New genomic insights into ciliates with loricae (Eukaryota: Alveolata)

Abstract Several ciliate taxa have evolved loricae as an adaptation for survival in specific environments. Previous studies of loricate ciliates have focused mainly on morphological and functional properties, whereas the molecular evolutionary biology of this particular group of ciliates, especially at the genomic level, has been largely overlooked. Here, we use omics data of selected loricate and aloricate ciliates to conduct a comparative genomics analysis. Molecular clock analysis estimated the origins of different loricate ciliate lineages. Functional enrichment analyses of significantly expanded gene families in loricate ciliates revealed that distantly related lineages possessing this convergent phenotype have developed similar functional adaptations. Notably, the expansion of amino acid and glycan metabolic pathways is consistent with the known biochemical composition of the lorica. Furthermore, the recurrent enrichment of the Hippo signalling pathway suggests its potential role in the development and maintenance of this loricate phenotype. Collectively, our comparative genomics study provides a new perspective on the adaptive evolution of loricate ciliates and will constitute a valuable resource for future investigations on this particular group of ciliates.