Preferential gene retention increases the robustness of cold regulation in Brassicaceae and other plants after polyploidization

Abstract

Cold stress profoundly affects plant growth and development and is a key factor affecting the geographic distribution and evolution of plants. Plants have evolved adaptive mechanisms to cope with cold stress. Here, through the genomic analysis of Arabidopsis, three Brassica species and 17 other representative species, we found that both cold-related genes (CRGs) and their collinearity were preferentially retained after polyploidization followed by genome instability, while genome-wide gene sets exhibited a variety of other expansion mechanisms. The coldrelated regulatory network was increased in Brassicaceae genomes, which were recursively affected by polyploidization. By combining our findings regarding the selective retention of CRGs from this ecological genomics study with the available knowledge of cold-induced chromosome doubling, we hypothesize that cold stress may have contributed to the success of polyploid plants through both increasing polyploidization and selectively maintaining CRGs during evolution. This hypothesis requires further biological and ecological exploration to obtain solid supporting evidence, which will potentially contribute to understanding the generation of polyploids and to the field of ecological genomics.

Identification, evolution and expression analyses of whole genome-wide TLP gene family in Brassica napus

“…The "L"and "D" indicates the loss and duplication, respectively. The number after "L" and "D" represents the number of genes families of B. rapa and B. napus, such as BES1, AP2/ERF, CO-Like, bHLH, BES1, HSF, GARS, and cold-related genes [36][37][38][39][40][41][42][43][44][45][46]. The methods, techniques, and experiences of these studies laid the foundation for an in-depth analysis of TLP gene family.…”

The ancient wave of polyploidization events in flowering plants and their facilitated adaptation to environmental stress

“…Through functional enrichment analysis of these gene pairs in grape and water lily, they are primarily related to environmental adaptability, such as responses to stresses ( Table 1). The γ events retained more cold resistance genes than that of Cretaceous-Paleogene whole-genome duplication, and recent whole-genome duplication (Song et al, 2020), indicating that the γ events retained more cold resistance genes as a result of selection. Therefore, after individual polyploidy events, the retention of stress-related resistance genes also illuminates the evolutionary significance of this wave of ancient whole-genome duplications to harsh environmental adaptation.…”

“…The diversification of angiosperms was likely related to the frequent occurrence of whole-genome duplication events (One Thousand Plant Transcriptomes, 2019; Ren et al, 2018;Zhang, Chen, et al, 2020). Multiple paleo-polyploidization events in flowering plants have made significant contributions to their adaptation to vastly different environments (Song et al, 2020;Wu, Han, & Jiao, 2020; K. Zhang, Wang, & Cheng, 2019). For example, cold resistance genes were preferentially retained after the gamma polyploidization in core eudicots (Song et al, 2020) occurred around the Cretaceous-Paleogene (K-Pg) boundary (Fawcett, Maere, & Van de Peer, 2009, PNAS;Vanneste et al, 2014, Genome Res.).…”

“…Multiple paleo-polyploidization events in flowering plants have made significant contributions to their adaptation to vastly different environments (Song et al, 2020;Wu, Han, & Jiao, 2020; K. Zhang, Wang, & Cheng, 2019). For example, cold resistance genes were preferentially retained after the gamma polyploidization in core eudicots (Song et al, 2020) occurred around the Cretaceous-Paleogene (K-Pg) boundary (Fawcett, Maere, & Van de Peer, 2009, PNAS;Vanneste et al, 2014, Genome Res.). The retained duplicated genes significantly enriched the ability of plants to respond to various stresses (Wu et al, 2020).…”

“…Thus, at least these four events constitute an ancient wave of whole-genome duplications during the early diversification of angiosperms. This ancient wave of whole-genome duplications appears to have played pivotal roles in the diversification and adaptation of angiosperms (Song et al, 2020;Wu et al, 2020;Zhang, Chen, et al, 2020). Here, we focused mainly on reviewing the polyploidization events of angiosperms from 100 to 120 million years ago, and their evolutionary contribution to the success of flowering plants.…”