Unravelling hybridization in Phytophthora using phylogenomics and genome size estimation by Kris Van Poucke, Annelies Haegeman, Thomas Goedefroit, Fran Focquet, Leen Leus, Marília Horta Jung, Corina Nave, Miguel Angel Redondo, Claude Husson, Kaloyan Kostov, Aneta Lyubenova, Petya Christova, Anne Chandelier, Slavcho Slavov, Arthur de Cock, Peter Bonants, Sabine Werres, Jonàs Oliva Palau, Benoit Marçais, Thomas Jung, Jan Stenlid, Tom Ruttink, Kurt Heungens

“…Hybrid species have previously been identified in at least six of the 12 phylogenetic clades. These hybrids can potentially infect a wider host range and display enhanced vigour compared to their progenitors. …”
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Comparative genomics analyses of Actinobacteriota identify Golgi phosphoprotein 3 (GPP34) as a widespread ancient protein family associated with sponge symbiosis by Cláudia Ferreira, Ilia Burgsdorf, Tzipora Perez, Gustavo Ramírez, Maya Lalzar, Dorothée Huchon, Laura Steindler

“…Furthermore, we identified GPP34 as a novel symbiosis-related gene family, found in two symbiotic Actinobacteriota clades, but not in their closely related free-living relatives. …”
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Identification and functional characterization of the RPP13 gene family in potato (Solanum tuberosum L.) for disease resistance by Baoqi Yuan, Chuang Li, Qingfeng Wang, Qi Yao, Xiaowei Guo, Yuhang Zhang, Zhongwei Wang

“…Phylogenetic analysis grouped these genes into four evolutionary clades, indicating a high level of conservation. Cis-regulatory element analysis identified that the promoter region of StRPP13-26 is enriched with pathogen-responsive elements such as the WUN-motif and MYC, suggesting its potential role in disease defense. …”
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Genome wide identification of MATE and ALMT gene family in lentil (Lens culinaris Medikus) and expression profiling under Al stress condition by Ankita Tripathi, Dharmendra Singh, Jyotika Bhati, Deepti Singh, Jyoti Taunk, Jawaher Alkahtani, Abdulrahman Al-Hashimi, Madan Pal Singh

“…Method and results In this study, 90 MATE and 14 ALMT genes were identified and clustered into four (MATE) and five (ALMT) subfamilies/clades with smaller subgroups. All the MATE and ALMT genes were unevenly dispersed across lentil chromosomes. …”
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Utilisation of an in vivo malaria model to provide functional proof for RhopH1/CLAG essentiality and conserved orthology with P. falciparum by Mitchell L. Trickey, Mrittika Chowdury, Georgina Bramwell, Natalie A. Counihan, Tania F. de Koning-Ward

“…Results It was revealed P. berghei CLAGX and CLAG9, which belong to two distinct phylogenetic clades, have separate non-complementary functions, and that clagX is the functional orthologue of P. falciparum clag3. …”
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New Resinogalea species from Araucaria araucana resin in Chile and reclassification of the genus in the Cryptocaliciomycetidae by Felipe Balocchi, Irene Barnes, Michael J. Wingfield, Rodrigo Ahumada, Cobus M. Visagie

“…A phylogenetic analysis based on the small subunit (SSU), internal transcribed spacer (ITS) and large subunit (LSU) rDNA regions resolved our strains into two clades with Cr. blascoi as its closest relative. Further analyses applying the Genealogical Concordance Phylogenetic Species Recognition (GCPSR) based on ITS, mini chromosome maintenance protein complex (MCM7), RNA polymerase II second largest subunit (RPB2) and translation elongation factor 1-alpha (TEF) gene regions, confirmed that strains represent two new species. …”
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Depletion of key gut bacteria predicts disrupted bile acid metabolism in inflammatory bowel disease by Daniel Peterson, Christopher Weidenmaier, Sonia Timberlake, Rotem Gura Sadovsky

