The rapid development of high-throughput sequencing techniques has led biology into the big-data era.Data analyses using various bioinformatics tools rely on programming and command-line environments,which are challen...The rapid development of high-throughput sequencing techniques has led biology into the big-data era.Data analyses using various bioinformatics tools rely on programming and command-line environments,which are challenging and time-consuming for most wet-lab biologists.Here,we present TBtools(a Toolkit for Biologists integrating various biological data-handling tools),a stand-alone software with a userfriendly interface.The toolkit incorporates over 130 functions,which are designed to meet the increasing demand for big-data analyses,ranging from bulk sequence processing to interactive data visualization.A wide variety of graphs can be prepared in TBtools using a new plotting engine("JIGplot")developed to maximize their interactive ability;this engine allows quick point-and-click modification of almost every graphic feature.TBtools is platform-independent software that can be run under all operating systems with Java Runtime Environment 1.6 or newer.It is freely available to non-commercial users at https://github.com/CJ-Chen/TBtools/releases.展开更多
The huge land areas in China provide highly diverse habitats for macrofungi.Of these macrofungi,many are directly related to people’s daily life and have been utilized by ancient Chinese for at least 6800 years.In th...The huge land areas in China provide highly diverse habitats for macrofungi.Of these macrofungi,many are directly related to people’s daily life and have been utilized by ancient Chinese for at least 6800 years.In this study,we evaluate the current known resource diversity of Chinese macrofungi.A total of 1662 taxa are summarized,and all species names and their authorities have been checked and corrected according to authentic mycological databases.Among the 1662 taxa,1020,692,and 480 are considered to be edible,medicinal and poisonous mushrooms,respectively.A few of edible macrofungi in China are commonly used for commercial production.All known medicinal functions are labeled for medicinal species.The most common medicinal functions possessed by Chinese macrofungi are antitumor or anticancer,followed by antioxidant and antimicrobial.A total of 277 Chinese macrofungi are edible simultaneously with certain medicinal functions and without known toxicity.These species could be treated as“Gold Mushrooms”.Contrarily,193 edible and/or medicinal species are also recognized as poisonous mushrooms.To avoid poisoning caused by these species,ingestion either in a proper way or in small amounts is important.However,the mycotoxins metabolized by these poisonous species could be a huge wealth of natural products yet to be explored.How to utilize these Chinese macrofungal resources is a critical to benefit humans worldwide.展开更多
A soil column method was used to compare the effect of drip fertigation (the application of fertilizer through drip irrigation systems, DFI) on the leaching loss and transformation of urea-N in soil with that of surfa...A soil column method was used to compare the effect of drip fertigation (the application of fertilizer through drip irrigation systems, DFI) on the leaching loss and transformation of urea-N in soil with that of surface fertilization combined with flood irrigation (SFI), and to study the leaching loss and transformation of three kinds of nitrogen fertilizers (nitrate fertilizer, ammonium fertilizer, and urea fertilizer) in two contrasting soils after the fertigation. In comparison to SFI, DFI decreased leaching loss of urea-N from the soil and increased the mineral N (NH4+-N + NO3- -N) in the soil. The N leached from a clay loam soil ranged from 5.7% to 9.6% of the total N added as fertilizer, whereas for a sandy loam soil they ranged between 16.2% and 30.4%. Leaching losses of mineral N were higher when nitrate fertilizer was used compared to urea or ammonium fertilizer. Compared to the control (without urea addition), on the first day when soils were fertigated with urea, there were increases in NH4+-N in the soils. This confirmed the rapid hydrolysis of urea in soil during fertigation. NH4+-N in soils reached a peak about 5 days after fertigation, and due to nitrification it began to decrease at day 10. After applying NH4+-N fertilizer and urea and during the incubation period, the mineral nitrogen in the soil decreased. This may be related to the occurrence of NH4+-N fixation or volatilization in the soil during the fertigation process.展开更多
Enhancing the terrestrial ecosystem carbon sink(referred to as terrestrial C sink) is an important way to slow down the continuous increase in atmospheric carbon dioxide(CO_(2)) concentration and to achieve carbon neu...Enhancing the terrestrial ecosystem carbon sink(referred to as terrestrial C sink) is an important way to slow down the continuous increase in atmospheric carbon dioxide(CO_(2)) concentration and to achieve carbon neutrality target.To better understand the characteristics of terrestrial C sinks and their contribution to carbon neutrality,this review summarizes major progress in terrestrial C budget researches during the past decades,clarifies spatial patterns and drivers of terrestrial C sources and sinks in China and around the world,and examines the role of terrestrial C sinks in achieving carbon neutrality target.According to recent studies,the global terrestrial C sink has been increasing from a source of (-0.2±0.9) Pg C yr^(-1)(1 Pg=1015g)in the 1960s to a sink of (1.9±1.1) Pg C yr^(-1) in the 2010s.By synthesizing the published data,we estimate terrestrial C sink of 0.20–0.25 Pg C yr^(-1) in China during the past decades,and predict it to be 0.15–0.52 Pg C