bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromatin accessibility and translational landscapes of tea plants under chilling stress
Authors: Wang Pengjie , Jin Shan , Chen Xuejin , Wu Liangyu , Zheng Yucheng , Yue Chuan , Guo Yongchun , Zhang Xingtan , Yang Jiangfan , Ye Naixing 
Published: May 2021

AbstractPlants have evolved regulatory mechanisms at multiple levels to regulate gene expression in order to improve their cold adaptability. However, limited information is available regarding the stress response at the chromatin and translational levels. Here, we characterize the chromatin accessibility, transcriptional, and translational landscapes of tea plants in vivo under chilling stress for the first time. Chilling stress significantly affected both the transcription and translation levels as well as the translation efficiency of tea plants. A total of 3010 genes that underwent rapid and independent translation under chilling stress were observed, and they were significantly enriched in the photosynthesis-antenna protein and phenylpropanoid biosynthesis pathways. A set of genes that were significantly responsive to cold at the transcription and translation levels, including four (+)-neomenthol dehydrogenases (MNDs) and two (E)-nerolidol synthases (NESs) arranged in tandem on the chromosomes, were also found. We detected potential upstream open reading frames (uORFs) on 3082 genes and found that tea plants may inhibit the overall expression of genes by enhancing the translation of uORFs under chilling stress. In addition, we identified distal transposase hypersensitive sites (THSs) and proximal THSs and constructed a transcriptional regulatory network for tea plants under chilling stress. We also identified 13 high-confidence transcription factors (TFs) that may play a crucial role in cold regulation. These results provide valuable information regarding the potential transcriptional regulatory network in plants and help to clarify how plants exhibit flexible responses to chilling stress.
Whole-genome resequencing of Osmanthus fragrans provides insights into flower color evolution
Authors: Chen Hongguo , Zeng Xiangling , Yang Jie , Cai Xuan , Shi Yumin , Zheng Riru , Wang Zhenqi , Liu Junyi , Yi Xinxin , Xiao Siwei , Fu Qiang , Zou Jingjing , Wang Caiyun 
Published: May 2021

AbstractOsmanthus fragransis a well-known ornamental plant that has been domesticated in China for 2500 years. More than 160 cultivars have been found during this long period of domestication, and they have subsequently been divided into four cultivar groups, including the Yingui, Jingui, Dangui, and Sijigui groups. These groups provide a set of materials to study genetic evolution and variability. Here, we constructed a reference genome ofO. fragrans‘Liuyejingui’ in the Jingui group and investigated its floral color traits and domestication history by resequencing a total of 122 samples, including 119O. fragransaccessions and three otherOsmanthusspecies, at an average sequencing depth of 15×. The population structure analysis showed that these 119 accessions formed an apparent regional cluster. The results of linkage disequilibrium (LD) decay analysis suggested that varieties with orange/red flower color in the Dangui group had undergone more artificial directional selection; these varieties had the highest LD values among the four groups, followed by the Sijigui, Jingui, and Yingui groups. Through a genome-wide association study, we further identified significant quantitative trait loci and genomic regions containing several genes, such as ethylene-responsive transcription factor 2 and Arabidopsis pseudoresponse regulator 2, that are positively associated with petal color. Moreover, we found a frameshift mutation with a 34-bp deletion in the first coding region of the carotenoid cleavage dioxygenase 4 gene. This frameshift mutation existed in at least one site on both alleles in all varieties of the Dangui group. The results from this study shed light on the genetic basis of domestication in woody plants, such asO. fragrans.
Transcriptomic and epigenomic remodeling occurs during vascular cambium periodicity in Populus tomentosa
Authors: Chen Bo , Xu Huimin , Guo Yayu , Grünhofer Paul , Schreiber Lukas , Lin Jinxing , Li Ruili 
Published: May 2021

