Homoeologous gene expression and co-expression network analyses and evolutionary inference in allopolyploids

G Hu, CE Grover, MA Arick, M Liu… - Briefings in …, 2021 - academic.oup.com
Polyploidy is a widespread phenomenon throughout eukaryotes. Due to the coexistence of
duplicated genomes, polyploids offer unique challenges for estimating gene expression …

[HTML][HTML] An interspecific fungal hybrid reveals cross-kingdom rules for allopolyploid gene expression patterns

MP Cox, T Dong, GG Shen, Y Dalvi, DB Scott… - PLoS …, 2014 - journals.plos.org
Polyploidy, a state in which the chromosome complement has undergone an increase, is a
major force in evolution. Understanding the consequences of polyploidy has received much …

Homeolog expression quantification methods for allopolyploids

TCY Kuo, M Hatakeyama, T Tameshige… - Briefings in …, 2020 - academic.oup.com
Genome duplication with hybridization, or allopolyploidization, occurs in animals, fungi and
plants, and is especially common in crop plants. There is an increasing interest in the study …

[HTML][HTML] Duplicate gene expression in allopolyploid Gossypiumreveals two temporally distinct phases of expression evolution

L Flagel, J Udall, D Nettleton, J Wendel - BMC biology, 2008 - Springer
Background Polyploidy has played a prominent role in shaping the genomic architecture of
the angiosperms. Through allopolyploidization, several modern Gossypium (cotton) species …

PolyCat: a resource for genome categorization of sequencing reads from allopolyploid organisms

JT Page, AR Gingle, JA Udall - G3: Genes, genomes, genetics, 2013 - academic.oup.com
Read mapping is a fundamental part of next-generation genomic research but is
complicated by genome duplication in many plants. Categorizing DNA sequence reads into …

[HTML][HTML] Homoeolog expression bias and expression level dominance in allopolyploid cotton

MJ Yoo, E Szadkowski, JF Wendel - Heredity, 2013 - nature.com
Allopolyploidy is an evolutionary and mechanistically intriguing process, in that it entails the
reconciliation of two or more sets of diverged genomes and regulatory interactions. In this …

[HTML][HTML] Polyploidy and the petal transcriptome of Gossypium

A Rambani, JT Page, JA Udall - BMC Plant Biology, 2014 - Springer
Background Genes duplicated by polyploidy (homoeologs) may be differentially expressed
in plant tissues. Recent research using DNA microarrays and RNAseq data have described …

A robust methodology for assessing differential homeolog contributions to the transcriptomes of allopolyploids

JL Boatwright, LM McIntyre, AM Morse, S Chen… - Genetics, 2018 - academic.oup.com
Polyploidy has played a pivotal and recurring role in angiosperm evolution. Allotetraploids
arise from hybridization between species and possess duplicated gene copies (homeologs) …

Unravelling gene expression of complex crop genomes

RJA Buggs - Heredity, 2013 - nature.com
Standing between us and global food shortage are high yielding varieties of wheat, oilseed
rape, potato, maize and sugarcane. These come from diverse plant families, but share the …

ccNET: Database of co-expression networks with functional modules for diploid and polyploid Gossypium

Q You, W Xu, K Zhang, L Zhang, X Yi… - Nucleic acids …, 2017 - academic.oup.com
Plant genera with both diploid and polyploid species are a common evolutionary
occurrence. Polyploids, especially allopolyploids such as cotton and wheat, are a great …