yr^(-1) by 2060.The terrestrial C sinks are mainly located in the mid-and high latitudes of the Northern Hemisphere,while tropical regions act as a weak C sink or source.The C balance differs much among ecosystem types:forest is the major C sink;shrubland,wetland and farmland soil act as C sinks;and whether the grassland functions as C sink or source remains unclear.Desert might be a C sink,but the magnitude and the associated mechanisms are still controversial.Elevated atmospheric CO_(2) concentration,nitrogen deposition,climate change,and land cover change are the main drivers of terrestrial C sinks,while other factors such as fires and aerosols would also affect ecosystem C balance.The driving factors of terrestrial C sink differ among regions.Elevated CO_(2) concentration and climate change are major drivers of the C sinks in North America and Europe,while afforestation and ecological restoration are additionally important forcing factors of terrestrial C sinks in China.For future studies,we recommend the necessity for intensive and long-term ec展开更多
Organochlorine pesticides （OCPs）, polychlorinated biphenyls （PCBs）, and polycyclic aromatic hydrocarbons （PAHs） were determined in nineteen surface sediment samples collected from Baiyangdian Lake and its inflow...Organochlorine pesticides （OCPs）, polychlorinated biphenyls （PCBs）, and polycyclic aromatic hydrocarbons （PAHs） were determined in nineteen surface sediment samples collected from Baiyangdian Lake and its inflowing river （Fuhe River） in North China. Total concentrations of OCPs, PCBs and PAHs in sediments ranged from 5.4 to 707.6 ng]g, 2.3 to 197.8 ng/g, and 101.3 to 6360.5 ng]g, respectively. The levels of contaminants in Fuhe River were significantly higher than those in Baiyandian Lake. For hexachlorocyclohexane （HCHs） and dichlorodiphenytrich/oroethanes （DDTs）, α-HCH and p,p＇-DDT were predominant isomers; while for PCBs, PCB 28/31, PCB 40/103, PCB 60, PCB 101, and PCB 118 were predominant congeners. Possible sources derived from historical usage for OCPs and incomplete combustion fuel, wood, and coal and exhaustion of boats or cars for PAHs. Risk assessment of sediment indicated that sediments in Fuhe River were likely to pose potential biological adverse impact.展开更多
Cultivated peanut (Arachis hypogaea) is an allotetraploid crop planted in Asia, Africa, and America for edible oil and protein. To explore the origins and consequences of tetraploidy, we sequenced the allotetraploid A...Cultivated peanut (Arachis hypogaea) is an allotetraploid crop planted in Asia, Africa, and America for edible oil and protein. To explore the origins and consequences of tetraploidy, we sequenced the allotetraploid A. hypogaea genome and compared it with the related diploid Arachis duranensis and Arachis ipaensis genomes. We annotated 39 888 A-subgenome genes and 41 526 B-subgenome genes in allotetraploid peanut. The A. hypogaea subgenomes have evolved asymmetrically, with the B subgenome resembling the ancestral state and the A subgenome undergoing more gene disruption, loss, conversion, and transposable element proliferation, and having reduced gene expression during seed development despite lacking genome-wide expression dominance. Genomic and transcriptomic analyses identified more than 2 500 oil metabolism-related genes and revealed that most of them show altered expression early in seed development while their expression ceases during desiccation, presenting a comprehensive map of peanut lipid biosynthesis. The availability of these genomic resources will facilitate a better understanding of the complex genome architecture, agronomically and economically important genes, and genetic improvement of peanut.展开更多
We used whole-tree agarwood-induction technology to produce agarwood from Aquilaria sinensis trees within 20 months, and evaluated the quality of this agarwood. The results showed its characteristics were similar to t...We used whole-tree agarwood-induction technology to produce agarwood from Aquilaria sinensis trees within 20 months, and evaluated the quality of this agarwood. The results showed its characteristics were similar to those of high-grade wild agarwood in terms of texture, chemical constituents, essential oil content, and ethanol-soluble extract content, with the lattermost quality far surpassing the requirement of traditional Chinese medicine agarwood, as indicated in Chinese Pharmacopoeia 2010. To the best of our knowledge, this is first study to show that high-quality agarwood can be produced in whole A. sinensis trees via a chemically induced technology.展开更多
Since the official release of the stand-alone bioinformatics toolkit TBtools in 2020,its superior functionality in data analysis has been demonstrated by its widespread adoption by many thousands of users and referenc...Since the official release of the stand-alone bioinformatics toolkit TBtools in 2020,its superior functionality in data analysis has been demonstrated by its widespread adoption by many thousands of users and references in more than 5000 academic articles.Now,TBtools is a commonly used tool in biological laboratories.Over the past 3 years,thanks to invaluable feedback and suggestions from numerous users,we have optimized and expanded the functionality of the toolkit,leading to the development of an upgraded version—TBtools-II.In this upgrade,we have incorporated over 100 new features,such as those for comparative genomics analysis,phylogenetic analysis,and data visualization.Meanwhile,to better meet the increasing needs of personalized data analysis,we have launched the plugin mode,which enables users to develop their own plugins and manage their selection,installation,and removal according to individual needs.To date,the plugin store has amassed over 50 plugins,with more than half of them being independently developed and contributed by TBtools users.These plugins offer a range of data analysis options including co-expression network analysis,single-cell data analysis,and bulked segregant analysis sequencing data analysis.Overall,TBtools is now transforming from a stand-alone software to a comprehensive bioinformatics platform of a vibrant and cooperative community in which users are also developers and contributors.By promoting the theme“one for all,all for one”,we believe that TBtools-II will greatly benefit more biological researchers in this big-data era.展开更多