AbstractTrees in temperate regions exhibit evident seasonal patterns, which play vital roles in their growth and development. The activity of cambial stem cells is the basis for regulating the quantity and quality of wood, which has received considerable attention. However, the underlying mechanisms of these processes have not been fully elucidated. Here we performed a comprehensive analysis of morphological observations, transcriptome profiles, the DNA methylome, and miRNAs of the cambium inPopulus tomentosaduring the transition from dormancy to activation. Anatomical analysis showed that the active cambial zone exhibited a significant increase in the width and number of cell layers compared with those of the dormant and reactivating cambium. Furthermore, we found that differentially expressed genes associated with vascular development were mainly involved in plant hormone signal transduction, cell division and expansion, and cell wall biosynthesis. In addition, we identified 235 known miRNAs and 125 novel miRNAs. Differentially expressed miRNAs and target genes showed stronger negative correlations than other miRNA/target pairs. Moreover, global methylation and transcription analysis revealed that CG gene body methylation was positively correlated with gene expression, whereas CHG exhibited the opposite trend in the downstream region. Most importantly, we observed that the number of CHH differentially methylated region (DMR) changes was the greatest during cambium periodicity. Intriguingly, the genes with hypomethylated CHH DMRs in the promoter were involved in plant hormone signal transduction, phenylpropanoid biosynthesis, and plant–pathogen interactions during vascular cambium development. These findings improve our systems-level understanding of the epigenomic diversity that exists in the annual growth cycle of trees.
CsTCPs regulate shoot tip development and catechin biosynthesis in tea plant (Camellia sinensis)
Authors: Yu Shuwei , Li Penghui , Zhao Xuecheng , Tan Mangmang , Ahmad Muhammad Zulfiqar , Xu Yujie , Tadege Million , Zhao Jian 
Published: May 2021

AbstractThe growth of leaves and biosynthesis of characteristic secondary metabolites are critically important for tea production and quality control. However, little is known about the coordinated regulation of leaf development and catechin biosynthesis in tea plants. Here, we reported that TCP TFs are involved in both catechin biosynthesis and leaf development. An integrated analysis of catechin profiling and CsTCP expression in different tissues of plants under various environmental conditions at different developmental stages indicated significant correlations between the transcript levels of CIN-type TCPs and catechin production. CIN-type CsTCP3 and CsTCP4 and PCF-type CsTCP14 interacted with the MYB-bHLH-WD40 repeat (MBW) complex by forming a CsTCP3-CsTT8 heterodimer and modulating the transactivation activity of the promoters of anthocyanin synthase (CsANS1) and anthocyanidin reductase (CsANR1). Four types of microRNA/target modules, miR319b/CsTCP3-4, miR164b/CsCUC, miR396/CsGRF-GIF, and miR165b/HD-ZIPIII ones, were also identified and characterized for their functions in the regulation of the development of tea plant shoot tips and leaf shape. The results of these modules were reflected by their different expression patterns in developing buds and leaves that had distinctly different morphologies in three different tea plant varieties. Their roles in the regulation of catechin biosynthesis were also further verified by manipulation of microRNA319b (miR319b), which targets the transcripts of CsTCP3 and CsTCP4. Thus, CsTCPs represent at least one of these important groups of TFs that can integrate tea plant leaf development together with secondary metabolite biosynthesis. Our study provides new insight into shoot tip development and catechin production in tea plants and lays a foundation for further mechanistic understanding of the regulation of tea plant leaf development and secondary metabolism.
Genetic basis of high aroma and stress tolerance in the oolong tea cultivar genome
Authors: Wang Pengjie , Yu Jiaxin , Jin Shan , Chen Shuai , Yue Chuan , Wang Wenling , Gao Shuilian , Cao Hongli , Zheng Yucheng , Gu Mengya , Chen Xuejin , Sun Yun , Guo Yuqiong , Yang Jiangfan , Zhang Xingtan , Ye Naixing 
Published: May 2021

Abstract
Tea plants (Camellia sinensis) are commercially cultivated in &gt;60 countries, and their fresh leaves are processed into tea, which is the most widely consumed beverage in the world. Although several chromosome-level tea plant genomes have been published, they collapsed the two haplotypes and ignored a large number of allelic variations that may underlie important biological functions in this species. Here, we present a phased chromosome-scale assembly for an elite oolong tea cultivar, “Huangdan”, that is well known for its high levels of aroma. Based on the two sets of haplotype genome data, we identified numerous genetic variations and a substantial proportion of allelic imbalance related to important traits, including aroma- and stress-related alleles. Comparative genomics revealed extensive structural variations as well as expansion of some gene families, such as terpene synthases (TPSs), that likely contribute to the high-aroma characteristics of the backbone parent, underlying the molecular basis for the biosynthesis of aroma-related chemicals in oolong tea. Our results uncovered the genetic basis of special features of this oolong tea cultivar, providing fundamental genomic resources to study evolution and domestication for the economically important tea crop.
The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative
Authors: Barrera-Redondo Josué , Sánchez-de la Vega Guillermo , Aguirre-Liguori Jonás A. , Castellanos-Morales Gabriela , Gutiérrez-Guerrero Yocelyn T. , Aguirre-Dugua Xitlali , Aguirre-Planter Erika , Tenaillon Maud I. , Lira-Saade Rafael , Eguiarte Luis E. 
Published: May 2021

