bluuebunny/crossref_metadata_2025_split huggingface dataset:
CRISPR/Cas9-mediated mutagenesis of VvbZIP36 promotes anthocyanin accumulation in grapevine (Vitis vinifera)
Authors: Tu Mingxing , Fang Jinghao , Zhao Ruikang , Liu Xingyu , Yin Wuchen , Wang Ya , Wang Xianhang , Wang Xiping , Fang Yulin 
Published: February 2022

Abstract
Anthocyanins are plant secondary metabolites that have a variety of biological functions, including pigmentation. The accumulation of anthocyanins is regulated by both transcriptional activators and repressors. Studies have shown that bZIP family members act primarily as positive regulators of anthocyanin biosynthesis, but there are few reports of negative regulation. Here, we report that a grapevine (Vitis vinifera) bZIP gene from group K, VvbZIP36, acts as a negative regulator of anthocyanin biosynthesis. Knocking out one allele of VvbZIP36 in grapevine with CRISPR/Cas9 promoted anthocyanin accumulation. Correlation analysis of transcriptome and metabolome data showed that a range of anthocyanin biosynthesis genes were activated in VvbZIP36 mutant plants relative to the wild type, resulting in the accumulation of related metabolites, including naringenin chalcone, naringenin, dihydroflavonols, and cyanidin-3-O-glucoside. The synthesis of stilbenes (α-viniferin), lignans, and some flavonols (including quercetin-3-O-rhamnoside, kaempferol-3-O-rhamnoside, and kaempferol-7-O-rhamnoside) was significantly inhibited, and several genes linked to their metabolism were downregulated in the mutant plants. In summary, our results demonstrate that VvbZIP36 is a negative regulator of anthocyanin biosynthesis that plays a role in balancing the synthesis of stilbenes (α-viniferin), lignans, flavonols, and anthocyanins.
Identification of a WRKY transcriptional activator from Camellia sinensis that regulates methylated EGCG biosynthesis
Authors: Luo Yong , Huang Xiang-xiang , Song Xiao-feng , Wen Bei-bei , Xie Nian-ci , Wang Kun-bo , Huang Jian-an , Liu Zhong-hua 
Published: February 2022

ABSTRACT
Naturally occurring methylated catechins, especially methylated EGCG in tea leaves, are known to have many health benefits. Although the genes involved in methylated EGCG biosynthesis have been studied extensively, the transcription factors that control methylated EGCG biosynthesis are still poorly understood. In the present study, a WRKY domain-containing protein termed CsWRKY57like was identified, which belongs to group IIc of the WRKY family and contains one conserved WRKY motif. CsWRKY57like was found to localize in the nucleus and function as a transcriptional activator; its expression was positively correlated with methylated EGCG level. In addition, CsWRKY57like activated the transcription of three genes related to methylated EGCG biosynthesis (CCoAOMT, CsLAR, and CsDFR), specifically interacting with their promoters by binding to the cis-acting element (C/T)TGAC(T/C). Further assays revealed that CsWRKY57like physically interacts with CsVQ4 and participates in the metabolic regulation of O-methylated catechin biosynthesis. We conclude that CsWRKY57like may positively impact the biosynthesis of methylated EGCG in the tea plant. These results comprehensively enrich the regulatory network of WRKY TFs associated with methylated EGCG and provide a potential strategy for the breeding of specific tea plant cultivars with high methylated EGCG levels.
Transcription factor CsWRKY40 regulates L-theanine hydrolysis by activating theCsPDX2.1promoter in tea leaves during withering
Authors: Cheng Haiyan , Wu Wei , Liu Xiaofen , Wang Yuefei , Xu Ping 
Published: February 2022

