Parasites, Hosts and Diseases

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Original Articles

Codon Usage Patterns of Tyrosinase Genes in Clonorchis sinensis: Young-An Bae; Korean J Parasitol 2017;55(2):175-183.
Published online April 30, 2017; DOI: https://doi.org/10.3347/kjp.2017.55.2.175

Abstract
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Codon usage bias (CUB) is a unique property of genomes and has contributed to the better understanding of the molecular features and the evolution processes of particular gene. In this study, genetic indices associated with CUB, including relative synonymous codon usage and effective numbers of codons, as well as the nucleotide composition, were investigated in the Clonorchis sinensis tyrosinase genes and their platyhelminth orthologs, which play an important role in the eggshell formation. The relative synonymous codon usage patterns substantially differed among tyrosinase genes examined. In a neutrality analysis, the correlation between GC₁₂ and GC₃ was statistically significant, and the regression line had a relatively gradual slope (0.218). NC-plot, i.e., GC₃ vs effective number of codons (ENC), showed that most of the tyrosinase genes were below the expected curve. The codon adaptation index (CAI) values of the platyhelminth tyrosinases had a narrow distribution between 0.685/0.714 and 0.797/0.837, and were negatively correlated with their ENC. Taken together, these results suggested that CUB in the tyrosinase genes seemed to be basically governed by selection pressures rather than mutational bias, although the latter factor provided an additional force in shaping CUB of the C. sinensis and Opisthorchis viverrini genes. It was also apparent that the equilibrium point between selection pressure and mutational bias is much more inclined to selection pressure in highly expressed C. sinensis genes, than in poorly expressed genes.

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Analysis of codon usage bias in mitochondrial CO gene among platyhelminthes
Gulshana A. Mazumder, Arif Uddin, Supriyo Chakraborty
Molecular and Biochemical Parasitology.2021; 245: 111410. CrossRef

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Molecular Detection of Spirometra decipiens in the United States: Hyeong-Kyu Jeon, Hansol Park, Dongmin Lee, Seongjun Choe, Woon-Mok Sohn, Keeseon S. Eom; Korean J Parasitol 2016;54(4):503-507.
Published online August 31, 2016; DOI: https://doi.org/10.3347/kjp.2016.54.4.503

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The genus Spirometra belongs to the family Diphyllobothriidae and order Pseudophyllidea, and includes intestinal parasites of cats and dogs. In this study, a plerocercoid labeled as Spirometra mansonoides from the USA was examined for species identification and phylogenetic analysis using 2 complete mitochondrial genes, cytochrome c oxidase I (cox1) and NADH dehydrogenase subunit 3 (nad3). The cox1 sequences (1,566 bp) of the plerocercoid specimen (USA) showed 99.2% similarity to the reference sequences of the plerocercoid of Korean Spirometra decipiens (GenBank no. KJ599679), and 99.1% similarity in regard to nad3 (346 bp). Phylogenetic tree topologies generated using 4 analytical methods were identical and showed high confidence levels with bootstrap values of 1.00, 100%, 100%, and 100% for Bayesian inference (BI), maximum-likelihood (ML), neighbor-joining (NJ), and maximum parsimony (MP) methods, respectively. Representatives of Diphyllobothrium and Spirometra species formed a monophyletic group, and the sister-genera status between these species was well supported. Trapezoic proglottids in the posterior 1/5 region of an adult worm obtained from an experimentally infected cat were morphologically examined. The outer uterine loop of the uterus coiling characteristically consisted of 2 complete turns. The results clearly indicated that the examined Spirometra specimen from the USA matched to S. decipiens very well, and indicated possible presence of the life cycle of this species in this region.

