of Botany,Chinese Academy Of Sciences
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Spatiotemporal dynamics of FERONIA reveal alternative endocytic pathways in response to flg22 elicitor stimuli
No full textThe plant receptor-like kinase FERONIA (FER) functions in the response to multiple extracellular signals, thereby regulating diverse cellular processes, such as polarized cell growth, hormone signaling and responses to pathogens. Here, we reported that in Arabidopsis thaliana, flagellin peptide flg22 stimulus significantly promoted the lateral mobility and dissociation of FER from the plasma membrane by inducing the association of FER with membrane microdomain components. FER underwent constitutive endocytosis and recycling in a brefeldin A (BFA)-sensitive manner via a clathrin-mediated pathway. Following flg22 elicitation, FER localized to bona fide endosomes via two distinct endocytic routes, showing differential sensitivity to BFA. These results at the single-particle level confirm that FER acts as an essential regulator during flg22 perception and immune activation, thus broadening our understanding of location-specific protein dynamics and membrane trafficking in receptor/receptor kinase signaling
Waxy is an important factor for grain fissure resistance and head rice yield as revealed by a genome-wide association study
No full textThe amylose synthase gene Waxyaffects grain fissure resistance and head rice yield by altering the layered structure of starch granules, thereby affecting their swelling response to moisture. Head rice yield (HRY) is an essential quality trait, and is sensitive to environmental stresses during the grain-filling, harvest, and postharvest stages. It is therefore important for rice production and global food security to select for superior HRY traits; however, the molecular basis of this trait remains unknown. Using diverse rice germplasm material, we performed a genome-wide association study of grain fissure resistance (GFR), the phenotype most associated with HRY, and found that the granule-bound starch synthase I gene Waxy is an important gene controlling GFR. Analysis of near-isogenic lines demonstrated that genetic variations in Waxy conferred different levels of tolerance to fissuring in grains. The null allele wx resulted in the highest GFR, while alleles that increased amylose synthesis reduced GFR. Increases in amylose content led to increases in the ratio of the widths of the amorphous layer to the semi-crystalline layer of the starch granules, and also to increased occurrence of chalkiness. The layer structure determined GFR by affecting the degree of swelling of granules in response to moisture, and chalkiness acted as an accelerator of moisture infiltration to rapidly increase the number of swelling granules. Our study reveals the molecular basis of GFR and HRY, thus opening the door for further understanding of the molecular networks of GFR and HRY
Ancient plastid genomes solve the tree species mystery of the imperial wood Nanmu in the Forbidden City, the largest existing wooden palace complex in the world
No full textSocietal Impact Statement Combining natural and social science approaches to conduct archeological research on wooden cultural relics is important for exploring major aspects of ancient civilizations. The Forbidden City in Beijing, China, is the largest existing wooden palace complex in the world. We examined ancient DNA of imperial wood Nanmu specimens taken from representative structural components of the Forbidden City, in order to provide a new perspective on the long-standing dispute about its species. This allowed us to accurately identify and properly restore these wooden artifacts and improved our understanding of the past interactions between plant distribution, forest resources, and human activities. Exploring the life styles and production methods of past generations using plant resources can help us to improve our understanding of human civilization. Nanmu, known for its high wood quality, was exclusively used for imperial palace construction in the 15th-19th centuries in China, yet its species has been a subject of long-standing debate. Here, we revisit this unresolved problem, using morphology and ancient DNA (aDNA) to analyze 21 centuries-old Nanmu specimens sampled from representative palaces of the Forbidden City. Cytochemical staining demonstrated that endogenous aDNA sporadically occurs in the wood ray parenchyma cells of Nanmu specimens. High-quality plastid genomes were retrieved from archeological woods for the first time via an aDNA capture method, with 90%-100% coverage (137,663-152,805 bp) and sequence depths of 27.05- to 1409.94-fold. Utilizing these ancient genomes, our results demonstrate that Phoebe zhennan and Phoebe hui are most likely the main species of Nanmu in the Forbidden City. This finding diverges from the prevailing view that Nanmu encompasses woods from the whole genus Phoebe and even its close relative Machilus. It also shows that stringent criteria were used when selecting construction materials for the Forbidden City. By combining morphological traits with aDNA analyses, we provide a new solution for identifying the species of timber used for ancient architecture, and we increase our understanding of the way in which forest resources were recognized and utilized by our ancestors despite the lack of a plant taxonomic framework in ancient times
A new model of two-sown regime for oat forage production in an alpine region of northern China
