Twenty years of plant genome sequencing: achievements and challenges

Y Sun, L Shang, QH Zhu, L Fan, L Guo - Trends in Plant Science, 2022 - cell.com
Publication of the complete genome sequence of Arabidopsis thaliana, the first plant
reference genome, in December 2000 heralded the beginning of the plant genome era …

Patterns, mechanisms, and consequences of homoeologous exchange in allopolyploid angiosperms: a genomic and epigenomic perspective

SK Deb, PP Edger, JC Pires, MR McKain - New Phytologist, 2023 - Wiley Online Library
Allopolyploids result from hybridization between different evolutionary lineages coupled with
genome doubling. Homoeologous chromosomes (chromosomes with common shared …

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 …

Genomic insights into the recent chromosome reduction of autopolyploid sugarcane Saccharum spontaneum

Q Zhang, Y Qi, H Pan, H Tang, G Wang, X Hua… - Nature Genetics, 2022 - nature.com
Saccharum spontaneum is a founding Saccharum species and exhibits wide variation in
ploidy levels. We have assembled a high-quality autopolyploid genome of S. spontaneum …

SubPhaser: a robust allopolyploid subgenome phasing method based on subgenome‐specific k‐mers

KH Jia, ZX Wang, L Wang, GY Li, W Zhang… - New …, 2022 - Wiley Online Library
With advanced sequencing technology, dozens of complex polyploid plant genomes have
been characterized. However, for many polyploid species, their diploid ancestors are …

Haplotype-resolved genomes of wild octoploid progenitors illuminate genomic diversifications from wild relatives to cultivated strawberry

X Jin, H Du, C Zhu, H Wan, F Liu, J Ruan, JP Mower… - Nature Plants, 2023 - nature.com
Strawberry is an emerging model for studying polyploid genome evolution and rapid
domestication of fruit crops. Here we report haplotype-resolved genomes of two wild …

Chromosome-level and haplotype-resolved genome provides insight into the tetraploid hybrid origin of patchouli

Y Shen, W Li, Y Zeng, Z Li, Y Chen, J Zhang… - Nature …, 2022 - nature.com
Abstract Patchouli (Pogostemon cablin (Blanco) Benth.), a member of the Lamiaceae family,
is an important aromatic plant that has been widely used in medicine and perfumery. Here …

Transposon signatures of allopolyploid genome evolution

AM Session, DS Rokhsar - Nature Communications, 2023 - nature.com
Hybridization brings together chromosome sets from two or more distinct progenitor species.
Genome duplication associated with hybridization, or allopolyploidy, allows these …

Genome sequencing reveals chromosome fusion and extensive expansion of genes related to secondary metabolism in Artemisia argyi

Y Miao, D Luo, T Zhao, H Du, Z Liu, Z Xu… - Plant biotechnology …, 2022 - Wiley Online Library
Artemisia argyi, as famous as Artemisia annua, is a medicinal plant with huge economic
value in the genus of Artemisia and has been widely used in the world for about 3000 years …

Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes

X Zeng, Z Yi, X Zhang, Y Du, Y Li, Z Zhou, S Chen… - Nature Plants, 2024 - nature.com
Scaffolding is crucial for constructing most chromosome-level genomes. The high-
throughput chromatin conformation capture (Hi-C) technology has become the primary …