AbstractL-Theanine is a crucial secondary metabolite in tea and positively determines the potential quality and health benefits of tea products. Previous work found that the content of L-theanine decreased during the withering process, although the specific mechanism is still unknown. Here, weighted gene co-expression network analysis (WGCNA) was performed based on transcriptome data obtained previously. The key hydrolysis gene CsPDX2.1 in L-theanine metabolism and seven candidate transcription factors were screened out. Among these transcription factors, CsWRKY40 displayed the strongest activation on the CsPDX2.1 promoter (373.18-fold) by binding to the W box element, based on dual luciferase assay and EMSA results. The CsWRKY40 protein was located in the nucleoplasm, whereas CsPDX2.1 was found in both the nucleoplasm and cytoplasm. Analysis of withering, water-retention, and water-loss treatments confirmed that water loss from tea leaves was the critical factor that affected ABA and L-theanine contents by activating the expression of CsWRKY40 and CsPDX2.1. Our results provide a new insight into the regulatory mechanism of L-theanine hydrolysis metabolism.
Genomic variation reveals demographic history and biological adaptation of the ancient relictual, lotus (Nelumbo Adans.)
Authors: Zheng Xingwen , Wang Tao , Cheng Teng , Zhao Lingling , Zheng Xingfei , Zhu Fenglin , Dong Chen , Xu Jinxing , Xie Keqiang , Hu Zhongli , Yang Liangbo , Diao Ying 
Published: February 2022

Abstract
Lotus (Nelumbo Adans.), a relict plant, is testimony to long-term sustained ecological success, but the underlying genetic changes related to its survival strategy remain unclear. Here, we assembled the high-quality lotus genome, investigated genome variation of lotus mutation accumulation (MA) lines and reconstructed the demographic history of wild Asian lotus. We identified and validated 43 base substitutions fixed in MA lines, implying a spontaneous mutation rate of 1.4 × 10−9 bases/generation in lotus shoot stem cells. The past history of the lotus revealed that the ancestors of the lotus in eastern and southern Asia could be traced back to ~20 million years ago and twice experienced significant bottlenecks and population splits. We further identified selected genes among three lotus groups in different habitats, suggesting that 453 differed genes between the tropical and temperate group and 410 differed genes between two subgroups from Northeastern China and the Yangtze River–Yellow River Basin might play important roles in natural selection in the lotus’s adaptation and resilience. Our findings not only improve understanding of the evolutionary history of the lotus and the genetic basis of its survival advantages, but also provide valuable data for addressing various questions in evolution and protection for relict plants.
Rootstock–scion exchanging mRNAs participate in the pathways of amino acid and fatty acid metabolism in cucumber under early chilling stress
Authors: Liu Wenqian , Wang Qing , Zhang Ruoyan , Liu Mengshuang , Wang Cuicui , Liu Zixi , Xiang Chenggang , Lu Xiaohong , Zhang Xiaojing , Li Xiaojun , Wang Tao , Gao Lihong , Zhang Wenna 
Published: February 2022

AbstractCucumber (Cucumis sativus L.) often experiences chilling stress that limits its growth and productivity. Grafting is widely used to improve abiotic stress resistance by exploiting a vigorous root system, suggesting there exists systemic signals communication between distant organs. mRNAs are reported to be evolving fortification strategies involving long-distance signaling when plants suffer from chilling stress. However, the potential function of mobile mRNAs in alleviating chilling stress in grafted cucumber is still unknown. Here, the physiological changes, mobile mRNA profiles, and transcriptomic and metabolomic changes in above- and underground tissues of all graft combinations of cucumber and pumpkin responding to chilling stress were established and analyzed comprehensively. The co-relationship between the cluster of chilling-induced pumpkin mobile mRNAs with differentially expressed genes and differentially intensive metabolites revealed that four key chilling-induced pumpkin mobile mRNAs were highly related to glycine, serine, and threonine synthesis and fatty acid β-oxidative degradation metabolism in cucumber tissues of heterografts. The verification of mobile mRNAs, potential transport of metabolites, and exogenous application of key metabolites of the glycerophospholipid metabolism pathway in cucumber seedlings confirmed the role of mobile mRNAs in regulating chilling responses in grafted cucumber. Our results build a link between the long-distance mRNAs of chilling-tolerant pumpkin and the fatty acid β-oxidative degradation metabolism of chilling-sensitive cucumber. They also help to uncover the mechanism of signaling interaction between scion and stock as a means of achieving chilling tolerance in grafted cucumber.
Evidence for two domestication lineages supporting a middle-eastern origin forBrassica oleraceacrops from diversified kale populations
Authors: Cai Chengcheng , Bucher Johan , Bakker Freek T , Bonnema Guusje 
Published: February 2022

