Genomic Convergence in the Adaptation to Extreme Environments

Xu, Shaohua; Wang, Jiayan; Guo, Zixiao; He, Ziwen; Shi, Suhua

doi:10.1016/j.xplc.2020.100117

Cited by 60 publications

(70 citation statements)

References 99 publications

(117 reference statements)

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“…Furthermore, most carnivorous plants live in wet soil environments that contain very limited nitrogenous material due to acidic or other unfavorable soil conditions (Xu et al, 2020). Such soil conditions may also restrict microbial growth.…”

Section: Nlr Contraction Tends To Occur In Aquatic Parasitic and Camentioning

confidence: 99%

An angiospermNLRatlas reveals thatNLRgene reduction is associated with ecological specialization and signal transduction component deletion

Liu

Zeng

et al. 2021

Preprint

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Nucleotide-binding site-leucine-rich repeat receptor (NLR) genes comprise the largest family of plant disease resistance genes. NLR genes are phylogenetically divided into the TNL, CNL, and RNL subclasses. NLR copy numbers and subclass composition vary tremendously across angiosperm genomes. However, the evolutionary associations between genomic NLR content and plant lifestyle, or between NLR content and signal transduction components, are poorly characterized due to limited genome availability. Here, we established an angiosperm NLR atlas (ANNA, http://compbio.nju.edu.cn/app/ANNA/), which includes NLR genes from over 300 angiosperm genomes. Using ANNA, we revealed that NLR copy numbers differ up to 66-fold among closely related species due to rapid gene loss and gain. Interestingly, NLR contraction was associated with adaptations to aquatic, parasitic, and carnivorous lifestyles. The convergent NLR reduction in aquatic plants resembles the long-term evolutionary silence of NLR genes in green algae before the colonization of land. A co-evolutionary pattern between NLR subclasses and plant immune-pathway components was also identified, suggesting that immune pathway deficiencies may drive TNL loss. Finally, we recovered a conserved TNL lineage that may function independently of the RNL pathway. Our findings provide new insights into the evolution of NLR genes in the context of plant lifestyles and genome content variation.

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Section: Nlr Contraction Tends To Occur In Aquatic Parasitic and Camentioning

confidence: 99%

An angiospermNLRatlas reveals thatNLRgene reduction is associated with ecological specialization and signal transduction component deletion

Liu

Zeng

et al. 2021

Preprint

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“…The generation of evolutionary innovations derived from gene duplication is often addressed in evolutionary biology (Panchy, Lehti-Shiu, & Shiu, 2016; Xu, Wang, Guo, He, & Shi, 2020). While attention has been paid to the acquisition of novel functions or increased protein abundance by duplicate genes, little is known about their roles in the expansion of evolutionary paths.…”

Section: Discussionmentioning

confidence: 99%

Gene expression shapes the patterns of parallel evolution of herbicide resistance in the agricultural weedMonochoria vaginalis

Tanigaki

Uchino

Okawa

et al. 2021

Preprint

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The evolution of herbicide resistance in weeds is an example of parallel evolution, through which genes encoding herbicide target proteins are repeatedly represented as evolutionary loci. The number of herbicide target-site genes differs among species, and little is known regarding the effects of duplicate gene copies on the evolution of herbicide resistance.　We investigated the evolution of herbicide resistance in Monochoria vaginalis, which carries five copies of sulfonylurea target-site acetolactate synthase (ALS) genes. Suspected resistant populations collected across Japan were investigated for herbicide sensitivity and ALS gene sequences, followed by functional characterisation and ALS gene expression analysis.　We identified over 60 resistant populations, all of which carried resistance-conferring amino acid substitutions exclusively in MvALS1 or MvALS3. All MvALS4 alleles carried a loss-of-function mutation. Although the enzymatic properties of ALS encoded by these genes were not markedly different, the expression of MvALS1 and MvALS3 was prominently higher among all ALS genes.　The higher expression of MvALS1 and MvALS3 is the driving force of the biased representation of genes during the evolution of herbicide resistance in M. vaginalis. Our findings highlight that gene expression is a key factor in creating evolutionary hotspots.

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“…Another perspective of mangrove adaptations to environmental constraints is driven by convergent evolution ( Ellison et al., 1999 ; Tomlinson, 2016 ). A worth reading review exclusively on genomic convergence of extreme adaptations was published recently by Xu et al. (2020) .…”

Section: Evolution Of Mangroves and Their Adaptations To Intertidal Environmentsmentioning

confidence: 99%

Genetic and molecular mechanisms underlying mangrove adaptations to intertidal environments

2022

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Mangroves are halophytic plants belonging to diverse angiosperm families that are adapted to highly stressful intertidal zones between land and sea. They are special, unique, and one of the most productive ecosystems that play enormous ecological roles and provide a large number of benefits to the coastal communities. To thrive under highly stressful conditions, mangroves have innovated several key morphological, anatomical, and physio-biochemical adaptations. The evolution of the unique adaptive modifications might have resulted from a host of genetic and molecular changes and to date we know little about the nature of these genetic and molecular changes. Although slow, new information has accumulated over the last few decades on the genetic and molecular regulation of the mangrove adaptations, a comprehensive review on it is not yet available. This review provides up-to-date consolidated information on the genetic, epigenetic, and molecular regulation of mangrove adaptive traits.

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Genomic Convergence in the Adaptation to Extreme Environments

Cited by 60 publications

References 99 publications

An angiospermNLRatlas reveals thatNLRgene reduction is associated with ecological specialization and signal transduction component deletion

An angiospermNLRatlas reveals thatNLRgene reduction is associated with ecological specialization and signal transduction component deletion

Gene expression shapes the patterns of parallel evolution of herbicide resistance in the agricultural weedMonochoria vaginalis

Genetic and molecular mechanisms underlying mangrove adaptations to intertidal environments

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