A Genomic Snapshot of the SARS-CoV-2 Pandemic in the Balearic Islands by Carla López-Causapé, Carla López-Causapé, Pablo A. Fraile-Ribot, Pablo A. Fraile-Ribot, Santiago Jiménez-Serrano, Gabriel Cabot, Gabriel Cabot, Ester del Barrio-Tofiño, Ester del Barrio-Tofiño, M. Carmen Prado, Juana María Linares, Aranzazu López, Adoración Hurtado, Elena Riera, Antoni Serra, Eva Roselló, Lluis Carbó, M. Victoria Fernández-Baca, Carmen Gallegos, Juan Saurina, Emilio Arteaga, M. Magdalena Salom, Antonia Salvá, Antoni Nicolau, Fernando González-Candelas, Fernando González-Candelas, Iñaki Comas, Iñaki Comas, Antonio Oliver, Antonio Oliver

“…Genetic diversity of circulating variants was assessed by lineage assignment of consensus whole genome sequences with PANGOLIN and investigation of additional spike mutations.Results: Consensus sequences were assigned to 46 different PANGO lineages and 75% of genomes were classified within a VOC, VUI, or VUM variant according to the WHO definitions. …”
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Genomic Regions Associated With Skeletal Type Traits in Beef and Dairy Cattle Are Common to Regions Associated With Carcass Traits, Feed Intake and Calving Difficulty by Jennifer L. Doyle, Jennifer L. Doyle, Donagh P. Berry, Roel F. Veerkamp, Tara R. Carthy, Siobhan W. Walsh, Ross D. Evans, Ross D. Evans, Deirdre C. Purfield

“…Analyses were carried out using linear mixed models on imputed whole genome sequence data separately in 1,444 Angus, 1,129 Hereford, 6,433 Charolais, 8,745 Limousin, 1,698 Simmental, and 4,494 Holstein-Friesian cattle, all scored for the linear type traits. …”
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Characterization and Comparative Genomic Analysis of a Deep-Sea <i>Bacillus</i> Phage Reveal a Novel Genus by Yuan Chen, Tianyou Zhang, Qiliang Lai, Menghui Zhang, Meishun Yu, Runying Zeng, Min Jin

“…A BLASTn search of the whole genome sequence of vB_BteM-A9Y against the GenBank revealed no existing homolog. …”
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High primary resistance to metronidazole and levofloxacin, and a moderate resistance to clarithromycin in Helicobacter pylori isolated from Karnataka patients by Vignesh Shetty, Binit Lamichhane, Chin Yen Tay, Ganesh C. Pai, Ramachandra Lingadakai, Girisha Balaraju, Shiran Shetty, Mamatha Ballal, Eng Guan Chua

“…In this study, 38 out of 113 H. pylori strains had been whole-genome sequenced. Based on the draft genomes, RdxA and/or FrxA inactivation mutations were found to present in 75% of metronidazole-resistant strains. …”
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A longitudinal study reveals persistence of antimicrobial resistance on livestock farms is not due to antimicrobial usage alone by Richard P. Smith, Hannah E. May, Manal AbuOun, Emma Stubberfield, Daniel Gilson, Kevin K. Chau, Derrick W. Crook, Derrick W. Crook, Derrick W. Crook, Liam P. Shaw, Daniel S. Read, Nicole Stoesser, Nicole Stoesser, Nicole Stoesser, Maria Jose Vilar, Muna F. Anjum

“…Up to 14 isolates per visit were whole genome sequenced to determine presence of AMR genes.ResultsSheep farms had very low AMU in comparison to the other species and very few sheep isolates were genotypically resistant at any time point. …”
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Multi-view information fusion using multi-view variational autoencoder to predict proximal femoral fracture load by Chen Zhao, Joyce H. Keyak, Xuewei Cao, Qiuying Sha, Li Wu, Zhe Luo, Lan-Juan Zhao, Qing Tian, Michael Serou, Chuan Qiu, Kuan-Jui Su, Hui Shen, Hong-Wen Deng, Weihua Zhou, Weihua Zhou

“…We performed genome-wide association studies (GWAS) to select 256 genetic variants with the lowest p-values for each proximal femoral strength and integrated whole genome sequence (WGS) features and DXA-derived imaging features to predict proximal femoral strength. …”
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Identification and Molecular Characterization of a Novel Carlavirus Infecting <i>Chrysanthemum morifolium</i> in China by Jiapeng Li, Xiaoyin Wu, Hui Liu, Xiaomei Wang, Shaokui Yi, Xueting Zhong, Yaqin Wang, Zhanqi Wang

