Strain identification method based on dunaliella core genome sequence

A genome sequence, Dunaliella technology, applied in the field of plant molecular identification, can solve the problems of lack of, long result output cycle, long calculation time, etc., to achieve broad application prospects, easy computer operation, and a wide range of software effects.

Active Publication Date: 2021-02-09
SHANXI UNIV
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  • Abstract
  • Description
  • Claims
  • Application Information

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 d

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  • Strain identification method based on dunaliella core genome sequence
  • Strain identification method based on dunaliella core genome sequence
  • Strain identification method based on dunaliella core genome sequence

Examples

Experimental program
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Embodiment 1

[0050] A method for de novo assembly of Dunaliella D.quartolecta whole genome sequencing and its core genome sequence fragments, comprising the following steps:

[0051] Step 1: Pick a single clone of the algal cells of a strain of Dunaliella D.quartolecta under sterile conditions, and carry out indoor expansion culture under sterile conditions after the microscopic examination is qualified. The indoor expansion culture conditions are as follows: the photoperiod is 18h: 6h, light intensity 19000lx, temperature: 23±3°C, maintain a sterile and ventilated environment, shake the culture dish every 5 days to prevent algae cells from adhering to the wall, and take 0.5-1mL algae liquid for microscopic examination, and the culture period is After 28±7 days, prepare the following medium solution for indoor expansion of the algae strains to be tested. The medium formula is as follows:

[0052] 30g / L NaCl, 1.5g / L NaNO 3 , 1.4g / L K 2 HPO 4 , 1.75g / L MgSO4 7H 2 O, 1.36g / LCaCl 2 ·7H 2...

Embodiment 2

[0123] A method for strain identification using the Dunaliella D.quartolecta core genome sequence, comprising the following steps:

[0124]Step 1, sample collection, purification and cultivation: collect the algae strain to be tested (tentatively named Dunaliella sp.), purify the algae strain to be tested and carry out indoor expansion culture, the specific steps are: aseptic Picking of single clones under the conditions, after the microscopic examination is qualified, carry out indoor expansion culture under sterile conditions, the indoor expansion culture conditions are: photoperiod 18h: 6h, light intensity 19000lx, temperature: 23±3℃, keep sterile In a ventilated environment, shake the culture dish every 5 days to prevent algae cells from adhering to the wall, and take 0.5~1mL algae liquid for microscopic examination. The culture period is 28±7 days. For expanded culture, the formula of the culture medium is as follows:

[0125] 30g / L NaCl, 1.5g / L NaNO 3 , 1.4g / L K 2 HPO...

Embodiment 3

[0170] Using the core genome data of Dunaliella D.quartolecta as a reference, the genetic variation and evolution characteristics of an identified strain Dq_SX genome were analyzed, including the following steps:

[0171] Step 1, referring to the method for screening and assembling Dunaliella D.quartolecta core genome sequencing data constructed in the present invention (see Example 1), use SOAPde novo 2.04 software to analyze the whole genome of an identified Dunaliella strain (tentatively named Dq_SX). The core fragment screening and de novo assembly were performed on the genome sequencing data (see Examples 1 and 2 for the method). The main indicators of the screened and assembled core genome sequence of the algae strain are shown in Table 4.

[0172] Step 2, use the LASTZ 1.02.00 software to perform collinearity analysis on the Dunaliella Dq_SX core genome assembly data constructed in step 1, and obtain the repeated fragments of the duplication events between different regi...

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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...

Claims

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Application Information

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IPC IPC(8): G16B30/10G16B20/30G16B30/20C12Q1/6895C12Q1/6869C12Q1/04C12R1/89
CPCG16B30/10G16B20/30G16B30/20C12Q1/6895C12Q1/6869C12Q2600/156C12Q2525/173C12Q2535/122
Inventor 高帆宋韡南芳茹冯佳谢树莲
Owner SHANXI UNIV
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