36 results about "Genomic research" patented technology

The invention relates to the technical field of biology, in particular to a molecular marker for accurately positioning centromere of chromosome of Chinese trumpet creeper, and the sequence of the molecular marker is as shown in SEQ ID NO.1 and SEQ ID NO.2. The method comprises the following steps: specifically enriching a DNA (Deoxyribose Nucleic Acid) sequence combined with a centromere specific histone CENH3 through a chromatin co-immunoprecipitation technology (ChIP), and sequencing the DNA sequence; sequencing data are analyzed to obtain a centromere sequence of the vicia villosa, and two specific repetitive sequences of the centromere of the vicia villosa are obtained after identification and optimization. Primers are designed according to the sequences, PCR amplification is carried out, amplification product sequences are marked, fluorescence in situ hybridization verification is carried out by analyzing a cytogenetics technology, it is proved that the primers are specifically distributed in a centromere area of vicia villosa, and the centromere specificity of the primers is proved. The marker can be used for genetic identification and accurate positioning of the centromere in genome research, and can also be used for cytological identification of the centromere and karyotype research such as chromosome counting and morphological analysis through centromere signal observation.

The invention relates to a construction method and application of a plant intra-genus generic transcriptome, and the method is realized by the following steps: obtaining second and third generation transcriptome data of different species in a genus and performing quality control, comparing a reference genome by using software such as HISAT2 and the like, and screening effective transcripts through gffcomplex after StringTie splicing; transcripts and genes are classified based on the ORF length (mRNA is greater than or equal to 100 aa, small peptide transcripts are from 10 aa to 99 aa, and ncRNA is smaller than 10 aa); the method comprises the following steps: analyzing sequence conservative properties among species through coding genes and non-coding genes, and dividing the genes into core, optional and specific types; and finally integrating and constructing a genus-level generic transcriptome containing three types of transcriptomes. According to the invention, the system construction of the plant intra-genus cross-species pan transcriptome is realized for the first time, the conservative property and difference of protein coding genes, small peptides and non-coding RNA can be analyzed, and a new tool is provided for the research of plant functional genomes.

This invention discloses a method for efficient genetic transformation of rice that overcomes genotype dependence and a dedicated culture medium, relating to the field of biotechnology. The dedicated culture medium comprises KCl, KH₂PO₄, MgSO₄·7H₂O, CaCl₂·2H₂O, disodium ethylenediaminetetraacetate, FeSO₄·7H₂O, MnSO₄·H₂O, ZnSO₄·7H₂O, H₃BO₃, KI, CoCl₂·6H₂O, CuSO₄·5H₂O, Na₂MoO₄·2H₂O, glutamine, aspartic acid, arginine, glycine, cyclohexanehexyl alcohol, thiamine hydrochloride, pyridoxine hydrochloride, nicotinic acid, and a carbon source. Using this dedicated culture medium can increase the number of rice cells containing the NiR gene. 375 S 453 The genetic transformation efficiency of haplotype rice varieties is of great significance for overcoming the bottleneck of rice genotype dependence, promoting functional genomics research and molecular breeding.

The invention discloses an application of a gene GmSW6 in regulation and control of plant grain weight and quality. GWAS is developed by using genotype and hundred-grain weight phenotype data, haplotype analysis, gene expression profile data and homologous gene function annotation are combined, and the grain weight related gene GmSW6 is successfully cloned by virtue of research means of molecular biology and comparative genomics. The function of the gene GmSW6 in regulating and controlling the plant grain weight is disclosed for the first time by utilizing a CRISPR-Cas9 system, and the target of increasing the hundred-grain weight of the plant is possibly achieved by knocking out a coding sequence of the GmSW6 gene or silencing the coding gene or reducing the expression level of the coding gene. Meanwhile, by introducing the gene into a target plant or over-expressing the gene in the plant, the grain weight of the plant can be regulated and controlled, the grain weight of the plant can be reduced, but the per unit yield can be increased under the condition, an important gene resource is provided for plant molecular breeding, and a new choice is provided for high yield of the plant.

