[HTML][HTML] Super-pangenome by integrating the wild side of a species for accelerated crop improvement

AW Khan, V Garg, M Roorkiwal, AA Golicz… - Trends in Plant …, 2020 - cell.com
The pangenome provides genomic variations in the cultivated gene pool for a given species.
However, as the crop's gene pool comprises many species, especially wild relatives with …

Current achievements and future prospects in the genetic breeding of chrysanthemum: a review

J Su, J Jiang, F Zhang, Y Liu, L Ding… - Horticulture …, 2019 - academic.oup.com
Abstract Chrysanthemum (Chrysanthemum morifolium Ramat.) is a leading flower with
applied value worldwide. Develo** new chrysanthemum cultivars with novel …

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 …

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 …

Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline

S Ou, W Su, Y Liao, K Chougule, JRA Agda… - Genome biology, 2019 - Springer
Background Sequencing technology and assembly algorithms have matured to the point
that high-quality de novo assembly is possible for large, repetitive genomes. Current …

A reference genome for pea provides insight into legume genome evolution

J Kreplak, MA Madoui, P Cápal, P Novák, K Labadie… - Nature …, 2019 - nature.com
We report the first annotated chromosome-level reference genome assembly for pea, Gregor
Mendel's original genetic model. Phylogenetics and paleogenomics show genomic …

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

MJ Roach, SA Schmidt, AR Borneman - BMC bioinformatics, 2018 - Springer
Background Recent developments in third-gen long read sequencing and diploid-aware
assemblers have resulted in the rapid release of numerous reference-quality assemblies for …

Massive haplotypes underlie ecotypic differentiation in sunflowers

M Todesco, GL Owens, N Bercovich, JS Légaré… - Nature, 2020 - nature.com
Species often include multiple ecotypes that are adapted to different environments.
However, it is unclear how ecotypes arise and how their distinctive combinations of adaptive …

The Rosa genome provides new insights into the domestication of modern roses

O Raymond, J Gouzy, J Just, H Badouin… - Nature …, 2018 - nature.com
Roses have high cultural and economic importance as ornamental plants and in the
perfume industry. We report the rose whole-genome sequencing and assembly and …

Genomic basis of the giga-chromosomes and giga-genome of tree peony Paeonia ostii

J Yuan, S Jiang, J Jian, M Liu, Z Yue, J Xu, J Li… - Nature …, 2022 - nature.com
Tree peony (Paeonia ostii) is an economically important ornamental plant native to China. It
is also notable for its seed oil, which is abundant in unsaturated fatty acids such as α …