A CACTA-like transposon in the Anthocyanidin synthase 1 (Ans-1) gene is responsible for apricot fruit colour in the raspberry (Rubus idaeus) cultivar 'Varnes'. by Daniel James Sargent, Matteo Buti, Stefan Martens, Claudio Pugliesi, Kjersti Aaby, Dag Røen, Chandra Bhan Yadav, Felicidad Fernández Fernández, Muath Alsheikh, Jahn Davik, R Jordan Price

“…By performing RNASeq, we revealed differential expression patterns in the apricot-fruited 'Varnes' for genes in the anthocyanin biosynthesis pathway and following whole genome sequencing using long-read Oxford Nanopore Technologies sequencing, we identified a CACTA-like transposable element (TE) in the second exon of the Anthocyanidin synthase (Ans) gene that caused a truncated predicted ANS protein. …”
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Long journey of 16S rRNA‐amplicon sequencing toward cell‐based functional bacterial microbiota characterization by Jianshi Jin, Xiongduo Liu, Katsuyuki Shiroguchi

“…Furthermore, we present the prospects for further technical development, including the combined use of high‐throughput methods and other informative analyses, such as whole‐genome sequencing in the common unit of the cell, which enables bacterial microbiota characterization based on both the number of cells and their functions.…”
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Genomic analysis of antimicrobial resistant Escherichia coli isolated from manure and manured agricultural grasslands by C. Tyrrell, C. M. Burgess, F. P. Brennan, D. Münzenmaier, D. Drissner, R. J. Leigh, F. Walsh

“…The E. coli isolates were phenotypically antimicrobial resistant, predominantly multidrug resistant. Whole genome sequencing identified 31 antimicrobial resistance genes, and mutations in the gyrA, parC, and parE genes, conferring fluoroquinolone resistance. …”
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Crown Gall Induced by a Natural Isolate of <i>Brucella</i> (<i>Ochrobactrum</i>) <i>pseudogrignonense</i> Containing a Tumor-Inducing Plasmid by Marjolein J. G. Hooykaas, Paul J. J. Hooykaas

“…Unexpectedly, we found evidence that a natural isolate from a rose crown gall, called NBC51/LBA8980, was a bacterium that did not belong to the <i>Rhizobiaceae</i> family. Whole-genome sequencing revealed that this bacterium contained three large DNA circles with rRNA and tRNA genes, representing one chromosome and two chromids, respectively, and two megaplasmids, including a Ti plasmid. …”
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Confirming Multiplex RT-qPCR Use in COVID-19 with Next-Generation Sequencing: Strategies for Epidemiological Advantage by Rob E. Carpenter, Vaibhav Tamrakar, Harendra Chahar, Tyler Vine, Rahul Sharma

“…All 78 samples were classified into WHO lineages by whole-genome sequencing and then compared with two commercially available RT-qPCR assays for spike protein mutation(s). …”
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Mutations in Mycobacterium tuberculosis Isolates with Discordant Results for Drug-Susceptibility Testing in Peru by L. Solari, D. Santos-Lazaro, Z. M. Puyen

“…Our objective was to identify mutations that could explain discordant results in the evaluation of susceptibility to rifampicin and isoniazid between molecular and phenotypic methods, using whole genome sequencing (WGS). Peruvian strains showing sensitive results in the GenoType MTBDRplus v2.0 test and resistant results in the proportions in the agar-plaque test for isoniazid or rifampin were selected. …”
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Complete genome of mangrove-derived anti-MRSA streptomycete, Streptomyces pluripotens MUSC 135T by Hooi-Leng Ser, Kok-Gan Chan, Wen-Si Tan, Wai-Fong Yin, Bey-Hing Goh, Nurul-Syakima Ab Mutalib, Learn-Han Lee

“…Thus, the strain was selected for whole genome sequencing as an attempt to explore its bioactive potential. …”
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First report of the chloroplast and mitochondrial genomes of the Indian pitcher plant, Nepenthes khasiana Hook.f. by Ruchishree Konhar, Debasis Dash, Devendra Kumar Biswal

“…These organelle genomes were assembled as part of a whole-genome sequencing project aimed at gaining deeper insights into their evolutionary relations with genomes of other carnivorous plants. …”
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Validation of Customized Cancer Panel for Detecting Somatic Mutations and Copy Number Alterations by Su-Hye Choi, Seung-Hyun Jung, Yeun-Jun Chung

“…With targeted sequencing, we can obtain deeper coverage of reads and handle data more easily with a relatively lower cost and less time than whole-exome or whole-genome sequencing. Recently, we designed a customized gene panel for targeted sequencing of major solid cancers. …”
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Faster model-based estimation of ancestry proportions by Santander, Cindy G., Refoyo Martinez, Alba, Meisner, Jonas

“…The ADMIXTURE software is a widely used model-based approach to account for population stratification, however, it struggles with convergence issues and does not scale to modern human datasets or the large number of variants in whole-genome sequencing data. Likelihood-free approaches optimize a least square objective and have gained popularity in recent years due to their scalability. …”
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Structural and functional divergence of homoeologous genes in allopolyploid plant genomes by A. Y. Glagoleva, O. Y. Shoeva, E. K. Khlestkina

