GBS-DP: a bioinformatics pipeline for processing data coming from genotyping by sequencing by A. Y. Pronozin, E. A. Salina, D. A. Afonnikov

“…Genotyping by sequencing (GBS) is used to identify genetic variability more rapidly, and is more cost-effective than whole-genome sequencing. GBS has demonstrated its reliability and flexibility for a number of plant species and populations. …”
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Discovery of two novel Flavobacterium species with potential for complex polysaccharide degradation by Xu-Dong Lian, Yong Guan, Yue Jiang, Dong-Heui Kwak, Mi-Kyung Lee, Zhun Li

“…Through comprehensive analyses, including 16S rRNA gene sequencing, whole-genome sequencing, and detailed morphological, physiological, and chemotaxonomic characterizations, these strains have been identified as new species within the genus Flavobacterium. …”
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Minimization of the Bacillus subtilis divisome suggests FtsZ and SepF can form an active Z-ring, and reveals the amino acid transporter BraB as a new cell division influencing fact... by Ilkay Celik Gulsoy, Terrens N V Saaki, Michaela Wenzel, Simon Syvertsson, Taku Morimoto, Tjalling K Siersma, Leendert W Hamoen

“…Viability of the multiple deletion mutant was not greatly affected, although the frequency of cell division was considerably reduced. Whole genome sequencing suggested that the construction of this minimal divisome strain was also possible due to the accumulation of suppressor mutations. …”
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Adaptive evolution of SARS-CoV-2 during a persistent infection for 521 days in an immunocompromised patient by Hanno Schmidt, Lea Schick, Jürgen Podlech, Angélique Renzaho, Bettina Lieb, Stefan Diederich, Thomas Hankeln, Bodo Plachter, Oliver Kriege

“…Virus samples from five time points were submitted to whole genome sequencing. Between the first detection of SARS-CoV-2 infection and its clearance, the patient’s virus population acquired 34 amino acid substitutions and 8 deletions in coding regions. …”
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LongReadSum: A fast and flexible quality control and signal summarization tool for long-read sequencing data by Jonathan Elliot Perdomo, Mian Umair Ahsan, Qian Liu, Li Fang, Kai Wang

“…We also demonstrate a few examples using LongReadSum to analyze cDNA sequencing, direct RNA sequencing, ONT reduced representation methylation sequencing (RRMS), and whole genome sequencing (WGS) data.…”
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In vitro long-term exposure to chlorhexidine or triclosan induces cross-resistance against azoles in Nakaseomyces glabratus by Kathrin Spettel, Dominik Bumberger, Richard Kriz, Sarah Frank, Madita Loy, Sonia Galazka, Miranda Suchomel, Heimo Lagler, Athanasios Makristathis, Birgit Willinger

“…Susceptibility testing and whole genome sequencing of yeast isolates pre- and post-exposure were performed. …”
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Development and validation of a minimal SNP genotyping panel for the differentiation of Cannabis sativa cultivars by Alex Cull, David L. Joly

“…Results In this study, we have conducted whole genome sequencing of 32 cultivars, mined the sequencing data for SNPs, developed a reduced SNP genotyping panel to discriminate between sequenced cultivars, then validated the 20-SNP panel using DNA from the sequenced cultivars and tested the assays on commercially available dried flower. …”
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Identification of DLEC1 D215N Somatic Mutation in Formalin Fixed Paraffin Embedded Melanoma and Melanocytic Nevi Specimens by Ricardo Vieira, Maria José Simões, Susana Carmona, Conceição Egas, Carlos Faro, Américo Figueiredo

“…DLEC1 D215N somatic mutation (COSM36702) was identified in a melanoma cell line through whole genome sequencing. However, little is known about the implication and prevalence of this mutation in primary melanomas or in melanocytic nevi. …”
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Molecular Epidemiology of Escherichia coli Resistant to Carbapenems, Fluoroquinolones, and Aminoglycosides Isolated from One of the Largest Hospitals in Vietnam in 2014–2019 by Tohru Miyoshi-Akiyama, Do Van Thanh, Truong Thai Phuong, Nguyen Quang Huy, Pham Thi Phuong Thuy, Teruo Kirikae, Pham Hong Nhung, Norio Ohmagari

“…This study was designed to clarify the molecular epidemiology of Escherichia coli isolates resistant to carbapenems, fluoroquinolones, and aminoglycosides isolated from patients admitted to one of the largest hospitals in Vietnam in 2014–2019 based on both whole-genome sequencing (WGS) and phenotypic data. Methodology. …”
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In Vivo Resistance to Ceftolozane/Tazobactam in Pseudomonas aeruginosa Arising by AmpC- and Non-AmpC-Mediated Pathways by Erik Skoglund, Henrietta Abodakpi, Rafael Rios, Lorena Diaz, Elsa De La Cadena, An Q. Dinh, Javier Ardila, William R. Miller, Jose M. Munita, Cesar A. Arias, Vincent H. Tam, Truc T. Tran