AbstractBrassica oleracea displays enormous phenotypic variation, including vegetables like cabbage, broccoli, cauliflower, kohlrabi, kales etc. Its domestication has not been clarified, despite several genetic studies and investigations of ancient literature. We used 14 152 high-quality SNP markers for population genetic studies and species-tree estimation (treating morphotypes as “species”) using SVD-quartets coalescent-modelling of a collection of 912 globally distributed accessions representing ten morphotypes of B. oleracea, wild B. oleracea accessions and nine related C9 Brassica species. Our genealogical tree provided evidence for two domestication lineages, the “leafy head” lineage (LHL) and the “arrested inflorescence” lineage (AIL). It also showed that kales are polyphyletic with regards to B. oleracea morphotypes, which fits ancient literature describing highly diverse kale types at around 400 BC. The SVD-quartets species tree topology showed that different kale clades are sister to either the LHL or the AIL. Cabbages from the middle-east formed the first-branching cabbage-clade, supporting the hypothesis that cabbage domestication started in the middle-east, which is confirmed by archeological evidence and historic writings. We hypothesize that cabbages and cauliflowers stem from kales introduced from Western Europe to the middle-east, possibly transported with the tin-trade routes in the Bronze age, to be re-introduced later into Europe. Cauliflower is the least diverse morphotype showing strong genetic differentiation with other morphotypes except broccoli, suggesting a strong genetic bottleneck. Genetic diversity reduced from landraces to modern hybrids for almost all morphotypes. This comprehensive Brassica C-group germplasm collection provides valuable genetic resources and a sound basis for B. oleracea breeding.
Ethylene precisely regulates anthocyanin synthesis in apple via a module comprising MdEIL1, MdMYB1, and MdMYB17
Authors: Wang Shuo , Li Li-Xian , Zhang Zhen , Fang Yue , Li Dan , Chen Xue-Sen , Feng Shou-Qian 
Published: February 2022

Abstract
Ethylene regulates anthocyanin synthesis in ripening apple fruit via the antagonistic activities of the R2R3-MYB repressors and activators. However, the molecular mechanism underlying this process remains unknown. In this study, ethylene significantly induced the expression of the R2R3-MYB gene MdMYB17 in apple fruit. Moreover, MdMYB17 was revealed to be an important repressor of anthocyanin synthesis. Specifically, MdMYB17 binds directly to the promoters of the ethylene-induced genes MdMYB1 and MdEIL1, which encode positive regulators of anthocyanin synthesis, and represses their expression. Additionally, MdMYB1 and MdEIL1 bind to the MdMYB17 promoter to activate its expression. Thus, MdMYB17, MdMYB1, and MdEIL1 form a regulatory module that controls the expression of the corresponding genes. MdMYB17 interacts with MdEIL1. The interaction between MdMYB17 and MdEIL1 attenuates the regulatory effects of MdMYB17 on MdMYB1 and MdEIL1 as well as the regulatory effects of MdEIL1 on MdMYB17. Overall, our results reveal the molecular mechanisms by which MdMYB17, MdMYB1, and MdEIL1 finely mediate ethylene-regulated anthocyanin synthesis in apple fruit.
Fruit transpiration drives interspecific variability in fruit growth strategies
Authors: Rossi Federica , Manfrini Luigi , Venturi Melissa , Corelli Grappadelli Luca , Morandi Brunella 
Published: February 2022