“…Thanks to the whole genome sequencing of a wide range of angiosperm species and comparative analysis of genome structure, the sequence of events that formed the genomes of modern plant taxa was restored. …”
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Recently Delisted Songbird Harbors Extensive Genomic Evidence of Inbreeding, Potentially Complicating Future Recovery by Anna María Calderón, Andrew W. Wood, Zachary A. Szpiech, David P. L. Toews

“…We explore the genomic consequences of this harsh bottleneck and recovery by comparing the genomic architecture of two closely related species whose population sizes have remained large and stable, Hooded Warblers (Setophaga citrina) and American Redstarts (Setophaga ruticilla). We used whole‐genome sequencing to characterize the distribution of runs of homozygosity and deleterious genetic variation. …”
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Resolving Rapid Radiation of Voles and Lemmings (Arvicolinae: Cricetinae, Rodentia) with QuaddRAD Sequencing and Transcriptome Analysis by Natalia Abramson, Elizaveta Skalon, Olga Bondareva, Semen Bodrov, Tatyana Petrova, Ivan Dvoyashov

“…For the first time, whole-genome sequencing data resolved relations within the third radiation wave of the subfamily’s taxa, namely the tribes Arvicolini, Lagurini, and Ellobiusini, which have formed polytomy in mitochondrial trees in earlier articles. …”
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Genomic characterization of foodborne Salmonella enterica and Escherichia coli isolates from Saboba district and Bolgatanga Municipality Ghana. by Gabriel Temitope Sunmonu, Frederick Adzitey, Erkison Ewomazino Odih, Boniface Awini Tibile, Rejoice Ekli, Martin Aduah, Anderson O Oaikhena, Olabisi C Akinlabi, Akebe Luther King Abia, Daniel Gyamfi Amoako, Iruka N Okeke

“…This study aimed to characterized previously isolated Salmonella (n = 14) and E. coli (n = 19) from milk, meat and its associated utensils in Ghana using whole-genome sequencing. Most of the Salmonella serovars (Fresno, Plymouth, Infantis, Give and Orleans) identified in this study are yet to be reported in Ghana. …”
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Evaluation of fecal occult blood testing for rapid diagnosis of invasive diarrhea in young children. by David A Kwasi, Pelumi D Adewole, Olabisi C Akinlabi, Stella E Ekpo, Iruka N Okeke

“…Presumptive pathogen isolates were identified biochemically and by PCR, and then confirmed by whole genome sequencing. Shigella, enteroinvasive Escherichia coli and Yersinia, pathogens that invariably cause invasive diarrhea, were detected in five of 46 specimens. …”
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Genomic and Drug Resistance Profile of Bovine Multidrug-Resistant <i>Escherichia coli</i> Isolated in Kazakhstan by Pavel G. Alexyuk, Andrey P. Bogoyavlenskiy, Yergali S. Moldakhanov, Kuralay S. Akanova, Adolat N. Manakbayeva, Timur Kerimov, Vladimir E. Berezin, Madina S. Alexyuk

“…While studying the prevalence and profile of antibiotic resistance among <i>E. coli</i> isolated from the feces of calves with signs of colibacillosis, a strain with a wide spectrum of drug resistance was isolated. Whole-genome sequencing, followed by bioinformatic processing and the annotation of genes of this strain, showed that the genome has a total length of 4,803,482 bp and contains 4986 genes, including 122 RNA genes. …”
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Potential links between human bloodstream infection by Salmonella enterica serovar Typhimurium and international transmission to Colombia. by Yan Li, Caisey V Pulford, Paula Díaz, Blanca M Perez-Sepulveda, Carolina Duarte, Alexander V Predeus, Magdalena Wiesner, Darren Heavens, Ross Low, Christian Schudoma, Angeline Montaño, Neil Hall, Jaime Moreno, Jay C D Hinton

“…Typhimurium isolates from bloodstream infection patients in Colombia, collected between 1997 and 2017. We used whole-genome sequencing to analyse multidrug-resistant (MDR) profiles, plasmid distribution, and to define phylogenetic relationships. …”
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Application of Genomic Selection in Beef Cattle Disease Prevention by Ramanathan Kasimanickam, Joao Carlos Pinheiro Ferreira, John Kastelic, Vanmathy Kasimanickam

“…By incorporating genomic technologies such as whole-genome sequencing, genotyping, and transcriptomics, researchers can identify specific genetic variants associated with resistance to pathogens like bovine respiratory disease and Johne’s disease. …”
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An insight into the genome-wide analysis of bacterial defense mechanisms in a uropathogenic Morganella morganii isolate from Bangladesh. by Syed Muktadir Al Sium, Barna Goswami, Sanjana Fatema Chowdhury, Showti Raheel Naser, Mihir Kanti Sarkar, Md Jobaid Faruq, Md Ahashan Habib, Shahina Akter, Tanjina Akhtar Banu, Md Murshed Hasan Sarkar, Md Salim Khan

“…A clinical isolate from a UTI patient in Bangladesh was subjected to high-throughput whole genome sequencing and extensive bioinformatics analysis in order to gather knowledge about the genomic basis of bacterial defenses and pathogenicity in M. morganii. …”
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Short-term evolutionary implications of an introgressed size-determining supergene in a vulnerable population by Pierre Lesturgie, John S. S. Denton, Lei Yang, Shannon Corrigan, Jeff Kneebone, Romuald Laso-Jadart, Arve Lynghammar, Olivier Fedrigo, Stefano Mona, Gavin J. P. Naylor

“…We conducted whole genome sequencing of samples collected across its range. …”
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