499 results about "Insertion" patented technology

Systems and methods for targeted gene modification, targeted insertion, perturbation of gene transcripts, and nucleic acid editing. Novel nucleic acid targeting systems comprise components of CRISPR systems and non-LTR retrotransposon elements.

The invention relates to a molecular marker closely linked with a pepper fruit length regulation gene CaFL1 and application of the molecular marker. The molecular marker is insertion / deletion of three basic groups GAC at 223149123-223149125th positions of chromosome 10 of a pepper genome, and the position of the molecular marker in the genome is determined according to a Qieme reference genome. Specifically, when the genotype of the molecular marker is InGAC: InGAC, the pepper has a long fruit phenotype, when the genotype is InGAC: DelGAC, the pepper has an intermediate phenotype, and when the genotype is DelGAC: DelGAC, the pepper has a short fruit phenotype. Through verification, the accuracy rate of the molecular marker reaches 100%, early, massive and accurate prediction and directional improvement of the pepper fruit length can be realized, and a new way is provided for screening and identifying the pepper fruit length and breeding the pepper fruit length.

The invention relates to the technical field of crop molecular genetic markers, and discloses an InDel molecular marker of avena nuda and application thereof.The molecular marker is a group of 314bp deletion variation and 2bp insertion variation in the 610439484-610440026 interval of the 5C chromosome position of a reference genome of an avena nuda variety OT3098, the nucleotide sequence of the deletion variation is shown as SEQ ID NO.1, the nucleotide sequence of the insertion variation is shown as SEQ ID NO.2, and the nucleotide sequence of the insertion variation is shown as SEQ ID NO.3. The nucleotide sequence of the insertion variation is 5 '-AA-3'. The molecular marker provided by the invention can realize stable detection in agarose gel electrophoresis by combining a specific primer pair (SEQ ID NO.2-3) with an optimized touchdown PCR (Polymerase Chain Reaction) program, has the advantage of being not influenced by a tissue part and a growth period, and provides an efficient and reliable technical means for oat germplasm identification, seed purity detection and molecular breeding.

The present disclosure provides compositions and methods for the targeted modification of RNA molecules by RNA prime editing. The compositions and methods may be conducted invitro or in vivo within cells (e.g., human cells) for the therapeutic correction of disease-causing mutations and / or installation of motifs or mutations in RNA molecules of interest as a tool for scientific research. The disclosure provides compositions and methods for conducting RNA prime editing of a target RNA molecule (e.g., an RNA transcript) that enables the incorporation of one or more nucleotide changes and / or targeted mutagenesis of a target RNA molecule. The nucleotide change can include a single-nucleotide change, an insertion of one or more nucleotides, or a deletion of one or more nucleotides. More in particular, the disclosure provides a variety of configurations of the RNA prime editors each comprising a nucleic acid programmable RNA binding proteins (napRNAbp), such as Cas13, and an RNA-dependent RNA polymerase (RDRP), which are provided as fusion proteins or which can be separately provided in trans. The RNA prime editors are guided to a target RNA site by a guide RNA, which can be a rpegRNA that includes a template region for the synthesis of an RNA sequence to be installed on the RNA molecule attached to an available 3′ terminus. In others embodiments, the RNA template can be provided in trans.

The invention discloses a molecular marker related to thousand seed weight of wheat, a detection primer and application of the molecular marker and the detection primer, and belongs to the technical field of molecular marker-assisted breeding. The nucleotide sequence of the molecular marker TaDTX50-STS is as shown in SEQ ID NO. 1; basic groups from the 502 site to the 661 site of the sequence as shown in SEQ ID NO. 1 have insertion / deletion mutation. The InDel molecular marker related to the thousand seed weight character in a wheat genome is identified and named as TaDTX50-STS, and by detecting the polymorphism or genotype of the InDel molecular marker, the InDel molecular marker can be used for identifying or assisting in identifying the thousand seed weight character of wheat, assisting in breeding dominant varieties with high thousand seed weight of wheat and improving the wheat breeding efficiency.

The invention discloses application of Indel marker dosage typing in detection of sweet potato soft rot resistance, and belongs to the technical field of plant genetic engineering. The Indel molecular marker related to the sweet potato soft rot resistance is obtained through screening, the nucleotide sequence of the Indel molecular marker is shown as SEQ ID NO.2, and an 8bp sequence is inserted into or deleted from the 161st site of the sequence shown as SEQ ID NO.2. Experiments find that target bands of amplification products are obtained through amplification of the Indel molecular marker and electrophoresis, dosage values of two genotypes are obtained according to gray values of the dyed electrophoretic bands, and results show that the insertion type Indel molecular marker is positively correlated with the sweet potato soft rot resistance. The method is of great significance to the dose effect research and molecular assisted breeding of sweet potato gene functions.

