Genome evolution following an ecological shift in nectar-dwelling Acinetobacter by Vivianna A. Sanchez, Tanya Renner, Lydia J. Baker, Tory A. Hendry

“…Most notably, nectar-dwelling Acinetobacter acquired the ability to degrade pectin from plant pathogens, and the genes underlying this ability have duplicated and are under selection within the clade. We hypothesize that this ability was a key trait for adaptation to floral nectar, as it could improve access to nutrients in the nutritionally unbalanced habitat of nectar. …”
Get full text

Révision de l’espèce Homo erectus (Dubois, 1893) by Valéry Zeitoun

“…The first step is to seek criteria allowing to define this species as a clade or as a grade; id est as a monophyletic unit or as an archaic evolutionary step of the species Homo sapiens. …”
Get full text

Spatial and temporal variation of Antarctic microbial interactions: a study around the west Antarctic Peninsula by Swan L. S. Sow, Willem H. van de Poll, Rachel Eveleth, Jeremy J. Rich, Hugh W. Ducklow, Patrick D. Rozema, Catherine M. Luria, Henk Bolhuis, Michael P. Meredith, Linda A. Amaral-Zettler, Julia C. Engelmann

“…Up to 62.3% of the negative causal effects were driven by Syndiniales at Rothera compared to only 13.5% at Palmer, suggesting that parasitism drives community dynamics at Rothera more strongly than at Palmer. Conversely, SAR11 Clade II, which was less abundant but persistent year-round at both sites, was the dominant driver at Palmer, evidenced by many (28.2% and 37.4% of positive and negative effects respectively) strong causal effects. …”
Get full text

Salivary peptidomic profiling of chronic gingivostomatitis in cats by matrix‐assisted laser desorption/ionization‐time‐of‐flight mass spectrometry and nanoscale liquid chromatograp... by Sekkarin Ploypetch, Apisit Pornthummawat, Sittiruk Roytrakul, Janthima Jaresitthikunchai, Narumon Phaonakrop, Sabrina Wahyu Wardhani, Sitthichok Lacharoje, Somporn Techangamsuwan

“…In FCGS, 26 salivary peptides were altered, including apolipoprotein A1, nuclear receptor subfamily 1 group I member 3, fibrinogen alpha chain, interleukin 2 receptor gamma, interleukin 23 receptor, hemoglobin subunit alpha, and serpin peptidase inhibitor clade A (alpha‐1 antiproteinase, antitrypsin) member 12, protein‐tyrosine‐phosphatase, and cholinergic receptor nicotinic alpha 10 subunit. …”
Get full text

Plastid genome comparison and phylogenetic analyses of the Chinese group of medicinal species and related taxa within Asparagus genus by Pingxuan Xie, Tinglu Wang, Jiawei Tan, Linyuan Fan, Changkun Liu, Hanjing Yan

“…Phylogenetic analyses yielded a robust phylogeny for Asparagus taxa, which were split into Clades I, II, and III. Notably, medicinal Asparagus species were mainly found in Clade III. …”
Get full text

Phylogenetic analysis, metabolic profiling, and environmental adaptation of strain LCG007: a novel Rhodobacteraceae isolated from the East China Sea intertidal zone by Cuizhu Liang, Jiahua Wang, Jie Liu, Zekai Wang, Junwei Cao, Xi Yu, Li Zhang, Jiasong Fang, Jiasong Fang

“…This study enhances our comprehension of the microbial taxonomy within the Roseobacter clade affiliated cluster, their survival strategies in intertidal ecosystems, and underscores the significance of their role in nutrient cycling. …”
Get full text

Genome-wide identification of the bHLH gene family in Scutellaria baicalensis and their relationship with baicalin biosynthesis under drought stress by Yingxin Sun, Beier Wang, Lichao Zhang, Xiaohan Zheng, Peng Xu, Meng Zhang, Meiguang Han, Peng Di, Mei Han, Lin Cheng, Limin Yang

“…Phylogenetic and conserved motif analyses revealed that the gene structures within each SbbHLH clade are relatively conserved. Gene duplication analysis identified 29 duplication events in the SbbHLH gene family, most of which involved gene pairs under purifying selection. …”
Get full text

Morphology, phylogeography, phylogeny, and taxonomy of Cyclorhiza (Apiaceae) by Bo-Ni Song, Xueyimu Aou, Rong-Ming Tian, Jing Cai, Wei-Yan Tan, Chang-Kun Liu, Chang-Kun Liu, Xing-Jin He, Song-Dong Zhou

“…The phylogenetic results showed that Cyclorhiza species clustered into a separate clade and S. purpureovaginatum nested within Cyclorhiza. …”
Get full text