Abstract
Fruit growth is a complex mechanism resulting from biochemical and biophysical events leading water and dry matter to accumulate in the fruit tissues. Understanding how fruits choose their growth strategies can help growers optimizing their resource management for a more sustainable production and a higher fruit quality. This paper compares the growth strategies adopted by different fruit crops, at different times during the season and relates their fruit surface conductance to key physiological parameters for fruit growth such as phloem and xylem inflows as well transpiration losses. Our results show how fruits capacity to transpire (determined by their surface conductance) is a key driver in determining the growth strategy adopted by a species and explains the inter-species variability existing among different crops. Indeed, fruits change their surface conductance depending on the species and the phenological stage. This has an impact on the fruit’s ability to lose water due to transpiration, affecting fruit pressure potential and increasing the force with which the fruit is able to attract xylem and phloem flows, with a considerable impact on fruit growth rate.
Comparative genomics analysis of bHLH genes in cucurbits identifies a novel gene regulating cucurbitacin biosynthesis
Authors: Xu Yuanchao , Zhang Huimin , Zhong Yang , Jiang Naiyu , Zhong Xiaoyun , Zhang Qiqi , Chai Sen , Li Hongbo , Zhang Zhonghua 
Published: February 2022

Abstract
The basic helix–loop–helix (bHLH) family of transcription factors (TFs) participate in a variety of biological regulatory processes in plants, and have undergone significant expansion during land plant evolution by gene duplications. In cucurbit crops, several bHLH genes have been found to be responsible for agronomic traits such as bitterness. However, the characterization of bHLH genes across the genomes of cucurbit species has not been reported, and how they have evolved and diverged remains largely unanswered. Here we identified 1,160 bHLH genes in seven cucurbit crops and performed a comprehensive comparative genomics analysis. We determined orthologous and paralogous bHLH genes across cucurbit crops by syntenic analysis between or within species. Orthology and phylogenetic analysis of the tandem-duplicated bHLH genes in the Bt cluster, which regulate the biosynthesis of cucurbitacins, suggest that this cluster is derived from three ancestral genes after the cucurbit-common tetraploidization event. Interestingly, we identified a new conserved cluster paralogous to the Bt cluster that includes two tandem bHLH genes, and the evolutionary history and expression profiles of these two genes in the new cluster suggest the involvement of one gene (Brp) in the regulation of cucurbitacin biosynthesis in roots. Further biochemical and transgenic assays in melon hairy roots supported the function of Brp. This study provides useful information for further investigating the functions of bHLH TFs and novel insights into the regulation of cucurbitacin biosynthesis in cucurbit crops and other plants.
Diversity and conservation of plant small secreted proteins associated with arbuscular mycorrhizal symbiosis
Authors: Hu Xiao-Li , Zhang Jin , Kaundal Rakesh , Kataria Raghav , Labbé Jesse L , Mitchell Julie C , Tschaplinski Timothy J , Tuskan Gerald A , Cheng Zong-Ming (Max) , Yang Xiaohan 
Published: February 2022

Abstract
Arbuscular mycorrhizal symbiosis (AMS) is widespread mutualistic association between plants and fungi, which plays an essential role in nutrient exchange, enhancement in plant stress resistance, development of host, and ecosystem sustainability. Previous studies have shown that plant small secreted proteins (SSPs) are involved in beneficial symbiotic interactions. However, the role of SSPs in the evolution of AMS has not been well studied yet. In this study, we performed computational analysis of SSPs in 60 plant species and identified three AMS-specific ortholog groups containing SSPs only from at least 30% of the AMS species in this study and three AMS-preferential ortholog groups containing SSPs from both AMS and non-AMS species, with AMS species containing significantly more SSPs than non-AMS species. We found that independent lineages of monocot and eudicot plants contained genes in the AMS-specific ortholog groups and had significant expansion in the AMS-preferential ortholog groups. Also, two AMS-preferential ortholog groups showed convergent changes, between monocot and eudicot species, in gene expression in response to arbuscular mycorrhizal fungus Rhizophagus irregularis. Furthermore, conserved cis-elements were identified in the promoter regions of the genes showing convergent gene expression. We found that the SSPs, and their closely related homologs, in each of three AMS-preferential ortholog groups, had some local variations in the protein structural alignment. We also identified genes co-expressed with the Populus trichocarpa SSP genes in the AMS-preferential ortholog groups. This first plant kingdom-wide analysis on SSP provides insights on plant-AMS convergent evolution with specific SSP gene expression and local diversification of protein structures.
Tea plant–legume intercropping simultaneously improves soil fertility and tea quality by changing Bacillus species composition
Authors: Huang Zhi , Cui Chunhong , Cao Yajun , Dai Jinghui , Cheng Xiaoyue , Hua Shaowei , Wang Wentao , Duan Yu , Petropoulos Evangelos , Wang Hui , Zhou Lixiang , Fang Wanping , Zhong Zengtao 
Published: February 2022

