Method for acquiring Minxian county Chinese Gentian chloroplast genome sequence by utilizing transcriptome data

Abstract

The invention discloses a method for utilizing transcriptome data to acquire Minxian county Chinese Gentian chloroplast genome sequence. The method comprises the steps that transcriptome sequencing raw data of Minxian county Chinese Gentian is acquired through a next-generation sequencing technique, chloroplast gene reads is screened out through filtration and comparison with the known Chinese Gentian chloroplast genome, the screened reads are assembled into contigs, the contigs are built into a local blast database to be compared with reference sequence, ordering and splicing are conducted according to the comparison result, the newly assembled sequence is compared with other chloroplast genome sequences after every 5-6kb is spliced to check the splice sequence, the sequences are assembled into a ring according to the overlapping areas at the head and tail, the gaps are filled through PCR and a first-generation sequencing technique, and the Minxian county Chinese Gentian chloroplast genome sequence is finally obtained. The method is beneficial to understand the important information such as Minxian county Chinese Gentian chloroplast genome structure, and further develops the valueof transcriptome data.

Description

technical field [0001] The invention relates to the field of biological sciences, in particular to a method for obtaining Gentiana chloroplast genome sequence in Minxian County by using transcriptome data. Background technique [0002] Obtaining the chloroplast genome sequence is of great significance to the study of energy metabolism processes such as photosynthesis of green plants and the phylogeny of species; there are three commonly used methods to obtain the chloroplast genome sequence: ① extract pure chloroplast DNA, and then obtain it by sequencing, This method has high requirements on experimental materials and is difficult to perform. ②The chloroplast DNA in the total plant DNA is amplified by long-segment PCR using universal primers, and then obtained by sequencing, but the primers used in this method often do not have a wide range of Versatility leads to the fact that the chloroplast DNA of many plant groups cannot be completely amplified. ③The total plant DNA is ...

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Problems solved by technology

[0002] Obtaining the chloroplast genome sequence is of great significance to the study of energy metabolism processes such as photosynthesis of green plants and the phylogeny of species; there are three commonly used methods to obtain the chloroplast genome sequence: ① extract pure chloroplast DNA, and then obtain it by sequencing, This method has high requirements on experimental materials and is difficult to perform. ②The chloroplast DNA in the total plant DNA is amplified by long-segment PCR using universal primers, and then obtained by sequencing, but the primers used in this method often do not have a wide range of Versatility leads to the fact that the chloroplast DNA of many plant groups cannot be completely amplified. ③The total plant DNA is directly sequenced, and then the chloroplast DNA is screened out by bioinformatics methods, and then obtained by splicing and assembly. However, the method’s In the sequencing results, non-chloroplast DNA (nuclear DNA and mitochondrial DNA) sequences often occupy a very large part of the data volume, resulting in high experimental costs