“…Pairwise sequence identity analysis showed that, except for CiCV1, CiCV1-CN has the highest whole-genome sequence identity of 71.3% to CVR-X6. At the amino acid level, the highest identities of predicted proteins encoded by the ORF1, ORF2, ORF3, ORF4, ORF5, and ORF6 of CiCV1-CN were 77.1% in the CVR-X21 ORF1, 80.3% in the CVR-X13 ORF2, 74.8% in the CVR-X21 ORF3, 60.9% in the CVR-BJ ORF4, 90.2% in the CVR-X6 and CVR-TX ORF5s, and 79.4% in the CVR-X21 ORF6. …”
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Composition and Diversity of CRISPR-Cas13a Systems in the Genus Leptotrichia by Shinya Watanabe, Bintao Cui, Kotaro Kiga, Yoshifumi Aiba, Xin-Ee Tan, Yusuke Sato’o, Moriyuki Kawauchi, Tanit Boonsiri, Kanate Thitiananpakorn, Yusuke Taki, Fen-Yu Li, Aa Haeruman Azam, Yumi Nakada, Teppei Sasahara, Longzhu Cui

“…Here, the complete whole genome sequences of 11 Leptotrichia strains were determined and compared with 18 publicly available Leptotrichia genomes in regard to the composition, occurrence and diversity of the CRISPR-Cas13a, and other CRISPR-Cas systems. …”
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Spatial Structure of <i>Yersinia pestis</i> Population Belonging to Altai Biovar, Subspecies central asiatica Acording to Genome-Wide Sequencing Data by K. A. Nikiforov, O. А. Morozov, G. A. Eroshenko, E. G. Oglodin, L. M. Kukleva, E. A. Naryshkina, Ya. M. Krasnov, V. M. Korzun, S. V. Balakhonov, V. V. Kutyrev

“…To determine the population structure of the biovar altaica ssp. central asiatica, 34 whole genome sequences were used (including 20 Y. pestis strains of the biovar altaica, 18 of which were sequenced by us). …”
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The impact of young age (< 40 years) on the outcome of a cohort of patients with primary non-metastatic breast cancer: analysis of 10-year survival of a prospective study by Youssef Bouferraa, Yolla Haibe, Andrea Chedid, Elio Jabra, Maya Charafeddine, Sally Temraz, Deborah Mukherji, Nagi El Saghir, Ali Shamseddine

“…Future studies of the whole genome sequences may reveal the genomic basis underlying the clinical differences we have observed.…”
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Sequence-based GWAS meta-analyses for beef production traits by Marie-Pierre Sanchez, Thierry Tribout, Naveen K. Kadri, Praveen K. Chitneedi, Steffen Maak, Chris Hozé, Mekki Boussaha, Pascal Croiseau, Romain Philippe, Mirjam Spengeler, Christa Kühn, Yining Wang, Changxi Li, Graham Plastow, Hubert Pausch, Didier Boichard

“…Abstract Background Combining the results of within-population genome-wide association studies (GWAS) based on whole-genome sequences into a single meta-analysis (MA) is an accurate and powerful method for identifying variants associated with complex traits. …”
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Molecular characterization of avian leukosis virus subgroup J in Chinese local chickens between 2013 and 2018 by Meige Ma, Mengmeng Yu, Fangfang Chang, Lixiao Xing, Yuanling Bao, Suyan Wang, Muhammad Farooque, Xinyi Li, Peng Liu, Yuntong Chen, Xiaole Qi, Qing Pan, Li Gao, Kai Li, Changjun Liu, Yanping Zhang, Hongyu Cui, Xiaomei Wang, Yanming Sun, Yulong Gao

“…To systematically analyze the molecular characteristics and the epidemic trend of ALV-J in Chinese local chickens, 260 clinical samples were collected for the period of 2013–2018; 18 ALV-J local chicken isolates were identified by antigen-capture enzyme-linked immunosorbent assay and subgroup A-, B-, and J-specific multiplex PCR. The whole genomic sequences of 18 isolates were amplified with PCR and submitted to GenBank. …”
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Lrp, a global regulator, regulates the virulence of Vibrio vulnificus by Yu-Chi Ho, Feng-Ru Hung, Chao-Hui Weng, Wei-Ting Li, Tzu-Hung Chuang, Tsung-Lin Liu, Ching-Yuan Lin, Chien-Jung Lo, Chun-Liang Chen, Jen-Wei Chen, Masayuki Hashimoto, Lien-I Hor

“…The purpose of this study was to map the mutation in this attenuated mutant and further explore how the gene thus identified is involved in virulence. Methods The whole genome sequence of mutant NY303 determined by next-generation sequencing was compared with that of strain YJ016 to map the mutations. …”
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Cancer origin tracing and timing in two high-risk prostate cancers using multisample whole genome analysis: prospects for personalized medicine by Anssi Nurminen, Serafiina Jaatinen, Sinja Taavitsainen, Gunilla Högnäs, Tom Lesluyes, Naser Ansari-Pour, Teemu Tolonen, Kerstin Haase, Antti Koskenalho, Matti Kankainen, Juho Jasu, Hanna Rauhala, Jenni Kesäniemi, Tiia Nikupaavola, Paula Kujala, Irina Rinta-Kiikka, Jarno Riikonen, Antti Kaipia, Teemu Murtola, Teuvo L. Tammela, Tapio Visakorpi, Matti Nykter, David C. Wedge, Peter Van Loo, G. Steven Bova

