The bacterial pangenome as a new tool for analysing pathogenic bacteria
New Microbes and New Infections, 2015 The bacterial pangenome was introduced in 2005 and, in recent years, has been the subject of many studies. Thanks to progress in next-generation sequencing methods, the pangenome can be divided into two parts, the core (common to the studied strains) and
Pierre-Édouard Fournier +2 more
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Comparative Genomic Analysis of Multidrug-Resistant Escherichia coli Across Poultry-Human-Environmental Interfaces. [PDF]
MicrobiologyopenWhole‐genome sequencing analysis of Escherichia coli isolates from broiler, layer and sonali chickens in Bangladesh shown extensive antimicrobial resistance, diverse virulence factors, plasmid‐mediated resistance, and a highly open pangenome. Comparative genomic analyses demonstrated close genetic relationships with global strains, highlighting the One
Shanto MRH +6 more
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Four haplotype-resolved genome assemblies and a reference-free 66-haplotype pangenome graph for Cannabis sativa [PDF]
Scientific DataWe present 4 haplotype-resolved, chromosome scale diploid assemblies of cannabis, assembled from ONT R9.4.1 reads via a novel pipeline based on Hi-C phasing.
Brett Pike +2 more
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A survey of sequence-to-graph mapping algorithms in the pangenome era
Genome BiologyA pangenome can reveal the genetic diversity across different individuals simultaneously. It offers a more comprehensive reference for genome analysis compared to a single linear genome that may introduce allele bias.
Yingbo Cui
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AlfaPang: alignment free algorithm for pangenome graph construction
Algorithms for Molecular BiologyThe success of pangenome-based approaches to genomics analysis depends largely on the existence of efficient methods for constructing pangenome graphs that are applicable to large genome collections.
Adam Cicherski +2 more
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Inversion characterization in Timema stick insects: from local PCA to pangenome approaches [PDF]
bioRxivDiana Tataru +3 more
europepmc +3 more sources
Frontiers in Genetics, 2023 Whole genome sequencing has revolutionized infectious disease surveillance for tracking and monitoring the spread and evolution of pathogens. However, using a linear reference genome for genomic analyses may introduce biases, especially when studies are ...
Zuyu Yang +12 more
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Human Pangenomics: Promises and Challenges of a Distributed Genomic Reference
Life, 2023 A pangenome is a collection of the common and unique genomes that are present in a given species. It combines the genetic information of all the genomes sampled, resulting in a large and diverse range of genetic material.
Paolo Abondio +2 more
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A pangenome analysis pipeline provides insights into functional gene identification in rice
Genome Biology, 2023 Background A pangenome aims to capture the complete genetic diversity within a species and reduce bias in genetic analysis inherent in using a single reference genome. However, the current linear format of most plant pangenomes limits the presentation of
Jian Wang +14 more
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A super-pangenome of the North American wild grape species
Genome Biology, 2023 Background Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated cultivars. Genetic
Noé Cochetel +10 more
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