sexual selection, chemical communication, and the dynamics of rapid range expansion at a behavioral and genetic level. However, the lack of a reference genome has limited insights into the genetic basis for these phenomena. Therefore, we assembled a high-quality chromosome-level reference genome of the European wasp spider as a tool for more in-depth future studies. Findings We generated, de novo, a 1.67 Gb genome assembly of A. bruennichi using 21.8× Pacific Biosciences sequencing, polished with 19.8× Illumina paired-end sequencing data, and proximity ligation (Hi-C)-based scaffolding. This resulted in an N50 scaffold size of 124 Mb and an N50 contig size of 288 kb. We found 98.4% of the genome to be contained in 13 scaffolds, fitting the expected number of chromosomes (n = 13). Analyses showed the presence of 91.1% of complete arthropod BUSCOs, indicating a high-quality assembly. Conclusions We present the first chromosome-level genome assembly in the order Araneae. With this genomic resource, we open the door for more precise and informative studies on evolution and adaptation not only in A. bruennichi but also in arachnids overall, shedding light on questions such as the genomic architecture of traits, whole-genome duplication, and the genomic mechanisms behind silk and venom evolution.

The Tetragnatha kauaiensis Genome Sheds Light on the Origins of Genomic Novelty in Spiders

“…From the available genomes, we selected those with a contig-N50 above 8,000 bp in order to avoid genomes that were highly fragmented. This included the genomes of S. mimosarum ( Sanggaard et al 2014 ), L. hesperus (BCM-HGSC website), P. tepidariorum ( Gendreau et al 2017 ), T. clavipes ( Babb et al 2017 ), D. silvatica ( Sánchez-Herrero et al 2019 ), A. ventricosus ( Kono et al 2019 ) and A. bruennichi ( Sheffer et al 2021 ). Additionally, we downloaded the genome of the bark scorpion C. sculpturatus ( Schwager et al 2017 ) as an outgroup.…”

“…Despite the advances in spider ecology, evolution, and systematics, knowledge of spider genomes still lags relative to other taxa. Most of the available spider genomes are of poor quality, being highly fragmented ( Garb et al 2018 ) and lack a substantial part of the genome, with only three recent exceptions involving chromosome-resolved genomes ( Escuer et al 2021 ; Fan et al 2021 ; Sheffer et al 2021 ). Several factors contribute to the sparse availability of high-quality spider genome assemblies, including the lack of a model organism among spiders (sensu Drosophila melanogaster in flies and Tribolium castaneum in beetles) ( Brewer et al 2014 ), and the challenges associated with sequencing spider genomes, which are characterized by high AT-content, repeats, heterozygosity, and often large genome sizes ( Garb et al 2018 ).…”

“…Under this framework, the retention of duplicated genes and other genetic components may act as “reservoirs of genetic variation,” through processes of gene neo- and sub-functionalization ( Lynch and Force 2000 ), and be of use when organisms encounter novel selective pressures ( Li et al 2018 ; Nieto Feliner et al 2020 ; Schmickl and Yant 2021 ). Considering the evidence for gene duplicates in spider genomes, including spidroins (silk genes) ( Sanggaard et al 2014 ; Clarke et al 2015 ; Babb et al 2017 ; Garb et al 2018 ; Sheffer et al 2021 ), venoms ( Sanggaard et al 2014 ; Gendreau et al 2017 ; Haney et al 2019 ), chemosensory (Vizueta et al 2018 , 2019 ; Vizueta, Escuer, et al 2020 ) gene families may yield insights on phenotypic innovation and the adaptation to novel environments. On the other hand, because genome duplication leads to a significant re-organization of the genome, it may cause deregulation of gene-expression networks or unlock the epigenetic suppression of transposable elements, which may proliferate across the genome and result in decreased fitness for the organism—“the genomic shock hypothesis” ( McClintock 1984 ; Choi et al 2020 ).…”

It takes Two: Discovery of Spider Pax2 Duplicates Indicates Prominent Role in Chelicerate Central Nervous System, Eye, as Well as External Sense Organ Precursor Formation and Diversification After Neo- and Subfunctionalization

“…In a second phylogenetic analysis only a subset of closely related Pax subfamilies was used (Pax2/5/8, Pax6, and poxn). Using the candidates for the respective groups recovered from P. tepidariorum, D. rerio Pax2/5/8 as well as D. melanogaster Pax2, poxn, and Pax6 orthologs were used to search for similar sequences in more chelicerate genomes including the xiphosuran Limulus polyphemus, and the spiders Argiope bruennichi (Sheffer et al, 2021), Stegodyphus dumicola (Liu et al, 2019) and Araneus ventricosus (Kono et al, 2019). Again, only unique hits with an e-value threshold lower than e-50 were kept (except for the xiphosuran L. polyphemus, for which only hits lower than e-100 were kept because of the large number of candidate hits).…”

Connecting materials, performance and evolution: a case study of the glue of moth-catching spiders (Cyrtarachninae)

“…Several recombinant studies have demonstrated that functional silk fibers, albeit with diminished mechanical properties, can be produced from the transgenic expression of constructs containing only the terminal and limited repetitive sequence from a single spidroin (Adrianos et al, 2013;Brooks et al, 2008;Heidebrecht et al, 2015;Saric et al, 2021;Xia et al, 2010;You et al, 2018). Second, recent advances in genomic technologies have made possible the discovery of complete silk gene sequences, which were previously inaccessible (Babb et al, 2017;Kono et al, 2019;Sheffer et al, 2021;Stellwagen and Burns, 2021;Stellwagen and Renberg, 2019;Zhou et al, 2021). Genomic comparisons coupled with our biomechanical tests will allow us to understand S1 and S2.…”