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The absence of a compiled large-scale catchment characteristics dataset is a key obstacle limiting the development of large-sample hydrology research in China. We introduce the first large-scale catchment attribute dataset in China. We compiled diverse data sources, including soil, land cover, climate, topography, and geology, to develop the dataset. The dataset also includes catchment-scale 31-year meteorological time series from 1990 to 2020 for each basin. Potential evapotranspiration time series based on Penman's equation are derived for each basin. The 4911 catchments included in the dataset cover all of China. We introduced several new indicators that describe the catchment geography and the underlying surface differently from previously proposed datasets. The resulting dataset has a total of 125 catchment attributes and includes a separate HydroMLYR (hydrology dataset for machine learning in the Yellow River Basin) dataset containing standardized weekly averaged streamflow for 102 basins in the Yellow River Basin. The standardized streamflow data should be able to support machine learning hydrology research in the Yellow River Basin. The dataset is freely available at https://doi.org/10.5281/zenodo.5729444 (Zhen et al., 2021). In addition, the accompanying code used to generate the dataset is freely available at https://github.com/haozhen315/CCAM-China-Catchment-Attributes-and-Meteorology-dataset (last access: 26 November 2021) and supports the generation of catchment characteristics for any custom basin boundaries. Compiled data for the 4911 basins covering all of China and the open-source code should be able to support the study of any selected basins rather than being limited to only a few basins.

The runoff amount, soil erosion amount and infiltration rate were analyzed on different rainfall and different underlying horizon in base of yellow river institute of hydraulic research at 2018. The date shows: the runoff amount of bare slope is 7 times that of grass slope, the runoff amount of heavy rainfall is 2 times that of middle rainfall and is 20 times that of small rainfall; the soil erosion amount of bare slope and arable slope is 100 times that of grass slope; the steady soil erosion amount of small rainfall is 1/4 times that of middle rainfall and is 1/30 times that of heavy rainfall on grass slope; the infiltration rate of bare slope and arable slope is 1/3 times of grass slope; the grass slope infiltration rate is about 0.6mm/min in small rainfall, the middle and heavy rainfall get the steady infiltration rate at experiment continue 30min and 12min.

Rainfall and raindrop characteristics have an important impact on the erosion of sandstone soil. The LPM laser raindrop spectrometer is used to analyze the rainfall characteristics of the Ordos City in the Yellow River Basin, including the distribution characteristics of the velocity and size of a natural rainfall raindrop. Statistical analysis shows that with the gradual strengthening of rainfall intensity, the number of raindrops per unit time, the size and speed of raindrops will increase parabolically. However, the natural rainfall process finds that the diameter and velocity of the raindrop are relatively scattered. During this measurement, the velocity of raindrops is mainly distributed between 1-3.4m / s, and most raindrops are distributed at 1-1.8m / s. The diameter of the raindrops is mainly distributed in the range of 0.125-0.5 mm. The raindrops with a diameter of 0.125mm are mainly distributed between 0.8-3.4m / s, the raindrops with a diameter of 0.25mm are mainly distributed between 1-2.6m / s, and the raindrops with a diameter of 0.375mm are mainly distributed between 1.0-2.2 m/s, and the diameter of 0.5 mm is mainly distributed in the range of 2.2-2.6 m / s.

Base the research of landform, soil erosion and vegetation characteristics, the comprehensive control model of soil and water conservation is summarized in Pisha stone area. The dates shows that: The general idea of this area is to take the construction of gully dam system as the starting point and to strengthen the construction of gully dam system with the main project of gully control. In line with local conditions, we will actively promote the construction of forest and grass vegetation, return farmland to forest and grassland, and implement large areas of closure and control, so as to give full play to the self-repair function of the ecosystem.