Novel H16N3 avian influenza viruses isolated from migratory gulls in China in 2023 by Peng Peng, Peng Peng, Peng Peng, Jinyan Shen, Wenjun Shi, Jing Guo, Mengjing Wang, Wenxi Li, Zhiqin Yue, Xiaohong Sun, Mengdi Guan, Lili Liu, Hongke Xu, Yujiao Xie, Anran Ren, Mingfeng Liu, Wenqiang Liu, Zhibin Zhang, Zhibin Zhang, Zhishu Xiao, Zhishu Xiao, Xuyong Li

“…Furthermore, the gull origin H13 and H16 viruses collectively served as gene donors for the newly emerged highly pathogenic clade 2.3.4.4b H5N1 viruses because the H13/H16-like PA, NP, and NS genes have been introduced into circulating H5N1 viruses since May 2022 in Europe. …”
Get full text

A Model H5N2 Vaccine Strain for Dual Protection Against H5N1 and H9N2 Avian Influenza Viruses by Jin-Ha Song, Seung-Eun Son, Ho-Won Kim, Se-Hee An, Chung-Young Lee, Hyuk-Joon Kwon, Kang-Seuk Choi

“…<b>Methods:</b> In this study, we generated a model PR8-derived recombinant H5N2 vaccine strain with hemagglutinin (HA) and neuraminidase (NA) genes from clade 2.3.2.1c H5N1 and Y439-like H9N2 viruses, respectively. …”
Get full text

Genomic characteristics of ST6115 carbapenem-resistant Klebsiella pneumoniae coharboring blaNDM-1 and blaIMP-4 by Xiaofang Xie, Xiaofang Xie, Yaxuan Zhai, Zhichen Zhu, Feinan Qian, Feinan Qian, Jie Zhu, Qizhao Gao, Hong Du, Hong Du

“…Finally, the conjugation transfer experiment was conducted to assess the transferability of the plasmid pHD8428-NDM-IMP.ResultsA comparable phylogenetic analysis revealed that ST6115 HD8428 and the majority of ST17 strains (9/12) were clustered on the same clade, which suggests a close relationship between two ST types. …”
Get full text

Energetic and genomic potential for hydrogenotrophic, formatotrophic, and acetoclastic methanogenesis in surface-expressed serpentinized fluids of the Samail Ophiolite by Alta E. G. Howells, Alta E. G. Howells, Lilja M. Quinn, Lilja M. Quinn, Miguel G. Silva, Miguel G. Silva, Kylie Akiyama, Kylie Akiyama, Lucas M. Fifer, Lucas M. Fifer, Grayson Boyer, Srishti Kashyap, Kirt Robinson, Kirt Robinson, Jared Broddrick, Everett L. Shock, Tori M. Hoehler

“…Acetoclastic methanogenesis is also shown to be energetically favorable in these fluids, and we report the first detection of a potential acetoclastic methanogen of the family Methanosarcinaceae, which forms a distinct clade with a genome from the serpentinizing seafloor hydrothermal vent field, Lost City. …”
Get full text

First report of serological, molecular detection, and characterization of human parvovirus B19 infections among sickle cell anaemia patients in Khartoum State, Sudan by Khalid Salman, Sittna Hayder El Nagar, Abdel Rahim M. El Hussein, Mohammed A. El Hussein, Hadi M. Yassine, Hebah A. Al Khatib, Mashael Ali Al- Badr, Ibrahim Farah, Khalid A. Enan

“…Phylogenetic analysis revealed two distinct Sudanese clusters: one (50 % of sequences) formed a unique clade with low similarity to existing genotypes, while the other (50 %) closely resembled genotype 1 A sequences from Iraq, Iran, and Tanzania. …”
Get full text

Genomic characterization of three marine fungi, including Emericellopsis atlantica sp. nov. with signatures of a generalist lifestyle and marine biomass degradation by Ole Christian Hagestad, Lingwei Hou, Jeanette H. Andersen, Espen H. Hansen, Bjørn Altermark, Chun Li, Eric Kuhnert, Russell J. Cox, Pedro W. Crous, Joseph W. Spatafora, Kathleen Lail, Mojgan Amirebrahimi, Anna Lipzen, Jasmyn Pangilinan, William Andreopoulos, Richard D. Hayes, Vivian Ng, Igor V. Grigoriev, Stephen A. Jackson, Thomas D. S. Sutton, Alan D. W. Dobson, Teppo Rämä

“…A six-gene phylogenetic analysis placed the isolate in the marine Emericellopsis clade and morphological examination confirmed that the isolate represents a new species, which is described here as E. atlantica. …”
Get full text

Differential vasoproliferative traits of Bartonella henselae strains associated with autotransporter BafA variants by Yuka Kondo, Masahiro Suzuki, Shingo Sato, Soichi Maruyama, Akiko Sei, Xingyan Ma, Kota Nakano, Yohei Doi, Kentaro Tsukamoto