“…A total of 22 whole genome-sequenced sites (16 primary cancer foci and 6 lymph node metastatic) were analyzed using evolutionary reconstruction tools and spatio-evolutionary models. …”
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Candidate genes for field resistance to cassava brown streak disease revealed through the analysis of multiple data sources by Morag E. Ferguson, Rodney P. Eyles, Ana Luísa Garcia-Oliveira, Fortunus Kapinga, Fortunus Kapinga, Esther A. Masumba, Esther A. Masumba, Teddy Amuge, Teddy Amuge, Jessen V. Bredeson, Daniel S. Rokhsar, Jessica B. Lyons, Trushar Shah, Steve Rounsley, Geoffrey Mkamilo

“…Further, we investigated the co-localization of QTL for CBSD resistance across populations and the genetic relationships of parents based on whole genome sequence information. Two QTL on chromosome 4 for resistance to CBSD foliar symptoms and one on each of chromosomes 11 and 18 for root necrosis were of interest. …”
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Retrospective analysis of Plasmodium vivax genomes from a pre-elimination China inland population in the 2010s by Ying Liu, Ying Liu, Ying Liu, Ying Liu, Ying Liu, Tao Zhang, Shen-Bo Chen, Shen-Bo Chen, Shen-Bo Chen, Shen-Bo Chen, Yan-Bing Cui, Yan-Bing Cui, Yan-Bing Cui, Yan-Bing Cui, Shu-Qi Wang, Hong-Wei Zhang, Hai-Mo Shen, Hai-Mo Shen, Hai-Mo Shen, Hai-Mo Shen, Jun-Hu Chen, Jun-Hu Chen, Jun-Hu Chen, Jun-Hu Chen, Jun-Hu Chen

“…This study aimed to examine genomic epidemiology during the pre-elimination stage by retrospectively reporting whole-genome sequence variation of 10 Plasmodium vivax isolates from inland China.MethodsThe samples were collected during the last few inland outbreaks from 2011 to 2012 when China implemented a malaria control plan. …”
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Emergence of coexistence of a novel blaNDM-5-harbouring IncI1-I plasmid and an mcr-1.1-harbouring IncHI2 plasmid in a clinical Escherichia coli isolate in China by Xiaofan Zhang, Lingxia Chen, Xia Zhang, Qian Wang, Jingjing Quan, Jintao He, Hongying Pan, Xi Li

“…In addition, the whole genome sequence of this strain was obtained and the genetic characteristics of the mcr-1.1- and blaNDM-5-harbouring plasmids were analyzed. …”
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Proteotyping of Clostridioides difficile as Alternate Typing Method to Ribotyping Is Able to Distinguish the Ribotypes RT027 and RT176 From Other Ribotypes by Matthias F. Emele, Felix M. Joppe, Thomas Riedel, Thomas Riedel, Jörg Overmann, Jörg Overmann, Maja Rupnik, Maja Rupnik, Paul Cooper, R. Lia Kusumawati, Fabian K. Berger, Friederike Laukien, Ortrud Zimmermann, Wolfgang Bohne, Uwe Groß, Oliver Bader, Andreas E. Zautner

“…MLST, based on whole genome sequences, and PCR-ribotyping were used as reference methods. …”
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Assessment of genotyping array performance for genome-wide association studies and imputation in African cattle by Valentina Riggio, Abdulfatai Tijjani, Rebecca Callaby, Andrea Talenti, David Wragg, Emmanuel T. Obishakin, Chukwunonso Ezeasor, Frans Jongejan, Ndudim I. Ogo, Fred Aboagye-Antwi, Alassane Toure, Jahashi Nzalawahej, Boubacar Diallo, Ayao Missohou, Adrien M. G. Belem, Appolinaire Djikeng, Nick Juleff, Josephus Fourie, Michel Labuschagne, Maxime Madder, Karen Marshall, James G. D. Prendergast, Liam J. Morrison

“…Because there is growing interest in performing GWAS in African breeds, we have assessed the performance of 23 commercial bovine genotyping arrays for capturing the diversity across African breeds and performing imputation. We used 409 whole-genome sequences (WGS) spanning global cattle breeds, and a real cohort of 2481 individuals (including African breeds) that were genotyped with the Illumina high-density (HD) array and the GeneSeek bovine 50 k array. …”
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Genome-wide investigation and expression profiling of polyphenol oxidase (PPO) family genes uncover likely functions in organ development and stress responses in Populus trichocarp... by Fang He, Yu-Jie Shi, Qian Zhao, Kuang-Ji Zhao, Xing-Lei Cui, Liang-Hua Chen, Han-Bo Yang, Fan Zhang, Jia-Xuan Mi, Jin-Liang Huang, Xue-Qin Wan

“…Polyphenol oxidase (PPO) is a ubiquitous metalloproteinase in plants, which plays crucial roles in mediating plant resistance against biotic and abiotic stresses. Although the whole genome sequence of Populus trichocarpa has long been published, little is known about the PPO genes in Populus, especially those related to drought stress, mechanical damage, and insect feeding. …”
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