Abstract
Spiders (Araneae) have a diverse spectrum of morphologies, behaviors, and physiologies. Attempts to understand the genomic-basis of this diversity are often hindered by their large, heterozygous, and AT-rich genomes with high repeat content resulting in highly fragmented, poor-quality assemblies. As a result, the key attributes of spider genomes, including gene family evolution, repeat content, and gene function, remain poorly understood. Here, we used Illumina and Dovetail Chicago technologies to sequence the genome of the long-jawed spider Tetragnatha kauaiensis, producing an assembly distributed along 3,925 scaffolds with an N50 of ∼2 Mb. Using comparative genomics tools, we explore genome evolution across available spider assemblies. Our findings suggest that the previously reported and vast genome size variation in spiders is linked to the different representation and number of transposable elements. Using statistical tools to uncover gene-family level evolution, we find expansions associated with the sensory perception of taste, immunity, and metabolism. In addition, we report strikingly different histories of chemosensory, venom, and silk gene families, with the first two evolving much earlier, affected by the ancestral whole genome duplication in Arachnopulmonata (∼450 Ma) and exhibiting higher numbers. Together, our findings reveal that spider genomes are highly variable and that genomic novelty may have been driven by the burst of an ancient whole genome duplication, followed by gene family and transposable element expansion.
Highlights
With nearly 50,000 described species (World Spider Catalog 2021), and dating back 350 Myr (Fernandez et al 2018), spiders (Chelicerata, Araneae) have conquered most terrestrial ecosystems, from the cold Arctic to arid deserts (Jackson and Cross 2011; Dimitrov et al 2012; Garrison et al 2016;ß The Author(s) 2021
When considering significant expansions in all Gene Ontology (GO) categories, we find expansions associated with taste
After querying these to the NCBI protein database, we identified one Flagelliform spidroin (Flag), four Aggregate spidroins (AgSp), eight Major Ampullate spidroins (MaSp), three Minor Ampullate spidroins (MiSp), one Tubuliform spidroins (TuSp), one Pyriform spidroin (PySp), and one Aciniform spidroin (AcSp)
Summary
With nearly 50,000 described species (World Spider Catalog 2021), and dating back 350 Myr (Fernandez et al 2018), spiders (Chelicerata, Araneae) have conquered most terrestrial ecosystems, from the cold Arctic to arid deserts (Jackson and Cross 2011; Dimitrov et al 2012; Garrison et al 2016;ß The Author(s) 2021. Despite being one of the most charismatic animal lineages, progress on spider genome evolution lags due to the challenges in sequencing and assembling their genomes, which involve genome size and repeat content. We sequence the genome of Tetragnatha kauaiensis, a spider endemic to Hawai’i, and compare it with other available spider genomes. We find variation in terms of repeats and transposable elements; expansions in gene-content associated with metabolism, sensory perception, and immunity; and wide variation of chemosensory genes and venom genes
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