Results 1 to 10 of about 4,042,841 (387)

An evolutionary view of the Fusarium core genome. [PDF]

BMC Genomics
Fusarium , a member of the Ascomycota fungi, encompasses several pathogenic species significant to plants and animals. Some phytopathogenic species have received special attention due to their negative economic impact on the agricultural industry around ...
Gomez-Chavarria DA, Rua-Giraldo AL, Alzate JF.   +2 more
europepmc   +5 more sources

Impact of homologous recombination on core genome phylogenies [PDF]

BMC Genomics, 2020
Core genome phylogenies are widely used to build the evolutionary history of individual prokaryote species. By using hundreds or thousands of shared genes, these approaches are the gold standard to reconstruct the relationships of large sets of strains ...
Caroline M. Stott, Louis‐Marie Bobay
semanticscholar   +6 more sources

Evolution of the orthopoxvirus core genome. [PDF]

Virus Res, 2023
Orthopoxviruses comprise several relevant pathogens, including the causative agent of smallpox and monkeypox virus. Analysis of orthopoxvirus genome evolution mainly focused on gene gains/losses. We instead analyzed core genes, which are conserved in all orthopoxviruses.
Molteni C, Forni D, Cagliani R, Mozzi A, Clerici M, Sironi M.   +5 more
europepmc   +6 more sources

Parsnp 2.0: scalable core-genome alignment for massive microbial datasets. [PDF]

Bioinformatics
Motivation Since 2016, the number of microbial species with available reference genomes in NCBI has more than tripled. Multiple genome alignment, the process of identifying nucleotides across multiple genomes which share a common ancestor, is used as the
Kille B, Nute MG, Huang V, Kim E, Phillippy AM, Treangen TJ.   +5 more
europepmc   +3 more sources

Introduction and benchmarking of pyMLST: open-source software for assessing bacterial clonality using core genome MLST. [PDF]

Microb Genom, 2023
Core genome multilocus sequence typing (cgMLST) has gained in popularity for bacterial typing since whole-genome sequencing (WGS) has become affordable.
Biguenet A, Bordy A, Atchon A, Hocquet D, Valot B.   +4 more
europepmc   +2 more sources

Identifying the core genome of the nucleus-forming bacteriophage family and characterization of Erwinia phage RAY. [PDF]

Cell Rep, 2023
We recently discovered that some bacteriophages establish a nucleus-like replication compartment (phage nucleus), but the core genes that define nucleus-based phage replication and their phylogenetic distribution were unknown.
Prichard A, Lee J, Laughlin TG, Lee A, Thomas KP, Sy AE, Spencer T, Asavavimol A, Cafferata A, Cameron M, Chiu N, Davydov D, Desai I, Diaz G, Guereca M, Hearst K, Huang L, Jacobs E, Johnson A, Kahn S, Koch R, Martinez A, Norquist M, Pau T, Prasad G, Saam K, Sandhu M, Sarabia AJ, Schumaker S, Sonin A, Uyeno A, Zhao A, Corbett KD, Pogliano K, Meyer J, Grose JH, Villa E, Dutton R, Pogliano J.   +38 more
europepmc   +2 more sources

Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus [PDF]

Nature Communications, 2020
Transferable DNA markers are essential for breeding and genetics. Grapevine (Vitis) breeders utilize disease resistance alleles from congeneric species ~20 million years divergent, but existing Vitis marker platforms have cross-species transfer rates as ...
Cheng Zou, Avinash Karn, Bruce I. Reisch, Allen Nguyen, Yongming Sun, Yun Bao, Michael S. Campbell, Deanna M. Church, Stephen R. Williams, Xia Xu, Craig A. Ledbetter, Sagar Patel, Anne Fennell, Jeffrey C. Glaubitz, Matthew D. Clark, Doreen Ware, Jason P. Londo, Qi Sun, Lance Cadle‐Davidson   +18 more
openalex   +2 more sources

Serotyping, MLST, and Core Genome MLST Analysis of Salmonella enterica From Different Sources in China During 2004–2019

Frontiers in Microbiology, 2021
Salmonella enterica (S. enterica) is an important foodborne pathogen, causing food poisoning and human infection, and critically threatening food safety and public health.
Shigan Yan, Wencheng Zhang, Chengyu Li, Xu Liu, Liping Zhu, Leilei Chen, Baowei Yang   +6 more
openalex   +2 more sources

KleTy: integrated typing scheme for core genome and plasmids reveals repeated emergence of multi-drug resistant epidemic lineages in Klebsiella worldwide. [PDF]

Genome Med
Clinically important lineages in Klebsiella, especially those expressing multi-drug resistance (MDR), pose severe threats to public health worldwide. They arose from the co-evolution of the vertically inherited core genome and horizontal gene transfers ...
Li H, Liu X, Li S, Rong J, Xie S, Gao Y, Zhong L, Jiang Q, Jiang G, Ren Y, Sun W, Hong Y, Zhou Z.   +12 more
europepmc   +2 more sources

A core genome approach that enables prospective and dynamic monitoring of infectious outbreaks [PDF]

Scientific Reports, 2019
Whole-genome sequencing is increasingly adopted in clinical settings to identify pathogen transmissions, though largely as a retrospective tool. Prospective monitoring, in which samples are continuously added and compared to previous samples, can ...
Helen van Aggelen, Raivo Kolde, Hareesh Chamarthi, Joshua Loving, Yu Fan, John T. Fallon, Weihua Huang, Guiqing Wang, Mary M. Fortunato-Habib, Juan J. Carmona, Brian D. Gross   +10 more
openalex   +2 more sources