Citations

Citations to this article as recorded by

Molecular confirmation of Spirometra mansoni (Cestoda: Diphyllobothriidae) in Javanese keelback water snake (Fowlea melanzosta) in Indonesia
Ryanka Edila, Seongjun Choe, Mustofa Helmi Effendi, Lucia Tri Suwanti, John Yew Huat Tang
International Journal for Parasitology: Parasites and Wildlife.2025; 28: 101150. CrossRef
Diversity and biology of Spirometra tapeworms (Cestoda: Diphyllobothriidea), zoonotic parasites of wildlife: A review
Roman Kuchta, Anna J. Phillips, Tomáš Scholz
International Journal for Parasitology: Parasites and Wildlife.2024; 24: 100947. CrossRef
Epidemiology, Diagnosis, and Prevention of Sparganosis in Asia
Wei Liu, Tengfang Gong, Shuyu Chen, Quan Liu, Haoying Zhou, Junlin He, Yong Wu, Fen Li, Yisong Liu
Animals.2022; 12(12): 1578. CrossRef
Genetic and Morphological Identification of Spirometra decipiens in Snakes and Domestic Dog Found in Cuba
Alexander Morales, Rebeca M. Laird-Pérez, Virginia Capó, Enrique Iglesias, Luis Fonte, Arturo Plascencia-Hernández, Enrique J. Calderón, Keeseon S. Eom, Yaxsier de Armas, Héctor R. Pérez-Gómez
Pathogens.2022; 11(12): 1468. CrossRef
Insight into One Health Approach: Endoparasite Infections in Captive Wildlife in Bangladesh
Tilak Chandra Nath, Keeseon S. Eom, Seongjun Choe, Shahadat Hm, Saiful Islam, Barakaeli Abdieli Ndosi, Yeseul Kang, Mohammed Mebarek Bia, Sunmin Kim, Chatanun Eamudomkarn, Hyeong-Kyu Jeon, Hansol Park, Dongmin Lee
Pathogens.2021; 10(2): 250. CrossRef
A Case of Sparganosis Caused by Spirometra decipiens on the Femur
Shoko YOGO, Sakurako IMAMURA, Kiko NAGAI, Kayo HARADA, Eiji NAGAYASU, Haruhiko MARUYAMA, Kazunori URABE
Nishi Nihon Hifuka.2021; 83(5): 453. CrossRef
Morphological Features and Structural Analysis of Plerocercoids of Spirometra erinaceieuropaei (Cestoda: Diphyllobothriidae) from European Pine Marten, Martes martes (Mammalia: Mustelidae) in Ukraine
Nataliya Yu. Rubtsova, Richard A. Heckmann
Comparative Parasitology.2020; 87(1): 109. CrossRef
Ocular Sparganosis: The First Report of Spirometra ranarum in Thailand
Wilai Saksirisampant, Chatanun Eamudomkarn, Hyeong-Kyu Jeon, Keeseon S. Eom, Buravej Assavapongpaiboon, Sunisa Sintuwong, Wasee Tulvatana
The Korean Journal of Parasitology.2020; 58(5): 577. CrossRef
Spirometra decipiens (Cestoda: Diphyllobothriidae) Collected in A Heavily Infected Stray Cat from the Republic of Korea
Hyeong-Kyu Jeon, Hansol Park, Dongmin Lee, Seongjun Choe, Keeseon S. Eom
The Korean Journal of Parasitology.2018; 56(1): 87. CrossRef
Molecular cloning, antiserum preparation and expression analysis during head regeneration of $$upalpha $$ α
Wen-Fang Dong, Hang Zhang, Ru-Meng Wang, Hong-Chun Pan
Journal of Genetics.2018; 97(4): 911. CrossRef
Human Sparganosis in Korea
Jeong-Geun Kim, Chun-Seob Ahn, Woon-Mok Sohn, Yukifumi Nawa, Yoon Kong
Journal of Korean Medical Science.2018;[Epub] CrossRef

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Codon Usage Bias and Determining Forces in Taenia solium Genome: Xing Yang, Xusheng Ma, Xuenong Luo, Houjun Ling, Xichen Zhang, Xuepeng Cai; Korean J Parasitol 2015;53(6):689-697.
Published online December 31, 2015; DOI: https://doi.org/10.3347/kjp.2015.53.6.689

Abstract
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The tapeworm Taenia solium is an important human zoonotic parasite that causes great economic loss and also endangers public health. At present, an effective vaccine that will prevent infection and chemotherapy without any side effect remains to be developed. In this study, codon usage patterns in the T. solium genome were examined through 8,484 protein-coding genes. Neutrality analysis showed that T. solium had a narrow GC distribution, and a significant correlation was observed between GC12 and GC3. Examination of an NC (ENC vs GC3s)-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENC (the effective number of codons) values were detected below the expected curve, suggesting that mutational bias plays a major role in shaping codon usage. The Parity Rule 2 plot (PR2) analysis showed that GC and AT were not used proportionally. We also identified 26 optimal codons in the T. solium genome, all of which ended with either a G or C residue. These optimal codons in the T. solium genome are likely consistent with tRNAs that are highly expressed in the cell, suggesting that mutational and translational selection forces are probably driving factors of codon usage bias in the T. solium genome.