No full textDemand for high forage production and quality has been increased markedly by development of animal husbandry in China. The lack of efficient planting regimes and key technologies greatly limits production of high-quality forage. Oat has become an important forage in animal husbandry in China due to its high nutritional value and forage yield as well as its great adaptation to harsh environment. To maximize oat forage production in an alpine region, we developed a new model of oat forage production known as two-sown regime, i.e., the first spring-sown and the second summer-sown, during a single growing season in an alpine region of Hulun Buir, Inner Mongolia Autonomous Region, China, using two early-matured oat species, Avena sativa (cv. Qinghai444, winner oat cultivar) and A. nuda (cv. Huazao2, spring oat cultivar). The key technologies and the underlying agronomic mechanisms were investigated across three experimental years of 2017-2019. The main results were as follows: (1) dry weight yield, crude protein yield, and relative feed value of forage in the two-sown regime were significantly increased by 53.6%, 48.9%, and 70.6% relative to traditional one-sown regime across the 3 years, respectively; (2) forage production was mainly achieved by an increase in plant height at the first spring-sown; and (3) forage yield resulted mainly from an increase in tiller density by increasing seeding rate under no-tillage treatment in the second summer-sown. The key technologies of the two-sown regime were the first spring-sown at the soil thawing depth 10-13 cm, followed by the second summer-sown with increasing seeding rate under no-tillage treatment. These findings highlight that the two-sown regime of oat forage can be widely used as an effective planting regime to maximize forage production in large alpine regions of northern China as well as in regions with similar climates
A case study in forensic soil comparison
No full textSoil examination can provide useful forensic information about the spatial location and suspect's activities. Many techniques have been applied for soil comparison and provenance determination in criminal investigations. Pollen and diatom identification, which has the potential to provide an independent ecological assessment of soil evidence, is currently underused in forensic soil analysis. This work presents a case study of application of these methods to help criminal investigation in a murder case, which happened in an irrigation ditch in Hunan Province, southern China. Soils from the suspect's clothes, the exact crime scene spot in the irrigation ditch, along the ditch and the reference ditches were collected and analyzed. In addition to the element and mineral analysis, pollen and diatom assemblages were analyzed for further comparison. The statistical methods of hierarchical cluster and cosine similarity analysis were carried out to assist in soil comparison and provenance determination. The results showed that soil on the suspect's clothes had a high probability to share the same source with the soil from the crime scene in the irrigation ditch. The suspect confessed to murder based largely on the soil examination result even without other evidences
Nonlinear responses of ecosystem carbon fluxes to nitrogen deposition in an old-growth boreal forest
No full textNitrogen (N) deposition is known to increase carbon (C) sequestration in N-limited boreal forests. However, the long-term effects of N deposition on ecosystem carbon fluxes have been rarely investigated in old-growth boreal forests. Here we show that decade-long experimental N additions significantly stimulated net primary production (NPP) but the effect decreased with increasing N loads. The effect on soil heterotrophic respiration (Rh) shifted from a stimulation at low-level N additions to an inhibition at higher levels of N additions. Consequently, low-level N additions resulted in a neutral effect on net ecosystem productivity (NEP), due to a comparable stimulating effect on NPP and Rh, while NEP was increased by high-level N additions. Moreover, we found nonlinear temporal responses of NPP, Rh and NEP to low-level N additions. Our findings imply that actual N deposition in boreal forests likely exerts a minor contribution to their soil C storage
Genome-wide analysis of the Glutathione S-Transferase family in wild Medicago ruthenica and drought-tolerant breeding application of MruGSTU39 gene in cultivated alfalfa
No full textKey message Transformation ofMruGSTU39inM. ruthenicaand alfalfa enhanced growth and survival of transgenic plants by up-regulating GST and glutathione peroxidase activity to detoxify ROS under drought stress. Glutathione S-transferases (GSTs) are ubiquitous supergene family which play crucial roles in detoxification of reactive oxygen species (ROS). Despite studies on GSTs, few studies have focused on them in perennial, wild plant species with high tolerance to environmental stress. Here, we identified 66 MruGST genes from the genome of Medicago ruthenica, a perennial legume species native to temperate grasslands with high tolerance to environmental stress. These genes were divided into eight classes based on their conserved domains, phylogenetic tree and gene structure, with the tau class being the most numerous. Duplication analysis revealed that GST family in M. ruthenica was expanded by segmental and tandem duplication. Several drought-responsive MruGSTs were identified by transcriptomic analyses. Of them, expression of MruGSTU39 was up-regulated much more in a tolerant accession by drought stress. Transformation of MruGSTU39 in M. ruthenica and alfalfa (Medicago sativa) enhanced growth and survival of transgenic seedlings than their wild-type counterparts under drought. We demonstrated that MruGSTU39 can detoxify ROS to reduce its damage to membrane by up-regulating activities of GST and glutathione peroxidase. Our findings provide full-scale knowledge on GST family in the wild legume M. ruthenica with high tolerance to drought, and highlight improvement tolerance of legume forages to drought using genomic information of M. ruthenica
