Decoding the anomalies: a genome-based analysis of Bacillus cereus group strains closely related to Bacillus anthracis by Thuto Gomolemo Magome, Marius Surleac, Marius Surleac, Ayesha Hassim, Cornelius Carlos Bezuidenhout, Henriette van Heerden, Kgaugelo Edward Lekota

“…Taxonomic challenges persist due to inconsistent classification methods, particularly for B. cereus isolates that resemble B. anthracis in genetic clustering.MethodsThis study investigated B. cereus group isolates from blood smears of animal carcasses in Kruger National Park, uncovering an unusual isolate with B. cereus features based on classical microbiological tests yet B. anthracis-like genomic similarities with an Average Nucleotide Identity (ANI) of ≥95%. Using comparative genomics, pan-genomics and whole genome Single Nucleotide Polymorphism (wgSNP) analysis, a total of 103 B. cereus group genomes were analyzed, including nine newly sequenced isolates from South Africa and a collection of isolates that showed some classification discrepancies, thus classified as “anomalous.”Results and discussionOf the 36 strains identified as B. anthracis in GenBank, 26 clustered phylogenetically with the four confirmed B. anthracis isolates from South Africa and shared 99% ANI. …”
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Prevalence and genomic insights of carbapenem resistant and ESBL producing Multidrug resistant Escherichia coli in urinary tract infections by Vidhyalakshmi Sivarajan, Amirtha Varshini Ganesh, Pavithra Subramani, Priyanka Ganesapandi, R. N. Sivanandan, Sneha Prakash, Nithyasri Manikandan, Arunasalam Dharmarajan, Frank Arfuso, Sudha Warrier, Marquess Raj, Kumar Perumal

“…The use of pangenome analysis enhances our understanding of resistance traits of isolates ST167, ST405, and ST448, offering valuable insights into comparative genomics of uropathogenic MDR E. coli.…”
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Genome evolution following an ecological shift in nectar-dwelling Acinetobacter by Vivianna A. Sanchez, Tanya Renner, Lydia J. Baker, Tory A. Hendry

“…Here, we investigate the genomic adaptations required to successfully colonize a novel habitat like floral nectar. We performed comparative genomics analyses between nectar-dwelling Acinetobacter and Acinetobacter species from other environments, like soil and water. …”
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Near telomere-to-telomere genome assemblies of Silkie Gallus gallus and Mallard Anas platyrhynchos restored the structure of chromosomes and “missing” genes in birds by Qiangsen Zhao, Zhongtao Yin, Zhuocheng Hou

“…The bird genome has more than tens of microchromosomes, but comparative genomics, annotations, and the discovery of variations are hindered by inadequate telomere-to-telomere level assemblies. …”
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Emergence of mcr-8.1-bearing MDR-hypervirulent Klebsiella pneumoniae ST307 by Jie Sheng, Rory Cave, Mary M. Ter-Stepanyan, Siyu Lu, Yingxiong Wang, Taihang Liu, Hermine V. Mkrtchyan

“…We report in-depth comparative genomics analyses of K. pneumoniae ST307 isolates recovered from patients in Armenia. …”
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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

“…The Pezizellaceae genome and the genome of the monotypic Amylocarpus genus represent the first published genomes of filamentous fungi that are restricted in their occurrence to the marine habitat and form thus a valuable resource for the community that can be used in studying ecological adaptions of fungi using comparative genomics.…”
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Evaluating the health risk of probiotic supplements from the perspective of antimicrobial resistance by Qiwen Tian, Hailv Ye, Xuan Zhou, Junyi Wang, Lifang Zhang, Wenxuan Sun, Chenxin Duan, Minyu Fan, Wei Zhou, Chuyun Bi, Qiong Ye, Aloysius Wong

“…Our data and future comparative genomics and metagenomics studies conducted on animal models and in healthy, immunocompromised, and/or antibiotic-treated human cohorts will contribute to a more comprehensive understanding of probiotic consumption, application, and safety.IMPORTANCEProbiotics are becoming increasingly popular, with promising applications in food and medicine, but the risk of transferring ARGs to disease-causing bacteria has raised concerns. …”
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Genomic insights into population dynamics and adaptive strategies of the endangered dipterocarp, Hopea chinensis by Wei-Min Xiang, Yu-Ting Jiang, Jie Zou, Yan Deng, Kai Jiang, Kai-Jian Zhang, Xin-Yu Zhou, Kai-Xi Quan, Zi-Wen Han, Wei-Chao Liu, Liang Tang, Yuan-Yuan Li, Simon T. Segar, Yuan-Ye Zhang, Xing-Hua Hu, Rong Wang, Xiao-Yong Chen

“…Furthermore, selective sweep analysis showed 12 genes associated with cold and drought tolerance and plant defense and immunity. Comparative genomics identified 125 specific and 30 lost gene families in the genome of H. chinensis, many of which were relevant to the responses to biotic and abiotic stresses. …”
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Chromosome-scale assembly and annotation of the wild wheat relative Aegilops comosa by Hongna Li, Shams ur Rehman, Rui Song, Liang Qiao, Xiaohua Hao, Jing Zhang, Kairong Li, Lifeng Hou, Wanyi Hu, Le Wang, Shisheng Chen

