Metagenomic global survey and in-depth genomic analyses of Ruminococcus gnavus reveal differences across host lifestyle and health status by S. Nooij, N. Plomp, I. M. J. G. Sanders, L. Schout, A. E. van der Meulen, E. M. Terveer, J. M. Norman, N. Karcher, M. F. Larralde, R. H. A. M. Vossen, S. L. Kloet, K. N. Faber, H. J. M. Harmsen, G. F. Zeller, E. J. Kuijper, W. K. Smits, Q. R. Ducarmon

“…Analysis of these genomes and publicly available high-quality draft genomes (N = 333 genomes) revealed multiple clades which separated Crohn’s-derived isolates from healthy-derived isolates. …”
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Subfamily evolution analysis using nuclear and chloroplast data from the same reads by Eranga Pawani Witharana, Takaya Iwasaki, Myat Htoo San, Nadeeka U. Jayawardana, Nobuhiro Kotoda, Masashi Yamamoto, Yukio Nagano

“…Our analysis revealed that incomplete lineage sorting predominantly drives these discordances, while introgression and ancient introgression also contribute to topological discrepancies within certain clades. This study underscores the cost-effectiveness of using the same raw sequencing data for both cp and nuclear DNA analyses in understanding plant evolutionary relationships.…”
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Systems Biology Profiling of AMD on the Basis of Gene Expression by Mones S. Abu-Asab, Jose Salazar, Jingsheng Tuo, Chi-Chao Chan

“…Cladograms exposed a highly heterogeneous transcriptomic profiles within all the conventional phenotypes. Moreover, clades and nodal synapomorphies did not support the classical AMD phenotypes as valid transcriptomal genotypes. …”
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Genetic diversity and population structure of the helminths intermediate host Anentome helena (von dem Busch, 1847) in northern Thailand by Nithinan Chomchoei, Chalobol Wongsawad, Preeyaporn Butboonchoo, Nattawadee Nantarat

“…The phylogenetic tree and haplotype network revealed three main clades and three haplogroups for each region (COI and 16S rRNA). …”
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Comparing subsampling strategies for metagenomic analysis in microbial studies using amplicon sequence variants versus operational taxonomic units. by Daniel Segura, Divya Sharma, Osvaldo Espin-Garcia

“…Although sampling using ASVs and OTUs typically lead to similar results for each subsample, ASVs had more clades that differed in expression levels between allergic and non-allergic individuals across all sample sizes compared to OTUs, and led to more biomarkers discovered at Phase 2-SM-seq level.…”
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Tracing the paths of modular evolution by quantifying rearrangement events of protein domains by Abdulbaki Coban, Erich Bornberg-Bauer, Carsten Kemena

“…Results Here we determine, at unprecedented completeness, the rates of fusion, fission, emergence and loss of domains in five eukaryotic clades (monocots, eudicots, fungi, insects, vertebrates). …”
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Strain-limited biofilm regulation through the Brg1-Rme1 circuit in Candida albicans by Min-Ju Kim, Aaron P. Mitchell

“…These strains represent diverse clades and biofilm/filament production abilities. …”
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Species delimitation in the Populus laurifolia complex (Salicaceae) based on phylogenetic and morphometric evidence by Xueya Wei, Xingyong Cui, Fulin Yuan, Kerou Zhou, Liwei Zhou, Changli Zhao, Shaoyu Guo, Ce Shang, Zhixiang Zhang

“…The results revealed that this complex, based on a series of significant character states, could be morphologically distinguished into three species—P. laurifolia (Populus pilosa considered a synonym of P. laurifolia), Populus talassica, and Populus pamirica—which also correspond to three well-supported clades in the phylogenetic trees. P. pamirica exhibits some degree of ecological niche differentiation from P. talassica and P. laurifolia, whereas the latter two show minimal differentiation. …”
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Genetic tracking of Crimean-Congo haemorrhagic orthonairovirus in Hyalomma population infesting cattle in Nigeria. by Oluwafemi Babatunde Daodu, Joseph Ojonugwa Shaibu, Rosemary Ajuma Audu, Daniel Oladimeji Oluwayelu

“…This study underscores the need for broader surveillance to understand the full spectrum of CCHFV strains and clades circulating in Nigeria.…”
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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

“…In conclusion, this study facilitates the understanding of the characteristics and sources of variation of CUB and the evolution of the surveyed cyanobacterial clades with different thermotolerance and provides insights into their adaptation to different environments.…”
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Population Structure Based on Microsatellite Length Polymorphism, Antifungal Susceptibility Profile, and Enzymatic Activity of <i>Candida auris</i> Clinical Isolates in Russia by Ellina Oganesyan, Victoria Klimenteva, Irina Vybornova, Valentina Venchakova, Ekaterina Parshikova, Sergey Kovyrshin, Olga Orlova, Alexander Kruglov, Svetlana Gordeeva, Natalya Vasilyeva, Anastasiya Taraskina