Increasing K＋ adsorption can be an effective alternative in building an available K pool in soils to optimize crop recovery and minimize losses into the environment. We hypothesized that long-term fertilization might...Increasing K＋ adsorption can be an effective alternative in building an available K pool in soils to optimize crop recovery and minimize losses into the environment. We hypothesized that long-term fertilization might change K＋ adsorption because of changes in the chemical and mineralogical properties of a rice （Oryza sativa L.）. The aims of this study were （i） to determine clay minerals in paddy soil clay size fractions using X-ray diffraction methods and a numerical diagramdecomposition method; （ii） to measure K＋ adsorption isotherms before and after H202 oxidation of organic matter, and （iii） to investigate whether K＋ adsorption is correlated with changes in soil chemical and mineral properties. The 30-yr longterm fertilization treatments caused little change in soil organic C （SOC） but a large variation in soil mineral composition. The whole-clay fraction （〈5 Jam） corresponded more to the fertilization treatment than the fine-clay fraction （〈1 gin） in terms of percentage of illite peak area. The total percentage of vermiculite-chlorite peak area was significantly negatively correlated with the total percentage ofillite peak area in the 〈5 lam soil particles （R=-0.946, P〈0.0006）. Different fertilization treatments gave significantly different results in K＋ adsorption. The SOC oxidation test showed positive effects of SOC on K＋ adsorption at lower K＋ concentration （≤120 mg L-0 and negative effects at higher K＋ concentration （240 mg L-l）. The K＋ adsorption by soil clay minerals after SOC oxidization accounted for 60-158% of that by unoxidized soils, suggesting a more important role of soil minerals than SOC on K＋ adsorption. The K＋ adsorption potential was significantly correlated to the amount of poorly crystallized illite present （R--0.879, P=0.012）. The availability of adsorbed K＋ for plant growth needs further study.展开更多
To provide a scientific basis for sustainable land management, a 20-year fertility experiment was conducted in Changwu County, Shaanxi Province, China to investigate the effects of long-term application of chemical fe...To provide a scientific basis for sustainable land management, a 20-year fertility experiment was conducted in Changwu County, Shaanxi Province, China to investigate the effects of long-term application of chemical fertilizers on wheat grain yield and yield stability on the Loess Plateau using regression and stability analysis. The experiment consisted of 17 fertilizer treatments, containing the combinations of different N and P levels, with three replications arranged in a randomized complete block design. Nitrogen fertilizer was applied as urea, and P was applied as calcium superphosphate. Fertilizer rates had a large effect on the response of wheat yield to fertilization. Phosphorus, combined with N, increased yield significantly （P 〈 0.01）. In the unfertilized control and the N or P sole application treatments, wheat yield had a declining trend although it was not statistically significant. Stability analysis combined with the trend analysis indicated that integrated use of fertilizer N and P was better than their sole application in increasing and sustaining the productivity of rainfed winter wheat.展开更多
The outbreak of COVID-19 started in mid-December2019 in Wuhan, China. Up to 29 February 2020,SARS-CoV-2(HCoV-19/2019-nCoV) had infected more than 85 000 people in the world. In this study,we used 93 complete genomes o...The outbreak of COVID-19 started in mid-December2019 in Wuhan, China. Up to 29 February 2020,SARS-CoV-2(HCoV-19/2019-nCoV) had infected more than 85 000 people in the world. In this study,we used 93 complete genomes of SARS-CoV-2 from the GISAID EpiFlu TM database to investigate the evolution and human-to-human transmissions of SARS-CoV-2 in the first two months of the outbreak.We constructed haplotypes of the SARS-CoV-2 genomes, performed phylogenomic analyses and estimated the potential population size changes of the virus. The date of population expansion was calculated based on the expansion parameter tau(τ)using the formula t=τ/2 u. A total of 120 substitution sites with 119 codons, including 79 non-synonymous and 40 synonymous substitutions, were found in eight coding-regions in the SARS-CoV-2 genomes.Forty non-synonymous substitutions are potentially associated with virus adaptation. No combinations were detected. The 58 haplotypes(31 found in samples from China and 31 from outside China)were identified in 93 viral genomes under study and could be classified into five groups. By applying the reported bat coronavirus genome(bat-RaTG13-CoV)as the outgroup, we found that haplotypes H13 and H38 might be considered as ancestral haplotypes,and later H1 was derived from the intermediate haplotype H3. The population size of the SARS-CoV-2 was estimated to have undergone a recent expansion on 06 January 2020, and an early expansion on 08 December 2019. Furthermore,phyloepidemiologic approaches have recovered specific directions of human-to-human transmissions and the potential sources for international infected cases.展开更多