“…We further found that bai genes from the Clostridium species best characterized as BA transformers were more prevalent in IBD patients than in non-IBD controls, while bai genes from uncharacterized taxa known only from MAGs were much more physiologically relevant in non-IBD samples. These un-isolated clades of BA-transforming bacteria merit further research; as beyond their prevalence in the human population, we found some cases in which they engrafted in IBD patients who had undergone fecal microbiota transplantation and experienced a clinical response.IMPORTANCEIn this paper, we identify specific bacteria that perform an important metabolic function in the human gut and demonstrate that in the guts of a large subset of patients with IBD, these bacteria are missing and the function is defective. …”
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The formulated microbicide RC-101 was safe and antivirally active following intravaginal application in pigtailed macaques. by Alexander M Cole, Dorothy L Patton, Lisa C Rohan, Amy L Cole, Yvonne Cosgrove-Sweeney, Nicole A Rogers, Deena Ratner, Alexandra B Sassi, Carol Lackman-Smith, Patrick Tarwater, Bharat Ramratnam, Piotr Ruchala, Robert I Lehrer, Alan J Waring, Phalguni Gupta

“…<h4>Background</h4>RC-101 is a congener of the antiretroviral peptide retrocyclin, which we and others have reported is active against clinical HIV-1 isolates from all major clades, does not hemagglutinate, and is non-toxic and non-inflammatory in cervicovaginal cell culture. …”
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Honoring the Afro-Colombian musical culture with the naming of Epipedobates currulao sp. nov. (Anura, Dendrobatidae), a frog from the Pacific rainforests by Mileidy Betancourth-Cundar, Juan Camilo Ríos-Orjuela, Andrew J. Crawford, David C. Cannatella, Rebecca D. Tarvin

“…Among species of Epipedobates, the new species has been previously confused with E. boulengeri, but the two species are allopatric and represent two divergent clades (1.77% divergent for 12S–16S and 5.39% for CYTB). …”
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Phylogenetic and pangenomic analyses of members of the family <i>Micrococcaceae</i> related to a plant-growth-promoting rhizobacterium isolated from the rhizosphere of potato (<i>S... by S. Yu. Shchyogolev, G. L. Burygin, L. A. Dykman, L. Yu. Matora

“…An important factor in this case may be the detailing of the gene composition of the strains and the taxonomic ratios resulting from analysis of the pangenomes of the corresponding clades.…”
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Genomic data suggest parallel dental vestigialization within the xenarthran radiation by Emerling, Christopher A, Gibb, Gillian C, Tilak, Marie-Ka, Hughes, Jonathan J, Kuch, Melanie, Duggan, Ana T, Poinar, Hendrik N, Nachman, Michael W, Delsuc, Frédéric

“…By contrast, in the two major armadillo clades, genes pertaining to the dento-gingival junction and amelogenesis appear to have been independently inactivated prior to losing all or some enamel. …”
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Most diverse, most neglected: weevils (Coleoptera: Curculionoidea) are ubiquitous specialized brood-site pollinators of tropical flora by Haran, Julien, Kergoat, Gael J., de Medeiros, Bruno A. S.

“…Our early estimates of the species richness of the corresponding weevil clades and the marked pattern of phylogenetic niche conservatism of host use further suggest that weevil-based pollination far exceeds the diversity of other brood-site mutualistic systems, which are generally restricted to one or a few groups of plants. …”
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In Silico Exploration of Staphylococcal Cassette Chromosome <i>mec</i> (SCC<i>mec</i>) Evolution Based on Phylogenetic Relationship of <i>ccrAB/C</i> by Huawei Wang, Jinxing He

“…Importantly, the phylogenetic relationship of <i>ccrAB/C</i> did not exhibit centralization over time; instead, similarly to <i>mecA</i>, <i>ccrAB/C</i> with similar identities had close clades across decades and geographical limits and different SCC<i>mec</i> types, which enabled us to discriminate SCC<i>mec</i> based on the sequence identity of <i>ccrAB/C</i>. …”
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Morphological and Molecular Characterization of Trichoderma Isolates from Vegetable Crop Rhizospheres in Nepal [version 2; peer review: 1 approved, 2 approved with reservations] by Arvind Kumar Keshari, Suraj Baidya, Aashaq Hussain Bhat, Ram B. Khadka, Puja Jaiswal

“…Results The morphological characteristics and phylogenetic trees for both regions provided a clear species resolution, with four main clades: Harzianum, Viride, Brevicompactum and Longibrachiatum with 12 species T. harzinaum, T. afroharzianum, T. lentiforme, T. inhamatum, T. camerunense, T. azevedoi, T. atroviride, T. asperellum, T. asperelloides, T. koningii, T. longibrachiatum and T. brevicompactum and nine species as a new country record. …”
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The complete chloroplast genome sequences of monotypic genus Pseudogalium, and comparative analyses with its relative genera by Wei Yu, Xiao-Juan Li, Zhen Lv, Li-E Yang, De-Li Peng

