Comparison of mitochondrial genome and development of specific PCR primers for identifying two scuticociliates, Pseudocohnilembus persalinus and Uronema marinum

• Published in: Parasites & vectors Vol. 14; no. 1; pp. 1 - 318
• Main Authors: Huang, Yu-Xi, Wang, Sen, Gao, Yan-Qi, Chen, Jie-Hu, Wang, Xiu-Li, Li, Rui-Jun
• Format: Journal Article
• Language: English
• Published: London BioMed Central Ltd 10.06.2021; BioMed Central; BMC
• Subjects: Amino acid sequence; Amino acid sequences; Amino acids; Ciliata; Ciliates; Classification; Codons; Comparative analysis; Design; Disease control; Distance; DNA; Genes; Genetic aspects; Genome comparison; Genomes; Identification; Identification and classification; Methods; Mitochondria; Morphology; Nucleotide sequence; Nucleotides; Parasitological research; PCR; Phylogenetics; Phylogeny; Polymerase chain reaction; Primers; Primers (Molecular genetics); Proteins; Pseudocohnilembus persalinus; Similarity; Species classification; Specific PCR primers; Uronema; Uronema marinum; China
• ISSN: 1756-3305; 1756-3305
• DOI: 10.1186/s13071-021-04821-3

Pseudocohnilembus persalinus and Uronema marinum (Ciliophora, Scuticociliatia), as parasitic scuticociliatid ciliates, were isolated from Scophthalmus maximus and Takifugu rubripes, respectively, in our previous studies. These ciliates are morphologically very similar; hence, it is difficult to identify specific scuticociliate species using traditional classification methods for performing taxonomic research and disease control studies. We annotated the mitochondrial genomes of these two scuticociliates on the basis of previous sequencing, including analyses of nucleotide composition, codon usage, Ka/Ks, and p-distance. We also compared the nucleotide and amino acid similarity of the mitochondrial genomes of P. persalinus, U. marinum, and other 12 related ciliates, and a phylogenetic tree was constructed using 16 common genes. We chose the nad4 and nad7 genes to design specific PCR primers for identification. P. persalinus and U. marinum were found to have a close evolutionary relationship. Although codon preferences were similar, differences were observed in the usage of codons such as CGA, CGC, and GTC. Both Ka/Ks and p-distance were less than 1. Except for yejR, ymf57, ymf67, and ymf75, the amino acid sequence similarity between P. persalinus and U. marinum was greater than 50%. The mitochondrial genomes of P. persalinus and U. marinum were thoroughly compared to provide a reference for disease prevention and control. The specific PCR primers enabled us to identify P. persalinus and U. marinum rapidly and accurately at the molecular level, thus providing a basis for classification and identification.