18 results about "Genome database" patented technology

The invention relates to the technical field of biological genetic engineering, in particular to application of a brassica napus BnaA01G0331000ZS gene in drought stress resistance. The BnaA01G0331000ZS gene is cloned by using cDNA of double 11 leaves as a template through a sequence published in a brassica napus genome database, an over-expression vector is constructed and genetically transformed into rape variety high oil for transgenic function verification, the drought resistance of the obtained over-expression transgenic line is obviously enhanced compared with that of a wild type, and the BnaA01G0331000ZS gene has the advantages that the BnaA01G0331000ZS gene is obtained; therefore, the gene can positively regulate the drought stress resistance of the rape. Therefore, the invention provides a new gene resource for adversity stress resistance of rape.

The invention provides application of a potato StMYB4 gene in regulation and control of solanine accumulation in potato tubers, the StMYB4 gene is cloned through a sequence published in a potato genome database by taking cDNA of leaves of cultivated species Hubei potato No.3 and AC142 as a template, an overexpression and knockout vector is constructed, genetic transformation is performed on the Hubei potato No.3 and AC142 respectively for transgenic function verification, and the solanine accumulation in the potato tubers is regulated and controlled. It is found that excessive StMYB4 genes can significantly promote synthesis of solanine in potato tubers, and knockout of the StMYB4 genes can significantly inhibit synthesis of solanine in potato tubers. The application of the potato StMYB4 gene to regulation and control of tuber solanine can be used for molecular marker development and low solanine variety breeding.

The invention relates to the technical field of oat breeding, and discloses a molecular marker related to the content of neutral detergent fibers in oat, a primer combination and application, the molecular marker is an insertion deletion (PAV) marker, the PAV molecular marker is located at a 5D chromosome of an oat reference genome, the physical position is 5D: 424169687, and 161bp deletion is achieved; the national genome database login number of the oat reference genome is GWHGDJH00000000.1, and the national genome database login number of the oat reference genome is According to the molecular marker related to the content of the neutral detergent fibers in the oats, the primer combination and the application, detection can be carried out in the seedling stage of the oats by adopting the molecular marker and the detection method, the breeding period is remarkably shortened, the breeding efficiency is improved, and the breeding cost is reduced; meanwhile, a PCR primer combination designed on the basis of the molecular marker is high in specificity and accuracy, can be used for predicting and screening the neutral detergent fiber content of the feeding oat and is used for genetic breeding of the oat.

The invention discloses a microbial community identification method and system, and particularly relates to the technical field of microbiomics. A hidden Markov model database constructed on the basis of multiple types of ribosome RNA sequences is adopted for global search, a huge whole genome database in the prior art is replaced, and the size of the database is reduced; moreover, the hypervariable region sequence is extracted from the identified ribosome RNA sequence in a targeted manner, and the extracted sequence data and the quality information in the original sequencing data are pasted back, so that the hypervariable region sequence file containing the complete quality information is generated. The sequence data contains sequence information for identification, and a ribosome RNA marker gene sequence can be accurately identified and extracted from metagenome or metatranscriptome sequencing data; the original sequencing data can be used for a traditional amplicon analysis process, and can also support downstream deep analysis, so that seamless connection with the traditional amplicon analysis process is realized.

The invention discloses a chlamydia psittaci cgMLST molecular typing method, and belongs to the field of microbial molecular typing and tracing. According to the invention, an operation technology for carrying out molecular typing on chlamydia psittaci by using a core genome multi-site sequence typing system (cgMLST) is established for the first time. The chlamydia psittaci cgMLST system is established through the processes of collecting chlamydia psittaci genomes in a disclosed genome database, obtaining core genomes through quality control screening and generic genome analysis, screening core genes suitable for typing under multiple screening conditions and the like. And comparing with a phylogenetic analysis result based on core genome SNP difference to confirm the resolution and reliability of the typing system. According to the typing technology, the core genome of the chlamydia psittaci is determined for the first time, and the typing technology can be used for molecular typing and epidemiological monitoring of the chlamydia psittaci.

