Spiders are a hyperdiverse taxon and among the most abundant predators in nearly all terrestrial habitats. Their success is often attributed to key developments in their evolution such as silk and venom production and major apomorphies such as a whole-genome duplication. Resolving deep relationships within the spider tree of life has been historically challenging, making it difficult to measure the relative importance of these novelties for spider evolution. Whole-genome data offer an essential resource in these efforts, but also for functional genomic studies. Here, we present de novo assemblies for three spider species: Ryuthela nishihirai (Liphistiidae), a representative of the ancient Mesothelae, the suborder that is sister to all other extant spiders; Uloborus plumipes (Uloboridae), a cribellate orbweaver whose phylogenetic placement is especially challenging; and Cheiracanthium punctorium (Cheiracanthiidae), which represents only the second family to be sequenced in the hyperdiverse Dionycha clade. These genomes fill critical gaps in the spider tree of life. Using these novel genomes along with 25 previously published ones, we examine the evolutionary history of spidroin gene and structural hox cluster diversity. Our assemblies provide critical genomic resources to facilitate deeper investigations into spider evolution. The near chromosome-level genome of the 'living fossil' R. nishihirai represents an especially important step forward, offering new insights into the origins of spider traits.

Centre for Molecular Biodiversity Research Leibniz Institute for the Analysis of Biodiversity Change Bonn Germany

Department of Biogeography Trier University Trier Germany

Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic

Ecology and Genetics Research Unit University of Oulu Oulu Finland

Evolutionary Genomics Unit Okinawa Institute of Science and Technology Okinawa Japan

Laboratory of Arachnid Cytogenetics Department of Genetics and Microbiology Faculty of Sciences Charles University Prague 2 Czech Republic

LOEWE Centre for Translational Biodiversity Genomics Frankfurt am Main Germany

Natural History Museum Vienna Central Research Laboratories Vienna Austria

Senckenberg Forschungsinstitut und Naturmuseum Frankfurt am Main Germany

South African National Biodiversity Institute National Zoological Garden Pretoria South Africa

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Mol Ecol Resour. 2025 May;25(4):e14093. doi: 10.1111/1755-0998.14093. PubMed

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