To better understand the effects of plastic film mulching on soil greenhouse gases（GHGs） emissions,we compared seasonal and vertical variations of GHG concentrations at seven soil depths in maize（Zea mays L.） fiel...To better understand the effects of plastic film mulching on soil greenhouse gases（GHGs） emissions,we compared seasonal and vertical variations of GHG concentrations at seven soil depths in maize（Zea mays L.） fields at Changwu station in Shaanxi,a semi-humid region,between 2012 and 2013.Gas samples were taken simultaneously every one week from non-mulched（BP） and plastic film-mulched（FM） field plots.The results showed that the concentration of GHGs varied distinctly at the soil-atmosphere interface and in the soil profile during the maize growing season（MS）.Both carbon dioxide（CO_2） and nitrous oxide（N_2O） concentrations increased with increasement of soil depth,while the methane（CH_4）concentrations decreased with increasement of soil depth.A strong seasonal variation pattern was found for CO_2 and N_2O concentrations,as compared to an inconspicuous seasonal variation of CH_4 concentrations.The mean CO_2 and N_2O concentrations were higher,but the mean CH_4 concentration in the soil profiles was lower in the FM plots than in the BP plots.The results of this study suggested that plastic film mulching significantly increased the potential emissions of CO_2and N_2O from the soil,and promoted CH_4 absorption by the soil,particularly during the MS.展开更多
While low-to-moderate resolution gridded climate data are suitable for climate-impact modeling at global and ecosystems levels, spatial analyses conducted at local scales require climate data with increased spatial ac...While low-to-moderate resolution gridded climate data are suitable for climate-impact modeling at global and ecosystems levels, spatial analyses conducted at local scales require climate data with increased spatial accuracy. This is particularly true for research focused on the evaluation of adaptive forest management strategies. In this study, we developed an application, Climate AP, to generate scale-free(i.e., specific to point locations) climate data for historical(1901–2015) and future(2011–2100)years and periods. Climate AP uses the best available interpolated climate data for the reference period 1961–1990 as baseline data. It downscales the baseline data from a moderate spatial resolution to scale-free point data through dynamic local elevation adjustments. It also integrates and downscales the historical and future climate data using a delta approach. In the case of future climate data, two greenhouse gas representative concentration pathways(RCP 4.5 and 8.5) and 15 general circulation models are included to allow for the assessment of alternative climate scenarios. In addition, Climate AP generates a large number of biologically relevant climate variables derived from primary monthly variables. The effectiveness of the local downscaling was determined based on the strength of the local linear regression for the estimate of lapse rate. The accuracy of the Climate AP output was evaluated through comparisons of Climate AP output against observations from 1805 weather stations in the Asia Pacific region. The local linear regression explained 70%–80% and 0%–50% of the total variation in monthly temperatures and precipitation, respectively, in most cases. Climate AP reduced prediction error by up to27% and 60% for monthly temperature and precipitation,respectively, relative to the original baselines data. The improvements for baseline portions of historical and futurewere more substantial. Applications and limitations of the software are discussed.展开更多
A field experiment with four treatments and four replicates in a randomized complete block design was conducted at the Changwu Experimental Station in Changwu County, Shaanxi Province, of Northwest China from 1998 to ...A field experiment with four treatments and four replicates in a randomized complete block design was conducted at the Changwu Experimental Station in Changwu County, Shaanxi Province, of Northwest China from 1998 to 2002. The local cropping sequence of wheat, wheat-beans, maize, and wheat over the 4-year period was adopted. A micro-plot study using ^15N-lahelled fertilizer was carried out to determine the fate of applied N fertilizer in the first year. When N fertilizer was applied wheat （years 1, 2 and 4） and maize （year 3） grain yield increased significantly （P 〈 0.05） （〉 30%）, with no significant yield differences in normal rainfall years （Years 1, 2 and 3） for N application at the commonly application rate and at 2/3 of this rate. Grain yield of wheat varied greatly between years, mainly due to variation in annual rainfall. Results of ^15N studies on wheat showed that plants recovered 36.6%-38.4% of the N applied, the N remained in soll （0-40 cm） ranged from 29.2% to 33.6%, and unaccounted-for N was 29.5%-34.2%. The following crop （wheat） recovered 2.1%- 2.8% of the residual N from N applied to the previous wheat crop with recovery generally decreasing in the subsequent three crops （beans, maize and wheat）.展开更多
基金This work was funded by the National Key Research and Developmental Program of China(2018YFD1000104)This work is also supported by awards to R.X.,Y.H.,and H.C.from the National Key Research and Developmental Program of China(2017YFD0101702,2018YFD1000500,2019YFD1000500)+4 种基金the National Science Foundation of China(#31872063)the Special Support Program of Guangdong Province(2019TX05N193)the Key-Area Research and Development Program of Guangdong Province(2018B020202011)the Guangzhou Science and Technology Key Project(201804020063)Support to M.H.F.comes from the NSF Faculty Early Career Development Program(IOS-1942437).
