A method for strain identification based on a Dunaliella core genome sequence

Abstract

The invention belongs to the technical field of plant molecular identification, in particular to a method for identification of strains based on a Dunaliella core gene sequence. The method mainly includes: sample collection, purification and culture; whole genome DNA extraction; construction of DNA sequencing library; acquisition of whole genome sequencing data of the algal strain to be tested and Dunaliella quartolecta; screening and de novo assembly of the core genome sequencing fragment of Dunaliella D. quartolecta , perform gene composition, protein function annotation and genome contig collinearity analysis on the assembled core genome sequence; use single nucleotide polymorphism to construct a phylogenetic tree, when the algal strain to be tested and Dunaliella tetraloba are clustered together, And the data support rate of the branch is between 0.99 and 1.00, and the percentage of genetic similarity is greater than or equal to 99%. The algal strain to be tested 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 kind of eukaryotic unicellular microalgae living in oceans, salt lakes and other extreme environments. It belongs to Chlorophyta, Chlorophyta, Volvox, Salinae and Dunaliella. No cell wall, with chromophore and protein nucleus, with flagella at the top of the cell. Dunaliella D.quartolecta is rich in glycerol, β-carotene, algal polysaccharide and other biologically active substances, and belongs to the characteristic economic microalgae. The characteristic strain of Dunaliella D.quartolecta is used as a bioreactor to extract and industrialize its active substances, which has important application prospects in food processing, medical care, biodiesel and other fields. However, a total of 23 Dunaliella species h...

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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