Breeding for postharvest physiological deterioration in cassava: problems and strategies by Wilton Mbinda, Asunta Mukami

“…With its extensive genomic resources including the public release of cassava reference genome sequence assembly and other and resources, and innovative plant breeding technologies, the crop offers an excellent opportunity to serve as a model to address postharvest spoilage and improve food security. …”
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Polygenic burden of short tandem repeat expansions promotes risk for Alzheimer’s disease by Michael H. Guo, Wan-Ping Lee, Badri Vardarajan, Gerard D. Schellenberg, Jennifer E. Phillips-Cremins

“…Here, we genotype 312,731 polymorphic STR tracts genome-wide using PCR-free whole genome sequencing data from 2981 individuals (1489 AD case and 1492 control individuals). …”
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A New Prognostic Indicator of Immune Microenvironment and Therapeutic Response in Lung Adenocarcinoma Based on Peroxisome-Related Genes by Zhen Xiong, Liwen Zhang, Wei Fan

“…However, the prognostic values of peroxisome-related genes (PRGs) were rarely reported. Genomic sequence, mutation, and clinical data of 535 LUAD tissues were obtained from TCGA data sets. …”
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An evaluation of the severe acute respiratory infection surveillance system in Ireland by Louise Marron, Roisin Duffy, Joan O’Donnell, Lisa Domegan

“…Time to receipt of whole genome sequencing (WGS) results was 40 days (IQR 30–61). …”
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Novel risk loci encompassing genes influencing STAT3, GPCR, and oxidative stress signaling are associated with co-morbid GERD and COPD. by Ava C Wilson, Alison Rocco, Joe Chiles, Vinodh Srinivasasainagendra, Wassim Labaki, Deborah Meyers, Bertha Hidalgo, Marguerite R Irvin, Surya P Bhatt, Hemant Tiwari, Merry-Lynn McDonald

“…We performed the first whole-genome sequence association analysis of comorbid GERD and COPD in 12,438 multi-ancestry participants. …”
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Pea (Pisum sativum L.): the uneasy fate of the first genetical object by O. E. Kosterin

“…Meanwhile, we await the completion of pea nuclear genome sequencing in 2016. For working out new molecular markers in pea, the synteny of its genome to the sequenced genome of Medicago truncatula is extensively used. …”
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“Sichuanvirus”, a novel bacteriophage viral genus, able to lyse carbapenem-resistant Klebsiella pneumoniae by Juan Li, Qingqing Fang, Huan Luo, Yan Feng, Yu Feng, Zhiyong Zong

“…We also obtained three bacterial mutants resistant to the phage and performed genome sequencing for them. We therefore discovered that the interruption of a capsular polysaccharide biosynthesis-related gene wcaJ by insertion sequences mediated the resistance to this phage. …”
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Pathogenicity of avian reovirus variant in the immune organs of broiler chicks by Haiyang Yu, Yudong Zhu, Qiong Wu, Wanjun Zhao, You Wang, Dong Wang, Huaguang Lu, Youxiang Diao, Yijing Li, Yi Tang

“…In this study, an ARV strain (Chicken/XJ/China/2022/01/16) was isolated from arthritic broiler chicks in Xinjiang province and whole genome sequencing of the ARV strain was performed using next generation sequencing (NGS) technology, and sequence analysis showed that the strain was a type V variant of the ARV gene. …”
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Comparison of SNP Variation and Distribution in Indigenous Ethiopian and Korean Cattle (Hanwoo) Populations by Zewdu Edea, Hailu Dadi, Sang Wook Kim, Tadelle Dessie, Kwan-Suk Kim

“…Although a large number of single nucleotide polymorphisms (SNPs) have been identified from the bovine genome-sequencing project, few of these have been validated at large in Bos indicus breeds. …”
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Decomposition of the pangenome matrix reveals a structure in gene distribution in the Escherichia coli species by Siddharth M. Chauhan, Omid Ardalani, Jason C. Hyun, Jonathan M. Monk, Patrick V. Phaneuf, Bernhard O. Palsson

“…ABSTRACT Thousands of complete genome sequences for strains of a species that are now available enable the advancement of pangenome analytics to a new level of sophistication. …”
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A chemical genetic screen with the EXO70 inhibitor Endosidin2 uncovers potential modulators of exocytosis in Arabidopsis by Xiaohui Li, Diwen Wang, Xianglin Yin, Mingji Dai, Christopher J. Staiger, Chunhua Zhang

“…Through a whole‐genome sequencing‐based mapping strategy, 14 nonallelic es2s mutants were mapped and the candidate mutations reported here. …”
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Sterol‐Targeted Laboratory Evolution Allows the Isolation of Thermotolerant and Respiratory‐Competent Clones of the Industrial Yeast Saccharomyces cerevisiae by Isabel‐Elena Sánchez‐Adriá, Jose A. Prieto, Gemma Sanmartín, Miguel Morard, Estéfani García‐Ríos, Francisco Estruch, Francisca Randez‐Gil

