56 results about "Pan-genome" patented technology

The invention belongs to the technical field of gene identification, and discloses a method for integrating multi-omics data to enhance genome prediction and candidate gene identification, candidate gene identification is verified through multi-layer evidence integration, and the verification comprises priority ordering based on gene contribution scores, function enrichment analysis, generic genome network verification and CRISPR / Cas9 experimental verification. Evaluation on a corn population (n = 174) containing complete genomics, transcriptomics, translational omics and proteomics maps shows that the framework is remarkably improved in grain character prediction and is improved by 2.9-12.3% compared with a genome selection baseline, and meanwhile candidate genes verified by experiments are recognized. The invention further verifies the universality of the framework to five traits on an arabidopsis thaliana population, and provides an open source software platform to promote the practical application of the framework in a breeding plan.

This invention provides a primer design method for multiplex PCR targeted sequencing technology. This method combines multiple indicators to carefully screen high-quality species genomes to design primers with high specificity and broad genome coverage. This method effectively optimizes the dimer formation of the primer system, improving the specificity and efficiency of detection. While ensuring high specificity, this technology significantly improves the performance of the multiplex primer system, optimizes the common dimer problem, and ensures the high efficiency of multiple pathogen detection.

The invention discloses a compression and decompression method based on generic genome expression, and relates to the technical field of compression and decompression of DNA next-generation sequencing data, in particular to the compression and decompression method based on generic genome expression. The method aims at solving the problems that in the prior art, the capacity of processing population genetic diversity is insufficient, original sequencing quality information cannot be effectively restored during decompression, and memory occupation is too high during large-scale data processing. Obtaining a to-be-compressed sequencing sequence data file, a reference genome sequence and a thousand-person genome variation sample; obtaining a haplotype list, a variation list and a haplotype offset list corresponding to each window block; storing the window number, the haplotype number, the haplotype offset, the head and tail unmatched sequences, the current sequence name and the quality score character string into a single compression block; carrying out binding storage; completing the compression processing of the mass fraction; and obtaining each to-be-compressed sequencing sequence based on the result of the compressed part.

The invention provides application of GW5 gene promoter methylation based on a multi-omics gene mining technology in regulation and control of rice grain length, and relates to the technical field of biology. On the basis of a generic genome micro-core germplasm population, multi-dimensional omics data such as a genome and an epigenome are integrated, a rice epigenome map is constructed, a stable methylation polymorphism marker in the map is utilized, a rice grain width phenotype is combined to carry out multi-omics association analysis, a new epigenetic allele of the GW5 gene is successfully mined, and the GW5 gene is successfully identified. It is found that the upstream promoter region of the GW5 gene has two epigenetic states of hypermethylation and hypomethylation in different rice germplasm backgrounds, and after demethylation editing is carried out on the region, the phenotype that the grain length is remarkably increased is shown. Therefore, detection of the rice grain length character can be realized according to the promoter methylation level of the GW5 gene, and regulation and control of the rice grain length character can be realized by regulating and controlling the promoter methylation level of the GW5 gene.

The present application relates to the technical field of gene sequence alignment, in particular to a pan-genome long read alignment method based on weighted syncmer; the method of the present application firstly processes the segment of the reference pan-genome graph based on the weighted syncmer sampling of frequency division weight reduction, filters high-frequency redundant k-mers, retains high-specificity k-mers, then constructs a hash index to realize the rapid matching of the k-mers of the query sequence, and generates a candidate anchor point array, which greatly reduces the false matching and improves the alignment efficiency; then, based on the topological information of the pan-genome graph, the best linear chain is selected by backtracking calculation and further expanded into the best graph chain, and the hierarchical screening strategy reduces the search complexity of the complex graph structure; finally, the candidate pan-genome graph chain set is integrated to output the alignment result, which guarantees the high precision and integrity of the result, and realizes the efficient and accurate alignment of the complex topological structure pan-genome graph.

