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CodonPlant system used for plant exogenous gene modification, and modification method thereof

A technology of exogenous genes and plants, applied in the field of genetic engineering, can solve problems such as insufficient translation of organisms

Active Publication Date: 2018-08-03
NANJING XIAOZHUANG UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

So for example genes are poorly translated in GC%-rich AT%-rich organisms due to lack of certain charged tRNAs

Method used

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  • CodonPlant system used for plant exogenous gene modification, and modification method thereof
  • CodonPlant system used for plant exogenous gene modification, and modification method thereof
  • CodonPlant system used for plant exogenous gene modification, and modification method thereof

Examples

Experimental program
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Effect test

Embodiment 1

[0052] A CodonPlant system for plant exogenous genetic modification, such as figure 1 As shown, it includes an input module, a processing module, and an output module; wherein, the input module is used for the user to input the gene sequence, codon usage frequency sorting table and the number of groups n (n >= 2 integer); the processing module is used to receive the input The codon information content and the codon usage frequency sorting table information content are effectively processed according to the group number n input by the user, and corresponding results are output through the output module.

[0053] The input module includes a sequence module, a codon usage frequency sorting table module, and a population number module. The sequence that can be input by the sequence module must be a multiple of three, and the input sequence is divided into triplets and sent to the processing module; the codon usage frequency The input format of the sorting table module is that syno...

Embodiment 2

[0147] Adopt the CodonPlant system for plant exogenous gene transformation of embodiment, carry out specific plant exogenous gene transformation, process is as follows:

[0148] The first step: input the NADH dehydrogenase original gene sequence of Bacillus thuringiensis bacteria (the sequence is shown in SEQ ID NO.1.)

[0149] Step 2: According to the sequence, 20 synonymous sequences (ie, different nucleotide sequences with the same protein) were randomly synthesized, numbered [0] to [19], and the corresponding sequences were shown in SEQ ID NO.2-21.

[0150] Step 3: Use roulette to randomly select 2 of these 20 entries. For example, the expected value of No. [0] is 0.2476, and the expected value of No. [3] is 0.2489. As parents, take half of the two sequences and perform cross-recombination to obtain a new sequence named new_seq, and carry out 5% of the new sequence. After the random synonymous mutation, scan the specific site in it again, perform fixed-point random mutati...

Embodiment 3

[0162] The method is the same as in Example 2, with the original sequence of cry9Aa-0 as shown in SEQ ID NO.24 (input sequence) for genetic modification, and the optimized sequence after 100 generations is shown in SEQ ID NO.25 (output result), Table 2 It is a comparison of the results before and after 100 generations.

[0163] Table 2 Comparison of results before and after 100 generations

[0164]

[0165]

[0166]

[0167]

[0168]

[0169] It can be seen from Table 2 that after the sequence was optimized for 100 generations, the expression level of the sequence increased significantly.

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Abstract

The invention discloses a CodonPlant system used for plant exogenous gene modification, and a modification method thereof. The CodonPlant system comprises an input module, a processing module and an output module, wherein the input module is used for a user to input a gene sequence, a codon use frequency sorting table and a group number n; and the processing module is used for receiving input codon information contents and codon use frequency sorting table information contents, carrying out effective processing on the basis of the number n of groups input by a user and outputting a corresponding result through the output module. By use of the system, parameters, including a shearing site, mRNA (Messenger Ribonucleic Acid) and the like, are subjected to fixed point mutation and put in a genetic algorithm to keep the diversity of populations in an evolution process, an exclusion mechanism is increased to make up the deficiencies of low astringency efficiency of the genetic algorithm, theoptimal solution searching ability of the algorithm can be improved, and the system is high in practicality.

Description

technical field [0001] The invention belongs to the technical field of genetic engineering, and in particular relates to a CodonPlant system and a transformation method for plant exogenous gene transformation. Background technique [0002] At present, commonly used codon optimization software optimizes for multiple objectives, and adopts different optimization methods. For example, Codon Optimizer (Fuglsang, 2003), JCat, OPTIMIZER OPTIMIZER (Puigbò et al., 2007) and ATGme (Daniel et al., 2015), etc. Recently, software with different ideas has been developed based on the multi-objective optimization algorithm. Among them, GeneDesigner, Upgene and GeMS first randomly generate a set of candidate sequences, and then perform filters according to predefined conditions. SGD (Wu et al., 2006) scans codons step by step along synthetic genes, selecting preferred codons based on a probabilistic model. DNAWorks (Hoover and Lubkowski, 2002) and EuGene (Gao et al., 2004) use simulated ...

Claims

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Application Information

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IPC IPC(8): G06F19/20G06F19/18
CPCG16B20/00G16B25/00
Inventor 续晨贲爱玲蔡小宁周加宝王立科钱保俐华春
Owner NANJING XIAOZHUANG UNIV
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