Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes  

Abstract

Gene duplication is a primary means to generate genomic novelties, playing an essential role in speciation and adaptation. Particularly in plants, a high abundance of duplicate genes has been maintained for significantly long periods of evolutionary time. To address the manner in which young duplicate genes were derived primarily from small-scale gene duplication and preserved in plant genomes and to determine the underlying driving mechanisms, we generated transcriptomes to produce the expression profiles of five tissues in Arabidopsis thaliana and the closely related species Arabidopsis lyrata and Capsella rubella. Based on the quantitative analysis metrics, we investigated the evolutionary processes of young duplicate genes in Arabidopsis. We determined that conservation, neofunctionalization, and specialization are three main evolutionary processes for Arabidopsis young duplicate genes. We explicitly demonstrated the dynamic functionalization of duplicate genes along the evolutionary time scale. Upon origination, duplicates tend to maintain their ancestral functions; but as they survive longer, they might be likely to develop distinct and novel functions. The temporal evolutionary processes and functionalization of plant duplicate genes are associated with their ancestral functions, dynamic DNA methylation levels, and histone modification abundances. Furthermore, duplicate genes tend to be initially expressed in pollen and then to gain more interaction partners over time. Altogether, our study provides novel insights into the dynamic retention processes of young duplicate genes in plant genomes.Gene duplication, which generates extra copies from ancestral genes, can provide raw materials for developing new functions and is one major means of contributing to the evolution of genomic novelty

Gene duplication and the evolution of phenotypic diversity in insect societies

“…It is notable that prior studies of this type also found that conservation was one of the most common mechanisms maintaining gene duplicates in mammals and plants (Assis and Bachtrog ; Wang et al. ). In contrast, neofunctionalization was found to be the most common process maintaining gene duplicates in Drosophila (Assis and Bachtrog ).…”

“…This suggests that the ancestral function of a pair of duplicates may limit their evolutionary trajectory (Wang et al. ). We also examined evolutionary and expression characteristics of duplicates that were maintained through the different evolutionary processes (Assis and Bachtrog , ).…”

“…Genes that are subject to the latter mechanisms generally displayed biased expression among phenotypes, leading to the development of new functions. This suggests that the ancestral function of a pair of duplicates may limit their evolutionary trajectory (Wang et al 2016). We also examined evolutionary and expression characteristics of duplicates that were maintained through the different evolutionary processes Bachtrog 2013, 2015).…”

“…We used sequence similarity measures from BLAST to classify each A. mellifera paralog in a pair as the “D1” or “D2” copy (Assis and Bachtrog ; Wang et al. ). We used BLASTp to compare each paralog to the single copy ortholog in B. terrestris , using the e‐value, identity, and alignment length as a measure of sequence similarity.…”

“…We identified genes that were duplicated in A. mellifera, but were in single copy in the social bee, Bombus terrestris, using custom perl scripts in the OrthoDB v9.1 database (Zdobnov et al 2017). We used sequence similarity measures from BLAST to classify each A. mellifera paralog in a pair as the "D1" or "D2" copy (Assis and Bachtrog 2013;Wang et al 2016). We used BLASTp to compare each paralog to the single copy ortholog in B. terrestris, using the e-value, identity, and alignment length as a measure of sequence similarity.…”