The application discloses a specific SNP site primer combination for identifying Taihe black-bone chicken varieties and application thereof. A chicken pan-genome containing a chicken reference genome GRCg7b and 2.49 Gb pan-sequence is taken as reference, WGS data of Taihe black-bone chicken and related chicken varieties is analyzed and screened to obtain two specific SNP sites, namely novel_th1 (G / T, dominant allele G) and novel_th2 (C / T, dominant allele C), wherein the T allele is medium to high frequency in most non-Taihe black-bone chicken varieties / strains. A FAM / VIC double-labeled TaqMan probe and a matching primer are designed based on the two sites to construct a real-time fluorescent quantitative PCR detection kit for joint typing of the two sites, and an amplification system and a Ct value judgment standard are established, so that 96 varieties / strains such as Taihe black-bone chicken, Zhushi chicken, other black-bone chicken, local chicken, white-feathered broiler and egg chicken can be quickly and accurately identified. The method has the advantages of high specificity, high sensitivity, simple operation and low cost, and is suitable for identification of authenticity of Taihe black-bone chicken and products thereof, purity monitoring and molecular-assisted breeding.

The invention discloses a sequencing data assembly method based on a reference genome, and belongs to the technical field of biological information. According to the method, the problems that the error rate of an existing assembling method is high and the integrity of an obtained assembling result is insufficient under the condition of ultra-low coverage are solved. According to the method, two comparison methods of a read segment and a linear reference genome and a read segment and a generic genome graph are adopted, a comparison tag graph is constructed on the basis of comparison results, then chromosome classification results of nodes in the comparison tag graph are further updated on the basis of bidirectional search and translocation variation detection, and then chromosome classification results of all the read segments are obtained. And finally, according to the chromosome classification result of each read, clustering each read into different chromosome sub-boxes, assembling the read in each chromosome sub-box, and combining the assembling results in each chromosome sub-box to generate a final genome assembling result. The method can be applied to sequencing data assembly.

This invention discloses a Dickeya solani This invention relates to specific targets for bacteria, their development methods, and applications. The specific targets possess DNA sequences as shown in SEQ ID No. 1. Based on comparative genomics, this invention utilizes the PGCGAP platform to call annotation and pan-genomics modules to mine specific target sites, overcoming [various challenges]. Dickeya The limitation that 16S and other common sequences of similar species are difficult to distinguish, establish D.solani This highly specific detection method can detect samples with a minimum copy count of 100, improving amplification efficiency and achieving higher detection rates, thus meeting the requirements for detecting low-copy templates. Furthermore, because the detection system utilizes the specificity of gene-editing probes, it exhibits high specificity.

The invention discloses a structural variation recognition method and system based on a generic genome map. The generic genome map is expanded / enhanced by using third-generation sequencing data; receiving input sequencing data, comparing the sequencing data with the expanded / enhanced generic genome map to obtain a map reference comparison result, identifying structural variation in the sequencing data based on the map reference comparison result, and generating a candidate structural variation set; and performing credibility evaluation and classification on the candidate structure variation set by adopting a pre-trained deep learning model to obtain a filtered high-credibility structure variation set. According to the method, on the basis of utilizing a standard generic genome map, high-quality three-generation sequencing data owned by a user is introduced to dynamically construct or expand the map, so that a reference structure can cover more unknown or individual specific structure variations, the sensitivity and the accuracy of structure variation recognition are improved, and the application prospect is wide. And the capturing capability on complex and individual specific variation is enhanced.

The invention discloses a hybrid calculation method for generic genome assembly, which is characterized in that based on a hybrid calculation framework guided by de novo assembly and a reference genome, the reference genome depth is integrated into the whole process of generic genome assembly, and the generic genome assembly is obtained by utilizing telomeres of a sibling and / or same species to telomere reference genome and 10-20kbHiFi read length. A high quality replacement long sequence is generated to simulate and / or replace up to millions of bp ONT reads, achieving continuous high precision generic genome assembly with low computational power consumption. According to the invention, the developed hybrid computing framework and algorithm tool are combined with de novo assembly and a hybrid computing tool based on a reference assembly method, so that the existing reference genome from the same or related species can be efficiently utilized, and a high-quality substitutive long sequence can be generated by combining PacBio HiFi read length; the sequences and de novo assembly results are integrated to improve the assembly quality of a group scale data set, and reliable gene information resources are provided for research and application of generic genomes.

