Brassicaceae transcriptomes reveal convergent evolution of super-accumulation of sinigrin

Yang, Jinghua; Li, Zhangping; Lian, Jinmin; Gao, Qi; Shi, Pibiao; He, Jiawei; Hu, Zhongyuan; Zhang, Mingfang

doi:10.1038/s42003-020-01523-x

Cited by 11 publications

(9 citation statements)

References 41 publications

(55 reference statements)

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“…To date, the cp genome sequences of cash crops such as Cannabis sativa [12], Citrus limon [13], and Momordica charantia L. [14] have been assembled, thus providing abundant idioplasmatic data for deeper evaluation and molecular breeding of these species. In recent years, studies of wasabi have primarily focused on its nutritional components and cultivation techniques [15,16]. A previous study sequenced the cp genome of E. japonicum, revealing that E. tenue (Gifu) had a close relationship with E. yunnanense, and asserted that they should be considered as a different species from other E. tenue species [17].…”

Section: Introductionmentioning

confidence: 99%

Analyses of Chloroplast Genome of Eutrema japonicum Provide New Insights into the Evolution of Eutrema Species

Zhang

et al. 2021

Agronomy

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Wasabi (Eutrema japonicum) is a vegetable of Brassicaceae family, currently cultivated in Southwest Asia. It is rich in nutritional and has a spicy flavour. It is regarded as a rare condiment worldwide. Its genetic profile for yield improvement and the development of E. japonicum germplasm resources remains unknown. Cognizant of this, this study sequenced and assembled the chloroplast (cp) genome of E. japonicum to enrich our genomic information of wasabi and further understand genetic relationships within the Eutrema species. The structural characteristics, phylogeny, and evolutionary relationship of cp genomes among other Brassicaceae plants were analyzed and compared to those of Eutrema species. The cp genome of E. japonicum has 153,851 bp with a typical quadripartite structure, including 37 tRNA genes, 8 rRNA genes, and 87 protein-coding genes. It contains 290 simple sequence repeats and prefers to end their codons with an A or T, which is the same as other Brassicaceae species. Moreover, the cp genomes of the Eutrema species had a high degree of collinearity and conservation during the evolution process. Nucleotide diversity analysis revealed that genes in the IR regions had higher Pi values than those in LSC (Large single copy) and SSC (Small single copy) regions, making them potential molecular markers for wasabi diversity studies. The analysis of genetic distance between Eutrema plants and other Brassicacea plants showed that intraspecies variation was found to be low, while large differences were found between genera and species. Phylogenetic analysis based on 29 cp genomes revealed the existence of a close relationship amongst the Eutrema species. Overall, this study provides baseline information for cp genome-based molecular breeding and genetic transformation studies of Eutrema plants.

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Section: Introductionmentioning

confidence: 99%

Analyses of Chloroplast Genome of Eutrema japonicum Provide New Insights into the Evolution of Eutrema Species

Zhang

et al. 2021

Agronomy

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“…This pattern strongly suggests frequent events of floral divergence and convergence during the evolution of the family (Pie & Weitz, 2005;Chartier et al, 2014). In fact, divergent, convergent, and parallel evolutionary patterns seem to be frequent in Brassicaceae (Huang et al, 2016;Zhong et al, 2019;Rellstab et al, 2020;Yang et al, 2020;Bohut ınsk a et al, 2021a,b).…”

Section: Brassicaceae Floral Diversificationmentioning

confidence: 94%

Phenotypic plasticity guidesMoricandia arvensisdivergence and convergence across the Brassicaceae floral morphospace

et al. 2021

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Many flowers exhibit phenotypic plasticity. By inducing the production of several phenotypes, plasticity may favour the rapid exploration of different regions of the floral morphospace. We investigated how plasticity drives Moricandia arvensis, a species displaying withinindividual floral polyphenism, across the floral morphospace of the entire Brassicaceae family.We compiled the multidimensional floral phenotype, the phylogenetic relationships, and the pollination niche of over 3000 species to construct a family-wide floral morphospace. We assessed the disparity between the two M. arvensis floral morphs (as the distance between the phenotypic spaces occupied by each morph) and compared it with the family-wide disparity. We measured floral divergence by comparing disparity with the most common ancestor, and estimated the convergence of each floral morph with other species belonging to the same pollination niches.Moricandia arvensis exhibits a plasticity-mediated floral disparity greater than that found between species, genera and tribes. The novel phenotype of M. arvensis moves outside the region occupied by its ancestors and relatives, crosses into a new region where it encounters a different pollination niche, and converges with distant Brassicaceae lineages.Our study suggests that phenotypic plasticity favours floral divergence and rapid appearance of convergent flowers, a process which facilitates the evolution of generalist pollination systems.

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“…The reads were mapped to the reference genome (Mus musculus mm10) with Bowtie2 v2.4.2 with default parameters 65 . The unmapped and duplicate reads were filtered with SAMtools v1.11 71 . The H3K9me2 peaks were determined with MACS2 v2.1.1.2 72 .…”

Section: Chip-seq Analysismentioning

confidence: 99%

Uncovering the role of G9a modulatory landscape promoting neuronal plasticity and neuroprotection in Alzheimer's disease

Bellver-Sanchis

Ávila-López²,

Companys-Alemany

et al. 2022

Preprint

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Epigenetic alterations are a fundamental pathological hallmark of Alzheimer’s disease (AD). Herein, we uncover the unknown G9a modulation pathways involved in AD, showing the upregulation of G9a and H3K9me2 in the brains of AD patients. Likewise, treatment with a G9a inhibitor in SAMP8 mice reversed the high levels of H3K9me2 and rescued the cognitive decline. Interestingly, a transcriptional profile analysis revealed induction of neuronal plasticity and a reduction of oxidative stress and neuroinflammation; the latter being also validated in cell cultures. Furthermore, an exploratory H3K9me2 ChIP-seq analysis demonstrated that during G9a inhibition treatment, the H3K9me2 mark is enriched at the promoter of genes associated with neural functions. Lastly, we showed in Caenorhabditis elegans (C. elegans) AD transgenic strains, similar epigenetic modifications and modulated pathways were altered with increased β-amyloid levels, which were reverted by the set-25 (in C. elegans is similar to the mammalian G9a protein) knockout, including the cognitive impairment. Therefore, our findings confirm that RNAi suppression of set-25 or pharmacological G9a inhibition promotes a positive outcome in AD, being a promising therapeutic strategy.

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Brassicaceae transcriptomes reveal convergent evolution of super-accumulation of sinigrin

Cited by 11 publications

References 41 publications

Analyses of Chloroplast Genome of Eutrema japonicum Provide New Insights into the Evolution of Eutrema Species

Analyses of Chloroplast Genome of Eutrema japonicum Provide New Insights into the Evolution of Eutrema Species

Phenotypic plasticity guidesMoricandia arvensisdivergence and convergence across the Brassicaceae floral morphospace

Uncovering the role of G9a modulatory landscape promoting neuronal plasticity and neuroprotection in Alzheimer's disease

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