Trends in genome diversity of small populations under a conservation program: a case study of two French chicken breeds by Bortoluzzi, Chiara, Restoux, Gwendal, Rouger, Romuald, Desnoues, Benoit, Petitjean, Florence, Bosse, Mirte, Tixier-Boichard, Michèle

“…We here used temporal whole-genome sequencing data to assess the effects of a conservation program on the genetic diversity (Δπ), deleterious variation (ΔL), and inbreeding (ΔF) of two local French chicken breeds, the Barbezieux and Gasconne. …”
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Deciphering the nature and statistical optimization of antimicrobial metabolites of two endophytic bacilli by Raghda S. Isleem, Ahmed M. Eid, Saad El-Din Hassan, Khaled M. Aboshanab, Ghadir S. El-Housseiny

“…Both bacterial isolates displayed antioxidant and antiviral activity and mild cytotoxic action. Genomic sequence and antiSMASH analysis showed that the biosynthetic gene clusters of bacillomycin, mycosubtilin, fengycin, and macrolactin H in B. velezensis CCASU-C6 and bacillibactin and Macrolactin H in B. subtilis CCASU-C11 showed 100% conservation.…”
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The Presence of Two Distinct Lineages of the Foot-And-Mouth Disease Virus Type A in Russia in 2013–2014 Has Significant Implications for the Epidemiology of the Virus in the Region... by Victor V. Nikiforov, Sergey A. Noskov, Alexander V. Sprygin, Mohammad Abed Alhussen, Anastasia S. Krylova, Taisia V. Erofeeva, Svetlana N. Fomina, Svetlana R. Kremenchugskaya, Fedor I. Korennoy, Maxim V. Patrushev, Ilya A. Chvala, Tamara K. Mayorova, Stepan V. Toshchakov

“…In this study, we investigated the FMDV strains circulating in Russia during the 2013–2014 period in geographically distant regions utilizing whole genome sequencing followed by maximum-likelihood phylogenetic reconstruction of whole genome and VP1 gene sequences. …”
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SMARCA4-related Coffin-Siris syndrome in newborn: a case report and literature review by Yuqian Wang, Li Zhang, Jing Zhu, Liu Yang, Chan Wang, Ning Zou

“…For patients with developmental abnormalities, whole-genome sequencing or whole-exome sequencing is particularly important to assist diagnosis. …”
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Liberties of the genome: insertions of mitochondrial DNA fragments into nuclear genome by M. V. Golubenko, V. P. Puzyrev

“…In some cases, the insertion of multiple copies of the complete mitochondrial genome sequence may mimic paternal inheritance of mtDNA. …”
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Insights into structure, codon usage, repeats, and RNA editing of the complete mitochondrial genome of Perilla frutescens (Lamiaceae) by Ru Wang, Yongjian Luo, Zheng Lan, Daoshou Qiu

“…While the nuclear and chloroplast genomes of P. frutescens have already been documented, the complete mitochondrial genome sequence remains unreported. To this end, the sequencing, annotation, and assembly of the entire Mitochondrial genome of P. frutescens were hereby conducted using a combination of Illumina and PacBio data. …”
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The Single-Nucleotide Polymorphism (SNP) Validity to Detect Omicron Variants by Lia Gardenia Partakusuma, Luhung Budiailmiawan, null Budiman, Ida Parwati, null Aryati, Basti Andriyoko, Louisa Markus, Corine Niswara, Cut Nur Cinthia Alamanda

“…Variants of SARS-CoV-2 are determined by the whole genome sequencing (WGS) assay, which is time-consuming, with limited availability (only in several laboratories). …”
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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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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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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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Pseudocitrobacter cyperus, a novel bacterial species recovered from Cyperus alternifolius in Egypt by Samira M. Hamed, Mai A. Amer

“…We provide a full description of the novel species and present its genome sequence and annotation. The discovery of this novel species highlights the potential of endophytic bacteria associated with unique plant hosts to harbor previously uncharacterized microbial diversity.…”
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Genome-wide analyses of genomic diversity, population structure and selection signatures in Italian turkey populations by Medhat S. Saleh, Vincenzo Landi, Martijn F.L. Derks, Gerardo Centoducati, Martien A.M. Groenen, Pasquale De Palo, Elena Ciani, Maria G. Strillacci, Alessandro Bagnato, Nicola Pugliese, Elena Circella, Antonio Camarda

“…Italian local turkey populations are an important source of genetic diversity that should be preserved through an in vivo approach. Whole genome sequencing (WGS) and genotyping datasets were used to assess genetic variability within and across populations, to perform a genome-wide comparative analysis among populations and to identify selection signatures in Italian turkey populations. …”
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Discovery of Novel Diagnostic Biomarkers for Common Pathogenic <i>Nocardia</i> Through Pan-Genome and Comparative Genome Analysis, with Preliminary Validation by Chaohong Wang, Xinmiao Jia, Ming Wei, Jun Yan, Qing Sun, Sibo Long, Maike Zheng, Yiheng Shi, Guanglu Jiang, Yan Zhao, Hairong Huang, Xinting Yang, Li Gu, Guirong Wang

