Nuclear genome annotation of wheel animals and thorny-headed worms: inferences about the last common ancestor of Syndermata (Rotifera s.l.)

Abstract

The basal splits within Syndermata probably date back hundreds of millions of years, and extant syndermatans greatly differ in reproduction modes (parthenogenesis, metagenesis, heterosexuality) and lifestyles (free-living, epizoic, endoparasitic). Against this background, the present investigation aims to reconstruct genome and transcriptome metrics in the last common ancestor (LCA) of Syndermata. We especially annotated nuclear genome assemblies of one representative, each, of monogononts (Brachionus plicatilis), bdelloids (Adineta vaga), seisonids (Seison nebaliae), and acanthocephalans (Pomphorhynchus laevis), S1 and additionally considered previously published data. Present results suggest that the syndermatan LCA possessed a compact nuclear genome of 50–100 Mb with a coding portion of ≥ 40%. Its ~ 17,000 protein-coding genes probably had about 4–6 exons and 3–5 introns on average. Long interspersed nuclear elements (LINEs) should have occupied 4–5% of the ancestral genome. Based on this, independent evolutionary trajectories involving gene loss, genome duplication, and repeat proliferation resulted in greatly varying genomes within the clade. Nevertheless, we identified 2114 clusters containing proteins of all four syndermatan taxa. About 200 of these clusters lacked sufficiently similar counterparts in the platyhelminths Macrostomum lignano and Schmidtea mediterranea. Gene ontologies assigned to these clusters might reference the muscular pharynx, light perception, and transposition, amongst others.