Citations

Citations to this article as recorded by

Distinct codon usage signatures reflecting evolutionary and pathogenic adaptation in the Acinetobacter baumannii complex
Ujwal Dahal, Anuj Sharma, Karan Paul, Anu Bansal, Shelly Gupta
European Journal of Clinical Microbiology & Infectious Diseases.2025; 44(11): 2803. CrossRef
Evolution of codon usage in Taenia saginata genomes and its impact on the host
Siddiq Ur Rahman, Hassan Ur Rehman, Inayat Ur Rahman, Muazzam Ali Khan, Fazli Rahim, Hamid Ali, Dekun Chen, Wentao Ma
Frontiers in Veterinary Science.2023;[Epub] CrossRef
Comparative analysis of codon usage patterns and phylogenetic implications of five mitochondrial genomes of the genus Japanagallia Ishihara, 1955 (Hemiptera, Cicadellidae, Megophthalminae)
Min Li, Jiajia Wang, Renhuai Dai, Guy Smagghe, Xianyi Wang, Siying You
PeerJ.2023; 11: e16058. CrossRef
Codon Usage is Influenced by Compositional Constraints in Genes Associated with Dementia
Taha Alqahtani, Rekha Khandia, Nidhi Puranik, Ali M. Alqahtani, Yahia Alghazwani, Saad Ali Alshehri, Kumarappan Chidambaram, Mohammad Amjad Kamal
Frontiers in Genetics.2022;[Epub] CrossRef
Analysis of codon usage bias of lumpy skin disease virus causing livestock infection
Siddiq Ur Rahman, Hassan Ur Rehman, Inayat Ur Rahman, Abdur Rauf, Abdulrahman Alshammari, Metab Alharbi, Noor ul Haq, Hafiz Ansar Rasul Suleria, Sayed Haidar Abbas Raza
Frontiers in Veterinary Science.2022;[Epub] CrossRef
Codon usage pattern in Gnetales evolved in close accordance with the Gnetifer hypothesis
Aasim Majeed, Harpreet Kaur, Amitozdeep Kaur, Sreemoyee Das, Josepheena Joseph, Pankaj Bhardwaj
Botanical Journal of the Linnean Society.2021; 196(4): 423. CrossRef
Analysis of codon usage bias in mitochondrial CO gene among platyhelminthes
Gulshana A. Mazumder, Arif Uddin, Supriyo Chakraborty
Molecular and Biochemical Parasitology.2021; 245: 111410. CrossRef
Genetic evolution and codon usage analysis of NKX-2.5 gene governing heart development in some mammals
Arup Kr. Malakar, Binata Halder, Prosenjit Paul, Himangshu Deka, Supriyo Chakraborty
Genomics.2020; 112(2): 1319. CrossRef
Selection constraints determine preference for A/U-ending codons in Taxus contorta
Aasim Majeed, Harpreet Kaur, Pankaj Bhardwaj
Genome.2020; 63(4): 215. CrossRef
Analysis of codon usage pattern of mitochondrial ND genes in Platyhelminthes
Gulshana A. Mazumder, Arif Uddin, Supriyo Chakraborty
Molecular and Biochemical Parasitology.2020; 238: 111294. CrossRef
Compositional Analysis of Flatworm Genomes Shows Strong Codon Usage Biases Across All Classes
Guillermo Lamolle, Santiago Fontenla, Gastón Rijo, Jose F. Tort, Pablo Smircich
Frontiers in Genetics.2019;[Epub] CrossRef
Compositional bias coupled with selection and mutation pressure drives codon usage in Brassica campestris genes
Prosenjit Paul, Arup Kumar Malakar, Supriyo Chakraborty
Food Science and Biotechnology.2018; 27(3): 725. CrossRef
Whole genome analysis of codon usage in Echinococcus
Lucas L. Maldonado, Georgina Stegmayer, Diego H. Milone, Guilherme Oliveira, Mara Rosenzvit, Laura Kamenetzky
Molecular and Biochemical Parasitology.2018; 225: 54. CrossRef
Comprehensive Analysis of Codon Usage on Rabies Virus and Other Lyssaviruses
Xu Zhang, Yuchen Cai, Xiaofeng Zhai, Jie Liu, Wen Zhao, Senlin Ji, Shuo Su, Jiyong Zhou
International Journal of Molecular Sciences.2018; 19(8): 2397. CrossRef
Codon Usage Patterns of Tyrosinase Genes in Clonorchis sinensis
Young-An Bae
The Korean Journal of Parasitology.2017; 55(2): 175. CrossRef