The soil covered Pisha stone area is the core source area of the coarse sediment in the Yellow River, it has become the focal point of the ecological control of the Yellow River Basin. It has important value to study the spatial distribution about geomorphologyl-vegetation- water Erosion coupling in the soil covered Pisha stone area. Some valuable research results have been obtained by using high-definition remote sensing aerial photographs and unmanned aerial vehicle high precision data interpretation, Especially the image resolution obtained by unmanned remote sensing to obtain the spatial structure features of small watershed topographic features or vegetation structure characteristics. Use remote sensing to study the spatial distribution characteristics of soil erosion in the Pisha stone area slope and the regular response with time change on the geomorphic spatial structure of the slope is very important, the negative response relation between the spatial structure of the vegetation community and the energy dissipation impedance erosion need be study. It will be an urgent scientific problem to promote the research progress of soil erosion in pisha stone area, which will directly affect the theoretical foundation of the comprehensive treatment model of soil erosion in Pisha stone area.

•allows the numerical simulation of the diffusion MRI signal arising from realistic neurons.•provides to the public the constructed finite element meshes for a group of 36 pyramidal neurons and a group of 29 spindle neurons whose morphological descriptions were found in the neuron repository NeuroMorpho.Org.•provides both whole neuron meshes as well as meshes of neuron component such as the soma and dendrite branches.•is available to the public and in open source. The diffusion MRI signal arising from neurons can be numerically simulated by solving the Bloch-Torrey partial differential equation. In this paper we present the Neuron Module that we implemented within the Matlab-based diffusion MRI simulation toolbox SpinDoctor. SpinDoctor uses finite element discretization and adaptive time integration to solve the Bloch-Torrey partial differential equation for general diffusion-encoding sequences, at multiple b-values and in multiple diffusion directions. In order to facilitate the diffusion MRI simulation of realistic neurons by the research community, we constructed finite element meshes for a group of 36 pyramidal neurons and a group of 29 spindle neurons whose morphological descriptions were found in the publicly available neuron repository NeuroMorpho.Org. These finite elements meshes range from having 15,163 nodes to 622,553 nodes. We also broke the neurons into the soma and dendrite branches and created finite elements meshes for these cell components. Through the Neuron Module, these neuron and cell components finite element meshes can be seamlessly coupled with the functionalities of SpinDoctor to provide the diffusion MRI signal attributable to spins inside neurons. We make these meshes and the source code of the Neuron Module available to the public as an open-source package. To illustrate some potential uses of the Neuron Module, we show numerical examples of the simulated diffusion MRI signals in multiple diffusion directions from whole neurons as well as from the soma and dendrite branches, and include a comparison of the high b-value behavior between dendrite branches and whole neurons. In addition, we demonstrate that the neuron meshes can be used to perform Monte-Carlo diffusion MRI simulations as well. We show that at equivalent accuracy, if only one gradient direction needs to be simulated, SpinDoctor is faster than a GPU implementation of Monte-Carlo, but if many gradient directions need to be simulated, there is a break-even point when the GPU implementation of Monte-Carlo becomes faster than SpinDoctor. Furthermore, we numerically compute the eigenfunctions and the eigenvalues of the Bloch-Torrey and the Laplace operators on the neuron geometries using a finite elements discretization, in order to give guidance in the choice of the space and time discretization parameters for both finite elements and Monte-Carlo approaches. Finally, we perform a statistical study on the set of 65 neurons to test some candidate biomakers that can potentially indicate the soma size. This preliminary study exemplifies the possible research that can be conducted using the Neuron Module.

Background: Understanding the DNA methylome and its relationship with non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), is essential for elucidating the molecular mechanisms underlying key biological processes in plants. Few studies have examined the functional roles of the DNA methylome in grass species with highly heterozygous polyploid genomes.Results: We performed genome-wide DNA methylation profiling in the tetraploid switchgrass (Panicum virgatum L.) cultivar ‘Alamo’ using bisulfite sequencing. Single-base-resolution methylation patterns were observed in switchgrass leaf and root tissues, which allowed for characterization of the relationship between DNA methylation and mRNA, miRNA, and lncRNA populations. The results of this study revealed that siRNAs positively regulate DNA methylation of the mCHH sites surrounding genes, and that DNA methylation interferes with gene and lncRNA expression in switchgrass. Ninety-six genes covered by differentially methylated regions (DMRs) were annotated by GO analysis as being involved in stimulus-related processes. Functionally, 82% (79/96) of these genes were found to be hypomethylated in switchgrass root tissue. Sequencing analysis of lncRNAs identified two lncRNAs that are potential precursors of miRNAs, which are predicted to target genes that function in cellulose biosynthesis, stress regulation, and stem and root development.Conclusions: This study characterized the DNA methylome in switchgrass and elucidated its relevance to gene and non-coding RNAs. These results provide valuable genomic resources and references that will aid further epigenetic research in this important biofuel crop.

