Challenges in Bringing Pangenome Research Into Breeding: A Case Study in Rice. [PDF]
Plant Biotechnol JABSTRACT Crop breeding has entered the pangenomics era, unlocking a far more comprehensive view of genetic diversity than a single reference genome can capture. In rice (Oryza sativa), a staple crop critical to global food security, the construction of pangenome resources has uncovered extensive structural variations (SVs), presence/absence variations (
Nie S +7 more
europepmc +2 more sources
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 +4 more
doaj +3 more sources
Pangenome Graph Indexing via the Multidollar-BWT. [PDF]
Indexing pangenome graphs is a major algorithmic challenge in computational pangenomics, a recent and active research field that seeks to use graphs as representations of multiple genomes. Since these graphs are constructed from whole genome sequences of a species population, they can become very large, making indexing one of the most challenging ...
Cozzi D. +5 more
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Pangenome-based association testing between a structural variant located upstream of the KIT gene and head depigmentation across a diverse panel of cattle breeds [PDF]
Genetics Selection EvolutionCoat color variation is a key phenotypic trait in domestic animals. Among the genetic factors involved, the KIT gene has frequently been associated with pigmentation diversity across species.
V. Sorin +8 more
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Pairwise graph edit distance characterizes the impact of the construction method on pangenome graphs. [PDF]
BioinformaticsInternational audienceMotivation: Pangenome variation graphs are an increasingly used tool to perform genome analysis, aiming to replace a linear reference in a wide variety of genomic analyses.
Dubois S +3 more
europepmc +2 more sources
Haplotype-aware sequence alignment to pangenome graphs. [PDF]
Genome Res, 2023 Modern pangenome graphs are built using haplotype-resolved genome assemblies. When mapping reads to a pangenome graph, prioritizing alignments that are consistent with the known haplotypes improves genotyping accuracy. However, the existing rigorous formulations for colinear chaining and alignment problems do not consider the ...
Chandra G, Gibney D, Jain C.
europepmc +3 more sources
Co-Linear Chaining on Pangenome Graphs [PDF]
, 2023 Pangenome reference graphs are useful in genomics because they compactly represent the genetic diversity within a species, a capability that linear references lack.
Jain, Chirag +2 more
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Assessing genome conservation on pangenome graphs with PanSel. [PDF]
Bioinform Adv1 Abstract Motivation With more and more telomere-to-telomere genomes assembled, pangenomes make it possible to capture the genomic diversity of a species. Because they introduce less biases, pangenomes, represented as graphs, tend to supplant the usual linear representation of a ...
Zytnicki M.
europepmc +3 more sources
WGT: Tools and algorithms for recognizing, visualizing, and generating Wheeler graphs
iScience, 2023 Summary: A Wheeler graph represents a collection of strings in a way that is particularly easy to index and query. Such a graph is a practical choice for representing a graph-shaped pangenome, and it is the foundation for current graph-based pangenome ...
Kuan-Hao Chao +3 more
doaj +1 more source
StrainFLAIR: strain-level profiling of metagenomic samples using variation graphs [PDF]
PeerJ, 2021 Current studies are shifting from the use of single linear references to representation of multiple genomes organised in pangenome graphs or variation graphs.
Kévin Da Silva +5 more
doaj +2 more sources