The invention belongs to the technical field of gene editing, and particularly relates to optimized omega RNA and gene editing application thereof. According to the optimized omega RNA, base mutation is carried out on the basis of wild type omega RNA with a gene sequence shown as SEQ ID NO.1, and by taking the 5'end of the wild type omega RNA, the 36th paired base UA is replaced with GC, the 37th paired base UA is replaced with AU, the 38th paired base UG is replaced with AU, the 50th paired base UG is replaced with CG, and the 51st paired base UA is replaced with GC. Compared with wild type omega RNA, the omega RNA has the advantages that the maximum enhancement multiple of the insertion and deletion activity is 16.7 times, 15 pairs of paired bases from the 40th site to the 54th site of the omega RNA are further deleted, and the editing efficiency is further improved.

The invention provides a cotton transformation event cD46-2 as well as a primer pair and a method for detecting the cotton transformation event cD46-2. The cotton plant carrying the cD46-2 transformation event comprises the event, namely the joint of an exogenous insertion DNA sequence and a cotton genome DNA sequence, on a group A chromosome 2. A detection primer can be designed by using an exogenous insertion DNA sequence and a DNA sequence of a junction region on a flanking cotton genome, and is used for specific detection of a cD46-2 event. The detection method aiming at the cD46-2 event can provide a convenient means for tracking the specific gene insertion event for the application of breeding by using the plant event, and the specific gene insertion event can be used as a molecular marker to improve the working efficiency of fiber improvement breeding by using the transformation event.

The invention discloses enterobacter mori capable of resisting fish aeromonas and application of the enterobacter mori, the bacterial strain is classified and named as enterobacter mori SCH0241, the enterobacter mori SCH0241 is preserved in the China Center for Type Culture Collection on October 17, 2024, and the preservation number is CCTCC NO: M 20242236. The enterobacter mori SCH0241 disclosed by the invention is derived from the intestinal tract of high-stress-resistance healthy hybrid crucian carassius auratus No. 2, has good contact dependence antibacterial activity on aeromonas veronii, and can improve the capability of resisting aeromonas veronii infection of zebra fish. Through construction of an insertion mutation library and phenotype screening, it is found that a gene cluster of SCH0241, which exerts contact inhibition toxicity, is T6SS-2. The enterobacter mori SCH0241 disclosed by the invention provides a new powerful tool for biological prevention and treatment of fish diseases caused by aeromonas veronii.

Among other things, provided herein are systems that replace the natural random integration activity of a retrovirus with site-specific integration machinery. This approach allows for a more precise targeting of a gene of interest into a human genome, e.g., for therapeutic purposes. The system may include integration-deficient retrovirus (e.g., lentivirus) (IDLV), in which the natural integration activity has been reduced (e.g., by mutation to the viral integrase polypeptide). Instead, the system may comprise a site-specific recombinase (e.g., a serine recombinase, e.g., a serine integrase) capable of directing insertion of a template DNA, or portion thereof, into a desired site in the human genome.

Compositions and methods comprising a deaminase for targeted editing of nucleic acids are provided. Also provided are compositions and methods for localizing a heterologous polypeptide to a target DNA molecule, and compositions and methods for targeted editing of nucleic acids. Fusion proteins comprising an RNA-guided nuclease (RGN) and at least one heterologous polypeptide inserted therein are provided, as well as fusion proteins comprising a DNA binding polypeptide and a deaminase. The heterologous polypeptide may be a pilot editing polypeptide or a base editing polypeptide. Compositions also include nucleic acid molecules encoding a deaminase or fusion protein. Vectors and host cells comprising the nucleic acid molecules encoding the deaminase or fusion protein are also provided.