The application discloses a primer, a probe composition for nontuberculous mycobacteria typing and application thereof, and provides a PCR primer and a probe for rapid detection and typing of 13 common NTM in clinic based on genome big data for carrying out pan-genomics analysis, and the specific genes of the common NTM in clinic are screened by using a pan-genomics method, and then typing primers and probes are designed based on the genes, so that the problems of insufficient accuracy and specificity in NTM typing are solved; the various NTM specific sequences screened guarantee the accuracy and specificity; the high sensitivity of the PCR method and the specificity of the sequences guarantee that various interference substances in the clinical samples can be avoided, and the clinical samples can be directly analyzed; the PCR detection is low in cost and low in equipment requirement, and can be carried out in primary hospitals, thereby providing an efficient and economical solution for the precise diagnosis of nontuberculous mycobacteria, the control of disease prevalence and the large-scale disease screening.

This invention discloses an algorithm, system, device, and medium for detecting structural variations based on third-generation sequencing data and a pan-genome. The detection algorithm includes: detecting SNARL structures in the pan-genome map; extracting reads corresponding to each SNARL path from the GAM alignment file; calculating the average coverage of all edges in each SNARL path and the number of edges with zero coverage; statistically analyzing the possible paths, path directions, reads aligned to the path, and path coverage information contained in each SNARL path; selecting the optimal path and the second path based on the read information and path coverage information; and comparing the optimized optimal path and the second path with the reference path to obtain variation information. This invention integrates the read information corresponding to the path, the base coverage information of the path, and the edge coverage information of the path as the basis for selecting potential variation paths, thus improving the accuracy of third-generation sequencing data detection.

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.

This invention discloses novel specific molecular targets for *Bacteroides fragilis* and its BFS17, along with a rapid detection method. The molecular target nucleotide sequence of *Bacteroides fragilis* is shown in SEQ ID NO.1, and the molecular target nucleotide sequence of *Bacteroides fragilis* BFS17 is shown in SEQ ID NO.2. This invention uses a pan-genomic approach to obtain the specific core genes of *Bacteroides fragilis* and the probiotic strain *Bacteroides fragilis* BFS17, and designs characteristic primers that can sensitively detect *Bacteroides fragilis* and the probiotic strain *Bacteroides fragilis* BFS17. Furthermore, this method can rapidly and easily distinguish *Bacteroides fragilis*, the probiotic strain *Bacteroides fragilis* BFS17, and other microbial strains. This invention has the advantages of being simple and rapid to operate, highly specific, quantifiable, and inexpensive.

The invention relates to the technical field of new strains for degrading cellulose, in particular to a pseudoxanthomonas strain JC1303 and application thereof. Through whole genome sequencing and function annotation, it is systematically revealed for the first time that the strain carries a complete cellulose degrading enzyme system including incision beta-1, 4-glucanase, cellulase and beta-glucosidase, has a plurality of central metabolic pathways supporting efficient degradation and utilization of cellulose, and can be used for degrading cellulose. And specific gene resources are determined through generic genome analysis. The strain has the remarkable technical effects that the strain shows higher cellulase activity after being cultured for 5 days, and cellulose materials such as agricultural wastes and the like can be stably and efficiently degraded in a salt-containing environment by virtue of the unique genetic background and marine source characteristics of the strain.

The present invention belongs to the field of crop molecular breeding and functional research, and specifically relates to a Triticeae D-genome pan-gene exon capture sequencing chip and its design method. The present invention integrates the Aegilops tauschii genome and the wheat D-subgenome, extracts gene coding region sequences by an iterative method, and uses Kmer classification and counting for grouped amplification to obtain Aegilops tauschii pan-genome capture probes, which are the Triticeae D-genome pan-gene exon capture sequencing chips. The present invention adopts the design of pan-genome probes, which can be better applied to the detection of different D-subgenome-derived materials and can cover the genetic variations of different Aegilops tauschii. The exon capture sequencing chip of the present invention can not only achieve high coverage of the exon regions of the whole genome derived from Aegilops tauschii, but also accurately identify exogenous fragments in introgression lines or synthetic materials derived from Aegilops tauschii, and greatly reduces the sequencing and analysis costs.

Provided herein are methods for assessing ageing process, lifespan, life expectancy, biological age and the rate of aging by determining pangenome gene alterations. Also provided are methods for increasing lifespan and / or inhibiting aging.

The invention discloses a gene for controlling existence of wheat tannin and a molecular marker and application thereof. The gene is positioned in a region of 701.8 to 704.3 Mb of a chromosome 3A of a reference genome of wheat in spring in China. According to a generic genome and gene expression result (RNA-seq), a candidate gene is locked and named as TaMYB10-3A, three primer markers are designed on the gene to form a primer combination, and the primer combination can be used for detecting whether wheat contains tannin or not, so that a new means is provided for identifying wheat tannin, and the application prospect is broad. The molecular marker primer combination can be applied to wheat tannin breeding practice in a simple, convenient, rapid and high-throughput mode, the wheat tannin character improvement process is accelerated, and the breeding accuracy and selection efficiency are improved.