AbstractDespite their economic importance and well-characterized domestication syndrome, the genomic impact of domestication and the identification of variants underlying the domestication traits in Cucurbita species (pumpkins and squashes) is currently lacking. Cucurbita argyrosperma, also known as cushaw pumpkin or silver-seed gourd, is a Mexican crop consumed primarily for its seeds rather than fruit flesh. This makes it a good model to study Cucurbita domestication, as seeds were an essential component of early Mesoamerican diet and likely the first targets of human-guided selection in pumpkins and squashes. We obtained population-level data using tunable Genotype by Sequencing libraries for 192 individuals of the wild and domesticated subspecies of C. argyrosperma across Mexico. We also assembled the first high-quality wild Cucurbita genome. Comparative genomic analyses revealed several structural variants and presence/absence of genes related to domestication. Our results indicate a monophyletic origin of this domesticated crop in the lowlands of Jalisco. We found evidence of gene flow between the domesticated and wild subspecies, which likely alleviated the effects of the domestication bottleneck. We uncovered candidate domestication genes that are involved in the regulation of growth hormones, plant defense mechanisms, seed development, and germination. The presence of shared selected alleles with the closely related species Cucurbita moschata suggests domestication-related introgression between both taxa.
CsbZIP1-CsMYB12 mediates the production of bitter-tasting flavonols in tea plants (Camellia sinensis) through a coordinated activator–repressor network
Authors: Zhao Xuecheng , Zeng Xiangsheng , Lin Ning , Yu Shuwei , Fernie Alisdair R. , Zhao Jian 
Published: May 2021

AbstractUnder high light conditions or UV radiation, tea plant leaves produce more flavonols, which contribute to the bitter taste of tea; however, neither the flavonol biosynthesis pathways nor the regulation of their production are well understood. Intriguingly, tea leaf flavonols are enhanced by UV-B but reduced by shading treatment. CsFLS, CsUGT78A14, CsMYB12, and CsbZIP1 were upregulated by UV-B radiation and downregulated by shading. CsMYB12 and CsbZIP1 bound to the promoters of CsFLS and CsUGT78A14, respectively, and activated their expression individually. CsbZIP1 positively regulated CsMYB12 and interacted with CsMYB12, which specifically activated flavonol biosynthesis. Meanwhile, CsPIF3 and two MYB repressor genes, CsMYB4 and CsMYB7, displayed expression patterns opposite to that of CsMYB12. CsMYB4 and CsMYB7 bound to CsFLS and CsUGT78A14 and repressed their CsMYB12-activated expression. While CsbZIP1 and CsMYB12 regulated neither CsMYB4 nor CsMYB7, CsMYB12 interacted with CsbZIP1, CsMYB4, and CsMYB7, but CsbZIP1 did not physically interact with CsMYB4 or CsMYB7. Finally, CsPIF3 bound to and activated CsMYB7 under shading to repress flavonol biosynthesis. These combined results suggest that UV activation and shading repression of flavonol biosynthesis in tea leaves are coordinated through a complex network involving CsbZIP1 and CsPIF3 as positive MYB activators and negative MYB repressors, respectively. The study thus provides insight into the regulatory mechanism underlying the production of bitter-tasting flavonols in tea plants.
Molecular and clinical determinants of response and resistance to rucaparib for recurrent ovarian cancer treatment in ARIEL2 (Parts 1 and 2)
Authors: Swisher Elizabeth M. , Kwan Tanya T. , Oza Amit M. , Tinker Anna V. , Ray-Coquard Isabelle , Oaknin Ana , Coleman Robert L. , Aghajanian Carol , Konecny Gottfried E. , O’Malley David M. , Leary Alexandra , Provencher Diane , Welch Stephen , Chen Lee-may , Wahner Hendrickson Andrea E. , Ma Ling , Ghatage Prafull , Kristeleit Rebecca S. , Dorigo Oliver , Musafer Ashan , Kaufmann Scott H. , Elvin Julia A. , Lin Douglas I. , Chambers Setsuko K. , Dominy Erin , Vo Lan-Thanh , Goble Sandra , Maloney Lara , Giordano Heidi , Harding Thomas , Dobrovic Alexander , Scott Clare L. , Lin Kevin K. , McNeish Iain A. 
Published: May 2021

