29 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 discloses a disease-resistant application of an arabidopsis thaliana AtRTP7 gene. The invention relates to application of inhibiting the expression of an arabidopsis thaliana AtRTP7 gene in enhancing the resistance of plants to pathogenic bacteria. The number of the arabidopsis thaliana AtRTP7 gene in an arabidopsis thaliana genome database is AT4G02820. The invention focuses on the S gene AtRTP7 of arabidopsis thaliana, the growth phenotype of the mutant is observed, and inoculation experiment is carried out on the mutant by using sclerotinia sclerotiorum and botrytis cinerea. The result shows that the growth of the AtRTP7 mutant is not obviously influenced, the AtRTP7 mutant shows obvious resistance to sclerotinia sclerotiorum and botrytis cinerea, and the scab area and the pathogenic bacterium biomass of the AtRTP7 mutant are obviously lower than those of a wild plant. Therefore, the S gene AtRTP7 of arabidopsis thaliana can be used as a potential gene resource for green prevention and control of sclerotinia rot of colza.

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.

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.

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 belongs to the technical field of molecular biology, and particularly relates to a molecular marker for identifying genetic sex of different populations of micropterus salmoides as well as a primer pair and application of the molecular marker. The invention provides a molecular marker for identifying genetic sex of different populations of micropterus salmoides. The molecular marker is located between the 35054224th site and the 35054476th site of a micropterus salmoides genome database ASM2243578v1 genetic sex number 15 linkage group. The used primer pair comprises M-F and M-R. PCR amplification is carried out through the primer pair, if two bands of 307 bp and 253 bp are obtained through amplification, the male is determined, and if only the band of 253 bp is determined, the female is determined. According to the method, the sex of the largemouth bass can be accurately identified, a result can be obtained on the same day, and the repeatability is high. The method lays a technical foundation for sex control breeding and unisexual breeding of the micropterus salmoides.

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 relates to the technical field of bioinformatics, in particular to a pathogenic microorganism genome, a construction method, a computer system and application. According to the method, a genome data quality control strategy in the pathogenic microorganism genome database creation process is innovated, ANI and AF double indexes are creatively adopted for classification error recognition, contig pollution sequence recognition and k-mer short sequence pollution recognition are combined for sequence pollution recognition and processing on genome data, the number of genomes is reserved to the maximum, and the number of the genomes is reduced to the maximum. According to the method, contig level sequence errors are accurately recognized, strain specific sequences are prevented from being mistakenly deleted, the diversity of species genomes is guaranteed, and the constructed database can improve the identification accuracy / sensitivity of pathogen infected species.

The invention relates to the technical field of bioinformatics, in particular to a construction method of a dehalogenation microorganism functional genome database and an analysis method of dehalogenation microorganisms. The construction method comprises the following steps: obtaining a dehalogenation reaction related gene; based on a Uniprot protein database, obtaining a seed sequence and a homologous sequence of a family to which a dehalogenation reaction related gene belongs to obtain a core database; comparing the core database with a homologous protein database, and combining the sequence of the dehalogenation functional gene family obtained by comparison with the core database to obtain a preliminary database; and comparing the preliminary database to a Refseq database of microorganisms in NCBI, and carrying out classification, homologous sequence merging and redundancy elimination to obtain a complete database. The accurate dehalogenation function gene database is constructed based on the analysis and search results of a plurality of databases, can be used for conveniently and accurately analyzing the dehalogenation microorganism function community in the environment, and has important application value.

The application discloses application of a rice fertility gene MS2. The application finds a gene MS2 for regulating rice fertility in a rice genome database, the gene is highly expressed during anther development period of rice, nucleotide sequences of the gene are shown in SEQ ID NO. 1, and the amino acid sequences are shown in SEQ ID NO. 2. Research shows that the MS2 gene is related to rice fertility, and influences rice pollen fertility, and knocking out the MS2 gene in wild type rice can make the rice pollen fertility significantly decrease, and the MS2 gene can be applied to creation of a rice sterile line and preparation of hybrid seeds. Meanwhile, the male sterile line generated by mutation of the MS2 gene is not influenced by environmental conditions such as illumination and temperature, the fertility of the male sterile line is stable, a new gene resource is provided for construction of a rice hybrid breeding system, and germplasm resources of the male sterile line are also expanded.