“…Phylogenetic analyses strongly supported the following proposals: (1) P. paradoxum can be isolated as a genus closely related to Galium; (2) P. paradoxum subsp. paradoxum and P. paradoxum subsp. duthiei form distinct clades, both of which can be considered as subspecies of P. paradoxum.…”
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Complete mitochondrial genome sequence analysis revealed double matrilineal components in Indian Ghoongroo pigs by Pranab Jyoti Das, Satish Kumar, Manasee Choudhury, Seema Rani Pegu, K. Meera, Rajib Deb, Sunil Kumar, Santanu Banik, Vivek Kumar Gupta

“…Phylogenetic analysis demonstrated a clear clustering of GH sequences into two clades, indicating the presence of two independent maternal lineages. …”
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A multigene phylogeny toward a new phylogenetic classification of Leotiomycetes by Peter R. Johnston, Luis Quijada, Christopher A. Smith, Hans-Otto Baral, Tsuyoshi Hosoya, Christiane Baschien, Kadri Pärtel, Wen-Ying Zhuang, Danny Haelewaters, Duckchul Park, Steffen Carl, Francesc López-Giráldez, Zheng Wang, Jeffrey P. Townsend

“…Such studies will ideally include designation of epitypes for the type species of those genera for which DNA is not able to be extracted from the original type specimen, and consideration of morphological characters whenever genetically defined clades are recognized as formal taxa within a classification.…”
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Phylogeography and genetic diversity of Ulmus elongata (Ulmaceae), a Tertiary relict tree with extremely small populations (PSESP) by Yakun Wang, Xiankun Wang, Junyuan Wu, Jun Yang, Yanpei Liu, Peng Guo, Fude Shang, Nan Lin

“…Analysis of molecular variance (AMOVA) showed that genetic variation in U. elongata occurs mainly between eight clades (60.95%). The Mantel tests indicated a significant correlation between genetic differentiation and geographical distances (r = 0.3777, p < 0.05) in U. elongata populations. …”
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Diversity and Distribution of <i>Phytophthora</i> Species Along an Elevation Gradient in Natural and Semi-Natural Forest Ecosystems in Portugal by Carlo Bregant, Eduardo Batista, Sandra Hilário, Benedetto Teodoro Linaldeddu, Artur Alves

“…Isolations performed from 138 symptomatic plant tissues and rhizosphere samples collected from 26 plant species yielded a total of 19 <i>Phytophthora</i> species belonging to 6 phylogenetic clades, including <i>P. cinnamomi</i> (36 isolates), <i>P. multivora</i> (20), <i>P. plurivora</i> (9), <i>P. cactorum</i> (8), <i>P. lacustris</i> (8), <i>P. pseudocryptogea</i> (8), <i>P. amnicola</i> (6), <i>P. hedraiandra</i> (6), <i>P. pseudosyringae</i> (5), <i>P. thermophila</i> (5), <i>P. bilorbang</i> (4), <i>P. inundata</i> (4), <i>P. asparagi</i> (3), <i>P. citricola</i> (3), <i>P. gonapodyides</i> (3), <i>P. rosacearum</i> (3), <i>P. chlamydospora</i> (2), <i>P. pachypleura</i> (2), and <i>P. syringae</i> (1). …”
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Phylogenetic inferences reveal multiple intra- and interhost genetic diversity among bat rabies viruses circulating in northeastern Brazil by Larissa Leão F. de Sousa, Mariana Dias Guilardi, Junior Olimpio Martins, Bruna Stefanie S. Alves, Luiz Henrique S. Tibo, Patrícia da Silva-Antunes, Gustavo Cabral-Miranda, Débora Bellini Caldeira, Paulo Eduardo Brandão, Fabrício Souza Campos, Luiz Mário R. Janini, Ricardo Durães-Carvalho

“…Phylogenetic reconstructions revealed three distinct and well-supported clusters and clades, indicating the cocirculation of different RABV lineages in the region and shedding light on both intra- and interhost diversity. …”
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