The application provides a multi-omics gene mining technology-based method for detecting and regulating rice grain length GW5 The application relates to the technical field of biology, and relates to application of gene promoter methylation in regulation of rice grain length. The application is based on a pan-genome micro-core germplasm population, integrates multi-dimensional omics data such as genomes and epigenomes, constructs an epigenome atlas of rice, and uses stable methylation polymorphic markers in the atlas to combine with a rice grain width phenotype to perform multi-omics correlation analysis, successfully mines a new epiallele of a gene, discovers GW5 a new epiallele of a gene, and discovers GW5 that a high-methylation and low-methylation epigenetic state exists in an upstream promoter region of the gene in different rice germplasm backgrounds, and that after demethylation editing is performed on the region, a phenotype of significantly increased grain length is exhibited. Therefore, according to GW5 a methylation level of a promoter of the gene, detection of a rice grain length trait can be realized, and by regulating GW5 a methylation level of a promoter of the gene, regulation of a rice grain length trait can be realized.

The invention discloses a structure variation analysis-oriented genome data visualization system and method, and the system comprises a data input module which is in data connection with a coordinate conversion module, an index module and a graph-comparison extraction module, the coordinate conversion module, the index module and the graph-comparison extraction module are in data connection with the function annotation visualization module, the coverage analysis module and the reading visualization module respectively, and the function annotation visualization module, the coverage analysis module and the reading visualization module jointly generate a group structure variation frequency visualization module. According to the method, the comparison result of the reading segment on the graphical generic genome is visualized in an interactive mode, and the limitation that a traditional linear genome browser cannot present graph structure comparison information is overcome; through the coordinate conversion module, the graphical generic genome is effectively connected with the traditional linear reference genome, and the system can automatically map a comparison result to the graphical genome and synchronously display corresponding function annotations, so that the operation intuition and compatibility are remarkably improved.

The invention discloses a real-time fluorescent quantitative PCR primer and probe design method based on generic genomics, and belongs to the field of bioinformatics and molecular biology. According to the method, an orthofinder homologous genome analysis function is flexibly applied, it is ensured that the screened target gene meets conservative and specific requirements at the same time, a high-quality target sequence is ensured, the risk that later primer and probe verification is unqualified is reduced, and primer development time is greatly shortened. Meanwhile, a program is specially designed to screen a multi-copy target gene, so that the primer designed by the invention has higher sensitivity. The technical scheme provided by the invention is wide in application range and can be applied to development of specific primers of various microorganisms such as bacteria, fungi and nematodes.

This invention relates to the field of species breeding technology, specifically to a genomic selection prediction model based on graph pan-genomics and deep learning, and its application. The selection prediction model provided by this invention obtains multi-type genetic variation information such as SNPs, INDELs, and SVs based on graph pan-genomics, constructs a target marker set by combining public GWAS data and known functional loci, and utilizes a deep learning framework to achieve the collaborative construction of multi-type variation information. This model can improve the accuracy of predicting rice agronomic traits under multiple environmental conditions, providing technical support for rice molecular design breeding and precision selection. This selection prediction model can solve the problems of insufficient utilization of complex genetic variations and limited predictive ability of complex agronomic traits under multiple environmental conditions in existing genomic selection methods, thereby improving the efficiency of crop molecular breeding and reducing breeding costs.

This application discloses an improved method for whole-genome selection of maize hybrids, belonging to the field of genetic breeding technology. To address the shortcomings of existing technologies, this application provides a computer device to implement the following steps: (A1) Construction of a maize pan-genome: screening core planting and breeding backbone parents, constructing libraries and sequencing, loading reference genomes and genome annotations, and iteratively assembling to construct a pan-genome to obtain a sequence / gene-based pan-genome; (A2) Construction of a maize haplotype library: setting chromosomal reference segments / genes and statistically analyzing the haplotypes of each reference segment to obtain a whole-genome haplotype library; (A3) Haplotype genotyping of the training population: obtaining haplotype data of the training population; (A4) Whole-genome prediction: training the training model data through evaluation dimensions such as haplotype effect value, parental combining ability, and / or prediction accuracy.

