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A method for assembling and forming circles of plant chloroplast genomes based on next-generation sequencing

A second-generation sequencing and genome-wide technology, applied in the field of bioinformatics, can solve problems such as unimaginable workload

Active Publication Date: 2021-11-09
KUNMING INST OF BOTANY - CHINESE ACAD OF SCI
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

In such a big data situation, if the assembly and stitching are done by hand, the workload is unimaginable

Method used

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  • A method for assembling and forming circles of plant chloroplast genomes based on next-generation sequencing
  • A method for assembling and forming circles of plant chloroplast genomes based on next-generation sequencing
  • A method for assembling and forming circles of plant chloroplast genomes based on next-generation sequencing

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Embodiment 1

[0042] The total DNA sample of LHT120202 was completed by Illumina's Hiseq2500 sequencing platform, and pair-end library construction was used for sequencing. The sequencing read length was 150bp, and the original data was about 2.2G.

[0043] Use the data filtering software Trimmomatic raw data to filter, remove joints and low-quality reads, and get clean reads. The command is: nohup java~ / Trimmomatic-0.32 / trimmomatic-0.32.jar PE-threads 2-phred33LHT120202_R1.fastq LHT120202_R2.fastq LHT120202_R1.trimLHT120202_R1.unpaired LHT120202_R2.trim LHT120202_R2.unpaired ILLUMINACLIP:~ / Trimmomatic-0.32 / adapters / TruSeq2-PE.fa:2:30:10 LEADING:5 TRAILING:5SLIDINGWINDOW:EN:180MIN;

[0044] Use SPAdes to assemble clean reads from scratch with multiple kmers to build Scaffolds. The command is: nohup python spades.py--careful-k 21,33,55,77,99,127-o~ / outsamplename--pe1-1~ / cpgenome / samplename --pe1-2~ / cpgenome / samplename &

[0045] Use the 4Kb sequence in the Arabidopsis chloroplast genome as...

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Abstract

The present invention is a method for assembling and constructing circles from whole genome data of plant chloroplasts based on next-generation sequencing data (eg, Illumina platform). The method provided by the present invention first uses the data filtering software Trimmomatic, the assembly software SPAdes and MASHMAP software, and then utilizes the ChloroplastCircle toolkit, combined with the Perl script language programming to realize the data flow process of assembling and forming a circle of the whole plant chloroplast whole genome. A large number of experiments prove that the method provided by the invention can quickly, accurately, batch and automatically complete the assembly and ring formation of the whole plant chloroplast genome. At present, the present invention has been implemented in the 10,000 plant chloroplast whole genome project, and good results have been achieved.

Description

technical field [0001] The invention belongs to the technical field of biological information, and in particular relates to a method for assembling and forming a ring of plant chloroplast whole genome sequences based on second-generation sequencing. Background technique [0002] Chloroplast is an important organelle for green plants on earth to convert light energy into chemical energy, and is an important place for photosynthesis. In the 1960s, researchers discovered chloroplast DNA (chloroplast DNA, cpDNA). Studies have shown that the size of the chloroplast genome is between 120kb and 217kb, with a relatively conservative ring structure. Analysis of the complete sequence of plant chloroplasts reveals that the cpDNA genome has the following characteristics: 1. The genome consists of two inverted repeat sequences (IR), a short single copy sequence (short single copy seguence, SSC) and a long single copy sequence (long single copy seguence, LSC) composition; 2. IRA and IRB...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B20/00G16B50/00
Inventor 赵磊李洪涛李德铢
Owner KUNMING INST OF BOTANY - CHINESE ACAD OF SCI