The invention discloses a DNA sequence reconstruction method and system based on multi-scale attention and contrast learning, and relates to the technical field of DNA storage data reconstruction. Comprising the following steps: collecting a plurality of DNA sequence copies, screening out abnormal length sequences, and constructing a standardized clustering data set; performing one-hot coding and filling processing on the DNA sequence; extracting context dependent features and cross-sequence variation features; an Inter-Sequence multi-head attention mechanism is constructed to calculate the similarity between the sequences, and a weighted sequence tensor is generated; a global dependency relationship in the sequence is extracted through an Intra-Sequence multi-head attention mechanism; local offset features caused by insertion and deletion errors are extracted through a multi-size convolutional network; inputting a double-layer long-short-term memory network for sequence-level modeling, and outputting base reconstruction probability distribution; and constructing positive and negative sample pairs, calculating comparison loss, combining cross entropy loss to form a joint loss function, and outputting a high-precision DNA sequence reconstruction result. The method has high accuracy and robustness under the conditions of complex noise and multiple types of errors.

The invention discloses an Indel marker related to a corn kernel protein content character and application of the Indel marker, and belongs to the technical field of plant molecular genetics and crop molecular design breeding. The Indel marker is located on a gdh2 gene of a chromosome 10 of a corn genome, and insertion or deletion of a nucleotide sequence as shown in SEQ ID NO.5 occurs in an intron region between a second exon and a third exon. By applying the molecular marker-assisted selection technology, high-protein new germplasms S3317 (the crude protein content is 17.0%) and JS231148 (the crude protein content is 15.6%) have been successfully cultivated, the increase amplitudes of the high-protein new germplasms and JS231148 are both more than 15% compared with those of the conventional control, and the lysine content reaches 0.41% and reaches the national high-quality protein corn standard.

Provided is a reverse prime editing system, which is used for achieving site-specific and precise small-fragment DNA editing upstream of a target site. In the reverse prime editing system, a targeted strand nickase (such as D10A-Cas9) is used to cleave a nick on a targeted strand, thereby enabling precise small-fragment DNA base insertion, deletion and substitution upstream of the target site under the action of a reverse transcriptase.

The invention belongs to the technical field of microbial engineering, and discloses a method for producing eicosapentaenoic acid (EPA) with high yield by schizochytrium limacinum based on random mutation and low-temperature screening and application, and the method comprises the following steps: driving overexpression of a G418 resistance gene through a P2520 promoter, constructing a random insertion mutant library, and screening to obtain a schizochytrium limacinum mutant strain with a randomly mutated genome; coating in a culture medium containing G418 resistance for culturing, and screening out strains which are resistant to low temperature and good in growth state at 15 DEG C; and inoculating into a fermentation culture medium, adding MgSO4 with the final mass concentration of 0.1% at the initial stage of fermentation, supplementing MnCl2 with the final mass concentration of 0.05% when fermentation is performed for 72 hours, and culturing to obtain a mutant strain. According to the invention, the G418 resistance gene carried by the plasmid is randomly inserted into the schizochytrium limacinum genome, and low-temperature induced screening is combined, so that the target limitation of traditional homologous recombination is broken through, and a stable strain with multiple mutation superposition can be obtained through enrichment.

Provided is an efficient and precise plant gene knockout method. First, a sequence containing a stop codon cluster is inserted into a genome by means of dual pegRNA to obtain, by means of screening, a stop codon cluster sequence capable of efficiently and precisely knocking out a target gene. A prime editing system and multiple pegRNA programming can be used in combination with the method to enable various genomic modifications such as efficient and precise knockout of one or more target genes, base substitutions, and small fragment insertions, deletions, and substitutions with just one prime editing protein.

The invention belongs to the technical field of crop molecular markers, and particularly discloses a molecular marker for identifying the salt tolerance of brassica napus in the germination period and application of the molecular marker. The molecular marker is located at the position of an A02 chromosome scafoldA028707654 of a brassica napus reference genome ZS11.v10, and the allelotype of the molecular marker is wild type C or mutant type CATATT insertion. The invention also provides a specific primer group for detecting the molecular marker, and the salt tolerance (sensitive type or tolerance type) of the brassica napus line can be quickly identified according to the existence of 411bp and 416bp bands through double PCR amplification and electrophoresis detection. The molecular marker is significantly associated with salt tolerance phenotypes, the detection method is rapid, accurate and low in cost, the molecular marker can be used for brassica napus salt tolerance germplasm resource screening and molecular marker-assisted breeding, and the breeding efficiency is significantly improved.