文摘The rapid development of high-throughput sequencing techniques has led biology into the big-data era.Data analyses using various bioinformatics tools rely on programming and command-line environments,which are challenging and time-consuming for most wet-lab biologists.Here,we present TBtools(a Toolkit for Biologists integrating various biological data-handling tools),a stand-alone software with a userfriendly interface.The toolkit incorporates over 130 functions,which are designed to meet the increasing demand for big-data analyses,ranging from bulk sequence processing to interactive data visualization.A wide variety of graphs can be prepared in TBtools using a new plotting engine("JIGplot")developed to maximize their interactive ability;this engine allows quick point-and-click modification of almost every graphic feature.TBtools is platform-independent software that can be run under all operating systems with Java Runtime Environment 1.6 or newer.It is freely available to non-commercial users at https://github.com/CJ-Chen/TBtools/releases.
基金supported by the National Natural Science Foundation of China(Project Nos.U1802231&31701978)the Second Tibetan Plateau Scientific Expedition and Research(STEP)Program(Grant No.2019QZKK0503)+2 种基金The Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment,China(2019HJ2096001006)LWZ and ZLY thanks to the financial supports by Youth Innovation Promotion Association CAS(No.2017240)the Yunling scholars funds of Yunnan Provincial Government,respectively.
文摘The huge land areas in China provide highly diverse habitats for macrofungi.Of these macrofungi,many are directly related to people’s daily life and have been utilized by ancient Chinese for at least 6800 years.In this study,we evaluate the current known resource diversity of Chinese macrofungi.A total of 1662 taxa are summarized,and all species names and their authorities have been checked and corrected according to authentic mycological databases.Among the 1662 taxa,1020,692,and 480 are considered to be edible,medicinal and poisonous mushrooms,respectively.A few of edible macrofungi in China are commonly used for commercial production.All known medicinal functions are labeled for medicinal species.The most common medicinal functions possessed by Chinese macrofungi are antitumor or anticancer,followed by antioxidant and antimicrobial.A total of 277 Chinese macrofungi are edible simultaneously with certain medicinal functions and without known toxicity.These species could be treated as“Gold Mushrooms”.Contrarily,193 edible and/or medicinal species are also recognized as poisonous mushrooms.To avoid poisoning caused by these species,ingestion either in a proper way or in small amounts is important.However,the mycotoxins metabolized by these poisonous species could be a huge wealth of natural products yet to be explored.How to utilize these Chinese macrofungal resources is a critical to benefit humans worldwide.
基金Project supported by the National Natural Science Foundation of China (Nos. 30230230 and 30370288)the NationalKey Laboratory for Soil Erosion and Dryland Farming on the Loess Plateau (No. 10501-116).
文摘A soil column method was used to compare the effect of drip fertigation (the application of fertilizer through drip irrigation systems, DFI) on the leaching loss and transformation of urea-N in soil with that of surface fertilization combined with flood irrigation (SFI), and to study the leaching loss and transformation of three kinds of nitrogen fertilizers (nitrate fertilizer, ammonium fertilizer, and urea fertilizer) in two contrasting soils after the fertigation. In comparison to SFI, DFI decreased leaching loss of urea-N from the soil and increased the mineral N (NH4+-N + NO3- -N) in the soil. The N leached from a clay loam soil ranged from 5.7% to 9.6% of the total N added as fertilizer, whereas for a sandy loam soil they ranged between 16.2% and 30.4%. Leaching losses of mineral N were higher when nitrate fertilizer was used compared to urea or ammonium fertilizer. Compared to the control (without urea addition), on the first day when soils were fertigated with urea, there were increases in NH4+-N in the soils. This confirmed the rapid hydrolysis of urea in soil during fertigation. NH4+-N in soils reached a peak about 5 days after fertigation, and due to nitrification it began to decrease at day 10. After applying NH4+-N fertilizer and urea and during the incubation period, the mineral nitrogen in the soil decreased. This may be related to the occurrence of NH4+-N fixation or volatilization in the soil during the fertigation process.