The invention belongs to the technical field of molecular biology, and discloses a saline-alkaline resistant gene MdLAC12 for enhancing apple and application thereof, an extraction method of the saline-alkaline resistant gene MdLAC12 for enhancing apple comprises the following steps: step 1, extracting total RNA (Ribonucleic Acid) from an apple rootstock M9-T337 root system, and taking cDNA (Complementary Deoxyribonucleic Acid) obtained by reverse transcription as a cloning template; 2, designing an MdLAC12 primer according to an apple genome database GDDH13, and carrying out a conventional polymerase chain reaction (PCR); and step 3, carrying out homologous recombination on the obtained PCR product of the MdLAC12 and pMD18-T, transforming a connection product into an escherichia coli DH5 alpha competent cell, and selecting resistant bacterial plaque for sequencing analysis to obtain a CDs sequence of the MdLAC12. The method is helpful for breeding excellent saline-alkaline tolerant apple rootstocks, and can also improve utilization of saline-alkaline land in a prebiotic area. The method has the advantages of simplicity in operation, high saline-alkaline tolerance and low production cost, and can be widely applied to the saline-alkaline tolerance germplasm resource breeding process.

The application discloses a bacterial identification method based on high-throughput sequencing data, comprising the following steps: (1) constructing a high-quality bacterial genome K-mer database and a high-quality bacterial marker gene database; (2) performing quality control on original sequencing data, removing low-quality sequences, adapter sequences and short fragments, and aligning the remaining sequences with a host reference genome to remove host-derived sequences and obtain pure microbial sequences; (3) inputting the pure microbial sequences into Kraken2 software and Metaphlan2 software respectively for independent species annotation to obtain two groups of annotation results; (4) performing cross-validation; (5) taking all retained 'high-confidence species' as final identification results, and calculating relative abundance based on the corresponding Bracken corrected abundance values. The method has important application value in the fields of clinical diagnosis, probiotic health products, pharmaceutical industry and the like.

The invention provides a method for constructing a clinical-grade respiratory tract pathogenic microorganism detection genome database. Key functions of screening of high-quality genome sequences of species, removal of redundant genome sequences, classification of wrong species of the genome, filtration of pollution sequences in the genome and the like are integrated.

The present application relates to the technical field of bioinformatics, and particularly relates to a construction method of a dehalogenating microorganism functional genome database and an analysis method of dehalogenating microorganisms. The construction method comprises the following steps: obtaining dehalogenation-related genes; obtaining seed sequences and homologous sequences of a family to which the dehalogenation-related genes belong based on a Uniprot protein database to obtain a core database; comparing the core database with a homologous protein database, merging sequences of dehalogenation functional gene families obtained through comparison with the core database to obtain a preliminary database; and comparing the preliminary database to a Refseq database of microorganisms in NCBI, and obtaining a complete database through classification, merging of homologous sequences and de-redundancy. The present application constructs an accurate dehalogenation functional gene database based on analysis and search results of multiple databases, which can be used to conveniently and accurately analyze dehalogenating microorganism functional communities in the environment, and has important application value.

The invention relates to the technical field of plant genetic engineering, in particular to application of a brassica napus BnPUB12 gene in regulation and control of plant waterlogging tolerance. The BnPUB12 gene is cloned through a sequence published in a brassica napus genome database by taking DNA (Deoxyribose Nucleic Acid) of Zhongdou-11 leaves as a template, a CRISPR / Cas9 gene editing vector targeting the BnPUB12 is successfully constructed and is genetically transformed into the Zhongdou-11 of a brassica napus variety for transgenosis function verification, and an obtained homozygous mutant material is obviously enhanced in waterlogging resistance compared with a wild type material and has a good application prospect. Therefore, the gene can remarkably and negatively regulate the waterlogging stress resistance of the rape. Therefore, the invention provides a new gene resource for adversity stress resistance of rape.

The invention discloses an information encryption method and system based on strain genome coding and identification. The method comprises the following steps: extracting target gene sequence features from a strain genome database, including conservative marker gene sequences, necessary functional gene sequences and genome variation site distribution, and generating a strain specific key matrix; after to-be-encrypted information is converted into binary codes, a dynamic mapping rule is established according to the strain specificity key matrix, the binary codes are converted into quaternary pseudo-gene sequences, and strain identity identification codes are embedded into the quaternary pseudo-gene sequences; a hierarchical coding mechanism is adopted to allocate different security levels according to strain system development levels, and multi-level key management and authority control are achieved; inserting a strain specific marker sequence and an integrity check code into the pseudo-gene sequence to generate a final biological ciphertext; according to the method, high-security quantum resistant encryption is realized by utilizing natural diversity and randomness of microbial genomes.

The invention belongs to the technical field of bioinformatics, and discloses a generic genome database and a construction method and system thereof. According to the method, microorganisms or parasites provided by a plurality of public databases and / or own databases are classified, genome sequences of the microorganisms or parasites are screened out by using different screening methods, the genome sequences are further cleaned to remove polluted sequences, and finally representative sequences are screened out from the cleaned genome sequences, so that the microorganisms or parasites are screened out. And summarizing all representative sequences to complete the construction of the generic genome database. According to the generic genome database constructed by the method, the accuracy and efficiency of metagenome sequencing are remarkably improved, and the method is suitable for rapid identification of clinical infection pathogens.