Abstract
The tea plant is an economically important crop in China, but long-term monoculture and substantial chemical nitrogen fertilizer input cause soil acidification, which in turn affects the nutrient supply and tea quality. Intercropping has drawn more attention in tea gardens because this pattern is expected to improve soil fertility and tea quality and change the soil microbial community composition. However, the roles of some key microorganisms in rhizosphere soils have not been well characterized. Here, a “soybean in summer and smooth vetch in winter” strategy was used in a tea garden to investigate the effects of intercropped legumes on soil fertility, tea quality, and potential changes in beneficial bacteria such as Bacillus. Our data showed that when soybeans were turned into the soil, the intercropping system exhibited higher soil organic matter (SOM), total nitrogen (TN), tea quality indices, and expression of the Camellia sinensis glutamine synthetase gene (CsGS). Notably, intercropping significantly affected the bacterial communities, decreasing the relative abundance of Bacillus but increasing its absolute abundance. Bacillus amyloliquefaciens BM1 was isolated from intercropped soil and showed outstanding plant growth-promoting (PGP) properties when co-inoculated with rhizobia. In winter, intercropping with smooth vetch had a beneficial effect on soil properties and tea quality. Co-inoculation with strain BM1 and Rhizobium leguminosarum Vic5 on smooth vetch (Vicia villosa) produced huge improvements in SOM, TN, and tea leaf quality, which were accompanied by the highest level of amino acids and the lowest levels of polyphenols and caffeine (p &lt; 0.05). Our findings demonstrate that intercropping with some legumes in the tea garden is a strategy that increases SOM, TN, and tea quality, and the optional use of some PGP Bacillus species produces an amplification effect.
An analysis of classical multidimensional scaling with applications to clustering
Authors: Little Anna , Xie Yuying , Sun Qiang 
Published: February 2022

Abstract
Classical multidimensional scaling is a widely used dimension reduction technique. Yet few theoretical results characterizing its statistical performance exist. This paper provides a theoretical framework for analyzing the quality of embedded samples produced by classical multidimensional scaling. This lays a foundation for various downstream statistical analyses, and we focus on clustering noisy data. Our results provide scaling conditions on the signal-to-noise ratio under which classical multidimensional scaling followed by a distance-based clustering algorithm can recover the cluster labels of all samples. Simulation studies confirm these scaling conditions are sharp. Applications to the cancer gene-expression data, the single-cell RNA sequencing data and the natural language data lend strong support to the methodology and theory.
Contracting scars from fibrin drops
Authors: Robinson Stephen , Parigoris Eric , Chang Jonathan , Hecker Louise , Takayama Shuichi 
Published: February 2022

AbstractThis paper describes a microscale fibroplasia and contraction model that is based on fibrin-embedded lung fibroblasts and provides a convenient visual readout of fibrosis. Cell-laden fibrin microgel drops are formed by aqueous two-phase microprinting. The cells deposit extracellular matrix (ECM) molecules such as collagen while fibrin is gradually degraded. Ultimately, the cells contract the collagen-rich matrix to form a compact cell-ECM spheroid. The size of the spheroid provides the visual readout of the extent of fibroplasia. Stimulation of this wound-healing model with the profibrotic cytokine TGF-β1 leads to an excessive scar formation response that manifests as increased collagen production and larger cell-ECM spheroids. Addition of drugs also shifted the scarring profile: the FDA-approved fibrosis drugs (nintedanib and pirfenidone) and a PAI-1 inhibitor (TM5275) significantly reduced cell-ECM spheroid size. Not only is the assay useful for evaluation of antifibrotic drug effects, it is relatively sensitive; one of the few in vitro fibroplasia assays that can detect pirfenidone effects at submillimolar concentrations. Although this paper focuses on lung fibrosis, the approach opens opportunities for studying a broad range of fibrotic diseases and for evaluating antifibrotic therapeutics.