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Brief Communication

Negligible Egg Positive Rate of Enterobius vermicularis and No Detection of Head Lice among Orphanage Children in Busan and Ulsan, Korea (2014): Dong-Hee Kim, Hyun-Mi Son, Sang Hwa Lee, Mi Kyung Park, Shin Ae Kang, Sang Kyun Park, Jun-Ho Choi, Jung Ha Park, Hak-Sun Yu; Korean J Parasitol 2015;53(4):497-499.
Published online August 25, 2015; DOI: https://doi.org/10.3347/kjp.2015.53.4.497

Abstract
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To determine whether pinworm infections and head lice infestations spread among children in orphanages, 117 children from 4 orphanages in Busan-si and Ulsan-si, Korea, were examined for enterobiasis and head lice infestation between January and February 2014. The overall rate of Enterobius vermicularis egg positivity was 0.85%, whereas none of the children had head lice infestations. The rate of pinworm infection was much lower among the orphanage children compared to the rates observed in previous studies among kindergarten and primary school students. Moreover, the risk factors for enterobiasis were less frequent among these subjects than previously reported. The personal hygiene and health of the orphanage children were supervised by a regular, employed nurse through a health education program. In conclusion, pinworm infection was efficiently controlled among the children in orphanages, and this might be related to good personal hygiene practices in Korea.

Citations

Citations to this article as recorded by

Enterobius vermicularis Infection among Preschool Children: A 12-Year (2008-2019) Survey in Large Cities and Provinces of the Republic of Korea
Hyejoo Shin, Bong-Kwang Jung, Seungwan Ryoo, Sooji Hong, Taehee Chang, Jiyeon Park, Keon Hoon Lee, Jeonggyu Lee, Jae Young Park, Hoo-Gn Jeoung, Jae Hyun Cho, Jong-Yil Chai
The Korean Journal of Parasitology.2021; 59(4): 421. CrossRef
A systematic scoping review of hygiene behaviors and environmental health conditions in institutional care settings for orphaned and abandoned children
Michelle Moffa, Ryan Cronk, Donald Fejfar, Sarah Dancausse, Leslie Acosta Padilla, Jamie Bartram
Science of The Total Environment.2019; 658: 1161. CrossRef
Status of common parasitic diseases in Korea in 2019
Sun Huh
Journal of the Korean Medical Association.2019; 62(8): 437. CrossRef
Prevalence ofEnterobius vermicularisamong preschool children in 2003 and 2013 in Xinxiang city, Henan province, Central China
Shuai Wang, Zhijun Yao, Yichen Hou, Dong Wang, Haizhu Zhang, Jingbo Ma, Luwen Zhang, Shiguo Liu
Parasite.2016; 23: 30. CrossRef

8,881 View
131 Download
5 Web of Science
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Original Article

Codon usage and bias in mitochondrial genomes of parasitic platyhelminthes: Thanh Hoa Le, Donald Peter McManus, David Blair; Korean J Parasitol 2004;42(4):159-167.
Published online December 20, 2004; DOI: https://doi.org/10.3347/kjp.2004.42.4.159