“…The genetic basis of ceftolozane/tazobactam resistance was evaluated, and β-lactam-resistant mechanisms were assessed by phenotypic assays. Whole genome sequencing identified mutations in AmpC including the mutation (V213A) and a deletion of 7 amino acids (P210–G216) in the Ω-loop. …”
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High-Resolution Melting Analysis to Detect Antimicrobial Resistance Determinants in South African Neisseria gonorrhoeae Clinical Isolates and Specimens by Nireshni Mitchev, Ravesh Singh, Veron Ramsuran, Arshad Ismail, Mushal Allam, Stanford Kwenda, Florah Mnyameni, Nigel Garrett, Khine Swe Swe-Han, Abraham J. Niehaus, Koleka P. Mlisana

“…Real-time PCR and high-resolution melting analysis were used to detect porA pseudogene (species-specific marker) and resistance-associated targets. Whole-genome sequencing was used as the gold standard for the presence of point mutations. …”
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Composition of the sputum bacterial microbiome of patients with different pathomorphological forms of non-small-cell lung cancer by V. G. Druzhinin, E. D. Baranova, P. S. Demenkov, L. V. Matskova, A. V. Larionov

“…Further research should be devoted to the search for microbiome biomarkers of lung cancer at the level of bacterial species using whole-genome sequencing.…”
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Comparison of Conservation Strategies for California Channel Island Oak (Quercus tomentella) Using Climate Suitability Predicted From Genomic Data by Alayna Mead, Sorel Fitz‐Gibbon, John Knapp, Victoria L. Sork

“…We performed whole‐genome sequencing on Island Oak individuals and Q. chrysolepis, a closely related species that hybridizes with Island Oak (127 total), to characterize genetic structure and introgression across its range and assess the relationship between genomic variation and climate. …”
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Spatio‐Temporal Changes in Effective Population Size in an Expanding Metapopulation of Eurasian Otters by Nia Evelyn Thomas, Elizabeth A. Chadwick, Michael W. Bruford, Frank Hailer

“…We obtained clear bottleneck signals in East England, and signals of recent population expansion in Wales and South West England in some analyses, consistent with national otter surveys and recent findings from whole‐genome sequencing. Analyses that did not account for spatial genetic structuring yielded strong spurious signals of United Kingdom‐wide population expansion, and Ne estimates from these analyses were suppressed by a factor of 3–4. …”
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Genomic and mutational analysis of Pseudomonas syringae pv. tagetis EB037 pathogenicity on sunflower by Jude E. Maul, John Lydon, Dilip Lakshman, Colin Willard, Hyesuk Kong, Daniel P. Roberts

“…Abstract Background Pseudomonas syringae pv. tagetis (Pstag) causes apical chlorosis on sunflower and various other plants of the Asteraceae family. Whole genome sequencing of Pstag strain EB037 and transposon-mutant derivatives, no longer capable of causing apical chlorosis, was conducted to improve understanding of the molecular basis of disease caused by this pathogen. …”
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Allele-specific PCR with fluorescently labeled probes: criteria for selecting primers for genotyping by V. A. Devyatkin, A. A. Shklyar, A. Zh. Fursova, Yu. V. Rumyantseva, O. S. Kozhevnikova

“…Single-nucleotide polymorphisms (SNPs) can serve as reliable markers in genetic engineering, selection, screening examinations, and other fields of science, medicine, and manufacturing. Whole-genome sequencing and genotyping by sequencing can detect SNPs with high specificity and identify novel variants. …”
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Virulence is not directly related to strain success in planta in Clavibacter nebraskensis by Molly Veregge, Cory D. Hirsch, Matthew J. Moscou, Liana Burghardt, Peter Tiffin, Devanshi Khokhani

“…Here, we used phenotypic assays and a high-throughput whole-genome sequencing approach to explore among-strain variation in virulence and multistrain reproductive success in planta. …”
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Intratumor heterogeneity of HPV integration in HPV-associated head and neck cancer by Noah Sasa, Toshihiro Kishikawa, Masashi Mori, Rie Ito, Yumie Mizoro, Masami Suzuki, Hirotaka Eguchi, Hidenori Tanaka, Takahito Fukusumi, Motoyuki Suzuki, Yukinori Takenaka, Keisuke Nimura, Yukinori Okada, Hidenori Inohara

“…Abstract Integration of human papillomavirus (HPV) into the host genome drives HPV-positive head and neck squamous cell carcinoma (HPV+ HNSCC). Whole-genome sequencing of 51 tumors revealed intratumor heterogeneity of HPV integration, with 44% of breakpoints subclonal, and a biased distribution of integration breakpoints across the HPV genome. …”
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Genome sequence and evaluation of safety and probiotic potential of Lacticaseibacillus paracasei LC86 and Lacticaseibacillus casei LC89 by Ting Chen, Yunjiao Zhao, Yunjiao Zhao, Yixuan Fan, Yao Dong, Zhonghui Gai

“…Secondly, whole-genome sequencing was performed on LC86 and LC89, and their antibiotic resistance, pathogenicity, and virulence genes were analyzed. …”
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Genome Analysis of Rhodococcus Sp. DSSKP-R-001: A Highly Effective β-Estradiol-Degrading Bacterium by Hongyan Zhao, Kejian Tian, Qing Qiu, Yu Wang, Hongyan Zhang, Shuang Ma, Shenbao Jin, Hongliang Huo

“…For a better understanding of the metabolic potential of the strain, whole genome sequencing of Rhodococcus DSSKP-R-001 and annotation of the functional genes were performed. …”
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