The application discloses a long-read data robust variant detection method and system based on data quality improvement, and belongs to the technical field of gene sequencing and biological information analysis. The method of the application is aimed at the characteristics of long-read data, and first, preprocessing is completed through sequence filtering and base correction, and a three-dimensional outlier feature system of sequencing support intensity, mapping quality reliability and strand-specific bias is constructed. Based on the median absolute deviation algorithm, the features are standardized and outlier scores are generated, a double-threshold dynamic optimization mechanism is constructed, and high-confidence data is screened. The variant candidate regions are identified through multi-tool joint comparison, the SNP and Indel are typed through a deep learning model, and the reliability of the results is ensured through triple cross-validation. The method does not need to manually set a fixed threshold, effectively suppresses interference factors, balances detection accuracy, robustness and scene universality, and provides high-quality variant data support for clinical diagnosis and genomics research.

The invention discloses a bombyx mori protein function prediction multi-modal fusion method based on a deep residual network, and the method comprises the steps: collecting the sequences and high-resolution three-dimensional structure data of bombyx mori proteins of different varieties and at different development stages from databases of bombyx mori genomes, protein crystal structures and the like by employing a data crawling and interface calling technology; and constructing a multi-modal data source. The sequence data are cleaned and coded in a one-hot mode, and the structural data are optimized and converted into a graph structure. Sequence and structure features are respectively extracted through a convolutional neural network and a GraphSAGE graph neural network, and the features are dynamically fused through an adaptive weight fusion strategy. And building a deep residual network training model, and realizing accurate prediction of the protein function category and confidence of the bombyx mori with unknown functions. According to the method, the precision and the high robustness of silkworm protein function prediction are improved through full-process technical optimization, and an efficient tool is provided for silkworm molecular breeding and functional genomics research.

The application discloses a chrysanthemum constitutive high-expression promoter and application thereof in gene editing. The nucleotide sequence of the promoter CmUbi is shown as SEQ ID NO. 4. Through double luciferase reporter experiments and stable genetic transformation experiments, it is proved that the expression activity of the CmUbi promoter in chrysanthemum protoplast and callus is significantly higher than that of commonly used CaMV 35S, AtRPS5a and corn ZmUbi promoters. A CRISPR / Cas9 gene editing vector is constructed by using the promoter, and a key gene of branch of hexaploid chrysanthemum is edited BRC1b , and a plurality of allele simultaneous mutation complete editing strains are successfully obtained, and the number of branches of the mutants is significantly increased. The endogenous high-activity promoter of the chrysanthemum provided by the application effectively solves the problems of low expression activity of an existing heterologous promoter in the chrysanthemum and poor gene editing efficiency of a polyploid, and provides an efficient and adaptive expression regulation element for chrysanthemum molecular breeding and functional genomics research.

The invention provides a method and system for gene expression quantitative trait locus analysis, and relates to the technical field of genomics, the method comprises the following steps: carrying out sample and locus level quality control on input genotype data, and generating a standardized genotype matrix; performing standardization processing and low expression gene filtering on the input gene expression data to generate a standardized expression quantity matrix; performing principal component analysis according to the standardized genotype matrix to obtain a group structure covariable; carrying out implicit factor analysis on the basis of the standardized expression quantity matrix to obtain a technical batch effect covariable; quantitative character site correlation analysis is carried out through a standardized genotype matrix, a standardized expression quantity matrix, a population structure covariable and a technical batch effect covariable. The method is suitable for functional genomics research, complex disease genetic mechanism analysis and precision medical related functional genetic variation mining scenes.

The invention relates to a device and a method for eluting, purifying and recovering oversized DNA (deoxyribonucleic acid) based on pulsed field gel electrophoresis, which are used for efficiently recovering complete DNA molecules from hundred kb level to Mb level. The device comprises an electrophoresis protection chamber with a polygonal container structure and a sample recovery chamber, the side edge of the protection chamber is provided with a semi-permeable membrane for current to pass through, and the recovery chamber is detachably placed in the center and comprises the semi-permeable membrane; the detachable and replaceable magnesium sheet is arranged in the protection chamber and is used for ionizing magnesium ions to promote DNA (Deoxyribose Nucleic Acid) compression; the method comprises the following steps: preparing a biological sample into an agarose gel block, cracking and cleaning the agarose gel block, placing the agarose gel block in a device, and adding a recovery protection solution containing PEG; under the condition of pulsed field gel electrophoresis, DNA migrates out of a gel block and is combined with magnesium ions to be compressed into spheres, and the spheres are collected in a recovery chamber after charges are neutralized. Compared with the prior art, the method provided by the invention overcomes the defects of low product purity and tedious steps of a traditional recovery method, realizes high-purity and high-efficiency integrated recovery, and is suitable for genomics research and biotechnology application.

