Widespread retention of ohnologs in key developmental gene families following whole genome duplication in arachnopulmonates

Abstract

<jats:p>Whole genome duplications (WGD) have occurred multiple times in the evolution of animals, including in the lineages leading to vertebrates, teleosts, horseshoe crabs and arachnopulmonates. These dramatic genomic events initially produce a wealth of new genetic material, which is generally followed by extensive gene loss. It appears that developmental genes such as homeobox genes, signalling pathway components and microRNAs, however, tend to be more frequently retained in duplicate following WGD (ohnologs). These not only provide the best evidence for the occurrence of WGD, but an opportunity to study its evolutionary implications. Although these genes are relatively well studied in the context of vertebrate WGD, genomic and transcriptomic data for independent comparison in other groups are scarce, with patchy sampling of only two of the five extant arachnopulmonate orders. To improve our knowledge of developmental gene repertoires, and their evolution since the arachnopulmonate WGD, we sequenced embryonic transcriptomes from two additional spider species and two whip spider species and surveyed them for three important gene families: Hox, Wnt and frizzled. We report extensive retention of ohnologs in all four species, further supporting the arachnopulmonate WGD. Thanks to improved sampling we were able to identify patterns of likely ohnolog retention and loss within spiders, including apparent differences between major clades. The two amblypygid species have larger ohnolog repertoires of these genes than both spiders and scorpions; including the first reported duplicated Wnt1/wg, the first Wnt10 recovered in an arachnid, and broad retention of frizzled genes. These insights shed light on the evolution of the enigmatic whip spiders, highlight the importance of the comparative approach within lineages, and provide substantial new transcriptomic data for future study.</jats:p>

Genomic resources and toolkits for developmental study of whip spiders (Amblypygi) provide insights into arachnid genome evolution and antenniform leg patterning

“…Our results suggest that Amblypygi retain a complete duplicated Hox complement with 20 genes. Similarly, a recent transcriptomic survey in Charinus acosta and Euphrynichus bacillifer reported duplications of nearly all Hox genes (excepting proboscipedia), as well as Wnt and Frizzled genes [83]. Taken together with the recent discovery of duplicated RDGN genes in Charinus, our results suggest that Amblypygi retain ohnologs of numerous developmental patterning genes, as a function of an ancient, shared whole genome duplication.…”

Lack of evidence for conserved parasegmental grooves in arthropods

“…Sequence information of en genes have been identified in a sequenced genome (Parasteatoda (Schwager et al 2017)) and sequenced embryonic transcriptomes (Cupiennius (Samadi et al 2015), Pholcus (Janssen et al 2015), Acanthoscurria (Pechmann 2020), Phalangium (Sharma et al 2012), Marpissa muscosa (Harper et al 2020), Charinus acosta (Harper et al 2020), and Euphrynichus bacillifer (Harper et al 2020). Potential orthologs were identified performing reciprocal tBLASTn searches against the single en gene of the onychophoran Euperipatoides kanangrensis (Eriksson et al 2009).…”

The evolution of Sox gene repertoires and regulation of segmentation in arachnids

“…Embryos were staged according to Mittmann and Wolff (2012) and fixed as described in Akiyama- Oda and Oda (2003). Embryos were collected and stored in RNAlater (Invitrogen) from captive mated females of the amblypygids Charinus acosta, at one day, one month and two months after the appearance of the egg sacs, and Euphrynichus bacillifer, at approximately 30% of embryonic development (Harper, et al 2020). Mixed stage embryos were collected from a female Pardosa amentata (collected in Oxford) and Marpissa muscosa (kindly provided by Philip Steinhoff and Gabriele Uhl) and stored in RNAlater (Harper, et al 2020).…”

“…RNA was extracted from the embryos of C. acosta, E. bacillifer, P. amentata and M. muscosa using QIAzol according to the manufacturer's guidelines (QIAzol Lysis Reagent, Qiagen) (Harper, et al 2020). Illumina libraries were constructed using a TruSeq RNA sample preparation kit and sequenced using the Illumina NovaSeq platform (100 bp PE) by Edinburgh Genomics (https://genomics.ed.ac.uk).…”

“…(available at https://github.com/FelixKrueger/TrimGalore) before de novo transcriptome assembly with Trinity (Haas, et al 2013). Transcriptome completeness was evaluated using BUSCO v4.0.2 (Seppey, et al 2019) along with the arachnid database (arachnida_odb10 created on 2019-11-2; 10 species, 2934 BUSCOs) (Harper, et al 2020). The transcriptomes will be made available on SRA upon publication.…”