Parasites, Hosts and Diseases

"base composition"

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
PDF

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

Citations to this article as recorded by

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
Gene.2021; 777: 145462. CrossRef
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
Genomics.2019; 111(3): 343. CrossRef
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
Characterization of the complete mitochondrial genomes from Polycladida (Platyhelminthes) using next-generation sequencing
M. Teresa Aguado, Cristina Grande, Michael Gerth, Christoph Bleidorn, Carolina Noreña
Gene.2016; 575(2): 199. CrossRef
The complete mitochondrial genome of the tapeworm Cladotaenia vulturi (Cestoda: Paruterinidae): gene arrangement and phylogenetic relationships with other cestodes
Aijiang Guo
Parasites & Vectors.2016;[Epub] CrossRef
A complete mitochondrial genome from Echinochasmus japonicus supports the elevation of Echinochasminae Odhner, 1910 to family rank (Trematoda: Platyhelminthes)
Thanh Hoa Le, Nga Thi Bich Nguyen, Khue Thi Nguyen, Huong Thi Thanh Doan, Do Trung Dung, David Blair
Infection, Genetics and Evolution.2016; 45: 369. CrossRef
Evolutionary Analysis of Mitogenomes from Parasitic and Free-Living Flatworms
Eduard Solà, Marta Álvarez-Presas, Cristina Frías-López, D. Timothy J. Littlewood, Julio Rozas, Marta Riutort, Hector Escriva
PLOS ONE.2015; 10(3): e0120081. CrossRef
An initial molecular signature of Indian isolates of Toxocara
K JEEVA, N CHATTERJEE, A K BERA, S MAITI, HIRA RAM, P S BANERJEE, T K GOSWAMI, P J DAS, J CHAMUA, A A P MILTON, M ARAVIND, G BHUVANAPRIYA, K THILAGAVATHI, S K GHOSH, S M DEB, D BHATTACHARYA
The Indian Journal of Animal Sciences.2015;[Epub] CrossRef
Genetic diversity of the Chinese liver fluke Clonorchis sinensis from Russia and Vietnam
Galina N. Chelomina, Yulia V. Tatonova, Nguyen Manh Hung, Ha Duy Ngo
International Journal for Parasitology.2014; 44(11): 795. CrossRef
Mutation and Selection Cause Codon Usage and Bias in Mitochondrial Genomes of Ribbon Worms (Nemertea)
Haixia Chen, Shichun Sun, Jon L. Norenburg, Per Sundberg, Tamir Tuller
PLoS ONE.2014; 9(1): e85631. CrossRef
Platyzoan mitochondrial genomes
Alexandra R. Wey-Fabrizius, Lars Podsiadlowski, Holger Herlyn, Thomas Hankeln
Molecular Phylogenetics and Evolution.2013; 69(2): 365. CrossRef
Analysis of synonymous codon usage patterns in different plant mitochondrial genomes
Meng Zhou, Xia Li
Molecular Biology Reports.2009; 36(8): 2039. CrossRef
DNA Asymmetric Strand Bias Affects the Amino Acid Composition of Mitochondrial Proteins
Xiang Jia Min, Donal A. Hickey
DNA Research.2007; 14(5): 201. CrossRef
Characterization of the Complete Mitochondrial Genome of Diphyllobothrium nihonkaiense (Diphyllobothriidae: Cestoda), and Development of Molecular Markers for Differentiating Fish Tapeworms
Kyu-Heon Kim, Hyeong-Kyu Jeon, Seokha Kang, Tahera Sultana, Gil Jung Kim, Keeseon S. Eom, Joong-Ki Park
Molecules and Cells.2007; 23(3): 379. CrossRef
Comparison of the phylogenetic performance of neodermatan mitochondrial protein‐coding genes
Michael Hardman, Lotta M. Hardman
Zoologica Scripta.2006; 35(6): 655. CrossRef
Complete mitochondrial genome sequences for Crown-of-thorns starfish Acanthaster planci and Acanthaster brevispinus
Nina Yasuda, Masami Hamaguchi, Miho Sasaki, Satoshi Nagai, Masaki Saba, Kazuo Nadaoka
BMC Genomics.2006;[Epub] CrossRef