AbstractARIEL2 (NCT01891344) is a single-arm, open-label phase 2 study of the PARP inhibitor (PARPi) rucaparib in relapsed high-grade ovarian carcinoma. In this post hoc exploratory biomarker analysis of pre- and post-platinum ARIEL2 samples, RAD51C and RAD51D mutations and high-level BRCA1 promoter methylation predict response to rucaparib, similar to BRCA1/BRCA2 mutations. BRCA1 methylation loss may be a major cross-resistance mechanism to platinum and PARPi. Genomic scars associated with homologous recombination deficiency are irreversible, persisting even as platinum resistance develops, and therefore are predictive of rucaparib response only in platinum-sensitive disease. The RAS, AKT, and cell cycle pathways may be additional modulators of PARPi sensitivity.
Population genomics provides insights into the evolution and adaptation to humans of the waterborne pathogen Mycobacterium kansasii
Authors: Luo Tao , Xu Peng , Zhang Yangyi , Porter Jessica L. , Ghanem Marwan , Liu Qingyun , Jiang Yuan , Li Jing , Miao Qing , Hu Bijie , Howden Benjamin P. , Fyfe Janet A. M. , Globan Maria , He Wencong , He Ping , Wang Yiting , Liu Houming , Takiff Howard E. , Zhao Yanlin , Chen Xinchun , Pan Qichao , Behr Marcel A. , Stinear Timothy P. , Gao Qian 
Published: May 2021

AbstractMycobacterium kansasii can cause serious pulmonary disease. It belongs to a group of closely-related species of non-tuberculous mycobacteria known as the M. kansasii complex (MKC). Here, we report a population genomics analysis of 358 MKC isolates from worldwide water and clinical sources. We find that recombination, likely mediated by distributive conjugative transfer, has contributed to speciation and on-going diversification of the MKC. Our analyses support municipal water as a main source of MKC infections. Furthermore, nearly 80% of the MKC infections are due to closely-related M. kansasii strains, forming a main cluster that apparently originated in the 1900s and subsequently expanded globally. Bioinformatic analyses indicate that several genes involved in metabolism (e.g., maintenance of the methylcitrate cycle), ESX-I secretion, metal ion homeostasis and cell surface remodelling may have contributed to M. kansasii’s success and its ongoing adaptation to the human host.
Responses of plant diversity to precipitation change are strongest at local spatial scales and in drylands
Authors: Korell Lotte , Auge Harald , Chase Jonathan M. , Harpole W. Stanley , Knight Tiffany M. 
Published: May 2021

AbstractMitigating and adapting to climate change requires an understanding of the magnitude and nature by which climate change will influence the diversity of plants across the world’s ecosystems. Experiments can causally link precipitation change to plant diversity change, however, these experiments vary in their methods and in the diversity metrics reported, making synthesis elusive. Here, we explicitly account for a number of potentially confounding variables, including spatial grain, treatment magnitude and direction and background climatic conditions, to synthesize data across 72 precipitation manipulation experiments. We find that the effects of treatments with higher magnitude of precipitation manipulation on plant diversity are strongest at the smallest spatial scale, and in drier environments. Our synthesis emphasizes that quantifying differential responses of ecosystems requires explicit consideration of spatial grain and the magnitude of experimental manipulation. Given that diversity provides essential ecosystem services, especially in dry and semi-dry areas, our finding that these dry ecosystems are particular sensitive to projected changes in precipitation has important implications for their conservation and management.
Nonequilibrium charge-density-wave order beyond the thermal limit
Authors: Maklar J. , Windsor Y. W. , Nicholson C. W. , Puppin M. , Walmsley P. , Esposito V. , Porer M. , Rittmann J. , Leuenberger D. , Kubli M. , Savoini M. , Abreu E. , Johnson S. L. , Beaud P. , Ingold G. , Staub U. , Fisher I. R. , Ernstorfer R. , Wolf M. , Rettig L. 
Published: May 2021