Provided are nucleic acids and nucleic acid constructs, nucleic acid sets and nucleic acid set constructs, compositions, recombinant vectors, recombinant host cells and kits comprising transposases. Further specifically provided is a method for introducing an exogenous nucleic acid fragment into a host cell genome, a method for editing a host cell genome, and a method for obtaining a host cell containing an exogenous nucleic acid fragment in the genome. Further specifically provided are transposases, nucleic acids and nucleic acid constructs, nucleic acid sets and nucleic acid set constructs, compositions, recombinant vectors or recombinant host cells for introducing an exogenous nucleic acid fragment gene into a host cell genome or for preparing a drug or preparation for gene therapy, cell therapy, genomic research or stem cell induction and post-induction differentiation.

The invention relates to a method for rapidly carrying out BSA (Bovine Serum Albumin) gene localization by utilizing a space mutation mutant. The method comprises the following steps: firstly, carrying propagules such as seeds through an aerospace craft, and constructing a broad-spectrum mutant library by utilizing space environment mutagenesis; returning to the ground, culturing and screening M1-generation mutants with target excellent characters, and hybridizing / backcrossing with a wild type to construct a character segregation population; by adopting a group separation analysis (BSA) strategy, selecting phenotype polar differentiation individuals, and respectively mixing the phenotype polar differentiation individuals to form a high-value pool and a low-value pool; and finally, carrying out whole genome high-throughput sequencing on the double pools and the parents, rapidly locking a genome region linked with a target character by combining bioinformatics analysis such as SNP-index and the like, and verifying candidate genes through gene annotation, molecular marking and gene editing. According to the invention, the broad spectrum of space mutagenesis and the high efficiency of the BSA-seq technology are integrated, the period from mutation creation to gene identification is remarkably shortened, and an innovative technical scheme is provided for crop genetic improvement and functional genomics research.

The invention discloses a pig whole genome low-density 5K SNP (Single Nucleotide Polymorphism) chip. The chip contains 5311 SNP loci. The SNP marker on the chip is fixed by a microarray technology, and high-throughput and high-precision genetic typing is realized by using hybridization and fluorescence detection technologies. According to the pig whole genome low-density 5K SNP chip disclosed by the invention, a breeding value prediction model is established by combining genotype data and phenotype data obtained by the chip, so that the accuracy of genetic evaluation is remarkably improved, different breeding targets can be realized, a breeding strategy can be optimized, and the progress of pig breeding and genome research can be accelerated.

The present invention relates to a method for preparing a single cell multi-sample multi-body library and a use thereof. The present invention relates to a method whereby an epigenome and a transcriptome can be simultaneously analyzed at a single cell level, and the principle of regulating the epigenome and the transcriptome has been identified. Accordingly, the present invention makes it possible to reduce reagent costs by about 1 / 10 compared to the prior art and simultaneously analyze six or more samples, thus being economical and having the advantage of being able to contribute to high-tech genomic research. According to the present invention, six samples can be simultaneously analyzed, and ATAC as an epigenome and 5 prime RNA information as a transcript can be simultaneously collected and used to clearly identify the starting point of gene expression that immediately responds to epigenetic changes.

The invention discloses application of a kelp endogenous promoter in kelp breeding and cultivation and a method, and relates to the technical field of biology. The invention provides a kelp endogenous promoter. The sequence of the kelp endogenous promoter is selected from one of the following sequences: (1) an amino acid sequence as shown in any one of SEQ ID NO: 1-3; (2) a sequence obtained by substituting, deleting or adding one or more nucleotides to the sequence shown in any one of SEQ ID NO: 1 to SEQ ID NO: 3; and (3) a sequence having 80% homology with the sequence as shown in SEQ ID NO: 1-3. The promoter can drive gene specific expression or main expression in a kelp gametophyte, can realize effective expression of a GUS reporter gene in transgenic kelp, and promotes development of kelp genetic engineering and functional genomics research.

