Subgenome-aware analyses reveal the genomic consequences of ancient allopolyploid hybridizations throughout the cotton family

P Sun, Z Lu, Z Wang, S Wang, K Zhao… - Proceedings of the …, 2024 - National Acad Sciences
Malvaceae comprise some 4,225 species in 243 genera and nine subfamilies and include
economically important species, such as cacao, cotton, durian, and jute, with cotton an …

Comparative genomics of Gossypium and Arabidopsis: unraveling the consequences of both ancient and recent polyploidy

J Rong, JE Bowers, SR Schulze… - Genome …, 2005 - genome.cshlp.org
Both ancient and recent polyploidy, together with post-polyploidization loss of many
duplicated gene copies, complicates angiosperm comparative genomics. To explore an …

Duplicate gene evolution, homoeologous recombination, and transcriptome characterization in allopolyploid cotton

LE Flagel, JF Wendel, JA Udall - BMC genomics, 2012 - Springer
Background Modern allotetraploid cotton contains an “A” and “D” genome from an ancestral
polyploidy event that occurred approximately 1–2 million years ago. Diploid A-and D …

Sequence-based ultra-dense genetic and physical maps reveal structural variations of allopolyploid cotton genomes

S Wang, J Chen, W Zhang, Y Hu, L Chang, L Fang… - Genome biology, 2015 - Springer
Background SNPs are the most abundant polymorphism type, and have been explored in
many crop genomic studies, including rice and maize. SNP discovery in allotetraploid cotton …

Persistence of subgenomes in paleopolyploid cotton after 60 my of evolution

S Renny-Byfield, L Gong, JP Gallagher… - … biology and evolution, 2015 - academic.oup.com
The importance of whole-genome multiplication (WGM) in plant evolution has long been
recognized. In flowering plants, WGM is both ubiquitous and in many lineages cyclical, each …

Dual domestication, diversity, and differential introgression in Old World cotton diploids

CE Grover, MA Arick, A Thrash… - Genome Biology and …, 2022 - academic.oup.com
Domestication in the cotton genus is remarkable in that it has occurred independently four
different times at two different ploidy levels. Relatively little is known about genome evolution …

Extensive intraspecific gene order and gene structural variations in upland cotton cultivars

Z Yang, X Ge, Z Yang, W Qin, G Sun, Z Wang… - Nature …, 2019 - nature.com
Multiple cotton genomes (diploid and tetraploid) have been assembled. However, genomic
variations between cultivars of allotetraploid upland cotton (Gossypium hirsutum L.), the …

Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing

JT Page, MD Huynh, ZS Liechty, K Grupp… - G3: Genes …, 2013 - academic.oup.com
Understanding the composition, evolution, and function of the Gossypium hirsutum (cotton)
genome is complicated by the joint presence of two genomes in its nucleus (AT and DT …

Jeans, genes, and genomes: cotton as a model for studying polyploidy

JF Wendel, LE Flagel, KL Adams - Polyploidy and genome evolution, 2012 - Springer
We present an overview of the cotton genus (Gossypium) as a model for the study of
polyploidy. A synopsis of the origin and evolution of polyploid cotton is provided, offering an …

Parallel and intertwining threads of domestication in allopolyploid cotton

D Yuan, CE Grover, G Hu, M Pan, ER Miller… - Advanced …, 2021 - Wiley Online Library
The two cultivated allopolyploid cottons, Gossypium hirsutum and Gossypium barbadense,
represent a remarkable example of parallel independent domestication, both involving …