Genotype imputation in human genomic studies by A. A. Berdnikova, I. V. Zorkoltseva, Y. A. Tsepilov, E. E. Elgaeva

“…When performing imputation, genotype information from the study sample, in which only part of the genetic variants are known, is complemented using the standard (reference) sample, which has more complete genotype data (most often the results of whole-genome sequencing). Imputation has become an integral part of human genomic research due to the benefits it provides and the increasing availability of imputation tools and reference sample data. …”
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Goat Genomic Resources: The Search for Genes Associated with Its Economic Traits by A. M. A. M. Zonaed Siddiki, Gous Miah, Md. Sirazul Islam, Mahadia Kumkum, Meheadi Hasan Rumi, Abdul Baten, Mohammad Alamgir Hossain

“…As a result, different whole-genome sequences along with annotated gene sequences, gene function, and other genomic information of different goats are available in different databases. …”
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Analysis of the ASMT Gene Family in Pepper (Capsicum annuum L.): Identification, Phylogeny, and Expression Profiles by Luzhao Pan, Jiaqiu Zheng, Jia Liu, Jun Guo, Fawan Liu, Lecheng Liu, Hongjian Wan

“…In this study, based on the whole genome sequence, we performed a systematic analysis for the ASMT gene family in pepper (Capsicum annuum L.) and analyzed their expression profiles during growth and development, as well as abiotic stresses. …”
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Genome Characterization of Mammalian Orthoreovirus and Porcine Epidemic Diarrhea Virus Isolated from the Same Fattening Pig by Xiaoxuan Li, Jiakai Zhao, Jingjie Li, Yangzong Xiri, Zhixiang Liu, Qin Zhao, Yani Sun

“…The viral RNA of MRV and PEDV was detected in the fecal samples. The genome sequences of MRV and PEDV were successfully amplified from the same fecal sample. …”
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Metatranscriptomics as a tool to identify fungal species and subspecies in mixed communities – a proof of concept under laboratory conditions by Vanesa R. Marcelino, Laszlo Irinyi, John-Sebastian Eden, Wieland Meyer, Edward C. Holmes, Tania C. Sorrell

“…Abstract High-throughput sequencing (HTS) enables the generation of large amounts of genome sequence data at a reasonable cost. Organisms in mixed microbial communities can now be sequenced and identified in a culture-independent way, usually using amplicon sequencing of a DNA barcode. …”
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Biallelic SLC13A1 loss-of-function variants result in impaired sulfate transport and skeletal phenotypes, including short stature, scoliosis, and skeletal dysplasia by Christina G. Tise, Katie Ashton, Lachlan de Hayr, Kun-Di Lee, Omkar L. Patkar, Emma Krzesinski, Jennifer A. Bassetti, Erin M. Carter, Cathleen Raggio, Andreas Zankl, Anas M. Khanshour, Kristhen N. Atala, Jonathan J. Rios, Carol A. Wise, Ying Zhu, Futao Zhang, Tony Roscioli, Michael Buckley, Robert J. Harvey, Paul A. Dawson

“…Methods: Probands were identified by exome or genome sequencing and GeneMatcher. Sulfate levels were quantified using ion chromatography. …”
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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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Physiological, biochemical and genetic bases of amaranth (Amaranthus L.) breeding for food and feed purposes (a review) by A. B. Shcherban

“…The presence of the complete genomic sequence of Amaranthus hypochondriacus L. makes it possible to identify orthologs of key biosynthetic genes. …”
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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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LEAF HAIRINESS IN POTATO Solanum tuberosum: MORPHOLOGY, FUNCTION AND METHODS OF ANALYSIS by A. V. Doroshkov, D. A. Afonnikov

“…The fundamental basis for identification of genes controlling pubescence in potato is currently sequence data from complete genome sequencing. By analysis of homology with the genes of model organisms, it allows candidate genes that control important traits in potato to be identified. …”
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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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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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Leveraging Quantum LSTM for High-Accuracy Prediction of Viral Mutations by Prashanth Choppara, Bommareddy Lokesh

“…To improve model predictions, we use two key preprocessing techniques TF-IDF for efficient feature extraction and PCA for dimensionality reduction of genomic sequences. TF-IDF helps the model focus on the most informative nucleotide features, while PCA reduces the size of the data, making the model computationally efficient without sacrificing important information. …”
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Application of DNA markers in molecular breeding and genetic studies of grapevine by E. T. Ilnitskaya, M. V. Makarkina

“…This article presents a review of the world’s main achievements in grapevine genetics and markerassisted selection after the Vitis genome sequence. The process of creating new forms of grapes, as well as all crops, is based on the use of existing genetic diversity. …”
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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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A genomic analysis of twinning rate and its relationship with other reproductive traits in Holstein-Friesian cattle by Brian W. Kirkpatrick, Donagh P. Berry

“…Genome-wide association analyses of twinning rate, calving interval, cow survival and age at first calving were conducted using de-regressed breeding values estimates for 2,656 Holstein-Friesian sires. Full genome sequence data imputed from ∼50,000 single nucleotide polymorphisms were available for all sires. …”
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Prospects for mineral biofortification of wheat: classical breeding and agronomy by I. N. Leonova, E. V. Ageeva, V. K. Shumny

“…The new markers obtained from wheat genome sequencing and application of bioinformatic methods (GWAS, meta-QTL analysis) has expanded our knowledge on the traits that determine the grain mineral concentration and has identified the key gene candidates. …”
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Genomic characterization of antimicrobial-resistance and virulence factors in Salmonella isolates obtained from pig farms in Antioquia, Colombia. by María Isabel García-Álvarez, Juana L Vidal, Pilar Donado-Godoy, Jared Smith, Nikki Shariat, María Fernanda Valencia, Luis M Gómez-Osorio, Sara López-Osorio, Jenny J Chaparro-Gutiérrez

“…A total of 28 isolates of Salmonella spp. were included, which presented phenotypic resistance to more than one antibiotic used in pig farms. Whole genome sequencing (WGS) was performed in the Unit of Genomic of Agrosavia using an automated pipeline from the GHRU- Sanger Institute, employing the Illumina MiSeq platform.…”
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Development of Genomic Simple Sequence Repeat Markers for Evaluating Resources of Armillaira ostoyae and Their Transferability to Armillaira gallica by Sohee Kim, Hwayong Lee

“…SSR markers were developed using the released A. ostoyae whole-genome sequence (GenBank assembly accession: GCA_900157425.1). …”
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Deciphering mixed infections by plant RNA virus and reconstructing complete genomes simultaneously present within-host. by Martine Bangratz, Aurore Comte, Estelle Billard, Abdoul Kader Guigma, Guillaume Gandolfi, Abalo Itolou Kassankogno, Drissa Sérémé, Nils Poulicard, Charlotte Tollenaere

“…In most cases, the complete genome sequences were obtained, which is particularly important for a better estimation of viral diversity and the detection of recombination events. …”
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