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Pan-Genome of Wild and Cultivated Soybeans [PDF]
Cell, 2020 Soybean is one of the most important vegetable oil and protein feed crops. To capture the entire genomic diversity, it is needed to construct a complete high-quality pan-genome from diverse soybean accessions. In this study, we performed individual de novo genome assemblies for 26 representative soybeans that were selected from 2,898 deeply sequenced ...
Zhixi Tian, Bin Han, Chengzhi Liang
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The Barley and Wheat Pan-Genomes
2022To unlock the genetic potential in crops, multi-genome comparisons are an essential tool. Decreasing costs and improved sequencing technologies have democratized plant genome sequencing and led to a vast increase in the amount of available reference sequences on the one hand and enabled the assembly of even the largest and most complex and repetitive ...
Kamal, N. +7 more
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Pan-genomics in the human genome era
Nature Reviews Genetics, 2020 Since the early days of the genome era, the scientific community has relied on a single 'reference' genome for each species, which is used as the basis for a wide range of genetic analyses, including studies of variation within and across species. As sequencing costs have dropped, thousands of new genomes have been sequenced, and scientists have come ...
Steven Salzberg, Rachel M Sherman
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Current Opinion in Genetics & Development, 2005
A decade after the beginning of the genomic era, the question of how genomics can describe a bacterial species has not been fully addressed. Experimental data have shown that in some species new genes are discovered even after sequencing the genomes of several strains.
Duccio, Medini +4 more
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A decade after the beginning of the genomic era, the question of how genomics can describe a bacterial species has not been fully addressed. Experimental data have shown that in some species new genes are discovered even after sequencing the genomes of several strains.
Duccio, Medini +4 more
openaire +2 more sources
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
openaire +3 more sources
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
openaire +2 more sources
Pan-Genome Storage and Analysis Techniques
2017Computational pan-genome analysis has emerged from the rapid increase of available genome sequencing data. Starting from a microbial pan-genome, the concept has spread to a variety of species, such as plants or viruses. Characterizing a pan-genome provides insights into intra-species evolution, functions, and diversity.
Zekic, Tina +5 more
openaire +3 more sources