Patterns and Consequences of Subgenome Differentiation Provide Insights into the Nature of Paleopolyploidy in Plants

• Published in: The Plant cell Vol. 29; no. 12; pp. 2974 - 2994
• Main Authors: Zhao, Meixia, Zhang, Biao, Lisch, Damon, Ma, Jianxin
• Format: Journal Article
• Language: English
• Published: England American Society of Plant Biologists 01.12.2017
• Subjects: Centromere - genetics; Chromosome rearrangements; Chromosomes, Plant - genetics; Corn; Deoxyribonucleic acid; Differentiation; DNA; DNA methylation; DNA Methylation - genetics; DNA Transposable Elements - genetics; Epigenesis, Genetic; Evolution, Molecular; Fractionation; Gene Duplication; Gene expression; Gene Expression Regulation, Plant; Gene Ontology; Genes; Genes, Duplicate; Genes, Plant; Genome, Plant; Genomes; Glycine max; Glycine max - genetics; Paleontology; Phaseolus - genetics; Plants - genetics; Polyploidy; Reproduction (copying); Retention; Retroelements - genetics; RNA, Small Interfering - metabolism; Selection, Genetic; Soybeans; Species Specificity; Synteny - genetics; Transposons; Zea mays; Zea mays - genetics
• ISSN: 1040-4651; 1532-298X; 1532-298X
• DOI: 10.1105/tpc.17.00595

Polyploidy is an important feature of plant genomes, but the nature of many polyploidization events remains to be elucidated. Here, we demonstrate that the evolutionary fates of the subgenomes in maize (Zea mays) and soybean (Glycine max) have followed different trajectories. One subgenome has been subject to relaxed selection, lower levels of gene expression, higher rates of transposable element accumulation, more small interfering RNAs and DNA methylation around genes, and higher rates of gene loss in maize, whereas none of these features were observed in soybean. Nevertheless, individual gene pairs exhibit differentiation with respect to these features in both species. In addition, we observed a higher number of chromosomal rearrangements and higher frequency of retention of duplicated genes in soybean than in maize. Furthermore, soybean “singletons” were found to be more frequently tandemly duplicated than “duplicates” in soybean, which may, to some extent, counteract the genome imbalance caused by gene loss. We propose that unlike in maize, in which two subgenomes were distinct prior to the allotetraploidization event and thus experienced global differences in selective constraints, in soybean, the two subgenomes were far less distinct prior to polyploidization, such that individual gene pairs, rather than subgenomes, experienced stochastic differences over longer periods of time, resulting in retention of the majority of duplicates.