“…In this study, complete or assembled genome sequences of common pathogenic <i>Nocardia</i> and closely related species were obtained from NCBI as discovery and validation sets, respectively. …”
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Genomic patterns of strain-specific genetic structure, linkage, and selection across fall armyworm populations by Ashley E. Tessnow, Rodney N. Nagoshi, Robert L. Meagher, Todd M. Gilligan, Ben M. Sadd, Yves Carrière, Holly N. Davis, Shelby J. Fleischer, Kelly Richers, John C. Palumbo, Patrick Porter, Jose Carlos Verle Rodrigues, Gregory A. Sword

“…Here, we used whole genome sequencing population genomics to unravel novel patterns of population structure, linkage, and selection across the genome of a notorious agricultural pest, the fall armyworm. …”
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The GWAS-MAP|ovis platform for aggregation and analysis of genome-wide association study results in sheep by A. V. Kirichenko, A. S. Zlobin, T. I. Shashkova, N. A. Volkova, B. S. Iolchiev, V. A. Bagirov, P. M. Borodin, L. С. Karssen, Y. A. Tsepilov, Y. S. Aulchenko

“…The platform currently contains information on more than 34 million associations between genomic sequence variants and traits of meat production in sheep. …”
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Antimicrobial susceptibility and epidemiological types of Legionella pneumophila human isolates from Italy (1987–2020) by Maria Scaturro, Alessio Lanni, Fabiola Mancini, Antonietta Girolamo, Silvia Fillo, Andrea Ciammaruconi, Florigio Lista, Clementina Elvezia Cocuzza, Rosario Musumeci, Christophe Ginevra, Ghislaine Descours, Sophie Jarraud, Jessica Iera, Paolo Visca, Maria Luisa Ricci

“…The presence of the lpeAB efflux pump genes was also investigated. The genome sequences of a subpopulation of isolates showing reduced susceptibility to azithromycin were also analysed. …”
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Duckweed: a starch-hyperaccumulating plant under cultivation with a combination of nutrient limitation and elevated CO2 by Ling Guo, Ling Guo, Yang Fang, Songhu Wang, Yao Xiao, Yanqiang Ding, Yanling Jin, Xueping Tian, Anping Du, Zhihua Liao, Kaize He, Shuang Chen, Yonggui Zhao, Li Tan, Zhuolin Yi, Yuqing Che, Lanchai Chen, Jinmeng Li, Leyi Zhao, Peng Zhang, Zhengbiao Gu, Fangyuan Zhang, Yan Hong, Qing Zhang, Hai Zhao

“…In this study, we integrated whole-genome sequencing, epigenomics, transcriptomics, enzyme activity, and composition variation to elucidate the mechanisms of efficient starch accumulation in duckweed in terms of starch accumulation and carbon partitioning, regulation of the expression of genes in the starch metabolic pathway, and sucrose biosynthesis and transportation.Results and discussionAlthough Landoltia punctata exhibits dramatic gene family contraction, its starch content and productivity reached 72.2% (dry basis) and 10.4 g m-2 d-1, respectively, in 10 days, equivalent to a yield of 38.0 t ha-1 y-1, under nutrient limitation treatment with elevated CO2 levels. …”
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Characterization of the Phosphotransferase from <i>Bacillus subtilis</i> 1101 That Is Responsible for the Biotransformation of Zearalenone by Yuzhuo Wu, Qiuyu Zhou, Junqiang Hu, Yunfan Shan, Jinyue Liu, Gang Wang, Yin-Won Lee, Jianrong Shi, Jianhong Xu

“…In this study, a ZEA phosphotransferase, ZPH1101, was identified from <i>Bacillus subtilis</i> 1101 using genome sequencing. The product transformed by ZPH1101 was identified as phosphorylated ZEA (ZEA-P) through LC-TOF-MS/MS analysis. …”
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SARS-CoV-2 excretion and genetic evolution in nasopharyngeal and stool samples from primary immunodeficiency and immunocompetent pediatric patients by Haifa Khemiri, Ilhem Ben Fraj, Alessio Lorusso, Najla Mekki, Iolanda Mangone, Mariem Gdoura, Adriano Di Pasqual, Cesare Cammà, Valeria Di Lollo, Asma Cherni, Henda Touzi, Amel Sadraoui, Zina Meddeb, Nahed Hogga, Imen Ben Mustapha, Mohamed-Ridha Barbouche, Monia Ouederni, Henda Triki, Sondes Haddad-Boubaker

“…RNA detection was performed using RT-qPCR, and whole-genome sequencing was conducted with the NexSeq 1000 platform. …”
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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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