Selection on synonymous codon usage in soybean (Glycine max) WRKY genes by Krishnendu Sinha, Sourav Jana, Payel Pramanik, Bithika Bera

“…This study examines the evolutionary dynamics of the GmWRKY gene family, focusing on its synonymous codon usage bias (CUB) in a comprehensive set of 179 coding sequences. …”
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Comparative genomics of thermosynechococcaceae and thermostichaceae: insights into codon usage bias by Qiao-Hui Mou, Zhe Hu, Jing Zhang, Maurycy Daroch, Jie Tang

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Codon usage bias is presumably affected by tRNA selection effects in Actinidia polyploidization events by Yi Zhou, Zhilu Sheng, Dongbin Li, Wencui Li, Yujia Peng, Zhaopeng Song, Zhanjun Quan, Yongbo Liu

“…Abstract Background Polyploidization is one of the main mechanisms in speciation, yet its effects on the frequency and distribution of synonymous codons remain unclear, which may lead to distinct patterns of codon usage bias (CUB) in polyploid species. …”
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Detection and Characterization of Colistin Heteroresistance in an Enterobacter cloacae ST48 Strain Isolated From Raw Milk in Algeria by Sedrati Tahar, Touati Abdelaziz, Tennah Safia, Menoueri M. Nabil, Seydina M. Diene

“…However, multiple non‐synonymous mutations, including a stop‐codon mutation in phoP gene, were found in the resistant subpopulation. …”
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Duplicated paralogous genes subject to positive selection in the genome of Trypanosoma brucei. by Richard D Emes, Ziheng Yang

“…We have investigated adaptive evolution in this class of genes in the human parasite Trypanosoma brucei, as indicated by the ratio of non-synonymous (amino-acid changing) to synonymous (amino acid retaining) nucleotide substitution rates.…”
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Distribution of Voltage-Gated Sodium Channel (Nav) Alleles among the Aedes aegypti Populations In Central Java Province and Its Association with Resistance to Pyrethroid Insecticid... by Sayono Sayono, Anggie Puspa Nur Hidayati, Sukmal Fahri, Didik Sumanto, Edi Dharmana, Suharyo Hadisaputro, Puji Budi Setia Asih, Din Syafruddin

“…The insecticide susceptibility tests demonstrated Ae, aegypti resistance to the pyrethroids, with mortality rates ranging from 1.6%-15.2%. Three non-synonymous polymorphisms (S989P, V1016G and F1534C) and one synonymous polymorphism (codon 982) were detected in the AaNaV gene. …”
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The Complete Mitochondrial Genome of <i>Thymus mongolicus</i> and Its Phylogenetic Relationship with Lamiaceae Species by Na Na, Zinian Wu, Zhiyong Wang, Yanting Yang, Chunyu Tian, Lin Zhu, Taiyou Ou, Xiaofei Chen, Hongyan Xia, Zhiyong Li

“…An analysis of the mitogenome codons revealed that synonymous codons generally end with A/U. …”
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Anticodon sequence determines the impact of mistranslating tRNAAla variants by Ecaterina Cozma, Megha Rao, Madison Dusick, Julie Genereaux, Ricard A. Rodriguez-Mias, Judit Villén, Christopher J. Brandl, Matthew D. Berg

“…For anticodons generating the same amino acid substitution, reduced growth generally correlated with the abundance of detected mistranslation events. Differences in decoding specificity, even between synonymous anticodons, resulted in each tRNAAla variant mistranslating unique sets of peptides and proteins. …”
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Phylogenomic Signatures of a Lineage of Vesicular Stomatitis Indiana Virus Circulating During the 2019–2020 Epidemic in the United States by Selene Zarate, Miranda Bertram, Case Rodgers, Kirsten Reed, Angela Pelzel-McCluskey, Ninnet Gomez-Romero, Luis L. Rodriguez, Christie Mayo, Chad Mire, Sergei L. Kosakovsky Pond, Lauro Velazquez-Salinas

“…Our analyses identified multiple codon sites under positive selection and the association of these sites with specific functional domains at P, M, G, and L proteins. …”
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Canadian 2021 H-type Bovine Spongiform Encephalopathy case associated with a novel E211K polymorphism in prion protein gene by Waqas Tahir, Sandor Dudas, Renee Anderson, Jianmin Yang, Sarah Bogart, Kristina Santiago-Mateo, Yuanmu Fang, Roberta Quaghebeur

“…Importantly, a non-synonymous mutation at codon 211 of the PRNP gene was detected and confirmed to be present as a germline mutation. …”
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Assembly and comparative analysis of the complete mitochondrial of Spodiopogon sagittifolius, an endemic and protective species from Yunnan, China by Chao Xu, Wei Bi, Ren-yi Ma, Pin-rong Li, Feng Liu, Zhen-wen Liu

“…Extensive RNA editing events were detected across 27 protein-coding genes, predominantly involving C-to-U conversions, with synonymous mutations accounting for 49.65% of the edits. …”
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The pre- and post-COVID-19 pandemic dengue fever patterns in southeastern coastal China in 2019 and 2024: molecular evolution and strain replacement by Tianran Zhang, Yaqi Shi, Leyi Zhang, Jian Wang, Chengchao Yu, Binbin Lv, Sisi Wu, Yiru Huang, Xuewei Liu, Hupiao Dai, Mingshi Zhou, Yanjuan Liao, Wei Wang, Guankai Lin

“…Recombination was analyzed using seven detection algorithms implemented in RDP4. Hamming distances were used to profile amino acid substitutions. …”
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The evolution of Vp1 gene in enterovirus C species sub-group that contains types CVA-21, CVA-24, EV-C95, EV-C96 and EV-C99. by Teemu Smura, Soile Blomqvist, Tytti Vuorinen, Olga Ivanova, Elena Samoilovich, Haider Al-Hello, Carita Savolainen-Kopra, Tapani Hovi, Merja Roivainen

“…Signs of positive selection were detected in some of these highly polymorphic sites, while strong negative selection was indicated in most of the codons. …”
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Variability of <I>omp25</I> and <I>omp2a</I> Genes in Brucella Strains of Different Taxonomic Position by N. A. Osina, E. G. Boolgakova, A. G. Osin, I. G. Shvidenko, S. A. Shcherbakova

“…In the omp25 gene, 11 non-synonymous and 24 synonymous mutations have been detected; two deletions: ∆103–108 bp – in В. nosferati, ∆562–597 bp – in В. …”
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Identification and Characterization of Novel Variations in Platelet G-Protein Coupled Receptor (GPCR) Genes in Patients Historically Diagnosed with Type 1 von Willebrand Disease. by Jacqueline Stockley, Shaista P Nisar, Vincenzo C Leo, Essa Sabi, Margaret R Cunningham, Jeroen C Eikenboom, Stefan Lethagen, Reinhard Schneppenheim, Anne C Goodeve, Steve P Watson, Stuart J Mundell, Martina E Daly, GAPP Study in Collaboration with the MCMDM-1VWD Study Group

“…Two synonymous single nucleotide variations were identified in F2RL3 (c.402C>G, p.A134 =; c.1029 G>C p.V343 =), both of which introduced less commonly used codons and were predicted to be deleterious, though neither of them affected PAR4 receptor expression. …”
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