Exception to the Rule: Genomic Characterization of Naturally Occurring Unusual Vibrio cholerae Strains with a Single Chromosome by Gary Xie, Shannon L. Johnson, Karen W. Davenport, Mathumathi Rajavel, Torsten Waldminghaus, John C. Detter, Patrick S. Chain, Shanmuga Sozhamannan

“…Here, we describe the genomic characterization of strains that are an exception to the two chromosome rules: naturally occurring single-chromosome V. cholerae. Whole genome sequence analyses of NSCV1 and NSCV2 (natural single-chromosome vibrio) revealed that the Chr1 and Chr2 fusion junctions contain prophages, IS elements, and direct repeats, in addition to large-scale chromosomal rearrangements such as inversions, insertions, and long tandem repeats elsewhere in the chromosome compared to prototypical two chromosome V. cholerae genomes. …”
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Successful Traceability of Wildlife Samples Contributes to Wildlife Conservation: A Case Study of Tracing the Snub-Nosed Monkey (<i>Rhinopithecus</i> spp.) by Xibo Wang, Ying Shen, Yang Teng, Ruifeng Wu, Shuhao Liu, Jilai Zhao, Can Hu, Ming Li, Huijuan Pan, Jiwei Qi

“…This pipeline has been applied to the whole-genome sequence (WGS) data of China’s flagship species, the snub-nosed monkey (<i>Rhinopithecus</i> spp.). …”
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Genome Resequencing of the Honeybee Apis mellifera jemenetica (Hymenoptera: Apidae): A Key Tool towards Characterization, Conservation, and Genomic Selection by Ahmad Alghamdi, Yehya Alattal

“…We report the whole-genome sequence of the Arabian honeybee (Apis mellifera jemenetica). …”
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The WRKY Transcription Factor Genes in Lotus japonicus by Hui Song, Pengfei Wang, Zhibiao Nan, Xingjun Wang

“…The recent release of the L. japonicus whole genome sequence provides an opportunity for a genome wide analysis of WRKY genes in this species. …”
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Essential oils modulate virulence phenotypes in a multidrug-resistant pyomelanogenic Pseudomonas aeruginosa clinical isolate by Jayalekshmi Haripriyan, Christy Rose Binu, Nitasha D Menon, Muralidharan Vanuopadath, Malavika B. Hari, N Namitha, Kesiya Binoy, Anil Kumar, Bipin G. Nair, Victor Nizet, Geetha B. Kumar

“…Abstract Pyomelanogenic P. aeruginosa, frequently isolated from patients with urinary tract infections and cystic fibrosis, possesses the ability to withstand oxidative stress, contributing to virulence and resulting in persistent infections. Whole genome sequence analysis of U804, a pyomelanogenic, multidrug-resistant, clinical isolate, demonstrates the mechanism underlying pyomelanin overproduction. …”
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Prevalence and methodologies for detection, characterization and subtyping of Listeria monocytogenes and L. ivanovii in foods and environmental sources by Jin-Qiang Chen, Patrick Regan, Pongpan Laksanalamai, Stephanie Healey, Zonglin Hu

“…In this review, we (A) described L. monocytogenes and L. ivanovii, world-wide incidence of listeriosis, and prevalence of various L. monocytogenes strains in food and environmental sources; (B) comprehensively reviewed different types of traditional and newly developed methodologies, including culture-based, antigen/antibody-based, LOOP-mediated isothermal amplification, matrix-assisted laser desorption ionization-time of flight-mass spectrometry, DNA microarray, and genomic sequencing for detection and characterization of L. monocytogenes in foods and environmental sources; (C) comprehensively summarized different subtyping methodologies, including pulsed-field gel electrophoresis, multi-locus sequence typing, ribotyping, and phage-typing, and whole genomic sequencing etc. for subtyping of L. monocytogenes strains from food and environmental sources; and (D) described the applications of these methodologies in detection and subtyping of L. monocytogenes in foods and food processing facilities.…”
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Transposable Elements and Genome Size Variations in Plants by Sung-Il Lee, Nam-Soo Kim

