Genomic characteristics of ST6115 carbapenem-resistant Klebsiella pneumoniae coharboring blaNDM-1 and blaIMP-4 by Xiaofang Xie, Xiaofang Xie, Yaxuan Zhai, Zhichen Zhu, Feinan Qian, Feinan Qian, Jie Zhu, Qizhao Gao, Hong Du, Hong Du

“…ObjectivesThe aim of this study is to characterize the genomic features of ST6115 carbapenem-resistant Klebsiella pneumoniae (CRKP) co-harboring blaNDM-1 and blaIMP-4.MethodsThe genome sequences of one ST6115 Klebsiella pneumoniae (KP) strain and 12 ST17 KP strain were obtained through whole genome sequencing (WGS). …”
Get full text

A Highly Divergent Mitochondrial Genome in Extant Cape Buffalo From Addo Elephant National Park, South Africa by Deon deJager, Marlo Möller, Eileen Hoal, Paul vanHelden, Brigitte Glanzmann, Cindy Harper, Paulette Bloomer

“…ABSTRACT The reduced cost of next‐generation sequencing (NGS) has allowed researchers to generate nuclear and mitochondrial genome data to gain deeper insights into the phylogeography, evolutionary history and biology of non‐model species. …”
Get full text

Genome-Wide Identification and Expression Analysis of PkNRT Gene Family in Korean Pine (<i>Pinus koraiensis</i>) by Xinyu Zhao, Haibo Wu, Boyang Li, Pengyang Wang, Peng Zhang, Hailong Shen, Jianfei Yang

“…Here, we present a comprehensive genome-wide analysis and characterization of the NRT gene family in Korean pine, an invaluable tree species cultivated extensively in northeastern China. …”
Get full text

Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data by Caitlin Guccione, Lucas Patel, Yoshihiko Tomofuji, Daniel McDonald, Antonio Gonzalez, Gregory D. Sepich-Poore, Kyuto Sonehara, Mohsen Zakeri, Yang Chen, Amanda Hazel Dilmore, Neil Damle, Sergio E. Baranzini, George Hightower, Teruaki Nakatsuji, Richard L. Gallo, Ben Langmead, Yukinori Okada, Kit Curtius, Rob Knight

“…Abstract As next-generation sequencing technologies produce deeper genome coverages at lower costs, there is a critical need for reliable computational host DNA removal in metagenomic data. …”
Get full text

Multi-ancestry genome-wide meta-analysis with 472,819 individuals identifies 32 novel risk loci for psoriasis by Min Zhang, Wenting Su, Jiahui Deng, Bin Zhai, Gaizhi Zhu, Ran Gao, Qi Zeng, Jinming Qiu, Ziqing Bian, He Xiao, Guoming Luan, Renxi Wang

“…Results We identified 74 genome-wide significant loci for psoriasis. Of 74 loci, 32 were novel psoriasis risk loci. …”
Get full text

Genomic insights and comparative analysis of Colletotrichum species associated with anthracnose fruit rot and crown rot of strawberry in North Carolina by Tika B. Adhikari, Norman Muzhinji, Ashley N. Philbrick, Frank J. Louws, Frank J. Louws

Subjects: Get full text

SOD1 Is Essential for the Viability of DT40 Cells and Nuclear SOD1 Functions as a Guardian of Genomic DNA by Eri Inoue, Keizo Tano, Hanako Yoshii, Jun Nakamura, Shusuke Tada, Masami Watanabe, Masayuki Seki, Takemi Enomoto

“…The results revealed that SOD1 was essential for viability and that depletion of SOD1, especially nuclear SOD1, increased sister chromatid exchange (SCE) frequency, suggesting that superoxide is generated in or near the nucleus and that nuclear SOD1 functions as a guardian of the genome. Furthermore, we found that ascorbic acid could offset the defects caused by SOD1 depletion, including cell lethality and increases in SCE frequency and apurinic/apyrimidinic sites.…”
Get full text

Gene expression signature of neuropathic pain: Unveiling compassion through pain genetics and genome-wide mRNA profiles by Ashok Kumar Saxena, Suman Choudhary, Geetanjali Chilkote

Get full text

Chloroplast genome characteristics and phylogenetic analysis of Macropanax rosthornii (Harms) C.Y. Wu ex G. Hoo (Araliaceae) by Shuxin Du, Huiying Huang, Shuhui Yang, Tianyi Gu, Mengli Zhou, Ruihong Wang

