一. Data overview This data interchange is the second data interchange of "genomics research on drought tolerance mechanism of typical desert plants in heihe basin", a key project of the major research program of "integrated research on eco-hydrological processes in heihe basin".The main research goal of this project is a typical desert sand Holly plants as materials, using the current international advanced a new generation of gene sequencing technology to the whole genome sequence and gene transcription of Holly group sequence decoding, so as to explore related to drought resistance gene and gene groups, and transgenic technology in model plants such as arabidopsis and rice) verify its drought resistance. 二, data content 1.Sequencing of the genome and transcriptome of lycophylla SPP. The genome size of Mongolian Holly was about 926 Mb, GC content 36.88%, repeat sequence proportion 66%, genome heterozygosity rate 0.56%, which indicated that the genome has many repeat sequences, high heterozygosity and belongs to a complex genome.Based on the predicted sequence results, we subsequently carried out in-depth sequencing of the genome of lysiopsis SPP. The obtained data were assembled to obtain a 937 Mb genome sequence (table 1), which was basically the same as the predicted genome size.Through to the sand Holly transcriptome sequencing and sequence assembly (table 2), received more than 77000 genes coding sequence (Unigene), these sequences are comments found that most of the gene sequence and legumes and soybean, garbanzo beans and bean has a higher similarity (figure 1), consistent with the fact of sand ilex leguminous plants. 一), and the sand Holly is a leguminous plants consistent with the fact. 2.Discovery of simple repeat sequence (SSR) molecular markers of sand Holly: There is a transcriptome data set of sand Holly in the network public database, and the sample collection site is zhongwei city, ningxia.But this is the location of the project team samples in minqin county, gansu province, in order to study whether this sand in different areas of the Holly sequence has sequence polymorphism, we first identify the minqin county plant samples in the genomes of simple sequence repeat (SSR) markers (table 3), and then, compares the transcriptome sequences of plant sample, found in part of SSR molecular marker polymorphism (table 4), these molecular markers could be used for the species of plant genetic map construction, QTL mapping and genetic diversity analysis in the study. 三, data processing instructions Sample collection place: minqin county, gansu province, latitude and longitude: N38 ° 34 '25.93 "E103 ° 08' 36.77".Genome sequencing: a total of 8 genomic DNA libraries of different sizes were constructed and determined by Illumina HiSeq 2500 instrument.Transcriptome sequencing: a library of 24 transcriptome mrnas was constructed and determined by Illumina HiSeq 4000. 四, the use of data and meaning We selected a typical desert plant as the research object, from the Angle of genomics, parse the desert plant genome and transcriptome sequences, excavated its precious drought-resistant gene resources, and to study their drought resistance mechanism of favorable sand Holly this ancient and important to the utilization of plant resources, as well as the heihe river basin of drought-resistant plant genetic breeding, ecological restoration and sustainable development.
HE Junxian, FENG Lei
In the previous project, three different types of desert investigation and observation sites in the lower reaches of Heihe River were set up. Different kinds of desert plants with the same average growth and size as the observation site were selected for the above ground biomass and underground biomass total root survey. The dry weight was the dry weight at 80 ℃, and the root shoot ratio was the dry weight ratio of the underground biomass to the aboveground biomass. Species: Elaeagnus angustifolia, red sand, black fruit wolfberry, bubble thorn, bitter beans, Peganum, Tamarix and so on.
"Hydrological ecological economic process coupling and evolution of Heihe River Basin Management under the framework of water rights" (91125018) project data collection 2 - Dunhuang comprehensive plan for rational utilization of water resources and ecological protection (2011-2020) Planning documents mainly include: 1. Current situation and existing problems of regional water resources utilization; 2. Guiding ideology, basic principles and planning objectives; 3. Analysis of economic, social and ecological water demand; 4. Plan for water resources allocation; 5. Construction of water right system; 6. Main engineering measures; 7. Environmental impact arrangement.
The data set is the physiological and ecological parameters of the dominant species of each ecosystem in Heihe River Basin. According to the requirements of tesim model, the data set divides Heihe River basin into seven ecosystems: deciduous broad-leaved forest ecosystem (BRD), evergreen coniferous forest ecosystem (CNF), agricultural field ecosystem (CRP), desert ecosystem (DST), meadow grassland ecosystem (MDS) Shrubbery ecosystem (SHB) and grassland ecosystem (STP). Some of the data in this data set are based on the measured data, some are obtained by reference documents, but after verification, they are applied to the Heihe River Basin. For the data in this data, each parameter of each ecosystem has three values, which are the value in the model, the minimum value and the maximum value of this parameter. The data can provide input parameters for the ecological process model, and the data set is still in further optimization.