Abstract
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Sequences of the complete protein-coding portions of the mitochondrial (mt) genome were analysed for 6 species of cestodes (including hydatid tapeworms and the pork tapeworm) and 5 species of trematodes (blood flukes and liver- and lung-flukes). A near-complete sequence was also available for an additional trematode (the blood flukeSchistosoma malayensis). All of these parasites belong to a large flatworm taxon named the Neodermata. Considerable variation was found in the base composition of the protein-coding genes among these neodermatans. This variation was reflected in statistically-significant differences in numbers of each inferred amino acid between many pairs of species. Both convergence and divergence in nucleotide, and hence amino acid, composition was noted among groups within the Neodermata. Considerable variation in skew (unequal representation of complementary bases on the same strand) was found among the species studied. A pattern is thus emerging of diversity in the mt genome in neodermatans that may cast light on evolution of mt genomes generally.

Citations

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Signatures of Endosymbiosis in Mitochondrial Genomes of Rhabdocoel Flatworms
M. Monnens, T. Artois, A. Briscoe, Y. L. Diez, K. P. P. Fraser, B. S. Leander, D. T. J. Littlewood, M. J. Santos, K. Smeets, N. W. L. Van Steenkiste, M. P. M. Vanhove
Molecular Ecology.2025;[Epub] CrossRef
Evolution of codon usage in Taenia saginata genomes and its impact on the host
Siddiq Ur Rahman, Hassan Ur Rehman, Inayat Ur Rahman, Muazzam Ali Khan, Fazli Rahim, Hamid Ali, Dekun Chen, Wentao Ma
Frontiers in Veterinary Science.2023;[Epub] CrossRef
Characterization of the complete mitochondrial genome of the fluke of turdus, Plagiorchis elegans, and phylogenetic implications
Rong Li, Hui-Mei Wang, Guo-Hua Liu, Ya Tu, Yuan-Ping Deng
Experimental Parasitology.2022; 242: 108387. CrossRef
Analysis of codon usage bias of lumpy skin disease virus causing livestock infection
Siddiq Ur Rahman, Hassan Ur Rehman, Inayat Ur Rahman, Abdur Rauf, Abdulrahman Alshammari, Metab Alharbi, Noor ul Haq, Hafiz Ansar Rasul Suleria, Sayed Haidar Abbas Raza
Frontiers in Veterinary Science.2022;[Epub] CrossRef
Understanding the codon usage patterns of mitochondrial CO genes among Amphibians
Parvin A. Barbhuiya, Arif Uddin, Supriyo Chakraborty
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Characterization of the complete mitochondrial genome of Diplostomum baeri
Toby Landeryou, Stephen M. Kett, Anne Ropiquet, Dirk Wildeboer, Scott P. Lawton
Parasitology International.2020; 79: 102166. CrossRef
Probing recalcitrant problems in polyclad evolution and systematics with novel mitochondrial genome resources
Nathan J. Kenny, Carolina Noreña, Cristina Damborenea, Cristina Grande
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The complete mitochondrial genome of Paragonimus ohirai (Paragonimidae: Trematoda: Platyhelminthes) and its comparison with P. westermani congeners and other trematodes
Thanh Hoa Le, Khue Thi Nguyen, Nga Thi Bich Nguyen, Huong Thi Thanh Doan, Takeshi Agatsuma, David Blair
PeerJ.2019; 7: e7031. CrossRef
Compositional Analysis of Flatworm Genomes Shows Strong Codon Usage Biases Across All Classes
Guillermo Lamolle, Santiago Fontenla, Gastón Rijo, Jose F. Tort, Pablo Smircich
Frontiers in Genetics.2019;[Epub] CrossRef
Compositional bias coupled with selection and mutation pressure drives codon usage in Brassica campestris genes
Prosenjit Paul, Arup Kumar Malakar, Supriyo Chakraborty
Food Science and Biotechnology.2018; 27(3): 725. CrossRef
Phenotypic plasticity of six unusual cercariae in nassariid gastropods and their relationships to the Acanthocolpidae and Brachycladiidae (Digenea)
Leonie J. Barnett, Terrence L. Miller
Parasitology International.2018; 67(2): 225. CrossRef
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Galina N. Chelomina, Yulia V. Tatonova, Nguyen Manh Hung, Ha Duy Ngo
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