Ultrastructure of Diophrys appendiculata and new systematic consideration of the euplotid family Uronychiidae (Protista, Ciliophora)

Dong, Jingyi; Liu, Yujie; Ma, Jun; Ma, Hongyu; Stoeck, Thorsten; Fan, Xinpeng

doi:10.1007/s42995-022-00153-y

Cited by 12 publications

(1 citation statement)

References 81 publications

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“…Most noncanonical genetic codes reported in ciliates can be classified as reassigned stop codons ( Kollmar and Mühlhausen 2017 ), which are used to encode amino acids instead of terminating translation. For example, in some species of Spirotrichea and Oligohymenophorea, TAA and TAG have been reassigned to encode glutamine (Q), and only TGA is used as the termination codon ( Kollmar and Mühlhausen 2017 ; Dong et al 2022 ; Wang et al 2022 ). Similarly, TAA/TAG is translated as tyrosine (Y) in Mesodinium ( Heaphy et al 2016 ) but glutamic acid (E) in several Sessilida species ( Heaphy et al 2016 ).…”

Section: Introductionmentioning

confidence: 99%

Stop or Not: Genome-Wide Profiling of Reassigned Stop Codons in Ciliates

Chen

Geng

Zhang

et al. 2023

Molecular Biology and Evolution

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Bifunctional stop codons that have both translation and termination functions in the same species are important for understanding the evolution and function of genetic codes in living organisms. Considering the high frequency of bifunctional codons but limited number of available genomes in ciliates, we de novo sequenced seven representative ciliate genomes to explore the evolutionary history of stop codons. We further propose a stop codon reassignment quantification method (stopCR) that can identify bifunctional codons and measure their frequencies in various eukaryotic organisms. Using our newly developed method, we found two previously undescribed genetic codes, illustrating the prevalence of bifunctional stop codons in ciliates. Overall, evolutionary genomic analyses suggest that gain or loss of reassigned stop codons in ciliates is shaped by their living environment, the eukaryotic release factor 1 (eRF1) and suppressor tRNAs (tRNAs with a stop codon anticodon). This study provides novel clues about the functional diversity and evolutionary history of stop codons in eukaryotic organisms.

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