“…ITS sequencing confirmed that all isolates belonged to a single ITS cluster (clades I and III). Fifteen distinct STR genotypes were identified, with genotype I being dominant (<i>n</i> = 53). …”
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Plant AT-rich protein and zinc-binding protein (PLATZ) family in Dendrobium huoshanense: identification, evolution and expression analysis by Fangli Gu, Yanshuang Ren, Muhammad Aamir Manzoor, Tingting Wang, Renshu Huang, Naifu Chen, Cheng Song, Yingyu Zhang

“…Eleven DhPLATZs were classified into three clades (I, II, and III) according to their evolutionary homology. …”
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Molecular and morphology identification of Squat lobster (Family Galatheidae) in Seribu Islands, Jakarta by Amanda Siregar Raissha, Putri Anggraini Nurlita, Restiana Endang Gelis Ester, Suryo Kusumo Bagus, Subhan Beginer, P Zamani Neviaty, Madduppa Hawis, Najwa Khalilah

“…The BLAST results on NCBI were identified as Allogalathea elegans, Allogalathea babai and Galathea sp. 2, which form 3 clades in the phylogenetic tree. Furthermore, we confirmed this type through morphological identification, which involves comparing the shape of the rostrum and the structure of the spines on the carapace. …”
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Probiogenomic analysis of Limosilactobacillus fermentum SD7, a probiotic candidate with remarkable aggregation abilities by Thunchanok Yaikhan, Monwadee Wonglapsuwan, Nuntiya Pahumunto, Natakorn Nokchan, Rawee Teanpaisan, Komwit Surachat

“…Using comprehensive genome analysis, we compared the genome of L. fermentum SD7 with 153 available genome sequences of L. fermentum strains and categorized the 154 strains into six distinct clades based on core gene single nucleotide polymorphisms. …”
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Identification and Characterization of the <i>ROP GTPase</i> Gene Family in Strawberry and the Positive Role of <i>FveROP4</i> in Fruit Resistance to Gray Mold by Shuai Zhao, Baode Zhu, Zhijun Zou, Yushan Zhai, Sufeng Liao, Ming Xu, Kunyang Li, Nasir Mehmood, Xiong Liao

“…Based on sequence homology, they were classified into three distinct phylogenetic clades. Detailed analysis of FveROP proteins revealed the presence of highly conserved catalytic G-domains, which are essential for their GTPase activity. …”
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Catfishes from the North-Western Part of Lake Tanganyika: Contribution to a Reference Library of DNA Barcodes by Archimède Mushagalusa Mulega, Arthur F. Boom, Imane Rahmouni, Hocein Bazairi, Abdelaziz Benhoussa, Maarten P. M. Vanhove, Maarten Van Steenberge

“…However, barcoding does seem promising as all the individual species are resolved as clades. Within <i>Synodontis</i>, the study found a strong similarity between <i>S. grandiops</i> and <i>S. multipunctatus</i>, highlighting a need for revision. …”
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Phylogenetic analysis of dermatophytes isolated from small domestic animals by A. M. Smagulova, E. V. Kukhar, T. I. Glotova, A. G. Glotov

“…The constructed phylogenetic trees reflecting the relationships of dermatophytes showed that, irrespective of the primer pairs used, the Microsporum and Trichophyton pathogens are in all cases reliably assigned to different clades. The analysis of ITS4F/ITS5R sequence fragment structures enabled the establish- ment of genetic relatedness between the Trichophyton benhamiae strains first isolated from cats in Russia and the Russian strain recovered from a guinea pig. …”
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Two new species of Plagiostomum (Prolecithophora, Plagiostomidae) from China with its morphology, phylogeny, and reproductive strategy by Leyuan Feng, Shiyan Zhang, Ming Tao, Ting Sun, Antai Wang

“…Kimura’s two-parameter distance and phylogenetic analyses further support the recognition of these two new species, showing that the three specimens of P. nanhaiensis sp. nov. and P. plagae sp. nov. form two separate clades within Plagiostomum with solid support. Moreover, these two new species exhibit similar habits and reproductive strategies, adopting hypodermic impregnation. …”
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Comparative plastome analyses and evolutionary relationships of 25 East Asian species within the medicinal plant genus Scrophularia (Scrophulariaceae) by Xia Wang, Lei Guo, Lulu Ding, Leopoldo Medina, Ruihong Wang, Pan Li

“…We categorized the 25 East Asian Scrophularia species into six distinct clades and further explored their interspecies relationships using morphological characteristics, such as flower color, the relative position of stamens and corolla, and plant height. …”
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Genome-Wide Identification of Superoxide Dismutase (<i>SOD</i>) Gene Family in <i>Cymbidium</i> Species and Functional Analysis of <i>CsSOD</i>s Under Salt Stress in <i>Cymbidium s... by Ruyi Li, Songkun Lin, Yin Yan, Yuming Chen, Linying Wang, Yuzhen Zhou, Shuling Tang, Ning Liu

“…These <i>SOD</i> genes were categorized into three clades: Cu/Zn-SOD, Fe-SOD, and Mn-SOD, with the Cu/Zn-SOD being the most abundant in these three types. …”
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