基金supported by the National Natural Science Foundation of China (31988102)。
文摘Enhancing the terrestrial ecosystem carbon sink(referred to as terrestrial C sink) is an important way to slow down the continuous increase in atmospheric carbon dioxide(CO_(2)) concentration and to achieve carbon neutrality target.To better understand the characteristics of terrestrial C sinks and their contribution to carbon neutrality,this review summarizes major progress in terrestrial C budget researches during the past decades,clarifies spatial patterns and drivers of terrestrial C sources and sinks in China and around the world,and examines the role of terrestrial C sinks in achieving carbon neutrality target.According to recent studies,the global terrestrial C sink has been increasing from a source of (-0.2±0.9) Pg C yr^(-1)(1 Pg=1015g)in the 1960s to a sink of (1.9±1.1) Pg C yr^(-1) in the 2010s.By synthesizing the published data,we estimate terrestrial C sink of 0.20–0.25 Pg C yr^(-1) in China during the past decades,and predict it to be 0.15–0.52 Pg C yr^(-1) by 2060.The terrestrial C sinks are mainly located in the mid-and high latitudes of the Northern Hemisphere,while tropical regions act as a weak C sink or source.The C balance differs much among ecosystem types:forest is the major C sink;shrubland,wetland and farmland soil act as C sinks;and whether the grassland functions as C sink or source remains unclear.Desert might be a C sink,but the magnitude and the associated mechanisms are still controversial.Elevated atmospheric CO_(2) concentration,nitrogen deposition,climate change,and land cover change are the main drivers of terrestrial C sinks,while other factors such as fires and aerosols would also affect ecosystem C balance.The driving factors of terrestrial C sink differ among regions.Elevated CO_(2) concentration and climate change are major drivers of the C sinks in North America and Europe,while afforestation and ecological restoration are additionally important forcing factors of terrestrial C sinks in China.For future studies,we recommend the necessity for intensive and long-term ec
基金supported by the National Basic Research Program (973) of China (No.2006CB403306)the National Natural Science Foundation of China (No.30870311)
文摘Organochlorine pesticides （OCPs）, polychlorinated biphenyls （PCBs）, and polycyclic aromatic hydrocarbons （PAHs） were determined in nineteen surface sediment samples collected from Baiyangdian Lake and its inflowing river （Fuhe River） in North China. Total concentrations of OCPs, PCBs and PAHs in sediments ranged from 5.4 to 707.6 ng]g, 2.3 to 197.8 ng/g, and 101.3 to 6360.5 ng]g, respectively. The levels of contaminants in Fuhe River were significantly higher than those in Baiyandian Lake. For hexachlorocyclohexane （HCHs） and dichlorodiphenytrich/oroethanes （DDTs）, α-HCH and p,p＇-DDT were predominant isomers; while for PCBs, PCB 28/31, PCB 40/103, PCB 60, PCB 101, and PCB 118 were predominant congeners. Possible sources derived from historical usage for OCPs and incomplete combustion fuel, wood, and coal and exhaustion of boats or cars for PAHs. Risk assessment of sediment indicated that sediments in Fuhe River were likely to pose potential biological adverse impact.
基金National Natural Science Foundation of China (31501246,31771841,31801401)the Natural Science Foundation of Guangdong Province (2017A030311007)+4 种基金the Modem Agroindustry Technology Research System (CARS-14)the Science and Technology Planning Project of Guangdong Province (2015B020231006, 2015A020209051, 2016B020201003, 2016LM3161, 2016LM3164, 2014A020208060 and S2013020012647)the International Science & Technology Cooperation Program of Guangdong Province (2013B050800021)the Agricultural Science and Technology Program of Guangdong (2013B020301014)the teamwork projects funded Guangdong Natural Science Foundation of Guangdong Province (no. 2017A030312004).
文摘Cultivated peanut (Arachis hypogaea) is an allotetraploid crop planted in Asia, Africa, and America for edible oil and protein. To explore the origins and consequences of tetraploidy, we sequenced the allotetraploid A. hypogaea genome and compared it with the related diploid Arachis duranensis and Arachis ipaensis genomes. We annotated 39 888 A-subgenome genes and 41 526 B-subgenome genes in allotetraploid peanut. The A. hypogaea subgenomes have evolved asymmetrically, with the B subgenome resembling the ancestral state and the A subgenome undergoing more gene disruption, loss, conversion, and transposable element proliferation, and having reduced gene expression during seed development despite lacking genome-wide expression dominance. Genomic and transcriptomic analyses identified more than 2 500 oil metabolism-related genes and revealed that most of them show altered expression early in seed development while their expression ceases during desiccation, presenting a comprehensive map of peanut lipid biosynthesis. The availability of these genomic resources will facilitate a better understanding of the complex genome architecture, agronomically and economically important genes, and genetic improvement of peanut.
基金supported by the National Key Technology R&D Program(No.2011BAI01B07)National Natural Science Foundation of China(Nos.81173481 and 31000136)+1 种基金Beijing Municipal Natural Science Foundation(No. 6102024)the key project in the Science & Technology Program of Hainan Provincial(No.ZDXM20120033)
文摘We used whole-tree agarwood-induction technology to produce agarwood from Aquilaria sinensis trees within 20 months, and evaluated the quality of this agarwood. The results showed its characteristics were similar to those of high-grade wild agarwood in terms of texture, chemical constituents, essential oil content, and ethanol-soluble extract content, with the lattermost quality far surpassing the requirement of traditional Chinese medicine agarwood, as indicated in Chinese Pharmacopoeia 2010. To the best of our knowledge, this is first study to show that high-quality agarwood can be produced in whole A. sinensis trees via a chemically induced technology.
基金supported by the Key Area Research and Development Program of Guangdong Province(2022B0202070003,and 2021B0707010004)supported by the National Science Foundation of China(#32072547,and#32102320)+5 种基金the National Key Research and Development Program(2021YFF1000101,and 2019YFD1000500)the Special Support Program of Guangdong Province(2019TX05N193)the Scientific Research Foundation of the Hunan Provincial Education Department(20A261),)the open competition program of top ten critical priorities of Agricultural Science and Technology Innovation for the 14th Five-Year Plan of Guangdong Province(2022SDZG05)C.C.is supported by the Guangzhou Municipal Science and Technology Plan Project(2023A04J0113)J.F.is supported by the Hainan Provincial Natural Science Foundation of China(323QN279).
