Results 121 to 130 of about 11,936 (226)

Salmonella pangenome genes [PDF]

<p>Our pangenome was created by concatenating our highest quality <em>Salmonella</em> short read metagenome assembled genome (Leleiwi et.al, 2023) and our best long read <em>Salmonella</em> assembled genome.
Wrighton, Kelly, Kokkinias, Katherine
core   +1 more source

PanCake: A Data Structure for Pangenomes.

, 2013
We present a pangenome data structure ("PanCake") for sets of related genomes, based on bundling similar sequence regions into shared features, which are derived from genome-wide pairwise sequence alignments. We discuss the design of the data structure, basic operations on it and methods to predict core genomes and singleton regions.
Ernst, Corinna, Rahmann, Sven
openaire   +3 more sources

Pangenome analysis reveals transposon-driven genome evolution in cotton

BMC Biology
Background Transposable elements (TEs) have a profound influence on the trajectory of plant evolution, driving genome expansion and catalyzing phenotypic diversification.
Xin He, Zhengyang Qi, Zhenping Liu, Xing Chang, Xianlong Zhang, Jianying Li, Maojun Wang   +6 more
doaj   +1 more source

Pan1c (Pangenome at chromosome level) [PDF]

Pan1c : a snakemake workflow for creating pangenomes at chromosome scale. Pan1c is a Snakemake workflow that simplifies pangenome creation by focusing on similar chromosome comparisons, using either PGGB or Minigraph-Cactus.
Klopp, Christophe, Gaspin, Christine, Mergez, Alexis, Legeai, Fabrice, Racoupeau, Martin, Choulet, Frédéric   +5 more
core   +4 more sources

Population-specific pangenome unveils a third FAD2 gene and solves the peanut mid-oleic fatty acid mystery

Nature Communications
Accumulating evidences have shown that the mid-oleic fatty acid phenotype in peanuts cannot be explained by the traditional two-gene model involving AhFAD2A and AhFAD2B, which are genes encoding fatty-acid desaturase 2.
Ethan Thompson, Walid Korani, Dongliang Wu, Vanika Garg, Brandon Tonnis, Mingli Wang, C. Corley Holbrook, Peggy Ozias-Akins, Albert K. Culbreath, Rajeev K. Varshney, Baozhu Guo, Josh P. Clevenger   +11 more
doaj   +1 more source

Cofitness network connectivity determines a fuzzy essential zone in open bacterial pangenome

mLife
Most in silico evolutionary studies commonly assumed that core genes are essential for cellular function, while accessory genes are dispensable, particularly in nutrient‐rich environments.
Pan Zhang, Biliang Zhang, Yuan‐Yuan Ji, Jian Jiao, Ziding Zhang, Chang‐Fu Tian   +5 more
doaj   +1 more source

First Pangenome of Corynebacterium rouxii, a Potentially Toxigenic Species of Corynebacterium diphtheriae Complex

Bacteria
Corynebacterium rouxii is one of the recently described species of the Corynebacterium diphtheriae complex. As this species can potentially infect different hosts and harbor the tox gene, producing diphtheria toxin, we present its first pangenomic ...
Fernanda Diniz Prates, Max Roberto Batista Araújo, Eduarda Guimarães Sousa, Juliana Nunes Ramos, Marcus Vinícius Canário Viana, Siomar de Castro Soares, Louisy Sanches dos Santos, Vasco Ariston de Carvalho Azevedo   +7 more
doaj   +1 more source

Evaluating data requirements for high-quality haplotype-resolved genomes for creating robust pangenome references

Genome Biology
Background Long-read technologies from Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have transformed genomics research by providing diverse data types like HiFi, Duplex, and ultra-long ONT.
Prasad Sarashetti, Josipa Lipovac, Filip Tomas, Mile Šikić, Jianjun Liu   +4 more
doaj   +1 more source

Genomic and Metabolomic Insights Into the Probiotic Potential of Weissella viridescens

Biology
Weissella viridescens has been proposed as a probiotic candidate, but strain-level multi-omics evidence remains limited. The complete genome of the human-derived W.
Shuwei Zhang, Ruiting Lan, Ruiqing Zhao, Ruoshi Wang, Liyun Liu, Jianguo Xu   +5 more
doaj   +1 more source

Comparative genomics profiling of Citrus species reveals the diversity and disease responsiveness of the GLP pangenes family

BMC Plant Biology
Citrus is an important nutritional fruit globally; however, its yield is affected by various stresses. This study presents the draft pangenome of Citrus, developed using 11 species to examine their genetic diversity and identify members of the germin ...
Muhammad Tahir ul Qamar, Kinza Fatima, Muhammad Junaid Rao, Qian Tang, Muhammad Sadaqat, Baopeng Ding, Ling-Ling Chen, Xi-Tong Zhu   +7 more
doaj   +1 more source