STADIUM: Species-Specific tRNA Adaptive Index Compendium by Jonghwan Yoon, Yeun-Jun Chung, Minho Lee

“…The index has been widely used in various fields of molecular evolution, genetics, and pharmacology. Afterwards, an improved version of the index, named specific tRNA adaptation index (stAI), was developed by adapting tRNA copy numbers in species. …”
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The complete mitochondrial genome of Ophiocordyceps gracilis and its comparison with related species by Aifeire Abuduaini, Yuan-Bing Wang, Hui-Ying Zhou, Rui-Ping Kang, Ming-Liang Ding, Yu Jiang, Fei-Ya Suo, Luo-Dong Huang

“…This study is the first to investigate the molecular evolution, phylogenetic pattern, and genetic structure characteristics of mitogenome in O. gracilis. …”
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First detection of recombinant variant of African swine fever virus in the Russian Federation (brief communication) by A. S. Igolkin, R. S. Chernyshev, N. G. Zinyakov, E. O. Morozova, A. R. Shotin, K. N. Gruzdev, I. A. Chvala, A. Mazloum

“…Given the accelerating rates of AFSV molecular evolution in the East Asian countries (China, Vietnam and the Far Eastern regions of Russia), it is required to improve control measures, general and specific prevention, national and international surveillance over the economically significant animal disease.…”
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Diagnosis of the mechanisms of different types of discordances between phylogenies inferred from nuclear and mitochondrial markers by A. A. Poroshina, D. Y. Sherbakov, T. E. Peretolchina

“…Here we use adaptive dynamics models to study neutral molecular evolution under various scenarios of interaction between sister species and the environment. …”
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Extrinsic mortality and senescence: a guide for the perplexed by de Vries, Charlotte, Galipaud, Matthias, Kokko, Hanna

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Comparative mitogenome analysis of two ectomycorrhizal fungi (Paxillus) reveals gene rearrangement, intron dynamics, and phylogeny of basidiomycetes by Qiang Li, Yuanhang Ren, Dabing Xiang, Xiaodong Shi, Jianglin Zhao, Lianxin Peng, Gang Zhao

“…This study is the first report on the mitogenomes of Paxillus, which will promote a better understanding of their contrasted ecological strategies, molecular evolution and phylogeny of these important ectomycorrhizal fungi and related basidiomycete species.…”
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The mitochondrial gene order and CYTB gene evolution in insects by F. S. Sharko, A. V. Nedoluzhko, S. M. Rastorguev, S. V. Tsygankova, E. S. Boulygina, A. A. Polilov, E. B. Prokhortchouk, K. G. Skryabin

“…It is known that molecular evolution goes by the way of not only single nucleotide substitutions, but also by larger genomic reorganizations, such as insertion or deletion of large genome fragments, and even changing the order of genes. …”
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Gene regulatory patterning codes in early cell fate specification of the C. elegans embryo by Alison G Cole, Tamar Hashimshony, Zhuo Du, Itai Yanai

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Mitogenomic Phylogenetic Analyses Reveal New Insights into the Taxonomy and Evolution of Parnassiinae Swallowtail Butterflies (Lepidoptera: Papilionidae) by Lu Song, Xiaoxiao Chen, Xiushan Li, Raul Narciso C. Guedes, Youssef Dewer, Suqin Shang, Jingjiang Zhou

“…Mitochondrial genomes provide powerful insights into insect phylogeny and molecular evolution, aiding in the clarification of complex taxonomic relationships. …”
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Unfolded protein response during the progression of colorectal carcinogenesis by Cesar Augusto Sobrinho, Alexandre Moreira de Almeida, Maytana Roberta Taschin Grigolo, Michele Selzler, Antônio Carlos de Abreu, Letícia Silva Fagundes, Almir Souza Martins, Durval Batista Palhares, Rondon Tosta Ramalho

“…ABSTRACT Purpose: To evaluate the molecular evolution of endoplasmic reticulum (ER) stress during colorectal cancer carcinogenesis. …”
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Potato spindle tuber viroid by A. V. Kochetov, A. Y. Pronozin, N. V. Shatskaya, D. A. Afonnikov, O. S. Afanasenko

