Strain identification method based on dunaliella core genome sequence

Abstract

The invention belongs to the technical field of plant molecular identification, and particularly relates to a strain identification method based on a dunaliella core gene sequence. The method mainly comprises the following steps: collecting, purifying and culturing a sample; extracting the DNA of the whole genome; constructing a DNA sequencing library; obtaining whole genome sequencing data of thealgae strain to be detected and the Dunaliella Quartolecta; screening and de novo assembly of sequencing fragments of the D. Quartolecta core genome are carried out, and genome segmentation, proteinfunction annotation and genome contig colinearity analysis are carried out on the assembled core genome sequence; constructing a phylogenetic tree by utilizing single nucleotide polymorphism, and whenan algae strain to be detected and Dunaliella Quartolecta are gathered into a cluster, the data support rate of branches is 0.99-1.00, the genetic similarity percentage is greater than or equal to 99%, and the algae strain to be detected is D.quartolecta.

Description

technical field [0001] The invention belongs to the technical field of plant molecular identification, and in particular relates to a method for strain identification based on a Dunaliella core genome sequence. Background technique [0002] Dunaliella quartolecta is a eukaryotic single-cell microalgae that lives in oceans, salt lakes and other extreme environments. It belongs to Chlorophyta, Chlorophyceae, Volvox, Salinaceae, and Dunaliella genus. No cell wall, containing chromatophore and protein nucleus, with flagella at the top of the cell. Dunaliella D.quartolecta is rich in biologically active substances such as glycerin, β-carotene, and algal polysaccharides, and belongs to characteristic economic microalgae. Using the characteristic strain of Dunaliella D.quartolecta as a bioreactor to extract and industrialize its active substances has important application prospects in food processing, medical care, biodiesel and other fields. However, there are currently 23 speci...

AI Technical Summary

Problems solved by technology

Although the reference genome sequencing data of D. salina was published in 2017 (Dunsal1 v.2), however, as another typical halophilic D. quartolecta, there is still no such strain Related reports on whole genome sequencing work

Using the current popular second-generation and third-generation sequencing technology to sequence the whole genome of a species, although relatively complete genetic information of the species can be obtained, there are still the following defects: (1) All sequencing fragments must be completely compared, and the calculation It takes a long time and produces a huge amount of data, which will consume a lot of time and resources of the computer, which is not conducive to the timely development of molecular identification; (2) Genome assembly and bioinformatics analysis are not only highly dependent on the second and third generation of sequencing companies at home and abroad High-throughput sequencing platforms, such as Illimina, Nanopore, PacBio, etc., are limited by the size of the genome of the species and the computing power of the platform. As a result, the output cycle is long and the cost is high, which is often difficult for ordinary laboratories; (3) for close relatives The molecular identification of species will be highly dependent on the quality of its whole genome resequencing, which is closely related to the quality of the genome of the reference species. If the genome sequencing depth of the reference species is insufficient and the assembly quality is not high, the resequencing results of the genome of the species to be tested will be affected. lead to biased species identification

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