“…This newly constructed reference genome of Ae. comosa will serve as an important genomic resource for comparative genomic studies and the cloning of agriculturally important genes.…”
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Fine-mapping of PmHHM, a broad-spectrum allele from a wheat landrace conferring both seedling and adult resistance to powdery mildew by Bisheng Fu, Bisheng Fu, Bisheng Fu, Zhixin Lin, Lijuan Yan, Qiaofeng Zhang, Caiyun Liu, Caiyun Liu, Jin Cai, Jin Cai, Wei Guo, Wei Guo, Ying Liu, Wenling Zhai, Shuangjun Gong, Feng Xu, Jizhong Wu, Jizhong Wu, Jizhong Wu

“…To map its PM resitance gene, bulked segregant analysis, molecular mapping and comparative genomic analysis were also used in the present study.ResultsHHM shows remarkable adult resistance in the field and is nearly immune to all 25 Bgt isolates used in seedling tests, making it an excellent source of PM resistance. …”
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Eukaryotic DNAJ/K Database: A Comprehensive Phylogenomic Analysis Platform for the DNAJ/K Family by Kyeongchae Cheong, Jaehyuk Choi, Jaeyoung Choi, Jongsun Park, Suwang Jang, Yong-Hwan Lee

“…Empowered by 'class', 'cluster', and 'taxonomy' browsers and the 'favorite' function, the EDD provides a versatile platform for comparative genomic analyses of DNAJ/K families.…”
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Genomic insights into familial adenomatous polyposis: unraveling a rare case with whole APC gene deletion and intellectual disability by Hiroki Tanabe, Masami Ijiri, Kenji Takahashi, Honoka Sasagawa, Tomomi Kamanaka, Shohei Kuroda, Hiroki Sato, Takeo Sarashina, Yusuke Mizukami, Yoshio Makita, Toshikatsu Okumura

“…Whole-genome array comparative genomic hybridization (aCGH) revealed germline deletions at chromosome 5q22.1-22.2 encompassing the entire APC gene. …”
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Heterogeneous Chromosomal Aberrations in Intraductal Breast Lesions Adjacent to Invasive Carcinoma by Michaela Aubele, Margaret Cummings, Axel Walch, Horst Zitzelsberger, Jörg Nährig, Heinz Höfler, Martin Werner

“…In this study we applied comparative genomic hybridization (CGH) to formalin‐fixed, paraffin‐embedded breast tissue with DH and DCIS, adjacent to invasive ductal carcinoma (IDC), to screen these potential precursor lesions for whole genomic chromosomal imbalances. …”
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Angelman-Like Syndrome: A Genetic Approach to Diagnosis with Illustrative Cases by Ho-Ming Luk

“…With the advancement of genomic technology like array comparative genomic hybridization and next generation sequencing methods, it is found that some patients of these test negative Angelman-like Syndromes actually have alternative diagnoses. …”
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Gene Array Studies in Renal Neoplasia by John P.T. Higgins

“…Renal cell carcinomas have also been studied by array based comparative genomic hybridization. The purpose of this review will be to summarize these studies, to compare the results of the different studies, and to suggest future areas of investigation with a particular emphasis on clinically relevant advances.…”
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Prenatal Diagnosis of Cystic Hygroma related to a Deletion of 16q24.1 with Haploinsufficiency of FOXF1 and FOXC2 Genes by Matthew J. Garabedian, Donna Wallerstein, Nubia Medina, James Byrne, Robert J. Wallerstein

“…We report the prenatal diagnosis of cystic hygroma that was subsequently identified to have haploinsufficiency of the FOXF1 and FOXC2 genes via array comparative genomic hybridization (aCGH). Deletion o f these genes has previously neither been associated with cystic hygroma nor prenatally diagnosed. …”
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First Trimester Diagnosis of Holoprosencephaly Secondary to a Ring Chromosome 7 by Lindsay B. Henderson, Virginia L. Corson, Daniel O. Saul, Cynthia Anderson, Sarah Millard, Denise A. S. Batista, Karin J. Blakemore, Cheryl DeScipio

“…To our knowledge, this is the first report of a prenatally identified r(7), molecularly characterized using array comparative genomic hybridization.…”
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Cytogenomic Characterization of Giant Ring or Rod Marker Chromosome in Four Cases of Well-Differentiated and Dedifferentiated Liposarcoma by Hongyan Chai, Fang Xu, Autumn DiAdamo, Brittany Grommisch, Huanzhi Mao, Peining Li

“…Chromosome and array comparative genomic hybridization (aCGH) analyses were performed on two cases of well-differentiated liposarcoma (WDLPS) and two cases of dedifferentiated liposarcoma (DDLPS). …”
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The clove (Syzygium aromaticum) genome provides insights into the eugenol biosynthesis pathway by Sonia Ouadi, Nicolas Sierro, Simon Goepfert, Lucien Bovet, Gaetan Glauser, Armelle Vallat, Manuel C. Peitsch, Felix Kessler, Nikolai V. Ivanov

“…Here, we present a 370-Mb high-quality chromosome-scale genome assembly for clove. Comparative genomic analysis between S. aromaticum and Eucalyptus grandis—both species of the Myrtaceae family—reveals good genome structure conservation and intrachromosomal rearrangements on seven of the eleven chromosomes. …”
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3p14 De Novo Interstitial Microdeletion in a Patient with Intellectual Disability and Autistic Features with Language Impairment: A Comparison with Similar Cases by Ana Belén de la Hoz, Hiart Maortua, Ainhoa García-Rives, María Jesús Martínez-González, Maitane Ezquerra, María-Isabel Tejada

“…An 8 Mb de novo interstitial deletion at 3p14.2-p14.1, from position 60.461.316 to 68.515.453, was revealed by means of array comparative genomic hybridization and confirmed using quantitative reverse-transcription polymerase chain reaction assays. …”
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