The invention belongs to the technical field of forest tree gene engineering, and particularly relates to a construction method of an agate red cherry seedling PDS gene virus-induced gene silencing (VIGS) system based on agrobacterium tumefaciens mediation. According to the method, a recombinant virus vector containing a PDS gene specific fragment as shown in SEQ ID NO.1 is constructed, the recombinant virus vector is introduced into an agate red cherry leaf tissue by utilizing an agrobacterium infection technology, and efficient silencing of a target gene is successfully realized. As a first VIGS technical platform established in the woody fruit tree agate red cherry, the system can visually verify the gene function by inducing the typical albino phenotype of the plant leaf of the agate red seedling, and breaks through the technical bottlenecks of long period and low efficiency of the traditional woody plant gene function research. The achievement fills the blank of a woody fruit tree VIGS technical system, provides a traceable research tool for analyzing a molecular mechanism formed by key traits of the agate red cherries, and has milestone significance for promoting functional genomics research of rosaceae fruit trees.

The application discloses a base recognition method based on semiconductor SERS technology and belongs to the technical field of biomedical detection. The specific method comprises the following steps: step one, synthesis of TiO2 nanoparticles; step two, preparation of a TiO2 / 4-MBA system; and step three, base recognition detection. The TiO2 / MBA system can be used for accurate and rapid DNA base recognition, and the developed TiO2 / MBA system is simple to prepare and has excellent base test performance, and has a high market application prospect. The application not only provides a novel base detection method, but also has high sensitivity and selectivity, can recognize and detect four bases and the non-covalent interaction between the four bases and 4-MBA in two pH environments, and has a simple and rapid operation process. The application not only provides a new method for base analysis, but also provides technical support for early diagnosis of DNA related diseases, genomics research and development of molecular sensors, and has a wide application prospect.

The invention belongs to the technical field of DNA extraction, and particularly relates to an efficient coral DNA extraction method. The invention provides a cell lysis solution, the cell lysis solution comprises PVP, sorbitol, sodium pyrosulfite and other substances, and the substances are specifically combined, so that mucoprotein and polysaccharide in a coral sample can be fully separated, and the DNA extraction quality is improved. On the basis, the invention also provides an efficient coral DNA extraction method, which not only improves the yield and quality of DNA extraction, but also shortens the experimental time. Compared with the prior art, the technical scheme provided by the invention has the advantages of low cost, short process and large-scale application, provides a standardized solution for coral genetics and genomics research, and has important scientific research value for coral biological research and protection.

The invention relates to the field of bioengineering technology and biomedicine, and discloses a nucleic acid modified protein and application thereof. The TdpC protein disclosed by the invention not only shows efficient catalytic activity in DNA phosphorus-sulfur acylation modification and specific adenylation of a DNA phosphate skeleton, but also can stably work in a high-temperature, strong-acidity or high-sulfur-enrichment extreme environment, so that the TdpC protein has wide application potential in the extreme environment. Experimental results fully prove that the method has high efficiency and applicability in the fields related to epigenetics research, genomics research and biological medicine.

The present invention concerns DNA motifs for identifying, isolating and assembling the nucleotide sequence of a chromosome centromere. In particular, these motifs are designed for the identification, isolation, and assembly of the nucleotide sequence of a chromosome's centromere. Additionally, the invention encompasses methods for validating these sequences within any human genome. The primary application of these DNA motifs and methods lies in their ability to facilitate the detailed characterization and analysis of centromeres and chromosomes. This innovation stands to make significant contributions to the fields of genomic research and diagnostic genetics, offering a novel approach to centromere study and genome assembly.

