Cotton Duplicated Genes Produced by Polyploidy Show Significantly Elevated and Unbalanced Evolutionary Rates, Overwhelmingly Perturbing Gene Tree Topology

Genes duplicated by polyploidy show unequal contributions to the transcriptome and organ-specific reciprocal silencing.

Most eukaryotes have genomes that exhibit high levels of gene redundancy, much of which seems to have arisen from one or more cycles of genome doubling. Polyploidy has been particularly prominent during flowering plant evolution, yielding duplicated genes (homoeologs) whose expression may be retained or lost either as an immediate consequence of polyploidization or on an evolutionary timescale....

Polyploidy and the Evolutionary History of Cotton

Expression Partitioning between Genes Duplicated by Polyploidy under Abiotic Stress and during Organ Development

Allopolyploidy has been a prominent mode of speciation and a recurrent process during plant evolution and has contributed greatly to the large number of duplicated genes in plant genomes [1-4]. Polyploidy often leads to changes in genome organization and gene expression [5-9]. The expression of genes that are duplicated by polyploidy (termed homeologs) can be partitioned between the duplicates ...

Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution.

To study the evolutionary effects of polyploidy on plant gene functions, we analyzed functional genomics data for a large number of duplicated gene pairs formed by ancient polyploidy events in Arabidopsis thaliana. Genes retained in duplicate are not distributed evenly among Gene Ontology or Munich Information Center for Protein Sequences functional categories, which indicates a nonrandom proce...

Evolutionary preservation of redundant duplicated genes.

Gene duplication events produce both perfect and imperfect copies of genes. Perfect copies are said to be functionally redundant when knockout of one gene produces no 'scoreable', phenotypic effects. Preserving identical, duplicate copies of genes is problematic as all copies are prone to accumulate neutral mutations as pseudogenes, or more rarely, evolve into new genes with novel functions. We...