“…Viroids belong to a very interesting class of molecules attracting researchers in phytopathology and molecular evolution. Here we review recent literature data concerning the genetics of Potato spindle tuber viroid (PSTVd) and the mechanisms related to its pathological effect on the host plants. …”
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Rapid diversification of St-genome-sharing species in wheat grasses (Triticeae: Poaceae) accompanied by diversifying selection of chloroplast genes by Li-Na Sha, Ning Chen, Shi-Yong Chen, Yue Zhang, Yi-Ran Cheng, Dan-Dan Wu, Yi Wang, Hou-Yang Kang, Hai-Qin Zhang, Xiao Ma, Yong-Hong Zhou, Xing Fan

“…While high level of genetic heterogeneity in plastome DNA due to a reticulate evolutionary event has been considered to link with the richness of the St-genome-sharing taxa, the relationship between the dynamics of diversification and molecular evolution is lack of understanding. Results Here, integrating 106 previously and 12 newly sequenced plastomes representing almost all previously recognized genomic types and genus of the Triticeae, this study applies phylogenetic reconstruction methods in combination with lineage diversification analyses, estimate of sequence evolution, and gene expression to investigate the dynamics of diversification in the tribe. …”
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Case report: an unusual long-term evolution of a diffuse midline glioma, H3K27 altered by Michael Griessmair, Michael Griessmair, Claire Delbridge, Claus Zimmer, Eva Mayr, Arthur Wagner, Julian Canisius, Marie-Christin Metz, Benedikt Wiestler, Benedikt Wiestler

“…Interestingly, MR imaging conducted for migraine diagnosis 6 years ago in retrospect already showed a small, nodular T2w hyperintense lesion in the right thalamus.ConclusionDespite a more precise, molecularly driven classification of pediatric HGG (high-grade glioma) in the 5th edition of the WHO classification of CNS tumors, many genetic factors influencing the biological tumor development as well as the precise molecular evolution of tumors remain unclear. Given the highly aggressive clinical course of these tumors, with a median overall survival around 16 to 18 months, our report of a (presumable) precursor lesion years before clinical manifestation point towards a complex, multi-stage evolution of this tumor entity. …”
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Spring reproductive success influences autumnal malarial load in a passerine bird by Pigeault, Romain, Cozzarolo, Camille-Sophie, Wassef, Jérôme, Gremion, Jérémy, Bastardot, Marc, Glaizot, Olivier, Christe, Philippe

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Evolutionary and functional divergence of Sfx, a plasmid-encoded H-NS homolog, underlies the regulation of IncX plasmid conjugation by Avril Wang, Martha Cordova, William Wiley Navarre

“…Overall, this work underscores the impact of protein diversification on plasmid biology, enhancing our understanding of how molecular evolution affects broader plasmid ecology.…”
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The Presence of Two Distinct Lineages of the Foot-And-Mouth Disease Virus Type A in Russia in 2013–2014 Has Significant Implications for the Epidemiology of the Virus in the Region... by Victor V. Nikiforov, Sergey A. Noskov, Alexander V. Sprygin, Mohammad Abed Alhussen, Anastasia S. Krylova, Taisia V. Erofeeva, Svetlana N. Fomina, Svetlana R. Kremenchugskaya, Fedor I. Korennoy, Maxim V. Patrushev, Ilya A. Chvala, Tamara K. Mayorova, Stepan V. Toshchakov

“…The phylogenetic data reported here provide insight into the molecular epidemiology of FMD in the Eurasia region, elucidating the circulation pattern, molecular evolution, and genetic diversity, which is highly valuable for guiding vaccine designs and improving regional eradication policies.…”
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Molecular Phylogenetic Analysis of 16S rRNA Sequences Identified Two Lineages of Helicobacter pylori Strains Detected from Different Regions in Sudan Suggestive of Differential Evo... by Abeer Babiker Idris, Hadeel Gassim Hassan, Maryam Atif Salaheldin Ali, Sulafa Mohamed Eltaher, Leena Babiker Idris, Hisham N. Altayb, Amin Mohamed Abass, Mustafa Mohammed Ahmed Ibrahim, El-Amin Mohamed Ibrahim, Mohamed A. Hassan

“…In this study, we analyzed the molecular evolution of H. pylori strains detected from different tribes and regions of Sudan using 16S rRNA gene and the phylogenetic approach. …”
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Genomic changes during the evolution of the Coxiella genus along the parasitism-mutualism continuum by Santos-Garcia, Diego, Morel, Olivier, Henri, Hélène, El Filali, Adil, Buysse, Marie, Noël, Valérie, McCoy, Karen D., Gottlieb, Yuval, Klasson, Lisa, Zenner, Lionel, Duron, Olivier, Vavre, Fabrice

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