文摘Since the official release of the stand-alone bioinformatics toolkit TBtools in 2020,its superior functionality in data analysis has been demonstrated by its widespread adoption by many thousands of users and references in more than 5000 academic articles.Now,TBtools is a commonly used tool in biological laboratories.Over the past 3 years,thanks to invaluable feedback and suggestions from numerous users,we have optimized and expanded the functionality of the toolkit,leading to the development of an upgraded version—TBtools-II.In this upgrade,we have incorporated over 100 new features,such as those for comparative genomics analysis,phylogenetic analysis,and data visualization.Meanwhile,to better meet the increasing needs of personalized data analysis,we have launched the plugin mode,which enables users to develop their own plugins and manage their selection,installation,and removal according to individual needs.To date,the plugin store has amassed over 50 plugins,with more than half of them being independently developed and contributed by TBtools users.These plugins offer a range of data analysis options including co-expression network analysis,single-cell data analysis,and bulked segregant analysis sequencing data analysis.Overall,TBtools is now transforming from a stand-alone software to a comprehensive bioinformatics platform of a vibrant and cooperative community in which users are also developers and contributors.By promoting the theme“one for all,all for one”,we believe that TBtools-II will greatly benefit more biological researchers in this big-data era.
基金funded by the the Public Service Sectors (Agriculture) Research Special Funds, China(201203013-06)supported in partial by the International Plant Nutrition Institute (IPNI ChinaProgram: Hunan-16)the Key Technologies R&D Program of China during the 12th Five-Year-Plan period(2012BAD05B05-3)
文摘Increasing K＋ adsorption can be an effective alternative in building an available K pool in soils to optimize crop recovery and minimize losses into the environment. We hypothesized that long-term fertilization might change K＋ adsorption because of changes in the chemical and mineralogical properties of a rice （Oryza sativa L.）. The aims of this study were （i） to determine clay minerals in paddy soil clay size fractions using X-ray diffraction methods and a numerical diagramdecomposition method; （ii） to measure K＋ adsorption isotherms before and after H202 oxidation of organic matter, and （iii） to investigate whether K＋ adsorption is correlated with changes in soil chemical and mineral properties. The 30-yr longterm fertilization treatments caused little change in soil organic C （SOC） but a large variation in soil mineral composition. The whole-clay fraction （〈5 Jam） corresponded more to the fertilization treatment than the fine-clay fraction （〈1 gin） in terms of percentage of illite peak area. The total percentage of vermiculite-chlorite peak area was significantly negatively correlated with the total percentage ofillite peak area in the 〈5 lam soil particles （R=-0.946, P〈0.0006）. Different fertilization treatments gave significantly different results in K＋ adsorption. The SOC oxidation test showed positive effects of SOC on K＋ adsorption at lower K＋ concentration （≤120 mg L-0 and negative effects at higher K＋ concentration （240 mg L-l）. The K＋ adsorption by soil clay minerals after SOC oxidization accounted for 60-158% of that by unoxidized soils, suggesting a more important role of soil minerals than SOC on K＋ adsorption. The K＋ adsorption potential was significantly correlated to the amount of poorly crystallized illite present （R--0.879, P=0.012）. The availability of adsorbed K＋ for plant growth needs further study.
基金Project supported by the Agricultural Development Program of the Chinese Academy of Sciences (No. KSCX1-YWN1504)the West Light Foundation of the Chinese Academy of Sciences (No. 2005404)the National Natural Science Foundation of China (Nos. 50479065 and 40601041).
文摘To provide a scientific basis for sustainable land management, a 20-year fertility experiment was conducted in Changwu County, Shaanxi Province, China to investigate the effects of long-term application of chemical fertilizers on wheat grain yield and yield stability on the Loess Plateau using regression and stability analysis. The experiment consisted of 17 fertilizer treatments, containing the combinations of different N and P levels, with three replications arranged in a randomized complete block design. Nitrogen fertilizer was applied as urea, and P was applied as calcium superphosphate. Fertilizer rates had a large effect on the response of wheat yield to fertilization. Phosphorus, combined with N, increased yield significantly （P 〈 0.01）. In the unfertilized control and the N or P sole application treatments, wheat yield had a declining trend although it was not statistically significant. Stability analysis combined with the trend analysis indicated that integrated use of fertilizer N and P was better than their sole application in increasing and sustaining the productivity of rainfed winter wheat.
基金Ten Thousand Talents Program of Yunnan for Top-notch Young Talentsthe open research project of“Cross-Cooperative Team”of the Germplasm Bank of Wild Species,Kunming Institute of Botany,Chinese Academy of Sciences.