This invention provides a germline mutation detection method and system with a low false positive rate. The system is computer-executed and includes: first, performing a PCR repeat cluster consistency test on sequence alignment files generated from high-throughput sequencing reads, down-regulating the base count weights of inconsistent sites within the cluster; then, based on the sample-specific background error baseline, calculating the variation confidence index of each genomic site using an empirical Bayesian framework to obtain candidate single nucleotide variants (SNPs); obtaining candidate insertion / deletion variants through read clustering and physical verification of insertion fragment lengths; subsequently, performing a dual-engine cross-feedback iteration on the two candidate types until convergence, integrating and filtering, and outputting a structured mutation detection report. This invention significantly reduces the false positive rate of both SNPs and insertion / deletion variants while maintaining sensitivity, and improves the detection capability of complex insertion / deletion variants.

The invention relates to an efficient guiding editing system for salvia miltiorrhiza and application of the efficient guiding editing system, and belongs to the technical field of gene editing. The invention provides a guided editing system suitable for salvia miltiorrhiza. The guided editing system comprises a U6complex promoter, a fusion protein and gRNA (guide Ribonucleic Acid), the fusion protein is a PEmax-MLH fusion protein; the nucleotide sequence for compiling the PEmax-MLH fusion protein is as shown in SEQ ID NO. 1; and the gRNA is pegRNA and sgRNA (small guide RNA). The constructed guided editing system realizes diversified and accurate editing in stable transformation of plants, the single-base replacement efficiency reaches 61.0%, the complex insertion replacement efficiency reaches 2.2%, the six-base replacement efficiency reaches 11.6%, and meanwhile, experiments prove that after the guided editing system is adopted to edit salvia miltiorrhiza, the accuracy of the edited salvia miltiorrhiza is greatly improved. The content of tanshinone and salvianolic acid of the edited plant is obviously improved.

The application discloses a KASP molecular marker of a Nicotiana benthamiana NbSAG101a gene and application thereof. The KASP molecular marker is an InDel insertion and deletion marker of the Nicotiana benthamiana NbSAG101a gene, is located at 256-262 bp of a second exon of the Nicotiana benthamiana NbSAG101a gene, and the nucleic acid sequence of the KASP molecular marker is shown as SEQ ID NO: 4. A wild-type allele of the Nicotiana benthamiana NbSAG101a gene is C, contains a 7 bp sequence shown as SEQ ID NO: 4, and a mutant-type allele is A, and the 7 bp sequence shown as SEQ ID NO: 4 is deleted. The KASP marker provided by the application can accurately and quickly distinguish wild-type homozygotes, heterozygotes and mutant-type homozygotes of the NbSAG101a gene, has high specificity, high accuracy, fast detection speed, low cost and high flux.

The invention provides methods for non-invasive prenatal testing that allow for detecting risk of chromosomal and subchromosomal abnormalities, including but not limited to aneuploidies, microdeletions and microduplications, insertions, translocations, inversions and small-size mutations including point mutations and mutational signatures. The methods of the invention utilize a pool of TArget Capture Sequences (TACS) to enrich for sequences of interest in a mixed sample containing both maternal and fetal DNA, followed by massive parallel sequencing and statistical analysis of the enriched population to thereby detect the risk of a genetic abnormality in the fetal DNA. Kits for carrying out the methods of the invention are also provided.

The present invention provides Lactiplantibacillus plantarum and a use thereof. A molecular marker gene for Lactiplantibacillus plantarum has a nucleotide sequence selected from one of the following: (1) a nucleotide sequence as shown in SEQ ID NO: 24; (2) a nucleotide sequence having at least 97%, 98%, 99% or higher homology with the nucleotide sequence as shown in SEQ ID NO: 24; and (3) a nucleotide sequence having one or more, e.g., 1, 2, 3, 4, 5, or more, nucleotide substitutions, deletions, or insertions in the nucleotide sequence as shown in SEQ ID NO: 24. The Lactiplantibacillus plantarum provided by the present invention has non-toxicity and good biological characteristics and has a good curative effect on the prevention and / or treatment of vaginal infection and related diseases thereof.

The present invention relates to methods of detecting region(s) of interest in a gene comprising a polyA tail. The region(s) of interest can include gene(s), region(s), mutation(s), deletion(s), insertion(s), indel(s), and / or translocation(s). The region(s) can be greater than or less than 1 kilobases from the polyA tail. Methods can include forming a library of single cell transcripts comprising the region(s) in close proximity to a cell barcode and a unique molecular identifier (UMI). Methods for distinguishing cells by genotype can include amplifying the transcripts using PCR methods and detecting the cell barcode and UMI using single cell sequencing methods. Transcripts can be enriched using tagged region-specific PCR primers. Cell barcodes can be brought into close proximity to the region(s) by circularizing the transcripts. Sequencing of the transcripts can include using primer binding sites added during PCR amplification and library indexes for multiplexed sequencing.