The invention discloses an application of a gene GmSW19 in regulation and control of plant grain weight and quality. GWAS is developed by using genotype and hundred-grain weight phenotype data, haplotype analysis, gene expression profile data and homologous gene function annotation are combined, and the grain weight related gene GmSW19 is successfully cloned by virtue of research means of molecular biology and comparative genomics. The function of the gene GmSW19 in regulating and controlling the grain weight and quality of the plant is disclosed for the first time through a CRISPR-Cas9 system, the target of increasing the hundred-grain weight, fat and per unit yield of the plant is possibly achieved by knocking out a coding sequence of the gene GmSW19 or silencing the coding gene of the gene GmSW19 or reducing the expression level of the gene GmSW19, an important gene resource is provided for molecular breeding of the plant, and the application of the gene GmSW19 in regulating and controlling the grain weight and quality of the plant is also facilitated. And a new choice is provided for high yield of plants.

Nucleic acids and nucleic acid constructs encoding transposase, nucleic acid groups and nucleic acid group constructs, compositions, recombinant vectors, recombinant host cells, and kits comprising transposase are provided. Further specifically provided are a method for introducing an exogenous nucleic acid fragment into the genome of a host cell, a method for editing the genome of a host cell, and a method for obtaining a host cell containing an exogenous nucleic acid fragment in the genome. Further specifically provided are transposase, nucleic acids and nucleic acid constructs, nucleic acid groups and nucleic acid group constructs, compositions, recombinant vectors, or recombinant host cells for introducing exogenous nucleic acid fragment genes into a host cell genome or for the preparation of transposase for gene therapy, cell therapy, cancer therapy, cancer therapy, cancer therapy, cancer therapy, cancer therapy, cancer therapy, cancer therapy, cancer therapy, etc. The invention relates to a drug or preparation for genome research or stem cell induction and induced post-differentiation.

The present invention belongs to the fields of molecular biology and biomedicine, and particularly relates to a highly active transposase and its applications. The amino acid sequence of the highly active transposase is shown as SEQ ID NO:2, and the coding nucleotide sequence of this amino acid sequence is shown as SEQ ID NO:3. The highly active transposase based on this amino acid sequence can significantly improve the gene transfer activity of transposons when used in a transposition system. The highly active transposase and the nucleotide sequence encoding this highly active enzyme can be used to construct a gene transfer system, and to prepare or serve as drugs, preparations or tools for genomic research, gene therapy, cell therapy, or the induction and / or differentiation of pluripotent stem cells, etc.

The invention belongs to the technical field of gene chips, and discloses a pine whole genome 50K liquid chip and application thereof. The liquid phase chip comprises a pine 50K site probe mixed solution and a hybridization capture reagent, and the pine tree 50K chip comprises information of 49693 sites. According to the present invention, the liquid phase chip design gives consideration to species specificity and transferability, is not only suitable for the target species, but also can be expanded to other related pine tree class groups, fills the blank in the tropical and subtropical pine tree genetic typing in the prior art, and provides the efficient and accurate tool for pine tree genetic resource protection, molecular breeding and genomics research; the method solves the problem of low conversion rate of pine tree molecular assisted breeding and whole genome selective breeding products, overcomes the defect of high application cost of pine trees in scientific research and practical application, and provides technical support for pine tree germplasm resource utilization and molecular breeding research.

The present invention relates to a method for constructing a pan-transcriptome within a plant genus and its application. The method is achieved by the following steps: obtaining and quality-controlling second- and third-generation transcriptome data from different species within the genus, aligning to a reference genome using software such as HISAT2, and screening for valid transcripts using gffcompare after StringTie splicing; classifying transcripts and genes based on ORF length (≥100 aa for mRNA, 10-99 aa for small peptide transcripts, and <10 aa for ncRNA); analyzing interspecies sequence conservation using coding and non-coding genes, and classifying genes into core, optional, and specific types; and finally integrating and constructing a genus-level pan-transcriptome encompassing these three transcriptome types. This method, for the first time, systematically constructs a cross-species pan-transcriptome within a plant genus, enabling analysis of the conservation and diversity of protein-coding genes, small peptides, and non-coding RNAs, providing a new tool for plant functional genomics research.

