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

Song, Xiaoming; Wang, Jinpeng; Sun, Pengchuan; Ma, Xiao; Yang, Qing; Hu, Jingjing; Sun, Shiqun; Li, Yuxian; Yu, Jigao; Feng, Shuyan; Pei, Qiaoying; Yu, Tong; Yang, Ning; Liu, Yinzhe; Li, Xiuqing; Paterson, Andrew H.; Wang, Xiyin

doi:10.1038/s41438-020-0253-0

Cited by 55 publications

(52 citation statements)

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“…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.…”

Section: Discussionmentioning

confidence: 99%

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

Wang

et al. 2020

BMC Genomics

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Background: Brassica is a very important genus of Brassicaceae, including many important oils, vegetables, forage crops, and ornamental horticultural plants. TLP family genes play important regulatory roles in the growth and development of plants. Therefore, this study used a bioinformatics approach to conduct the systematic comparative genomics analysis of TLP gene family in B. napus and other three important Brassicaceae crops. Results: Here, we identified a total of 29 TLP genes from B. napus genome, and they distributed on 16 chromosomes of B. napus. The evolutionary relationship showed that these genes could be divided into six groups from Group A to F. We found that the gene corresponding to Arabidopsis thaliana AT1G43640 was completely lost in B. rapa, B. oleracea and B. napus after whole genome triplication. The gene corresponding to AT1G25280 was retained in all the three species we analysed, belonging to 1:3:6 ratios. Our analyses suggested that there was a selective loss of some genes that might be redundant after genome duplication. This study proposed that the TLP genes in B. napus did not directly expansion compared with its diploid parents B. rapa, and B. oleracea. Instead, an indirect expansion of TLP gene family occurred in its two diploid parents. In addition, the study further utilized RNA-seq to detect the expression pattern of TLP genes between different tissues and two subgenomes. Conclusions: This study systematically conducted the comparative analyses of TLP gene family in B. napus, discussed the loss and expansion of genes after genome duplication. It provided rich gene resources for exploring the molecular mechanism of TLP gene family. Meanwhile, it provided guidance and reference for the research of other gene families in B. napus.

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Section: Discussionmentioning

confidence: 99%

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

Wang

et al. 2020

BMC Genomics

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“…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.…”

Section: The Ancient Whole-genome Duplication Events Contribute Tomentioning

confidence: 95%

“…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.).…”

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confidence: 99%

“…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).…”

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“…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.…”

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

Zhang

Chang

et al. 2020

Plant Cell & Environment

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Flowering plants, or angiosperms, consist of more than 300,000 species, far more than any other land plant lineages. The accumulated evidence indicates that multiple ancient polyploidy events occurred around 100 to 120 million years ago during the Cretaceous and drove the early diversification of four major clades of angiosperms: gamma whole-genome triplication in the common ancestor of core eudicots, tau whole-genome duplication during the early diversification of monocots, lambda whole-genome duplication during the early diversification of magnoliids, and pi whole-genome duplication in the Nymphaeales lineage. These four polyploidy events have played essential roles in the adaptive evolution and diversification of major clades of flowering plants. Here, we specifically review the current understanding of this wave of ancient whole-genome duplications and their evolutionary significance. Notably, although these ancient whole-genome duplications occurred independently, they have contributed to the expansion of many stress-related genes (e.g., heat shock transcription factors and Arabidopsis response regulators)，and these genes could have been selected for by global environmental changes in the Cretaceous. Therefore, this ancient wave of paleopolyploidy events could have significantly contributed to the adaptation of angiosperms to environmental changes, and potentially promoted the wide diversification of flowering plants.

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Neopolyploidy‐induced changes in giant duckweed (Spirodela polyrhiza) alter herbivore preference and performance and plant population performance

Assour,

Ashman,

Turcotte

2024

American J of Botany

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PremisePolyploidy is a widespread mutational process in angiosperms that may alter population performance of not only plants but also their interacting species. Yet, knowledge of whether polyploidy affects plant–herbivore dynamics is scarce. Here, we tested whether aphid herbivores exhibit preference for diploid or neopolyploid plants, whether polyploidy impacts plant and herbivore performance, and whether these interactions depend on the plant genetic background.MethodsUsing independently synthesized neotetraploid strains paired with their diploid progenitors of greater duckweed (Spirodela polyrhiza), we evaluated the effect of neopolyploidy on duckweed's interaction with the water‐lily aphid (Rhopalosiphum nymphaeae). Using paired‐choice experiments, we evaluated feeding preference of the herbivore. We then evaluated the consequences of polyploidy on aphid and plant performance by measuring population growth over multiple generations.ResultsAphids preferred neopolyploids when plants were provided at equal abundances but not at equal surface areas, suggesting the role of plant population surface area in driving this preference. Additionally, neopolyploidy increased aphid population performance, but this result was dependent on the plant's genetic lineage. Lastly, the impact of herbivory on neopolyploid vs. diploid duckweed varied greatly with genetic lineage, where neopolyploids appeared to be variably tolerant compared to diploids, sometimes mirroring the effect on herbivore performance.ConclusionsBy experimentally testing the impacts of polyploidy on trophic species interactions, we showed that polyploidization can impact the preference and performance of herbivores on their plant hosts. These results have significant implications for the establishment and persistence of plants and herbivores in the face of plant polyploidy.

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

Cited by 55 publications

References 72 publications

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

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

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

Neopolyploidy‐induced changes in giant duckweed (Spirodela polyrhiza) alter herbivore preference and performance and plant population performance

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