A method for detecting de novo structural variations includes: a genome analysis apparatus extracting k-mer data of a target individual from genome sequencing data of a target individual. The method may include: extracting k-mer data of a target individual from genome sequencing data, comparing a reference-genome k-mer database—including parents' and pan-genome k-mers—with the target individual's k-mers to select target-individual-specific k-mers, determining target-individual-specific reads, identifying candidate de novo structural-variation regions, predicting discordant read pairs using a machine-learning model, selecting final de novo regions based on an estimated variant allele frequency, and generating a clinical report.

The invention belongs to the technical field of gene sequence comparison, and particularly relates to a haplotype sensing sequence-to-graph comparison method, system, device and medium, and the method directly embeds haplotype information into an edge correlation structure of a generic genome graph, so that the graph structure has the ability of expressing a haplotype path. And then, an improved haplotype perception partial sequence comparison algorithm is adopted to map the sequence to the graph, so that the graph can identify and utilize embedded haplotype information, and the global consistency of a comparison result is ensured. And finally, an optimal comparison path is obtained by adopting path multiplexing backtracking based on global cache, so that the algorithm efficiency is remarkably improved while the precision is ensured.

This invention discloses a wheat ultra-high-density gene chip probe and its preparation method, belonging to the fields of plant functional genomics, population genetics, and molecular breeding technology. Based on wheat pan-genome information, this invention uses resequencing data and exon capture sequencing data from large-scale natural wheat populations to perform variation analysis and obtain ultra-large-scale whole-genome variation information. High-quality SNPs and INDEL loci with population and individual representativeness are obtained through filtering and screening. Simultaneously, harmful mutation sites are identified, and publicly published genetic loci related to important wheat yield and quality traits are integrated and extracted. Polymorphic loci regions are determined by combining genome annotation and variation annotation. Finally, ultra-high-density liquid-phase probes are synthesized at the pan-genome level. Because this invention only sequences target gene regions, it reduces sequencing costs by more than 90% for the same gene sequencing depth.

The invention provides a design and application method of a plant generic genome exon chip, and aims to reduce the genome sequencing cost of wheat and other complex genome crops and improve the sequencing efficiency. The technology comprises the following steps: 1, designing an efficient liquid phase capture probe through an iterative algorithm, and ensuring that the probe can cover more than 99% of exon regions of a target genome; 2, calculating an original probe template for grouping and synthesizing the exon chips by adopting an algorithm; 3, preparing a liquid phase capture probe by using an ultramicro amplification method; 4, performing experimental hybridization through a grouping gradient hybridization method to ensure efficient capture of a target area; and 5, performing high-throughput sequencing on the captured sample by using a next-generation sequencing platform to obtain high-quality exon region data. The technology can be applied to the fields of genetic research, breeding, whole genome selection and the like of wheat and other complex genome crops. By optimizing probe design, hybridization probe preparation and capture methods, the sequencing cost of plants with complex genomes is remarkably reduced, the coverage degree and data accuracy of important regions of the genomes are improved, and the method is suitable for large-scale plant genomics research, germplasm resource evaluation and identification and large-scale mutant library digitization.

This invention belongs to the field of gene sequence alignment technology, specifically relating to a haplotype-aware sequence-to-graph alignment method, system, device, and medium. This method directly embeds haplotype information into the edge association structure of a pan-genome graph, enabling the graph structure itself to express haplotype paths. Then, an improved haplotype-aware partial order alignment algorithm is used to map the sequence onto this graph, allowing it to identify and utilize the embedded haplotype information, ensuring global consistency of the alignment results. Finally, a path reuse backtracking based on global caching is used to obtain the optimal alignment path, significantly improving algorithm efficiency while maintaining accuracy.

The invention discloses a metagenome species level classification method based on a Debrueine graph, which takes a linear genome and a generic genome as a complementary reference framework, and adopts a two-stage process: firstly, executing approximate member query by utilizing HIBF, and screening out candidate species and strains from a database in a high-recall and low-overhead manner; and then ccDBG is constructed around the candidates, and the attribution of each read length is finely judged on the strain scale. The method has the rapid screening capability of linear reference and high-resolution capture of a generic genome on intra-population differences, so that the problems of fuzzy and confusion of species classification in a traditional process are remarkably relieved.