On the shoulder of giants: Mitogenome recovery from non-targeted genome projects for phylogenetic inference and molecular evolution studies

Abstract

The advent of high-throughput sequencing technologies (HTS) has generated an unprecedented amount of genomic and transcriptomic information. A vast amount of these data is not even used in targeted projects but is made available in public repositories. Previous studies have demonstrated that HTS data constitute a valuable resource to recover mitogenomic information, which is most relevant for studies of non-model and undersampled taxa. The spider family Dysderidae exemplifies well this situation: It is a highly diverse group, exceptionally well-suited for evolutionary and ecological research, but with a sparse mitogenomic record. In this study, we used public and in-house HTS data to assemble and annotate at no cost 13 complete and 6 partial Dysderidae mitogenomes, as well as 34 partial mitogenomes belonging to other taxa within the Synspermiata clade, to which Dysderidae belongs. The mitogenomic information was further used to interrogate on a diverse array of evolutionary questions posed by the family. Phylogenetic inference clarified the evolutionary scenario of the colonization of the Canary Islands by the genus Dysdera, supporting two independent colonizations from the continent. Synteny analyses indicated that gene organization at the mitogenomic level is overall conserved within Dysderidae, the only exceptions being two cave-dwelling species, each of them with a unique putative transposition not described before in spiders. Finally, tRNA secondary structure reconstruction confirmed that the extreme compaction of tRNA is conserved across the family, suggesting that its origin could be traced back to approximately 100 million years ago (Mya). Altogether, this study demonstrates the potential of publicly available HTS data to conduct low-cost evolutionary research at different biological levels.