NAC proteins comprise of a plant-specific transcription factor (TF) family and play important roles in plant development and stress responses. Switchgrass ( Panicum virgatum ) is the prime candidate and model bioenergy grass across the world. Excavating agronomically valuable genes is important for switchgrass molecular breeding. In this study, a total of 251 switchgrass NAC ( PvNAC s) family genes clustered into 19 subgroups were analyzed, and those potentially involved in stress response or tissue-specific expression patterns were pinpointed. Specifically, 27 PvNAC s were considered as abiotic stress-related including four membrane-associated ones. Among 40 tissue-specific PvNAC s expression patterns eight factors were identified that might be relevant for lignin biosynthesis and/or secondary cell wall formation. Conserved functional domains and motifs were also identified among the PvNACs and potential association between these motifs and their predicted functions were proposed, that might encourage experimental studies to use PvNACs as possible targets to improve biomass production and abiotic stress tolerance.

Polyploidization is a significant source of genomic and organism diversification during plant evolution, and leads to substantial alterations in plant phenotypes and natural fitness. To help understand the phenotypic and molecular impacts of autopolyploidization, we conducted epigenetic and full-transcriptomic analyses of a synthesized autopolyploid accession of switchgrass (Panicum virgatum) in order to interpret the molecular and phenotypic changes. We found that mCHH levels were decreased in both genic and transposable element (TE) regions, and that TE methylation near genes was decreased as well. Among 142 differentially expressed genes involved in cell division, cellulose biosynthesis, auxin response, growth, and reproduction processes, 75 of them were modified by 122 differentially methylated regions, 10 miRNAs, and 15 siRNAs. In addition, up-regulated PvTOE1 and suppressed PvFT probably contribute to later flowering time of the autopolyploid. The expression changes were probably associated with modification of nearby methylation sites and siRNAs. We also experimentally demonstrated that expression levels of PvFT and PvTOE1 were regulated by DNA methylation, supporting the link between alterations in methylation induced by polyploidization and the phenotypic changes that were observed. Collectively, our results show epigenetic modifications in synthetic autopolyploid switchgrass for the first time, and support the hypothesis that polyploidizationinduced methylation is an important cause of phenotypic alterations and is potentially important for plant evolution and improved fitness.

Drought stress is a global problem, and the lack of water is a key factor that leads to agricultural shortages. MicroRNAs play a crucial role in the plant drought stress response; however, the microRNAs and their targets involved in drought response have not been well elucidated. In the present study, we used Illumina platform (https://www.illumina.com/) and combined data from miRNA, RNA, and degradome sequencing to explore the drought- and organ-specific miRNAs in orchardgrass (Dactylis glomerata L.) leaf and root. We aimed to find potential miRNA–mRNA regulation patterns responding to drought conditions. In total, 519 (486 conserved and 33 novel) miRNAs were identified, of which, 41 miRNAs had significant differential expression among the comparisons (p < 0.05). We also identified 55,366 unigenes by RNA-Seq, where 12,535 unigenes were differently expressed. Finally, our degradome analysis revealed that 5950 transcripts were targeted by 487 miRNAs. A correlation analysis identified that miRNA ata-miR164c-3p and its target heat shock protein family A (HSP70) member 5 gene comp59407_c0 (BIPE3) may be essential in organ-specific plant drought stress response and/or adaptation in orchardgrass. Additionally, Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analyses found that “antigen processing and presentation” was the most enriched downregulated pathway in adaptation to drought conditions. Taken together, we explored the genes and miRNAs that may be involved in drought adaptation of orchardgrass and identified how they may be regulated. These results serve as a valuable genetic resource for future studies focusing on how plants adapted to drought conditions.