“…With a wealth of information on whole-genome sequences in plant genomes, it was revealed that several genome-purging mechanisms have been employed, depending on plant taxa. …”
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Newly developed genomic SSR markers revealed the population structure and genetic characteristics of abaca (Musa textilis Nee) by Mariecris Rizalyn R. Mendoza, Antonio C. Laurena, Maria Genaleen Q. Diaz, Eureka Teresa M. Ocampo, Tonette P. Laude, Antonio G. Lalusin

“…To address this, we developed 50 genome-specific molecular markers based on the recently released whole genome sequence assembly of Abaca var. Abuab by Galvez et al. (2021). …”
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Development of Genomic Simple Sequence Repeat Markers for Evaluating Resources of Armillaira ostoyae and Their Transferability to Armillaira gallica by Sohee Kim, Hwayong Lee

“…SSR markers were developed using the released A. ostoyae whole-genome sequence (GenBank assembly accession: GCA_900157425.1). …”
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Novel risk loci encompassing genes influencing STAT3, GPCR, and oxidative stress signaling are associated with co-morbid GERD and COPD. by Ava C Wilson, Alison Rocco, Joe Chiles, Vinodh Srinivasasainagendra, Wassim Labaki, Deborah Meyers, Bertha Hidalgo, Marguerite R Irvin, Surya P Bhatt, Hemant Tiwari, Merry-Lynn McDonald

“…We performed the first whole-genome sequence association analysis of comorbid GERD and COPD in 12,438 multi-ancestry participants. …”
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Attenuation and Immunogenicity of a Live High Pathogenic PRRSV Vaccine Candidate with a 32-Amino Acid Deletion in the nsp2 Protein by Wenhui Lu, Baoli Sun, Jianyue Mo, Xiduo Zeng, Guanqun Zhang, Lianxiang Wang, Qingfeng Zhou, Ling Zhu, Zhili Li, Qingmei Xie, Yinzuo Bi, Jingyun Ma

“…Furthermore, we determined the whole genome sequences of these four intermediate viruses. …”
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Expert Consensus on Molecular Tumor Boards in Taiwan: Joint Position Paper by the Taiwan Oncology Society and the Taiwan Society of Pathology by Ming-Huang Chen, Wan-Shan Li, Bin-Chi Liao, Chiao-En Wu, Chien-Feng Li, Chia-Hsun Hsieh, Feng-Che Kuan, Huey-En Tzeng, Jen-Fan Hang, Nai-Jung Chiang, Tse-Ching Chen, Tom Wei-Wu Chen, John Wen-Cheng Chang, Yao-Yu Hsieh, Yen-Lin Chen, Yi-Chen Yeh, Yi-Hsin Liang, Yu-Li Su, Chiung-Ru Lai, James Chih-Hsin Yang

“…Results: The joint statement proposes key recommendations: (1) MTB discussions encompass diverse molecular analyses including next-generation sequencing (NGS), RNA sequencing, whole-exon sequencing, and whole-genomic sequencing addressing relevant genomic changes, tumor mutation burden, microsatellite instability, and specific biomarkers for certain cancers. (2) MTB meetings should involve multidisciplinary participants who receive regular updates on NGS-related clinical trials. (3) Prioritize discussing cases with unique clinical needs, gene alterations lacking treatments, untreatable neoplasms, or oncogenes unresponsive to targeted therapies. (4) Base MTB discussions on comprehensive patient data, including genetics, pathology, timing of specimen collection, and NGS outcomes. (5) MTBs offer treatment recommendations: standard therapies, off-label use, clinical trials, genetic counseling, and multidisciplinary reviews. (6) MTB effectiveness can be gauged by member composition, case reviews, treatment suggestions, and patient outcomes. …”
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Goat Genomic Resources: The Search for Genes Associated with Its Economic Traits by A. M. A. M. Zonaed Siddiki, Gous Miah, Md. Sirazul Islam, Mahadia Kumkum, Meheadi Hasan Rumi, Abdul Baten, Mohammad Alamgir Hossain