文摘The outbreak of COVID-19 started in mid-December2019 in Wuhan, China. Up to 29 February 2020,SARS-CoV-2(HCoV-19/2019-nCoV) had infected more than 85 000 people in the world. In this study,we used 93 complete genomes of SARS-CoV-2 from the GISAID EpiFlu TM database to investigate the evolution and human-to-human transmissions of SARS-CoV-2 in the first two months of the outbreak.We constructed haplotypes of the SARS-CoV-2 genomes, performed phylogenomic analyses and estimated the potential population size changes of the virus. The date of population expansion was calculated based on the expansion parameter tau(τ)using the formula t=τ/2 u. A total of 120 substitution sites with 119 codons, including 79 non-synonymous and 40 synonymous substitutions, were found in eight coding-regions in the SARS-CoV-2 genomes.Forty non-synonymous substitutions are potentially associated with virus adaptation. No combinations were detected. The 58 haplotypes(31 found in samples from China and 31 from outside China)were identified in 93 viral genomes under study and could be classified into five groups. By applying the reported bat coronavirus genome(bat-RaTG13-CoV)as the outgroup, we found that haplotypes H13 and H38 might be considered as ancestral haplotypes,and later H1 was derived from the intermediate haplotype H3. The population size of the SARS-CoV-2 was estimated to have undergone a recent expansion on 06 January 2020, and an early expansion on 08 December 2019. Furthermore,phyloepidemiologic approaches have recovered specific directions of human-to-human transmissions and the potential sources for international infected cases.
基金financially supported by the National Natural Science Foundation of China(31270553,51279197,41401343)the Special Fund for Agricultural Profession, China(201103003)
文摘To better understand the effects of plastic film mulching on soil greenhouse gases（GHGs） emissions,we compared seasonal and vertical variations of GHG concentrations at seven soil depths in maize（Zea mays L.） fields at Changwu station in Shaanxi,a semi-humid region,between 2012 and 2013.Gas samples were taken simultaneously every one week from non-mulched（BP） and plastic film-mulched（FM） field plots.The results showed that the concentration of GHGs varied distinctly at the soil-atmosphere interface and in the soil profile during the maize growing season（MS）.Both carbon dioxide（CO_2） and nitrous oxide（N_2O） concentrations increased with increasement of soil depth,while the methane（CH_4）concentrations decreased with increasement of soil depth.A strong seasonal variation pattern was found for CO_2 and N_2O concentrations,as compared to an inconspicuous seasonal variation of CH_4 concentrations.The mean CO_2 and N_2O concentrations were higher,but the mean CH_4 concentration in the soil profiles was lower in the FM plots than in the BP plots.The results of this study suggested that plastic film mulching significantly increased the potential emissions of CO_2and N_2O from the soil,and promoted CH_4 absorption by the soil,particularly during the MS.
基金funded by a research grant"Adaptation of Asia-Pacific Forests to Climate Change"(APFNet/2010/PPF/001)funded by the Asia-Pacific Network for Sustainable Forest Management and Rehabilitation
文摘While low-to-moderate resolution gridded climate data are suitable for climate-impact modeling at global and ecosystems levels, spatial analyses conducted at local scales require climate data with increased spatial accuracy. This is particularly true for research focused on the evaluation of adaptive forest management strategies. In this study, we developed an application, Climate AP, to generate scale-free(i.e., specific to point locations) climate data for historical(1901–2015) and future(2011–2100)years and periods. Climate AP uses the best available interpolated climate data for the reference period 1961–1990 as baseline data. It downscales the baseline data from a moderate spatial resolution to scale-free point data through dynamic local elevation adjustments. It also integrates and downscales the historical and future climate data using a delta approach. In the case of future climate data, two greenhouse gas representative concentration pathways(RCP 4.5 and 8.5) and 15 general circulation models are included to allow for the assessment of alternative climate scenarios. In addition, Climate AP generates a large number of biologically relevant climate variables derived from primary monthly variables. The effectiveness of the local downscaling was determined based on the strength of the local linear regression for the estimate of lapse rate. The accuracy of the Climate AP output was evaluated through comparisons of Climate AP output against observations from 1805 weather stations in the Asia Pacific region. The local linear regression explained 70%–80% and 0%–50% of the total variation in monthly temperatures and precipitation, respectively, in most cases. Climate AP reduced prediction error by up to27% and 60% for monthly temperature and precipitation,respectively, relative to the original baselines data. The improvements for baseline portions of historical and futurewere more substantial. Applications and limitations of the software are discussed.
基金Project supported by the International Atom Energy Agency (IAEA) (NO. 302-D1-CRP-9986) and the National Basic Research Program of China (NO. 2005CB121102).
文摘A field experiment with four treatments and four replicates in a randomized complete block design was conducted at the Changwu Experimental Station in Changwu County, Shaanxi Province, of Northwest China from 1998 to 2002. The local cropping sequence of wheat, wheat-beans, maize, and wheat over the 4-year period was adopted. A micro-plot study using ^15N-lahelled fertilizer was carried out to determine the fate of applied N fertilizer in the first year. When N fertilizer was applied wheat （years 1, 2 and 4） and maize （year 3） grain yield increased significantly （P 〈 0.05） （〉 30%）, with no significant yield differences in normal rainfall years （Years 1, 2 and 3） for N application at the commonly application rate and at 2/3 of this rate. Grain yield of wheat varied greatly between years, mainly due to variation in annual rainfall. Results of ^15N studies on wheat showed that plants recovered 36.6%-38.4% of the N applied, the N remained in soll （0-40 cm） ranged from 29.2% to 33.6%, and unaccounted-for N was 29.5%-34.2%. The following crop （wheat） recovered 2.1%- 2.8% of the residual N from N applied to the previous wheat crop with recovery generally decreasing in the subsequent three crops （beans, maize and wheat）.
