Pangenome graphs and their applications in biodiversity genomics
S Secomandi, GR Gallo, R Rossi… - Nature Genetics, 2025 - nature.com
Complete datasets of genetic variants are key to biodiversity genomic studies. Long-read
sequencing technologies allow the routine assembly of highly contiguous, haplotype …
sequencing technologies allow the routine assembly of highly contiguous, haplotype …
A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species
Chinese indicine cattle harbor a much higher genetic diversity compared with other
domestic cattle, but their genome architecture remains uninvestigated. Using PacBio HiFi …
domestic cattle, but their genome architecture remains uninvestigated. Using PacBio HiFi …
A unified framework to analyze transposable element insertion polymorphisms using graph genomes
Transposable elements are ubiquitous mobile DNA sequences generating insertion
polymorphisms, contributing to genomic diversity. We present GraffiTE, a flexible pipeline to …
polymorphisms, contributing to genomic diversity. We present GraffiTE, a flexible pipeline to …
Fitness consequences of structural variation inferred from a House Finch pangenome
Genomic structural variants (SVs) play a crucial role in adaptive evolution, yet their average
fitness effects and characterization with pangenome tools are understudied in wild animal …
fitness effects and characterization with pangenome tools are understudied in wild animal …
[HTML][HTML] Application of Pan-Omics Technologies in Research on Important Economic Traits for Ruminants
Z Gao, Y Lu, M Li, Y Chong, J Hong, J Wu… - International Journal of …, 2024 - mdpi.com
The economic significance of ruminants in agriculture underscores the need for advanced
research methodologies to enhance their traits. This review aims to elucidate the …
research methodologies to enhance their traits. This review aims to elucidate the …
Graph construction method impacts variation representation and analyses in a bovine super-pangenome
Background Several models and algorithms have been proposed to build pangenomes from
multiple input assemblies, but their impact on variant representation, and consequently …
multiple input assemblies, but their impact on variant representation, and consequently …
A near complete genome assembly of the East Friesian sheep genome
X You, Q Fang, C Chen, J Cao, S Fu, T Zhang, S Wang… - Scientific Data, 2024 - nature.com
Advancements in sequencing have enabled the assembly of numerous sheep genomes,
significantly advancing our understanding of the link between genetic variation and …
significantly advancing our understanding of the link between genetic variation and …
Small polymorphisms are a source of ancestral bias in structural variant breakpoint placement
High-quality genome assemblies and sophisticated algorithms have increased sensitivity for
a wide range of variant types, and breakpoint accuracy for structural variants (SVs,≥ 50 bp) …
a wide range of variant types, and breakpoint accuracy for structural variants (SVs,≥ 50 bp) …
Genome-wide expansion and reorganization during grass evolution: from 30 Mb chromosomes in rice and Brachypodium to 550 Mb in Avena
Q Liu, L Ye, M Li, Z Wang, G **ong, Y Ye, T Tu… - BMC Plant …, 2023 - Springer
Abstract Background The BOP (Bambusoideae, Oryzoideae, and Pooideae) clade of the
Poaceae has a common ancestor, with similarities to the genomes of rice, Oryza sativa (2 n …
Poaceae has a common ancestor, with similarities to the genomes of rice, Oryza sativa (2 n …
Duck pan‐genome reveals two transposon insertions caused bodyweight enlarging and white plumage phenotype formation during evolution
K Wang, G Hua, J Li, Y Yang, C Zhang, L Yang, X Hu… - Imeta, 2024 - Wiley Online Library
Structural variations (SVs) are a major source of domestication and improvement traits. We
present the first duck pan‐genome constructed using five genome assemblies capturing∼ …
present the first duck pan‐genome constructed using five genome assemblies capturing∼ …