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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Comparative Genomics Reveals Pathogenicity-Related Loci in Shewanella algae by Jui-Hsing Wang, Guo-Cheng He, Yao-Ting Huang, Po-Yu Liu

“…In this study, we aim to determine the occurrence of common virulence genes in S. algae using whole-genome sequence and comparative genomic analysis. Comparative genomics reveals putative-virulence genes related to bile resistance, chemotaxis, hemolysis, and motility. …”
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misMM: An Integrated Pipeline for Misassembly Detection Using Genotyping-by-Sequencing and Its Validation with BAC End Library Sequences and Gene Synteny by Young-Joon Ko, Jung Sun Kim, Sangsoo Kim

“…As next-generation sequencing technologies have advanced, enormous amounts of whole-genome sequence information in various species have been released. …”
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Updated review on diagnosis of Helicobacter pylori by R. Ugiagbe, S. Smith

“…Molecular diagnostic techniques include H. pylori reflexive stool testing, whole genomic sequencing as well as PCR diagnostics and clarithromycin resistance testing.…”
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First isolation and characterization of SARS-CoV-2 from COVID-19 patient of North East India by Aniruddha Jakharia, Biswajyoti Borkakoty, Sumi Pait, Gautam Baruah, Rahul Hazarika, Dipankar Biswas

“…Phylogenetic analyses of the whole genome sequences of the SARS-CoV-2 isolate (EPI_ISL_2501532 | 2020-05-19) showed monophyletic clade G and lineage B.1.1.…”
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Research Note: Novel reassortant avian influenza A(H9N2) Viruses in Wild Birds in Shanghai, China, 2020–2023 by Jie Hu, Yuting Xu, Min Ma, Chenyao Zhao, Yue Yuan, Guimei He

“…To better understand the genetic characteristics of these H9N2 viruses in Shanghai, the whole genome sequences were analyzed. Phylogenetical analysis showed that the nine H9N2 viruses have undergone complicated reassortment with waterfowl viruses along the East Asian-Australasian flyways. …”
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Genomic signatures of adaptation in native lizards exposed to human-introduced fire ants by Braulio A. Assis, Alexis P. Sullivan, Stephanie Marciniak, Christina M. Bergey, Vanessa Garcia, Zachary A. Szpiech, Tracy Langkilde, George H. Perry

“…Here, we investigate potential lizard adaptation to invasive fire ants by generating whole-genome sequences from 420 lizards across three populations: one with long exposure to fire ants, and two unexposed populations. …”
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Urinary Catheter Colonization by Multidrug-Resistant Cedecea neteri in Patient with Benign Prostatic Hyperplasia by Peter S. Ginn, Serina B. Tart, Stephen M. Sharkady, Dorothea K. Thompson

“…This C. neteri isolate was resistant or intermediate to second-generation cephalosporins, penicillins, and certain β-lactamase inhibitor/β-lactam combinations. Analysis of whole genome sequence information for a representative C. neteri strain indicated the presence of multiple open reading frames with sequence similarity to β-lactamases, including a chromosome-encoded AmpC β-lactamase and metallo-β-lactamases, consistent with the resistance phenotype of this bacterium. …”
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Chromosome-level reference genome assembly of the gyrfalcon (Falco rusticolus) and population genomics offer insights into the falcon population in Mongolia by Farooq Omar Al-Ajli, Giulio Formenti, Olivier Fedrigo, Alan Tracey, Ying Sims, Kerstin Howe, Ikdam M. Al-Karkhi, Asmaa Ali Althani, Erich D. Jarvis, Sadequr Rahman, Qasim Ayub

“…Here, we generated a chromosome-level gyrfalcon reference genome using the Vertebrate Genomes Project (VGP) assembly pipeline. Using whole genome sequences of 49 falcons from different species and populations, including “Altai” falcons, we analyzed their population structure, admixture patterns, and demographic history. …”
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Mining the Proteome of subsp. ATCC 25586 for Potential Therapeutics Discovery: An Approach by Abdul Musaweer Habib, Md. Saiful Islam, Md. Sohel, Md. Habibul Hasan Mazumder, Mohd. Omar Faruk Sikder, Shah Md. Shahik

“…In this study, we adopted subtractive genomics approach to analyze the whole genome sequence of the Fusobacterium nucleatum, a human oral pathogen having association with colorectal cancer. …”
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Genome analysis and prevalence of SARS-CoV-2 Indonesian variants and the correlation with the outbreak timeline by Maria Prevyolita Indra Muliawan, Timotius Christopher Tantokusumo, Amalda Siti Anisa, Kholis Abdurachim Audah

“…Methods: We analyzed whole genome sequences of SARS-CoV-2 wild type and variants isolated from Indonesian samples, sourced from GenBank and the GISAID EpiCoV database. …”
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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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Occurrence of <i>Salmonella</i> and presumptive <i>Bacillus cereus</i> in sesame products from Swiss retail stores by Karen Barmettler, Sara Boss, Michael Biggel, Roger Stephan

“…The 11 isolates identified by matrix-assisted laser desorption ionization-time of flight were whole-genome sequenced with Illumina technology to confirm the identity of the pathogen, determine its toxin gene profile, and perform panC typing. …”
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