Nucleic acids and nucleic acid constructs encoding transposase, nucleic acid groups and nucleic acid group constructs, compositions, recombinant vectors, recombinant host cells, and kits comprising transposase are provided. Further specifically provided are a method for introducing an exogenous nucleic acid fragment into the genome of a host cell, a method for editing the genome of a host cell, and a method for obtaining a host cell containing an exogenous nucleic acid fragment in the genome. Further specifically provided are transposase, nucleic acids and nucleic acid constructs, nucleic acid groups and nucleic acid group constructs, compositions, recombinant vectors, or recombinant host cells for introducing exogenous nucleic acid fragment genes into a host cell genome or for the preparation of transposase for gene therapy, cell therapy, cancer therapy, cancer therapy, cancer therapy, cancer therapy, cancer therapy, cancer therapy, cancer therapy, cancer therapy, etc. The invention relates to a drug or preparation for genome research or stem cell induction and induced post-differentiation.

Provided are nucleic acids and nucleic acid constructs encoding transposases, nucleic acid panels and nucleic acid panel constructs, compositions, recombinant vectors, recombinant host cells, and kits comprising transposases. Further specifically provided are a method for introducing an exogenous nucleic acid fragment into a host cell genome, a method for editing a host cell genome, and a method for obtaining a host cell containing an exogenous nucleic acid fragment in a genome. Further specifically provided are transposases, nucleic acids and nucleic acid constructs, nucleic acid panels and nucleic acid panel constructs, compositions, recombinant vectors, or recombinant host cells for use in introducing an exogenous nucleic acid fragment gene into a host cell genome or in the preparation of a medicament or a preparation for gene therapy, cell therapy, genomic research, or stem cell induction and post-induction differentiation.

The invention belongs to the field of bioinformatics and genomics, and discloses a method for rapidly and accurately predicting an intron splicing site of a target species. The method comprises the following steps: 1) obtaining a genome sequence and transcriptome sequencing data of a target species; 2) screening annotation genes and constructing a training set and a test set; 3) performing learning training on splicing site information by adopting a deep learning model architecture combining a convolutional neural network, a bidirectional long-short-term memory network and a self-attention structure; 4) performing bit-by-bit prediction on the input gene sequence by using the model obtained by training; and 5) judging the position of the splicing site according to the prediction score, and labeling and re-evaluating the abnormal or low-credibility splicing site. The calculation model provided by the invention can learn key sequence features at splicing sites, and can be extended to various species through transfer learning to realize high-precision introne boundary prediction. According to the method, the gene annotation efficiency can be remarkably improved, splicing abnormity caused by mutation can be accurately recognized, and the method has important application value for genomics research and gene function analysis and regulation.

The invention discloses a method for realizing wheat whole genome large-scale mutation and germplasm creation by editing repetitive sequences. CRISPR / Cas9 target sites with the copy number higher than 20,000 in wheat genomes are screened, tandem repeat sequences and dispersed repeat sequences are edited in a targeted mode, and heritable large-scale variation, chromosome structure variation and agronomic character variation of the whole genome scale are induced and generated in progeny plants. By editing repetitive sequences, large-scale mutation with chromosome and subgenome specificity can be realized, the created mutant library not only provides heritable variation mutant types different from those of traditional physical and chemical mutagenesis methods, but also generates materials such as chromosome aneuploidy (such as monosome, tetrasome and whole-arm deletion) and the like. And a unique genetic resource is provided for wheat functional genomics research and germplasm improvement.

Provided is a separated transposase and its uses. Also provided are a nucleic acid encoding the transposase, a nucleic acid construct, a nucleic acid group, a nucleic acid group construct, and a composition, a recombinant vector, a recombinant host cell, and a kit containing the transposase. Also provided are a method for introducing an exogenous nucleic acid fragment into the genome of a host cell, a method for editing the genome of a host cell, and a method for obtaining a host cell containing an exogenous nucleic acid fragment in the genome. Also provided are the uses of the transposase, the nucleic acid, the nucleic acid construct, the nucleic acid group, the nucleic acid group construct, the composition, the recombinant vector or the recombinant host cell for introducing a foreign nucleic acid fragment gene into the genome of a host cell or for preparing a drug or a preparation for gene therapy, cell therapy, genomic research, or stem cell induction and post-induction differentiation.