Plant pan-genomes are the new reference

PE Bayer, AA Golicz, A Scheben, J Batley, D Edwards - Nature plants, 2020‏ - nature.com
Recent years have seen a surge in plant genome sequencing projects and the comparison
of multiple related individuals. The high degree of genomic variation observed led to the …

Grey mould of strawberry, a devastating disease caused by the ubiquitous necrotrophic fungal pathogen Botrytis cinerea

S Petrasch, SJ Knapp, JAL Van Kan… - Molecular plant …, 2019‏ - Wiley Online Library
The fungal pathogen Botrytis cinerea causes grey mould, a commercially damaging disease
of strawberry. This pathogen affects fruit in the field, storage, transport and market. The …

Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance

PF Ma, YL Liu, C Guo, G **, ZH Guo, L Mao… - Nature Genetics, 2024‏ - nature.com
Polyploidy (genome duplication) is a pivotal force in evolution. However, the interactions
between parental genomes in a polyploid nucleus, frequently involving subgenome …

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

H Cheng, GT Concepcion, X Feng, H Zhang, H Li - Nature methods, 2021‏ - nature.com
Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence
variations in a genome. However, existing algorithms either collapse heterozygous alleles …

Analyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum

A Song, J Su, H Wang, Z Zhang, X Zhang… - Nature …, 2023‏ - nature.com
Abstract Chrysanthemum (Chrysanthemum morifolium Ramat.) is a globally important
ornamental plant with great economic, cultural, and symbolic value. However, research on …

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars

J Salojärvi, A Rambani, Z Yu, R Guyot, S Strickler… - Nature …, 2024‏ - nature.com
Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the
source of approximately 60% of coffee products worldwide, and its cultivated accessions …

Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages

T Zhang, W Huang, L Zhang, DZ Li, J Qi… - Nature communications, 2024‏ - nature.com
Poaceae members shared a whole-genome duplication called rho. However, little is known
about the evolutionary pattern of the rho-derived duplicates among Poaceae lineages and …

Reference genome assemblies reveal the origin and evolution of allohexaploid oat

Y Peng, H Yan, L Guo, C Deng, C Wang, Y Wang… - Nature Genetics, 2022‏ - nature.com
Common oat (Avena sativa) is an important cereal crop serving as a valuable source of
forage and human food. Although reference genomes of many important crops have been …

Highly accurate long-read HiFi sequencing data for five complex genomes

T Hon, K Mars, G Young, YC Tsai, JW Karalius… - Scientific data, 2020‏ - nature.com
Abstract The PacBio® HiFi sequencing method yields highly accurate long-read sequencing
datasets with read lengths averaging 10–25 kb and accuracies greater than 99.5%. These …

Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass

JT Lovell, AH MacQueen, S Mamidi, J Bonnette… - Nature, 2021‏ - nature.com
Long-term climate change and periodic environmental extremes threaten food and fuel
security and global crop productivity,–. Although molecular and adaptive breeding strategies …