AbstractThe interaction of many-body systems with intense light pulses may lead to novel emergent phenomena far from equilibrium. Recent discoveries, such as the optical enhancement of the critical temperature in certain superconductors and the photo-stabilization of hidden phases, have turned this field into an important research frontier. Here, we demonstrate nonthermal charge-density-wave (CDW) order at electronic temperatures far greater than the thermodynamic transition temperature. Using time- and angle-resolved photoemission spectroscopy and time-resolved X-ray diffraction, we investigate the electronic and structural order parameters of an ultrafast photoinduced CDW-to-metal transition. Tracking the dynamical CDW recovery as a function of electronic temperature reveals a behaviour markedly different from equilibrium, which we attribute to the suppression of lattice fluctuations in the transient nonthermal phonon distribution. A complete description of the system’s coherent and incoherent order-parameter dynamics is given by a time-dependent Ginzburg-Landau framework, providing access to the transient potential energy surfaces.
Sex differences in fear memory consolidation via Tac2 signaling in mice
Authors: Florido A. , Velasco E. R. , Soto-Faguás C. M. , Gomez-Gomez A. , Perez-Caballero L. , Molina P. , Nadal R. , Pozo O. J. , Saura C. A. , Andero R. 
Published: May 2021

AbstractMemory formation is key for brain functioning. Uncovering the memory mechanisms is helping us to better understand neural processes in health and disease. Moreover, more specific treatments for fear-related disorders such as posttraumatic stress disorder and phobias may help to decrease their negative impact on mental health. In this line, the Tachykinin 2 (Tac2) pathway in the central amygdala (CeA) has been shown to be sufficient and necessary for the modulation of fear memory consolidation. CeA-Tac2 antagonism and its pharmacogenetic temporal inhibition impair fear memory in male mice. Surprisingly, we demonstrate here the opposite effect of Tac2 blockade on enhancing fear memory consolidation in females. Furthermore, we show that CeA-testosterone in males, CeA-estradiol in females and Akt/GSK3β/β-Catenin signaling both mediate the opposite-sex differential Tac2 pathway regulation of fear memory.
Consequences of spatial patterns for coexistence in species-rich plant communities
Authors: Wiegand Thorsten , Wang Xugao , Anderson-Teixeira Kristina J. , Bourg Norman A. , Cao Min , Ci Xiuqin , Davies Stuart J. , Hao Zhanqing , Howe Robert W. , Kress W. John , Lian Juyu , Li Jie , Lin Luxiang , Lin Yiching , Ma Keping , McShea William , Mi Xiangcheng , Su Sheng-Hsin , Sun I-Fang , Wolf Amy , Ye Wanhui , Huth Andreas 
Published: May 2021

AbstractEcology cannot yet fully explain why so many tree species coexist in natural communities such as tropical forests. A major difficulty is linking individual-level processes to community dynamics. We propose a combination of tree spatial data, spatial statistics and dynamical theory to reveal the relationship between spatial patterns and population-level interaction coefficients and their consequences for multispecies dynamics and coexistence. Here we show that the emerging population-level interaction coefficients have, for a broad range of circumstances, a simpler structure than their individual-level counterparts, which allows for an analytical treatment of equilibrium and stability conditions. Mechanisms such as animal seed dispersal, which result in clustering of recruits that is decoupled from parent locations, lead to a rare-species advantage and coexistence of otherwise neutral competitors. Linking spatial statistics with theories of community dynamics offers new avenues for explaining species coexistence and calls for rethinking community ecology through a spatial lens.
Customized depolarization spatial patterns with dynamic retardance functions
Authors: Marco David , López-Morales Guadalupe , Sánchez-López María del Mar , Lizana Ángel , Moreno Ignacio , Campos Juan 
Published: May 2021

AbstractIn this work we demonstrate customized depolarization spatial patterns by imaging a dynamical time-dependent pixelated retarder. A proof-of-concept of the proposed method is presented, where a liquid–crystal spatial light modulator is used as a spatial retarder that emulates a controlled spatially variant depolarizing sample by addressing a time-dependent phase pattern. We apply an imaging Mueller polarimetric system based on a polarization camera to verify the effective depolarization effect. Experimental validation is provided by temporal integration on the detection system. The effective depolarizance results are fully described within a simple graphical approach which agrees with standard Mueller matrix decomposition methods. The potential of the method is discussed by means of three practical cases, which include non-reported depolarization spatial patterns, including exotic structures as a spirally shaped depolarization pattern.