National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022, Zhoushan, China
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Marine Science and Technology College, Zhejiang Ocean University, 316022, Zhoushan, China
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This work was supported by the Basic Scientific Research Operating Expenses of Zhejiang Provincial Universities under contract 2021JZ003, Zhoushan Science and Technology Bureau under contract No. 2021C21007, Natural Science Foundation of Zhejiang Province under contract Y21C190023 and National Natural Science Foundation of China under contract 31272273.
The conventional theory of concerted evolution has been used to explain the lack of sequence variation in ribosomal RNA (rRNA) genes across diverse eukaryotic species. However, recent investigations into rRNA genes in flatfish genome have resulted in controversial findings. This study focuses on 18S rRNA genes of the widely distributed tongue sole, Cynoglossus abbreviatus (Pleuronectiformes: Cynoglossidae), aiming to explore sequence polymorphism. Five distinct 18S rDNA sequence types (Type A, B, R1, R2, and R3) were identified, suggesting a departure from concerted evolution. A combination of general criteria and variations in highly conserved regions were employed to detect pseudogenes. The results pinpointed Type A sequences as potential pseudogenes due to significant sequence variations and deviations in secondary structure within highly conserved regions. Three types (Type R1, R2, and R3) were identified as recombinants between Type A and B sequences, with simple crossing over and gene conversion as the most likely recombination mechanisms. These findings not only contribute to rRNA pseudogene identification but also shed light on the evolutionary dynamics of rRNA genes in teleost genomes.
Figure 1. Sequence alignment of distinct 18S rDNA sequences within the Cynoglossus abbreviatus genome (A) and a schematic representation illustrating the plausible recombinant generation process (B). Dashes (-) indicate deletions or insertions, with colors used to distinguish different types of sequences.
Figure 2. A schematic illustration depicting potential mechanisms for the formation of recombinants.
Figure 3. Sequence alignment of 18S rDNA in Soleoidei species (partial). The specific singleton sites and insertions in C. pur_A are labelled with solid circles and triangles; respectively. Dots (.) denote the conserved sites, dashes (−) denote the deletion or insertion. Abbreviations in 16 Soleoidei species are as follows. Z. zeb: Zebrias zebrinus; Z. qua: Zebrias quagga; Z. cro: Zebrias crossolepis; P. pav: Pardachirus pavoninus; S. ova: Solea ovata; S. sen: Solea senegalensis; B. ori: Brachirus orientalis; D. cad: Dagetichthys cadenati; C. iti: Cynoglossus itinus; C. rou: Cynoglossus roulei C. oli: Cynoglossus oligolepis; C. bro: Cynoglossus browni; P. jap: Paraplagusia japonica; C. pun: Cynoglossus puncticeps; C. zan: Cynoglossuszanzibarensis; C. pur_B: Cynoglossusabbreviatus Type B; C. pur_A: Cynoglossusabbreviatus Type A.
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