“…The clones were categorised into two groups based on their respiratory competence or deficiency, the latter associated with mtDNA loss, an event seemingly linked to FCNZ and heat tolerance. Genome sequencing and ploidy‐level analysis of all strains revealed aneuploidies, copy number variations (CNVs), and single nucleotide polymorphisms (SNPs). …”
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Adaptive evolution of stress response genes in parasites aligns with host niche diversity by Armando J. Cruz-Laufer, Maarten P. M. Vanhove, Lutz Bachmann, Maxwell Barson, Hassan Bassirou, Arnold R. Bitja Nyom, Mare Geraerts, Christoph Hahn, Tine Huyse, Gyrhaiss Kapepula Kasembele, Samuel Njom, Philipp Resl, Karen Smeets, Nikol Kmentová

“…We comparatively investigated antioxidant, heat shock, osmoregulatory, and behaviour-related genes (foraging) in two model parasitic flatworm lineages with contrasting ecological diversity, Cichlidogyrus and Kapentagyrus (Platyhelminthes: Monopisthocotyla), through whole-genome sequencing of 11 species followed by in silico exon bait capture as well as phylogenetic and codon analyses. …”
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Multidrug-Resistant Salmonella enterica Serovar Rissen Clusters Detected in Azores Archipelago, Portugal by Leonor Silveira, Miguel Pinto, Joana Isidro, Ângela Pista, Patrícia Themudo, Luís Vieira, Jorge Machado, João Paulo Gomes

“…In the present study, we analyzed by whole genome sequencing (WGS) all clinical, animal, food, and environmental isolates received up to 2017 in the Portuguese Reference Laboratories. …”
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Genome-wide characterization of the MADS-box gene family in Paeonia ostii and expression analysis of genes related to floral organ development by Xueting Yang, Qi Guo, Shaodan Liu, Duoduo Wang, Dingding Zuo, Tongfei Niu, Dongfeng Wei, Lili Guo, Xiaogai Hou

“…A total of 857 SSRs were identified by analysing the genome sequences of identified genes. We additionally created protein‒protein interaction networks for PoMADS proteins and analysed proteins that could interact among PoMADSs in Arabidopsis thaliana and grape. …”
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Auditory Phenotype of a Novel Missense Variant in the CEACAM16 Gene in a Large Russian Family With Autosomal Dominant Nonsyndromic Hearing Loss by Tatiana G. Markova, Natalia N. Alekseeva, Oxana P. Ryzhkova, Olga L. Shatokhina, Anna A. Orlova, Viktoriia V. Zabnenkova, Olga S. Groznova, Olesya V. Sagaydak, Svetlana S. Chibisova, Alexander V. Polyakov, George A. Tavartkiladze

“…Genetic testing was performed, including whole-genome sequencing for the proband’s son and Sanger sequence analysis for the proband and for all available family members. …”
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Subtle genomic differences in Klebsiella pneumoniae sensu stricto isolates indicate host adaptation by Bridget O'Brien, Alla Yushchenko, Jinha Suh, Dongyun Jung, Zhangbin Cai, Ngoc Sang Nguyen, Makeda Semret, Simon Dufour, Séamus Fanning, Jennifer Ronholm

“…A total of 128 KpI strains (bovine n = 65; human n = 63) were whole genome sequenced and human and bovine strains were compared based on phylogenomics, the pangenome, mobile genetic elements, and differential gene abundance. …”
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Insufficient gene expression and lost gene regulatory network may underlie the mechanism of Hirschsprung Disease in 5p–syndrome by Yizhao Luan, Peng Li, Yuanyuan Luo, Hong Zhang, Xiaochun Zhu, Yan Zhang, Aihua Yin, Qiang Wu, Chengwei Chai

“…Here, we conducted a study on two patients with CDC and HSCR using whole genome sequencing (WGS) analyses. Our WGS data confirmed the deletion regions on 5p associated with CDC and indicated potential unknown genetic mechanisms underlying HSCR. …”
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Pseudomonas azotoformans and Pseudomonas putida: Novel kiwifruit-native biological control agents against Pseudomonas syringae pv. actinidiae by Cristiana Correia, Antonio Cellini, Irene Donati, Panagiotis Voulgaris, Adebayo Ebenezer Obafemi, Elia Soriato, Elodie Vandelle, Conceição Santos, Francesco Spinelli

“…In vitro metabolic analysis together with genome sequencing and annotation revealed siderophore production, in particular pyoverdine, which may limit iron availability to the pathogen. …”
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The study of organelle DNA variability in alloplasmic barley lines in the NGS era by M. G. Siniauskaya, A. M. Makarevich, I. M. Goloenko, V. S. Pankratov, A. D. Liaudanski, N. G. Danilenko, N. V. Lukhanina, A. M. Shimkevich, O. G. Davydenko

“…Whole chloroplast (cp) and mitochondrial (mt) genome sequences were obtained by the MiSeq System (Illumina). …”
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