Results 81 to 90 of about 15,819 (203)

Revisiting pangenome openness with k-mers

Peer Community Journal
Pangenomics is the study of related genomes collectively, usually from the same species or closely related taxa. Originally, pangenomes were defined for bacterial species. After the concept was extended to eukaryotic genomes, two definitions of pangenome
Parmigiani, Luca, Wittler, Roland, Stoye, Jens   +2 more
doaj   +1 more source

ImpuT2T: Pangenome-Based Patching for Human Genome Assemblies

With improvements in sequencing and assembly have come many high-quality telomere-to-telomere assemblies and reference pangenomes. However, the long-read sequencing recipes needed for high quality assemblies are expensive, and out of reach for many ...
Ben Langmead, Human Pangenome Reference Consortium, Mao-Jan Lin, Vikram S Shivakumar   +3 more
core   +1 more source

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

Supporting data for "Towards a Standardized Framework for Pangenome Graph Evaluation: Assessing Crop Plant Pangenome Variation Graph Construction from Multiple Assemblies"

El dataset se puede consultar y descargar en el siguiente enlace https://doi.org/10.5524/102758This dataset was created to support the benchmarking of pangenome graph assembly pipelines in plants.
Zanini, Silvia F., Golicz, Agnieszka A., Morales-Díaz, Noemia, Kopalli, Venkataramana, Arslan, Kübra   +4 more
core   +1 more source

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

Pangenome-aware DeepVariant

Population-scale genomics information provides valuable prior knowledge for various genomic analyses, especially variant calling. A notable example of such application is the human pangenome reference released by the Human Pangenome Reference Consortium,
Carroll, Andrew, Paten, Benedict, Asri, Mobin, Brambrink, Lucas, Kolesnikov, Alexey, Sirén, Jouni, Novak, Adam M, Dorfman, Lizzie, Eskandar, Parsa, Webster, Dale R, Shafin, Kishwar, Chang, Pi-Chuan, Mier, Juan Carlos, Cook, Daniel E, Hickey, Glenn   +14 more
core   +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

Building pangenome graphs

Pangenome graphs can represent all variation between multiple reference genomes, but current approaches to build them exclude complex sequences or are based upon a single reference.
Guarracino, A., Weigel, D. ; https://orcid.org/, Rusholme-Pilcher, R., Nobrega, F., Williams, R., Hagmann, J. ; https://orcid.org/, Golicz, A., Vorbrugg, S. ; https://orcid.org/, Yang, Z., Liti, G., Mwaniki, M., Villani, F., Wu, Y., Heumos, S., Huang, S., Kubica, C. ; https://orcid.org/, Nahnsen, S., Prins, P., Bao, Z. ; https://orcid.org/, Tattini, T., Garrison, E., Marco-Sola, S., Rudbeck, E., Sudmant, P., Chen, H., Soranzo, N., Ashbrook, G., Thorell, K., Colonna, V., de Ligt, J.   +29 more
core   +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

Defining Orthologs and Pangenome Size Metrics

, 2015
Since the advent of ultra-massive sequencing techniques, the consequent drop-off in both price and time required made feasible the sequencing of increasingly more genomes from microbes belonging to the same taxonomic unit.
Emanuele Bosi, Renato Fani, Fondi, Marco, Fondi M., Marco Fondi, Bosi, Emanuele, Fani, Renato, Fani R., Bosi E.   +8 more
core   +1 more source