Method for assembling chloroplast genome sequence

A chloroplast genome and sequence technology, applied in the field of bioinformatics, can solve the problems of high requirements for separation and purification equipment, time-consuming, expensive, laborious, and difficult problems

Inactive Publication Date: 2015-03-25
SOUTHWEST UNIVERSITY
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AI Technical Summary

Problems solved by technology

Although a lot of research has been carried out by many top scientific research institutions and personnel, a lot of progress has been made in accurately assembling large fragments from a large number of sequenced small fragments, but it is still extremely difficult to assemble a large complete genome, especially the nuclear genome. mo

Method used

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Embodiment 1

[0028] 1. Resequence the data of sweet orange.

[0029] Our sweet orange resequencing was completed by Illumina's Hiseq2000 sequencing platform, using pair-end mode library construction and sequencing, with a sequencing read length of 100bp, and a total of about 25.53 million paired-reads were obtained, with a total data volume of about 5.1G, covering about citrus Haploid genome 14 times.

[0030] The pair-end mode library construction sequencing can calculate the theoretical coverage in the subsequent assembly analysis, and provide a basis for selecting a few similar sequences at the same location through the difference in coverage.

[0031] 2. Acquisition of reference genome sequence and screening of sequencing reads.

[0032] Using the published sweet orange chloroplast genome sequence (Bausher MG, Singh ND, Lee SB, Jansen RK, Daniell H (2006) The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var'Ridge Pineapple': organization and phylogenetic relatio...

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Abstract

The invention discloses a method for assembling a chloroplast genome sequence. According to the method, the chloroplast does not need to be separated specially; a sample is sequenced by use of a new generation sequencing technique; Reads available in mapping into a reference genome are selected according to a reference chloroplast genome sequence; the Reads obtained by screening are assembled with a plurality of kmers to construct Contigs; the sequence of the Contigs and the reference chloroplast genome sequence are compared and ranked; the assembly and ranking result of one kmer is selected as the principal result, the extension of the sequence is realized according to the ranking result; the overlay regions of the polymerous sequences at the head and the tail are combined to obtain the complete sequence of the reference assembled chloroplast genome. The method for assembling the chloroplast genome sequence has the advantages that DeNovo assembly is performed by directly utilizing NGS genome sequencing data to obtain the complete chloroplast genome sequence, effective self-assembly and verified closed loop are realized, and the quality of the assembled sequence can be evaluated and determined.

Description

technical field [0001] The invention belongs to the technical field of biological information, and in particular relates to a method for assembling a chloroplast genome sequence. Background technique [0002] NGS Genome Sequencing (Next Generation Sequencing) is a next-generation DNA sequencing method with higher throughput and efficiency than traditional Sanger Sequencing. Roche's GS FLX sequencing system, ABI's (Applied Biosystems) SOLiD sequencing platform, and Illumina's Solexa sequencing platform are currently the world's leading NGS sequencing platforms. Compared with traditional Sanger sequencing, they all have higher throughput. , but each has different advantages and disadvantages. GS FLX sequencing has obvious advantages in read length. When the read length exceeds 400 bases, its accuracy can still reach more than 99%. However, the disadvantages of cost and throughput have limited its competition in NGS. The biggest advantage of SOLiD is High accuracy, the accura...

Claims

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Application Information

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IPC IPC(8): C12N15/10C12Q1/68
Inventor 洪棋斌龚桂芝
Owner SOUTHWEST UNIVERSITY
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