Multiple whole-genome duplications (WGDs) are found in most sequenced angiosperms. WGDs help plants to survive in extreme environments and contribute to phenotypic innovations. Duplicated genes following WGD often have different fates: they can quickly disappear again, be retained for long(er) periods, or subsequently undergo small-scale duplications. Why different genes have different fates following a WGD? How different expression, epigenetic regulation, and functional constraints can be associated with these different gene fates following a WGD? To answer these questions, it requires a model plant with a single WGD during its evolutionary past, such as lotus (Nelumbo nucifera).  

Researchers from Wuhan Botanical Garden, Ghent University, University of Maryland and Sun Yat-sen University investigated lotus, an angiosperm with a single WGD during the K-pg boundary. 

Relying on an improved intraspecific-synteny identification by a high-throughput  chromosome conformation capture (Hi-C) based genome assembly, transcriptome, and bisulfite sequencing, they explored not only the fundamental distinctions in genomic features, expression, and methylation patterns of genes of different fates after a WGD, but also what shaped post-WGD expression divergence and expression bias between duplicates.  

Also, they found biases in expression level between different subgenomes reflecting subgenome dominance, which were associated with the bias of subgenome fractionation. Based on the observed subgenome pattern, they suggested that lotus might be an ancient allopolyploid. 

To sum up, this study on the genome duplication of lotus emphasizes the impact of functional constraints on gene fate and post-WGD duplicates divergence in plants.            

This article entitled “Distinct expression and methylation patterns for genes with different fates following a single whole-genome duplication in flowering plant” is now published in Molecular Biology and Evolution.  

This project was supported by grants from the Strategic Priority Research Program of Chinese Academy of Sciences, the National Natural Science Foundation of China, Youth Innovation Promotion Association of Chinese Academy of Sciences, Hubei Provincial Natural Science Foundation of China, and Hubei Chenguang Talented Youth Development Foundation. 

CG, CHG and CHH methylation patterns of the lotus genes with different duplication status (fate after a WGD) (Image by SHI Tao)