“…A core genome SNP analysis of strains using whole genome sequencing data divided B. henselae strains into four clades, with each clade corresponding to BafA variants 1–4. …”
Get full text

Morphological Characteristics, Mitochondrial Genome, and Evolutionary Insights Into a New Sea Squirt From the Beibu Gulf by Yichuan Zhang, Yuting Qin, Yueying Wu, Liping Liu, Wenguang Zhang, Ling Ding, Xiangpei Ya, Zhiting Wen, Kuaili Feng, Hong Wang, Yujun Wang

“…Interestingly, YZ‐2024 belongs to Pyuridae, but it clustered with 12 species of Styelidae into a clade. Based on this, it can be suggested that YZ‐2024 is a new species of sea squirt in the northern Beibu Gulf of the South China Sea. …”
Get full text

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding? by Robert Lücking, M. Catherine Aime, Barbara Robbertse, Andrew N. Miller, Hiran A. Ariyawansa, Takayuki Aoki, Gianluigi Cardinali, Pedro W. Crous, Irina S. Druzhinina, David M. Geiser, David L. Hawksworth, Kevin D. Hyde, Laszlo Irinyi, Rajesh Jeewon, Peter R. Johnston, Paul M. Kirk, Elaine Malosso, Tom W. May, Wieland Meyer, Maarja Öpik, Vincent Robert, Marc Stadler, Marco Thines, Duong Vu, Andrey M. Yurkov, Ning Zhang, Conrad L. Schoch

“…Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. …”
Get full text

Vertical bacterial variability in oxidation ponds in the tropical zone by C. Tudsanaton, T. Pattamapitoon, O. Phewnil, W. Wararam, K. Chunkao, P. Maskulrath, M. Srichomphu

“…Amongst these phyla, the Actinobacteriota dominated (25.35 to 28.23 percent), followed by Cyanobacteria (19.49 to 21.57percent), Planctomycetota (15.50 to 17.41 percent), Firmicutes (9.97 to 10.79 percent), Proteobacteria (9.73 to 10.79 percent), Verrucomicrobiota (6.47 to 7.69 percent), Chloroflexi (2.79 to 2.99 percent), Bacteriota (0.96 to 1.41 percent), Acidobacteriota (0.70 to 0.80 percent) and SAR324 clade (marine group B) (0.69 to 0.61 percent). Four organic substances were found in contaminated domestic wastewater. 1) Photosynthetic cyanobacteria and phytoplankton performed aerobic degradation and accounted for the dissolved oxygen levels of 7.76, 7.45 and 7.42 milligrams per liter, respectively at various depths along the vertical profile. 2) Bacteria and archaeans that participate in carbon compound treatment included Planctomycetes, Verrucomicrobiota, Bacteroidota and Euryarcheota. …”
Get full text

TALome and phenotypic analysis of Pakistani Xanthomonas oryzae pv. oryzae population revealed novel virulent TALEs contributing to bacterial blight of rice by Syed Mashab Ali Shah, Rafia Ahsan, Linlin Liu, Ying Li, Qi Wang, Yong Wang, Jiali Yan, Moein Khojasteh, Xiameng Xu, Zhengyin Xu, Awais Rasheed, Muhammad Zakria, Gongyou Chen

“…Interestingly, the expression analysis of six clade-III OsSWEET genes suggests that novel TALE/s targeting unidentified susceptibility gene/s. …”
Get full text

Preparedness, prevention and control related to zoonotic avian influenza by EFSA Panel on Animal Health and Animal Welfare (AHAW), ECDC, Julio Alvarez, Anette Boklund, Sabine Dippel, Fernanda Dórea, Jordi Figuerola, Mette S. Herskin, Virginie Michel, Miguel Ángel Miranda Chueca, Eleonora Nannoni, Søren Saxmose Nielsen, Romolo Nonno, Anja B. Riber, Jan Arend Stegeman, Karl Ståhl, Hans‐Hermann Thulke, Frank Tuyttens, Christoph Winckler, Claire Brugerolles, Thorsten Wolff, Anna Parys, Erika Lindh, Neus Latorre‐Margalef, Marie‐Anne Rameix Welti, Ralf Dürrwald, Ramona Trebbien, Sylvie Van der Werf, Magnus Gisslén, Isabella Monne, Alice Fusaro, Claire Guinat, Alessio Bortolami, Leonidas Alexakis, Theresa Enkirch, Olov Svartstrom, Katriina Willgert, Francesca Baldinelli, Ludovica Preite, Malin Grant, Alessandro Broglia, Angeliki Melidou

“…In the EU/EEA, H5Nx viruses of clade 2.3.4.4b, which have increased opportunities for evolution due to widespread circulation in birds and occasional cases/outbreaks in mammals, have acquired the highest number of zoonotic traits. …”
Get full text