Plant pan-genomics and its applications
J Shi, Z Tian, J Lai, X Huang - Molecular Plant, 2023 - cell.com
Plant genomes are so highly diverse that a substantial proportion of genomic sequences are
not shared among individuals. The variable DNA sequences, along with the conserved core …
not shared among individuals. The variable DNA sequences, along with the conserved core …
A review of the pangenome: how it affects our understanding of genomic variation, selection and breeding in domestic animals?
Y Gong, Y Li, X Liu, Y Ma, L Jiang - Journal of Animal Science and …, 2023 - Springer
As large-scale genomic studies have progressed, it has been revealed that a single
reference genome pattern cannot represent genetic diversity at the species level. While …
reference genome pattern cannot represent genetic diversity at the species level. While …
A common resequencing‐based genetic marker data set for global maize diversity
Maize (Zea mays ssp. mays) populations exhibit vast ranges of genetic and phenotypic
diversity. As sequencing costs have declined, an increasing number of projects have sought …
diversity. As sequencing costs have declined, an increasing number of projects have sought …
Exploring pan-genomes: an overview of resources and tools for unraveling structure, function, and evolution of crop genes and genomes
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 …
explore intra-and inter-specific genomic comparisons at higher resolution and build clade …
Plant pangenomes for crop improvement, biodiversity and evolution
Plant genome sequences catalogue genes and the genetic elements that regulate their
expression. Such inventories further research aims as diverse as mapping the molecular …
expression. Such inventories further research aims as diverse as mapping the molecular …
Gene expression and expression quantitative trait loci analyses uncover natural variations underlying the improvement of important agronomic traits during modern …
C Li, Y Li, G Song, D Yang, Z Xia, C Sun… - The Plant …, 2023 - Wiley Online Library
Maize (Zea mays L.) is a major staple crop worldwide, and during modern maize breeding,
cultivars with increased tolerance to high‐density planting and higher yield per plant have …
cultivars with increased tolerance to high‐density planting and higher yield per plant have …
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 …
DNA sequence within a species or clade. Pangenome analysis predominantly leverages …
Pangenome of water caltrop reveals structural variations and asymmetric subgenome divergence after allopolyploidization
X Zhang, Y Chen, L Wang, Y Yuan, M Fang… - Horticulture …, 2023 - academic.oup.com
Abstract Water caltrop (Trapa spp., Lythraceae) is a traditional but currently underutilized
non-cereal crop. Here, we generated chromosome-level genome assemblies for the two …
non-cereal crop. Here, we generated chromosome-level genome assemblies for the two …
Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea
Abstract Chickpea (Cicer arietinum L.)—an important legume crop cultivated in arid and
semiarid regions—has limited genetic diversity. Efforts are being undertaken to broaden its …
semiarid regions—has limited genetic diversity. Efforts are being undertaken to broaden its …
Going broad and deep: sequencing‐driven insights into plant physiology, evolution, and crop domestication
S Gui, FJ Martinez‐Rivas, W Wen, M Meng… - The Plant …, 2023 - Wiley Online Library
Deep sequencing is a term that has become embedded in the plant genomic literature in
recent years and with good reason. A torrent of (largely) high‐quality genomic and …
recent years and with good reason. A torrent of (largely) high‐quality genomic and …