Exploring pan-genomes: an overview of resources and tools for unraveling structure, function, and evolution of crop genes and genomes

S Naithani, CH Deng, SK Sahu, P Jaiswal - Biomolecules, 2023 - mdpi.com
The availability of multiple sequenced genomes from a single species made it possible to
explore intra-and inter-specific genomic comparisons at higher resolution and build clade …

Accurate and fast graph-based pangenome annotation and clustering with ggCaller

ST Horsfield, G Tonkin-Hill, NJ Croucher… - Genome …, 2023 - genome.cshlp.org
Bacterial genomes differ in both gene content and sequence mutations, which underlie
extensive phenotypic diversity, including variation in susceptibility to antimicrobials or …

PanKmer: k-mer-based and reference-free pangenome analysis

AJ Aylward, S Petrus, A Mamerto, NT Hartwick… - …, 2023 - academic.oup.com
Pangenomes are replacing single reference genomes as the definitive representation of
DNA sequence within a species or clade. Pangenome analysis predominantly leverages …

Seven quick tips for gene-focused computational pangenomic analysis

V Bonnici, D Chicco - BioData Mining, 2024 - Springer
Pangenomics is a relatively new scientific field which investigates the union of all the
genomes of a clade. The word pan means everything in ancient Greek; the term …

Comparative Genome Annotation

S Nachtweide, L Romoth, M Stanke - Comparative Genomics: Methods …, 2024 - Springer
Newly sequenced genomes are being added to the tree of life at an unprecedented fast
pace. A large proportion of such new genomes are phylogenetically close to previously …

Strain heterogeneity in a non-pathogenic Aspergillus fungus highlights factors associated with virulence

DC Rinker, TJC Sauters, K Steffen, A Gumilang… - Communications …, 2024 - nature.com
Fungal pathogens exhibit extensive strain heterogeneity, including variation in virulence.
Whether closely related non-pathogenic species also exhibit strain heterogeneity remains …

Adaptation of Fusarium Head Blight Pathogens to Changes in Agricultural Practices and Human Migration

M Yang, S Smit, D de Ridder, J Feng, T Liu… - Advanced …, 2024 - Wiley Online Library
Fusarium head blight (FHB) is one of the most destructive wheat diseases worldwide. To
understand the impact of human migration and changes in agricultural practices on crop …

Lactuca super-pangenome reduces bias towards reference genes in lettuce research

DJM van Workum, SL Mehrem, BL Snoek… - BMC Plant …, 2024 - Springer
Abstract Background Breeding of lettuce (Lactuca sativa L.), the most important leafy
vegetable worldwide, for enhanced disease resistance and resilience relies on multiple wild …

Cross-species transcriptomics reveals differential regulation of essential photosynthesis genes in Hirschfeldia incana

F Garassino, S Bengoa Luoni… - G3: Genes …, 2024 - academic.oup.com
Photosynthesis is the only yield-related trait not yet substantially improved by plant breeding.
Previously, we have established H. incana as the model plant for high photosynthetic light …

[PDF][PDF] Inferring long-term and short-term determinants of genetic diversity in honey bees: Beekee** impact and conservation strategies

T Leroy, P Faux, B Basso, S Eynard… - Molecular Biology …, 2024 - academic.oup.com
Bees are vital pollinators in natural and agricultural landscapes around the globe, playing a
key role in maintaining flowering plant biodiversity and ensuring food security. Among the …