Seasonal and interannual variations of ecosystem photosynthetic characteristics in a semi-arid grassland of Northern China
No full textThe ecosystem apparent quantum yield (alpha), maximum rate of gross CO2 assimilation (P-max) and daytime ecosystem respiration rate (R-d), reflecting the physiological functioning of ecosystem, are vital photosynthetic parameters for the estimation of ecosystem carbon budget. Climatic drivers may affect photosynthetic parameters both directly and indirectly by altering the response of vegetation. However, the relative contribution and regulation pathway of environmental and physiological controls remain unclear, especially in semi-arid grasslands. We analyzed seasonal and interannual variations of photosynthetic parameters derived from eddy-covariance observation in a typical semi-arid grassland in Inner Mongolia, Northern China, over 12 years from 2006 to 2017. Regression analyses and a structural equation model (SEM) were adopted to separate the contributions of environmental and physiological effects. The photosynthetic parameters showed unimodal seasonal patterns and significantly interannual variations. Variations of air temperature (T-a) and soil water content (SWC) drove the seasonal patterns of photosynthetic parameters, while SWC predominated their interannual variations. Moreover, contrasting with the predominant roles of T-a on alpha and R-d, SWC explained more variance of P-max than T-a. Results of SEM revealed that environmental factors impacted photosynthetic parameters both directly and indirectly through regulating physiological responses reflected by stomatal conductance at the canopy level. Moreover, leaf area index (LAI) directly affected alpha, P-max and R-d and dominated the variation of P-max. On the other hand, SWC influenced photosynthetic parameters indirectly through LAI and canopy surface conductance (gc). Our findings highlight the importance of physiological regulation on the photosynthetic parameters and carbon assimilation capacity, especially in water-limited grassland ecosystems
RaacFold: a webserver for 3D visualization and analysis of protein structure by using reduced amino acid alphabets
No full textProtein structure exhibits greater complexity and diversity than DNA structure, and usually affects the interpretation of the function, interactions and biological annotations. Reduced amino acid alphabets (Raaa) exhibit a powerful ability to decrease protein complexity and identify functional conserved regions, which motivated us to create RaacFold. The RaacFold provides 687 reduced amino acid clusters (Raac) based on 58 reduction methods and offers three analysis tools: Protein Analysis, Align Analysis, and Multi Analysis. The Protein Analysis and Align Analysis provide reduced representations of sequence-structure according to physicochemical similarities and computational biology strategies. With the simplified representations, the protein structure can be viewed more concise and clearer to capture biological insight than the unreduced structure. Thus, the design of artificial protein will be more convenient, and redundant interference is avoided. In addition, Multi Analysis allows users to explore biophysical variation and conservation in the evolution of protein structure and function. This supplies important information for the identification and exploration of the nonhomologous functions of paralogs. Simultaneously, RaacFold provides powerful 2D and 3D rendering performance with advanced parameters for sequences, structures, and related annotations. RaacFold is freely available at http://bioinfor.imu.edu.cn/raacfold. [GRAPHICS]
The genome of Prunus humilis provides new insights to drought adaption and population diversity
No full textPrunus humilis (2n = 2x = 16) is a dwarf shrub fruit tree native to China and distributed widely in the cold and arid northern region. In this study, we obtained the whole genome sequences of P. humilis by combining Illumina, PacBio and HiC sequencing technologies. This genome was 254.38 Mb long and encodes 28,301 putative proteins. Phylogenetic analysis indicated that P. humilis shares the same ancestor with Prunus mume and Prunus armeniaca at similar to 29.03 Mya. Gene expansion analysis implied that the expansion of WAX-related and LEA genes might be associated with high drought tolerance of P. humilis and LTR maybe one of the driver factors for the drought adaption by increase the copy number of LEAs. Population diversity analysis among 20 P. humilis accessions found that the genetic diversity of P. humilis populations was limited, only 1.40% base pairs were different with each other, and more wild resources need to be collected and utilized in the breeding and improvement. This study provides new insights to the drought adaption and population diversity of P. humilis that could be used as a potential model plant for horticultural research