Subjects: Get full text

Computational analysis of SARS-CoV-2, SARS-CoV, and MERS-CoV genome using MEGA by Vipan Kumar Sohpal

“…Genomics & Informatics…”
Get full text

The genome sequence of the tawny cockroach, Ectobius (Ectobius) pallidus (Olivier, 1789) [version 1; peer review: 2 approved] by Tony Hunter

Subjects: Get full text

Genome-wide identification of the adaptor protein complexes and its expression patterns analysis in foxtail millet (Setaria italica L.) by Dan Wang, Min Su, Jian-Hong Hao, Zi-Dong Li, Shuqi Dong, Xiangyang Yuan, Xiaorui Li, Lulu Gao, Xiaoqian Chu, Guanghui Yang, Jia-Gang Wang, Huiling Du

Subjects: Get full text

Using Quantitative Trait Locus Mapping and Genomic Resources to Improve Breeding Precision in Peaches: Current Insights and Future Prospects by Umar Hayat, Cao Ke, Lirong Wang, Gengrui Zhu, Weichao Fang, Xinwei Wang, Changwen Chen, Yong Li, Jinlong Wu

Subjects: Get full text

Exploration of migration directions in different populations of Eothenomys miletus in the Hengduan Mountains of Yunnan Province: a genome-based analysis by Yanfei Cai, Ting Jia, Wanlong Zhu, Wanlong Zhu, Wanlong Zhu

“…Additionally, we focused on identifying genomic signatures of selection and local adaptation among the different populations. …”
Get full text

Mitochondrial genome and nuclear ribosomal RNA analysis place Alveonasus lahorensis within the Argasinae and suggest that the genus Alveonasus is paraphyletic by Ben J. Mans, Lidia Chitimia-Dobler, Ronel Pienaar, Minique de Castro, Mehran Khan, Mashal M. Almutairi, Abdulaziz Alouffi, Abid Ali, Ala Tabor

“…In addition, the mitochondrial genomes for Argas reflexus and Alectorobius kelleyi are reported from Germany and the USA, respectively. …”
Get full text

Modification and analysis of context-specific genome-scale metabolic models: methane-utilizing microbial chassis as a case study by M. A. Kulyashov, R. Hamilton, Y. Afshin, S. K. Kolmykov, T. S. Sokolova, T. M. Khlebodarova, M. G. Kalyuzhnaya, I. R. Akberdin

Subjects: “…context-specific genome-scale metabolic modeling…”
Get full text

Recombinant AAV batch profiling by nanopore sequencing elucidates product-related DNA impurities and vector genome length distribution by Florian Dunker-Seidler, Kathrin Breunig, Magdalena Haubner, Florian Sonntag, Markus Hörer, Rebecca C. Feiner

“…During production, recombinant adeno-associated virus (rAAV) capsids are equipped with heterogeneous genetic payloads including undesired DNA impurities as well as truncated vector genomes. Comprehensive analysis of encapsidated DNA by long-read next-generation sequencing is destined to guide platform optimization and provide crucial insights into safety of gene therapies. …”
Get full text

Detecting gene copy number alterations by Oncomine Comprehensive genomic profiling in a comparative study on FFPE tumor samples by Fabio Bozzi, Elena Conca, Marco Silvestri, Gianpaolo Dagrada, Alice Ardore, Donata Penso, Daniele Lorenzini, Chiara Costanza Volpi, Desirè Viola Trupia, Adele Busico, Iolanda Capone, Federica Perrone, Elena Tamborini, Andrea Vingiani, Luca Agnelli, Giancarlo Pruneri

“…The introduction of other procedures, such as Next-Generation Sequencing has dramatically improved CNAs discovery at genome-wide level. The detection of CNAs by NGS in FFPE material is, nonetheless, a complex issue, which still requires validation studies. …”
Get full text

Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes by Yihan Wang, Daniel A. Armendariz, Lei Wang, Huan Zhao, Shiqi Xie, Gary C. Hon

Subjects: Get full text

Genome-wide association study analysis of single nucleotide variants in L. infantum associated with IL-6 inflammatory response in visceral leishmaniasis by Amanda Miranda da Silva, Kátia Silene Sousa Carvalho, Caio Andrey Bezerra Januário, Raquel Gomes de Sena Carneiro Caldas, Bianka Lopes da Silva Paulino, Débora Cavalcante Braz, Dorcas Lamounier Costa, Gabriel da Luz Wallau, Wilson Jose da Silva Junior, Carlos Henrique Nery Costa

Subjects: Get full text