Abstract
The comparison of chromosome-level genomes allows biologists to investigate new axes of organismal evolution. Spiders comprise a significant proportion of known arachnid diversity, with many complex morphologies and unique natural histories, yet comparative genomics in spiders has been limited due to the number of available genomes. We present a de novo chromosomal reference genome of a mature male tarantula, Aphonopelma marxi, and comparatively examine spider genome evolution across the order Araneae. Using PacBio HiFi and Hi-C sequencing, the final 6.5 Gb assembly consists of 17 autosomes, 1 X chromosome, and 127 unplaced scaffolds, with an N50 of 370 Mb and Arachnida (odb10; 2,934 genes) BUSCO of 96.7%. By comparing 20 additional spider genomes from 15 families, we find mygalomorphs (trapdoor spiders and their kin) generally possess more repetitive genomes with similar composition compared to their much more diverse sister lineage, the araneomorphs. We report mygalomorphs recover a lower number of completed BUSCOs than araneomorph spiders, a finding not correlated with sequencing coverage, as mygalomorphs have a portion of missing or derived BUSCOs in the current arachnid dataset. Across the Araneoidea (orb-weaving spiders and their kin), there is a correlation between decreasing genome size and repeat content, suggesting repetitive elements are being lost or removed. Importantly, visualization of macrosynteny across available genomes highlights structural rearrangements and allows identification of previously unreported sex chromosomes. This new, high-quality mygalomorph genome will provide new avenues of exploration for arachnid evolutionary biology.