The invention belongs to the field of gene identification, and particularly relates to a method for identifying an invasive plant in a soil environment DNA sample by using chloroplast genome data, which comprises the following steps: constructing an invasive plant chloroplast whole-genome database; collecting samples at a plurality of sample points; eDNA in the sample is extracted; carrying out PCR (Polymerase Chain Reaction) amplification on the extracted eDNA to obtain an amplicon product; sequencing the amplicon product by using a high-throughput sequencing technology to obtain high-throughput data; comparing the intrusive plant chloroplast whole-genome database with the high-throughput data to obtain the species of the intrusive plant species; according to the method, only the extracted eDNA is subjected to chloroplast gene PCR amplification, and exfoliates of animals and microorganisms are screened out, so that the DNA data volume is simplified, and the analysis of invasive plant species in a region can be accurately and comprehensively completed.

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 a database cleaning method and device, computer equipment and a storage medium. The method comprises the steps that a to-be-cleaned database is obtained, the to-be-cleaned database comprises whole genome sequences of different target species, the whole genome sequences of all the target species are preprocessed, a short sequence fragment set of all the target species is obtained, preprocessing at least comprises splitting and duplicate removal, and a short sequence fragment set of all the target species is obtained; the short sequence fragment set of each target species is compared with a preset gene sequence database of different dimensions to obtain a signal-to-signal comparison result, the gene sequence database at least comprises a target species whole genome database, and a target species whole genome database is obtained based on the signal-to-signal comparison result. And screening out polluted short sequence fragments from the short sequence fragment set of each target species, and carrying out signal generation modification on the whole genome sequence corresponding to the polluted short sequence fragments to obtain a cleaned database. By adopting the method, the reliability of the database can be improved.

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.

Embodiments are directed to systems and methods for pathogen detection using next-generation sequencing (NGS) analysis of a sample. Embodiments may apply alignment algorithms (e.g., SNAP and / or RAPSearch alignment algorithms) to align individual sequence reads from a sample in a next-generation sequencing (NGS) dataset against reference genome entries in a classified reference genome database. Embodiments of the present invention may include classifying, filtering, and displaying results to a clinician that can then quickly and easily obtain the results of the sequencing to identify a pathogen or other genetic material in a sample that is being tested. A negative sample and a corresponding database can be used to remove contaminants from a list of candidate pathogens. Thus, embodiments are directed to a system that is configured to filter the results of a sequencing alignment and classify a sample quickly.

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.

The present invention belongs to the field of biotechnology, and specifically relates to a method for establishing a mitochondrial DNA gene library and a method for obtaining a mitochondrial genome sequence. The method for establishing the library is as follows: (1) after hybridization of the total DNA of the sample with an RNA probe, the target sequence is captured; (2) the target sequence is collected and amplified to obtain the amplified mitochondrial DNA. The amplified DNA is fragmented, blunt-end repaired, connected to a sequencing adapter, and indexed by PCR to construct a library. The obtained gene library is sequenced, and the sequencing results are assembled. The scheme of the present invention enriches the original long-fragment mitochondrial DNA before constructing the sequencing library, so that more mitochondrial DNA data can be obtained, thereby improving the enrichment efficiency, increasing the proportion and coverage of the mitochondrial genome data, and achieving complete assembly; at the same time, the amount of data required for assembly is reduced, and the sequencing cost is greatly reduced. The present invention does not require a reference genome of the corresponding species, and can relatively quickly and economically obtain the complete mitochondrial genome of various vertebrates, providing a feasible technical route for establishing a vertebrate environmental DNA mitochondrial genome database.

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 invention relates to the technical field of genome database construction, and in particular to a method for constructing a pathogenic microorganism genome database. The method comprises the following steps: performing pathogenic characteristic point analysis on the pathogenic microorganism genome sequence to obtain pathogenic characteristic point data; performing physiological and biochemical characteristic analysis on the pathogenic microorganism genome sequence based on the pathogenic characteristic point data, and performing genome evolution relationship simulation, and then performing pre-relationship linkage identification to obtain pre-relationship linkage data; performing relationship nesting structure analysis on the pre-relationship linkage data, and constructing a relationship coding index to obtain a linkage relationship coding index; performing dynamic search condition matching on the linkage relationship coding index, and constructing a genome database to obtain a pathogenic microorganism genome database. The present invention improves the genome database construction technology by improving the genome database construction technology.

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.