The application provides a potato StTST1 gene and its application in cold resistance and drought resistance, and discloses the following technical scheme: through a sequence published in a potato genome database, total RNA of a low-temperature sensitive e potato No.3 (E3) is taken as a template to prepare cDNA by reverse transcription, the cDNA is taken as a template to clone a StTST1 gene, an overexpression vector is constructed, genetic transformation is carried out on E3 to verify the gene function, and the endogenous StTST1 gene of the interference E3 is found to be able to improve the cold resistance and reduce the drought resistance by combining with the interference strain obtained in the early stage; the overexpression StTST1 gene is able to improve the drought resistance and reduce the cold resistance.

A method of constructing a microbial identification database, the method comprising: (ST02) acquiring genome data for microorganisms from a genome database; (ST06) determining whether a criterion is satisfied by the genome data thus acquired; (ST16) for respective sets of the genome data that were determined that they satisfied the criterion, predicting proteins to be expressed; and (ST20A, 20C) constructing a mass-to-charge ratio database including mass-to-charge ratio lists, the mass-to-charge ratio lists being predicted for the respective sets of the genome data based on the proteins thus predicted.

This invention discloses a method for obtaining SSR molecular marker information based on high-throughput sequencing technology, belonging to the field of molecular biology. The method includes: selecting a reference genome in a genome database; collecting biological samples of the target species for high-throughput sequencing; obtaining raw sequencing data; analyzing the raw data to obtain a genome variation record file; performing a whole-genome scan of the reference genome; identifying and obtaining all SSR loci that meet the screening parameters; generating an analysis background file; performing joint analysis with the genome variation record files of each individual; extracting SSR loci information that have mutated relative to the reference genome in each individual; generating a cleaned SSR locus information file; constructing a whole-genome SSR molecular marker identification file; or performing joint analysis of multiple locus information files to generate population genetic data. This invention can provide efficient and highly adaptable core technical support for molecular genetic research and breeding applications in various species.

The present application relates to the breeding technology field of oat, and discloses a molecular marker, primer combination and application related to the neutral detergent fiber content of oat, wherein the molecular marker is a PAV marker, the PAV molecular marker is located on the 5D chromosome of the oat reference genome, the physical position is 5D:424169687, and 161 bp is deleted; the accession number of the national genome database of the oat reference genome is GWHGDJH00000000.1. The molecular marker, primer combination and application related to the neutral detergent fiber content of oat are used, the molecular marker and the detection method are used, the detection can be performed on the oat seedling stage, the breeding cycle is significantly shortened, the breeding efficiency is improved, and the breeding cost is reduced, meanwhile, the PCR primer combination designed based on the molecular marker has high specificity and high accuracy, can be used for the prediction and screening of the neutral detergent fiber content of the forage oat, and is used for the genetic breeding of the oat.

The invention discloses an analysis method of a malassezia generic genome, which comprises the following steps of: searching 'Malassezia' from a public genome database to obtain whole genome sequence data of the malassezia; calculating ANI values between every two genome sequence data, and constructing a phylogenetic tree according to a distance matrix of the ANI values; performing gene prediction on the data and translating the data into a protein coding gene sequence; performing generic genome analysis on the data, drawing a dilution curve or an accumulation curve of malassezia, and fitting the curve to obtain a function; and comparing and annotating the protein coding gene sequence and the public function database, and analyzing the functional difference between different genomes. The analysis method for the malassezia generic genome has the advantages of being high in universality, convenient and fast to operate and the like, the method is simple, convenient and reliable, high in accuracy and easy to understand, and the operation process is simple and convenient.

This invention discloses a method and system for identifying microbial communities, particularly relating to the field of microbiome technology. By employing a Hidden Markov Model database constructed based on multiple types of ribosomal RNA sequences for global searching, it replaces the massive whole-genome databases of existing technologies, reducing database size. Furthermore, this invention generates a hypervariable region sequence file containing complete quality information by targeting and extracting hypervariable regions from the identified ribosomal RNA sequences and then back-linking the extracted sequence data with the quality information from the original sequencing data. The sequence data contains sequence information for identification, enabling accurate identification and extraction of ribosomal RNA marker gene sequences from metagenomic or metatranscriptomical sequencing data. The original sequencing data can be used for traditional amplicon analysis workflows and also supports downstream in-depth analysis, achieving seamless integration with traditional amplicon analysis workflows.