Comparative transcriptomics of Entelegyne spiders (Araneae, Entelegynae), with emphasis on molecular evolution of orphan genes

Abstract

Next-generation sequencing technology is rapidly transforming the landscape of evolutionary biology, and has become a cost-effective and efficient means of collecting exome information for non-model organisms. Due to their taxonomic diversity, production of interesting venom and silk proteins, and the relative scarcity of existing genomic resources, spiders in particular are excellent targets for next-generation sequencing (NGS) methods. In this study, the transcriptomes of six entelegyne spider species from three genera (Cicurina travisae, C. vibora, Habronattus signatus, H. ustulatus, Nesticus bishopi, and N. cooperi) were sequenced and de novo assembled. Each assembly was assessed for quality and completeness and functionally annotated using gene ontology information. Approximately 100 transcripts with evidence of homology to venom proteins were discovered. After identifying more than 3,000 putatively orthologous genes across all six taxa, we used comparative analyses to identify 24 instances of positively selected genes. In addition, between ~ 550 and 1,100 unique orphan genes were found in each genus. These unique, uncharacterized genes exhibited elevated rates of amino acid substitution, potentially consistent with lineage-specific adaptive evolution. The data generated for this study represent a valuable resource for future phylogenetic and molecular evolutionary research, and our results provide new insight into the forces driving genome evolution in taxa that span the root of entelegyne spider phylogeny.

Ultraconserved elements (UCEs) resolve the phylogeny of Australasian smurf-weevils

“…In invertebrates, UCEs have been used in Hymenoptera (primarily ants [ 8 , 21 , 11 , 57 – 60 ]), but also Coleoptera [ 61 ] and arachnids [ 62 ]. Transcriptome-based analyses constitute another major source of phylogenomic data in arthropods [ 63 – 69 ]. For hyperdiverse beetles, there is great potential for both UCE- and exon-based markers to help resolve relationships within this diverse group.…”

Venom gland size and venom complexity—essential trophic adaptations of venomous predators: A case study using spiders

“…It is also likely that phylogenetically unrelated species achieved similar toxicity by employing different types of toxins. Indeed, spiders use different substances to immobilize prey: For example, araneids appear to rely on substances of low molecular mass (e.g., Carlson & Hedin, 2017), while sicariids and theridiids mainly use proteins (Vassilevski et al, 2009).…”

Transcriptome responses to elevated CO2 level and Wolbachia‐infection stress in Hylyphantes graminicola (Araneae: Linyphiidae)

“…The rapid development of high‐throughput sequencing technologies and transcriptome profiling (RNA‐seq) has enabled the investigation of species without a reference genome (Wang et al ., ). Most previous studies on transcriptional regulation of gene expression have been conducted on model organisms, including Drosophila , nematodes, and Arabidopsis thaliana (Gardner et al ., ; Moskalev et al ., ; Zinta et al ., ), with few studies targeting spiders (Haney et al ., ; Carlson & Hedin, ).…”