Provided herein are fusion proteins and related methods and systems for increasing the efficiency of genome editing using site-specific nuclease enzymes. These fusion proteins, systems, and methods may selectively increase a desired editing outcome (e.g., insertion of a donor polynucleotide sequence). Also provided are various useful compositions for producing and using these fusion proteins and practicing these methods.

The present application relates to a gene GmPMT for regulating soybean root nodule symbiotic nitrogen fixation and application thereof. Specifically, the present application relates to an isolated gene for regulating soybean root nodule symbiotic nitrogen fixation or nodule number, the coding region sequence of the gene is shown as SEQ ID NO:1 or a homologous sequence thereof has one or more substitutions, deletions and / or insertions of nucleotides compared with the sequence shown as SEQ ID NO:1. The present application also provides the use of the gene as described above in breeding soybeans with increased yield or changed nodule number, optionally, the changed nodule number is manifested as increased nodule number, nodule number per root and / or nodule number per unit root length, optionally, the changed nodule number is manifested as decreased nodule number, nodule number per root and / or nodule number per unit root length. The present application has great theoretical and application value for regulating soybean root nodule symbiotic nitrogen fixation or nodule number and its related application research.

Provided in the present invention are the use of insertion / deletion polymorphism genetic markers in detecting the copy number of human chromosomal subtelomeric regions, a reagent panel for detecting the insertion / deletion polymorphisms genetic markers, and a method for detecting the copy number of human chromosomal subtelomeric regions.

Provided are polynucleotides comprising a mobile bacterial island nucleotide sequence (B-INS) comprising one or more modifications (a modified B-INS) that include deletion or modification of restriction enzyme recognition sites to inhibit restriction enzyme cleavage of the B-INS, and an insertion of at least one cargo sequence into the B-INS. The B-INS is packaged within a bacterium into a phage-like particle that contains a bacteriophage capsid, tail and tail fiber proteins. The phage-like particle function as an antibacterial drone "ABD" and infects bacteria. The cargo sequence is introduced into bacteria infected by the ABD and kills the infected bacteria or inhibits growth of infected bacteria.

The invention provides a papaya CpMp gene, a protein, a primer pair, a recombinant expression vector and application, and belongs to the technical field of plant genetic engineering. The nucleotide sequence of the papaya CpMp gene is as shown in SEQ ID No. 1. The papaya CpMp gene has the effect of regulating and controlling the length of inflorescence stalks. According to the present invention, by using the difference of the CpMp gene on the Y chromosome and the Yh chromosome, i.e., the 4691bp transposon insertion exists on the CpMp promoter on the Yh chromosome, and the transposon insertion does not exist on the CpMp on the Y chromosome, the CpMp gene is adopted as the molecular marker to distinguish the male plant from the male-female plant, and the difference can be used in the early sex verification work of the papaya;

The invention discloses a primer group, a chip, a kit and a method for detecting mutation of a virulence gene SLC25A13 of Hilteline deficiency. The primer group comprises a primer group 1 and / or a primer group 2. According to the method for detecting mutation IVS16ins3kb and IVS4ins6kb of the Hilteline deficiency disease-causing gene SLC25A13, provided by one embodiment of the invention, two insertion variation types IVS16ins3kb and IVS4ins6kb of the SLC25A13 gene can be detected at the same time through one-time multiple LA-PCR reaction, and the method has the characteristics of short time consumption, low cost and high specificity; and the method is suitable for conventional clinical verification work and is easy to popularize.

This invention proposes a molecular marker for *Lactobacillus japonicus*, which was deposited on February 7, 2023, at the China General Microbiological Culture Collection Center (CGMCC) with accession number CGMCC No. 26505. The molecular marker comprises a nucleotide sequence selected from one of the following: (1) the nucleotide sequence shown in SEQ ID NO: 24; (2) a nucleotide sequence having at least 97%, 98%, 99%, or higher homology to the nucleotide sequence shown in SEQ ID NO: 24; or (3) a nucleotide sequence having one or more nucleotide substitutions, deletions, or insertions in the nucleotide sequence shown in SEQ ID NO: 24. Using the molecular marker of this invention, not only can the target *Lactobacillus japonicus* be screened quickly and easily, but it can also highly specifically identify the target *Lactobacillus japonicus*, eliminating interference from other strains.