“…As a result, different whole-genome sequences along with annotated gene sequences, gene function, and other genomic information of different goats are available in different databases. …”
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Analysis of the ASMT Gene Family in Pepper (Capsicum annuum L.): Identification, Phylogeny, and Expression Profiles by Luzhao Pan, Jiaqiu Zheng, Jia Liu, Jun Guo, Fawan Liu, Lecheng Liu, Hongjian Wan

“…In this study, based on the whole genome sequence, we performed a systematic analysis for the ASMT gene family in pepper (Capsicum annuum L.) and analyzed their expression profiles during growth and development, as well as abiotic stresses. …”
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Subtle genomic differences in Klebsiella pneumoniae sensu stricto isolates indicate host adaptation by Bridget O'Brien, Alla Yushchenko, Jinha Suh, Dongyun Jung, Zhangbin Cai, Ngoc Sang Nguyen, Makeda Semret, Simon Dufour, Séamus Fanning, Jennifer Ronholm

“…A total of 128 KpI strains (bovine n = 65; human n = 63) were whole genome sequenced and human and bovine strains were compared based on phylogenomics, the pangenome, mobile genetic elements, and differential gene abundance. …”
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Identification of two new genetic loci for high-resolution genotyping of Enterocytozoon bieneusi by Meng Xinan, Ou Yonglin, Jiang Wen, Guo Yaqiong, Xiao Lihua, Feng Yaoyu, Li Na

“…In this study, comparison of a clinical genome sequence (C44566) with the whole genome sequence of an E. bieneusi isolate (H348) in GenBank led to the selection of the hypothetical protein 1 (hp1) and tubulin 1 (tub1) loci. …”
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Structure of a Sulfated Capsular Polysaccharide from the Marine Bacterium <i>Cobetia marina</i> KMM 1449 and a Genomic Insight into Its Biosynthesis by Maxim S. Kokoulin, Yulia V. Savicheva, Alina P. Filshtein, Ludmila A. Romanenko, Marina P. Isaeva

“…To elucidate the genetic basis of the CPS biosynthesis, the whole genomic sequence of <i>C. marina</i> KMM 1449 was obtained. …”
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Molecular Identification and Antimicrobial Potential of Streptomyces Species from Nepalese Soil by Karan Khadayat, Dawa Dindu Sherpa, Krishna Prakash Malla, Sunil Shrestha, Nabin Rana, Bishnu P. Marasini, Santosh Khanal, Binod Rayamajhee, Bibek Raj Bhattarai, Niranjan Parajuli

“…Here, we have also analyzed 16S rRNA in 27 Streptomyces species whose whole-genome sequence is available, which has revealed that some species have multiple copies of the 16S gene (∼1.5 kb) with significant variation in nucleotides. …”
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Taxonomic refinement of Bacillus thuringiensis by Nagham Shiekh Suliman, Reza Talaei-Hassanloui, Hamid Abachi, Sadegh Zarei, Ebrahim Osdaghi

“…By October 2023, whole genome sequences (WGS) of 885 bacterial strains were labeled as B. thuringiensis in the NCBI GenBank database. …”
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The extremely halotolerant black yeast Hortaea werneckii - a model for intraspecific hybridization in clonal fungi by Polona Zalar, Jerneja Zupančič, Cene Gostinčar, Janja Zajc, G. Sybren de Hoog, Filomena De Leo, Armando Azua-Bustos, Nina Gunde-Cimerman

“…Analysis of the BTB and MCM7 genes showed that in some cases two copies of the gene from the same genome are positioned in distant phylogenetic clusters of the intraspecific gene tree. Analysis of whole-genome sequences of selected H. werneckii strains generally confirmed the phylogenetic distances estimated on the basis of ribosomal genes, but also showed substantial reticulation within the phylogenetic history of the strains. …”
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