Background: this data interchange is the first data interchange of the key project of "integrated study of eco-hydrological processes in heihe basin", "genomics research on drought tolerance mechanism of typical desert plants in heihe basin".The main research targets of the key projects is a typical sand desert plants are Holly, using the current international advanced a new generation of gene sequencing technology to the whole genome sequence and gene transcription of Holly group sequence decoding, so as to explore related to drought resistance gene and gene groups, and transgenic technology in model to verify their drought resistance in plants. Process and content: as genome sequencing requires special sequencing equipment, the project is huge and the process is complex (mainly including genome library construction, sequencing, data analysis and genome assembly), so it needs to be completed by a professional sequencing company.After contacting with sequencing companies, we learned that before sequencing an unknown genome, the size and complexity of the genome should be predicted, which is a necessary prerequisite for designing sequencing schemes and strategies.Therefore, in 2013, we mainly predicted the chromosome composition, genome size and complexity of sand Holly, and successfully established the extraction and purification method of its genomic DNA.The results showed that the plant was diploid, the genome was composed of 9 staining lines (18 lines of diploid), and the genome size was 1.07G.The quality test results of the genomic DNA indicated that the requirements of the obtained DNA complex sequencing have been sent to the sequencing company for library construction and sequencing, which is now in progress.In addition, in order to obtain a large number of uniform plant materials, we have discussed the induction of callus, which has been successful.Due to these reasons, we were unable to complete the genome sequencing and submit the relevant data of sand Holly in accordance with the original plan of the project this year, mainly because we did not count the predicted contents of the genome before. Data usage: the data obtained in this year on ploidy, karyotype composition and genome size of lycopodium SPP.The success of the callus induction provides a high-quality material guarantee for the subsequent transcriptome sequencing and drought-resistance mechanism research experiments, and it is also a new contribution to the cytological and physiological research of the plant.
HE Junxian, GU Lifei
The dataset investigated the growth status of plants and leaf morphological indexes of single and conjoined red sand and pearl in the middle and lower reaches of heihe river basin in 2013. The growth indexes were crown width, plant height, and biomass of fine roots and thick roots.Leaf shape indicators are: length, width, thickness, and leaf area, volume, etc.The experimental observation indexes are: leaf nitrogen content, water potential, gas exchange data, chlorophyll fluorescence data. Data include: field observation data and explanatory documents.
As determined in mid-august 2013, planting species: bubbly spines (different habitats are mid-range intermountain lowland and gobi), red sand (different habitats are mid-range gobi and downstream gobi). Using the brother company of LI - 6400 Portable Photosynthesis System (Portable Photosynthesis System, LI - COR, USA) and LI - 3100 leaf area meter, etc., to the desert plant photosynthetic physiological characteristics were observed. The symbolic meaning of the observed data is as follows: Obs，observation frequency ； Photo ，net photosynthetic rate，μmol CO2•m–2•s–1； Cond stomatal conductance，mol H2O•m–2•s–1 ; Ci, Intercellular CO2 concentration, μmol CO2•mol-1； Trmmol，transpiration rate，mmol H2O•m–2•s–1； Vpdl，Vapor pressure deficit，kPa； Area，leaf area，cm2； Tair，free air temperature ，℃； Tleaf，Leaf temperature，℃； CO2R，Reference chamber CO2 concentration，μmol CO2•mol-1； CO2S，Sample chamber CO2 concentration，μmol CO2•mol-1； H2OR，Reference chamber moisture，mmol H2O•mol-1； H2OS，Sample chamber moisture，mmol H2O•mol-1； PARo，photon flux density，μmol•m–2•s–1； RH-R，Reference room air relative humidity，%； RH-S，Relative humidity of air in sample room，%； PARi，Photosynthetic effective radiation，μmol•m–2•s–1； Press，barometric pressure，kPa； Others are the state parameters of the instrument at the time of measurement.
On the basis of physiological and biochemical analysis of photosynthetic organs (leaves or assimilating branches) of typical desert plants in heihe river basin collected in mid-july 2011, some photosynthetic organs of desert plants were collected in mid-july 2012 and put into a liquid nitrogen tank and brought back to the laboratory for determination. Physiological analysis indexes mainly include: soluble protein unit: mg/g;Free amino acid unit: g/g;Chlorophyll content unit: mg/g;Superoxide dismutase (SOD) unit: U/g FW;Catalase (CAT) unit: U/(g•min);POD unit: U/(g•min);Proline (Pro) unit: g/g; Soluble sugar unit: g/g;Malondialdehyde (MDA) is given in moles per liter.
At the end of September and the beginning of October, 2013, desert plants in typical areas of heihe basin stopped their growth period to conduct year-end ecological survey. There are altogether 8 survey and observation fields, which are: piedmont desert, piedmont gobi, middle reaches desert, middle reaches gobi, middle reaches desert, lower reaches desert, lower reaches gobi and lower reaches desert, with a size of 40m×40m. Three 20m×20m large quadrats were fixed in each observation field, named S1, S2 and S3, and regular shrub surveys were conducted.Each large quadrat was fixed with 4 5m x 5m small quadrats, named A, B, C, D, for the herbal survey.
In mid-july 2011, photosynthetic organs (leaves or assimilating branches) of typical desert plants were collected and brought back to the laboratory in a liquid nitrogen tank for determination. The analysis indexes mainly include soluble protein unit: mg/g;Free amino acid unit: g/g;Chlorophyll content unit: mg/g;Superoxide dismutase (SOD) unit: U/g FW;Catalase (CAT) unit: U/(g•min);POD unit: U/(g•min);Proline (Pro) unit: g/g; Soluble sugar unit: g/g;Malondialdehyde (MDA) is given in moles per liter.
Contact SupportNorthwest Institute of Eco-Environment and Resources, CAS 0931-4967287 firstname.lastname@example.org
LinksNational Tibetan Plateau Data Center