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Plant pan-genomics and its applications
Molecular Plant, 2023Plant genomes are so highly diverse that a substantial proportion of genomic sequences are not shared among individuals. The variable DNA sequences, along with the conserved core sequences, compose the more sophisticated pan-genome that represents the collection of all non-redundant DNA in a species.
Junpeng, Shi +3 more
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The Core and Pan-Genome of the Vibrionaceae
2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, 2009Species of the family Vibrionaceae are ubiquitous in marine environments and the family contains numerous important pathogens of humans and marine species. In order to find the core, accessory and pan-proteome of this family, we deduced the complete set of orthologs for eleven strains from this family.
Timothy G. Lilburn +2 more
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Plant Pan-Genomics Comes of Age
Annual Review of Plant Biology, 2021A pan-genome is the nonredundant collection of genes and/or DNA sequences in a species. Numerous studies have shown that plant pan-genomes are typically much larger than the genome of any individual and that a sizable fraction of the genes in any individual are present in only some genomes.
Li, Lei +5 more
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Gene, 2017
A decade after the concept of Pan-genome was first introduced; research in this field has spread its tentacles to areas such as pathogenesis of diseases, bacterial evolutionary studies and drug resistance. Gene content-based differentiation of virulent and a virulent strains of bacteria and identification of pathogen specific genes is imperative to ...
Iyyappan Yuvaraj +3 more
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A decade after the concept of Pan-genome was first introduced; research in this field has spread its tentacles to areas such as pathogenesis of diseases, bacterial evolutionary studies and drug resistance. Gene content-based differentiation of virulent and a virulent strains of bacteria and identification of pathogen specific genes is imperative to ...
Iyyappan Yuvaraj +3 more
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Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics, 2013
Bacterial genomes at NCBI represent a large collection of strains with different levels of sequence and assembly quality as well as sampling density. Among these, there are densely-sampled sets of related genomes, usually human pathogens, whose organization and protein content could be directly analyzed within the concept of pan-genome.
Leonid Zaslavsky +2 more
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Bacterial genomes at NCBI represent a large collection of strains with different levels of sequence and assembly quality as well as sampling density. Among these, there are densely-sampled sets of related genomes, usually human pathogens, whose organization and protein content could be directly analyzed within the concept of pan-genome.
Leonid Zaslavsky +2 more
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2018
The pan-genome of a species is comprised of genes/sequences that are present in all individuals in the species (core genome) and genes/sequences that are present in only a subset of individuals within the species (dispensable genome). In maize, the study of the pan-genome began in the 1940s through cytogenetic experiments and has seen an increased ...
Alex B. Brohammer +2 more
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The pan-genome of a species is comprised of genes/sequences that are present in all individuals in the species (core genome) and genes/sequences that are present in only a subset of individuals within the species (dispensable genome). In maize, the study of the pan-genome began in the 1940s through cytogenetic experiments and has seen an increased ...
Alex B. Brohammer +2 more
openaire +1 more source
Orthopoxvirus pan-genomic DNA assay
Journal of Virological Methods, 2007A genome-spanning assay is described that enables laboratory confirmation of infections with orthopoxviruses (OPVs), particularly Vaccinia, Monkeypox, and Variola viruses, which can cause vesiculo-pustular rash illnesses in humans. The assay uses a series of polymerase chain reaction (PCR) amplicons that overlap to span the approximately 200kilobase ...
Yu, Li +4 more
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2019
Due to their tendency to have a high recombination rate, bacterial genomes are highly diverse across different strains. This diversity may even be in the form of the presence or absence of entire genes; therefore, each strain might have its own combination of genes. The pan-genome represents the complete gene pool of a species.
Arash Iranzadeh, Nicola Jane Mulder
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Due to their tendency to have a high recombination rate, bacterial genomes are highly diverse across different strains. This diversity may even be in the form of the presence or absence of entire genes; therefore, each strain might have its own combination of genes. The pan-genome represents the complete gene pool of a species.
Arash Iranzadeh, Nicola Jane Mulder
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Transposable elements and the plant pan-genomes
Current Opinion in Plant Biology, 2007The comparative sequencing of several grass genomes has revealed that transposable elements are largely responsible for extensive variation in both intergenic and local genic content, not only between closely related species but also among individuals within a species.
MORGANTE, Michele +2 more
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Estimating the size of the bacterial pan-genome
Trends in Genetics, 2009The 'pan-genome' denotes the set of all genes present in the genomes of a group of organisms. Here, we extend the pan-genome concept to higher taxonomic units. Using 573 sequenced genomes, we estimate the size of the bacterial pan-genome based on the frequency of occurrences of genes among sampled genomes. Using gene- and genome-centered approaches, we
Pascal, Lapierre, J Peter, Gogarten
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