Evolution of Homeologous Gene Expression in Polyploid Wheat

Polyploidization has played a prominent role in the evolutionary history of plants. Two recent and sequential allopolyploidization events have resulted in the formation of wheat species with different ploidies, and which provide a model to study the effects of polyploidization on the evolution of gene expression. In this study, we identified differentially expressed genes (DEGs) between four BBAA tetraploid wheats of three different ploidy backgrounds. DEGs were found to be unevenly distributed among functional categories and duplication modes. We observed more DEGs in the extracted tetraploid wheat (ETW) than in natural tetraploid wheats (TD and TTR13) as compared to a synthetic tetraploid (AT2). Furthermore, DEGs showed higher Ka/Ks ratios than those that did not show expression changes (non-DEGs) between genotypes, indicating DEGs and non-DEGs experienced different selection pressures. For A-B homeolog pairs with DEGs, most of them had only one differentially expressed copy, however, when both copies of a homeolog pair were DEGs, the A and B copies were more likely to be regulated to the same direction. Our results suggest that both cis- and inter-subgenome trans-regulatory changes are important drivers in the evolution of homeologous gene expression in polyploid wheat, with ploidy playing a significant role in the process.

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Exploring the Evolutionary History of the Differentially Expressed Genes between Human Populations: Action of Recent Positive Selection

Evolutionary Bioinformatics ◽

10.4137/ebo.s744 ◽

2008 ◽

Vol 4 ◽

pp. EBO.S744 ◽

Cited By ~ 1

Author(s):

Wei Zhang ◽

M. Eileen Dolan

Keyword(s):

Positive Selection ◽

Differentially Expressed Genes ◽

Evolutionary History ◽

Differentially Expressed ◽

Human Populations ◽

Recent Positive Selection ◽

History Of

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Genetic diversity, distribution and domestication history of the neglected GGAtAt genepool of wheat

10.1101/2021.01.10.426084 ◽

2021 ◽

Author(s):

Ekaterina D. Badaeva ◽

Fedor A. Konovalov ◽

Helmut Knüpffer ◽

Agostino Fricano ◽

Alevtina S. Ruban ◽

...

Keyword(s):

Evolutionary History ◽

Chromosomal Rearrangements ◽

Tetraploid Wheat ◽

Wheat Breeding ◽

Intraspecific Diversity ◽

Wheat Improvement ◽

Comprehensive Survey ◽

History Of ◽

Diversity Sampling ◽

Wheat Wild Relatives

AbstractBackgroundWheat yields are stagnating around the world and new sources of genes for resistance or tolerances to abiotic traits are required. In this context, the tetraploid wheat wild relatives are among the key candidates for wheat improvement. Despite of its potential huge value for wheat breeding, the tetraploid GGAtAt genepool is largely neglected. Understanding the population structure, native distribution range, intraspecific variation of the entire tetraploid GGAtAt genepool and its domestication history would further its use for wheat improvement.ResultsWe report the first comprehensive survey of genomic and cytogenetic diversity sampling the full breadth and depth of the tetraploid GGAtAt genepool. We show that the extant GGAtAt genepool consists of three distinct lineages. We provide detailed insights into the cytogenetic composition of GGAtAt wheats, revealed group-, and population-specific markers and show that chromosomal rearrangements play an important role in intraspecific diversity of T. araraticum. We discuss the origin and domestication history of the GGAtAt lineages in the context of state-of-the-art archaeobotanical finds.ConclusionsWe shed new light on the complex evolutionary history of the GGAtAt wheat genepool. We provide the basis for an increased use of the GGAtAt wheat genepool for wheat improvement. The findings have implications for our understanding of the origins of agriculture in southwest Asia.

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Corrigendum to “Polyphenol oxidase genes as integral part of the evolutionary history of domesticated tetraploid wheat” [Genomics 113 (2021) 2989–3001]

Genomics ◽

10.1016/j.ygeno.2021.12.006 ◽

2021 ◽

Author(s):

Francesca Taranto ◽

Giacomo Mangini ◽

Monica Marilena Miazzi ◽

Piergiorgio Stevanato ◽

Pasquale De Vita

Keyword(s):

Polyphenol Oxidase ◽

Evolutionary History ◽

Tetraploid Wheat ◽

History Of

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A quantitative framework for characterizing the evolutionary history of mammalian gene expression

Genome Research ◽

10.1101/gr.237636.118 ◽

2018 ◽

Vol 29 (1) ◽

pp. 53-63 ◽

Cited By ~ 23

Author(s):

Jenny Chen ◽

Ross Swofford ◽

Jeremy Johnson ◽

Beryl B. Cummings ◽

Noga Rogel ◽

...

Keyword(s):

Gene Expression ◽

Evolutionary History ◽

Mammalian Gene ◽

History Of ◽

Mammalian Gene Expression

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Evolutionary history of host use, rather than plant phylogeny, determines gene expression in a generalist butterfly

BMC Evolutionary Biology ◽

10.1186/s12862-016-0627-y ◽

2016 ◽

Vol 16 (1) ◽

Cited By ~ 17

Author(s):

Maria de la Paz Celorio-Mancera ◽

Christopher W. Wheat ◽

Mikael Huss ◽

Francesco Vezzi ◽

Ramprasad Neethiraj ◽

...

Keyword(s):

Gene Expression ◽

Evolutionary History ◽

Host Use ◽

Plant Phylogeny ◽

History Of

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Conservation and trans-regulation of histone modification in the A and B subgenomes of polyploid wheat during domestication and ploidy transition

BMC Biology ◽

10.1186/s12915-021-00985-7 ◽

2021 ◽

Vol 19 (1) ◽

Cited By ~ 1

Author(s):

Zhenling Lv ◽

Zijuan Li ◽

Meiyue Wang ◽

Fei Zhao ◽

Wenjie Zhang ◽

...

Keyword(s):

Gene Expression ◽

Histone Modification ◽

Hexaploid Wheat ◽

Epigenetic Modification ◽

Expression Profiles ◽

Tetraploid Wheat ◽

Gene Expression Profiles ◽

Great Majority ◽

D Genome ◽

Polyploid Wheat

AbstractBackgroundPolyploidy has played a prominent role in the evolution of plants and many other eukaryotic lineages. However, how polyploid genomes adapt to the abrupt presence of two or more sets of chromosomes via genome regulation remains poorly understood. Here, we analyzed genome-wide histone modification and gene expression profiles in relation to domestication and ploidy transition in the A and B subgenomes of polyploid wheat.ResultsWe found that epigenetic modification patterns by two typical euchromatin histone markers, H3K4me3 and H3K27me3, for the great majority of homoeologous triad genes in A and B subgenomes were highly conserved between wild and domesticated tetraploid wheats and remained stable in the process of ploidy transitions from hexaploid to extracted tetraploid and then back to resynthesized hexaploid. However, a subset of genes was differentially modified during tetraploid and hexaploid wheat domestication and in response to ploidy transitions, and these genes were enriched for particular gene ontology (GO) terms. The extracted tetraploid wheat manifested higher overall histone modification levels than its hexaploid donor, and which were reversible and restored to normal levels in the resynthesized hexaploid. Further, while H3K4me3 marks were distally distributed along each chromosome and significantly correlated with subgenome expression as expected, H3K27me3 marks showed only a weak distal bias and did not show a significant correlation with gene expression.ConclusionsOur results reveal overall high stability of histone modification patterns in the A and B subgenomes of polyploid wheat during domestication and in the process of ploidy transitions. However, modification levels of a subset of functionally relevant genes in the A and B genomes weretrans-regulated by the D genome in hexaploid wheat.

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