CN105734134A - Method of molecularly identifying crassostrea rivularis and crassostrea sikamea - Google Patents
Method of molecularly identifying crassostrea rivularis and crassostrea sikamea Download PDFInfo
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Abstract
The invention relates to a method of molecularly identifying crassostrea rivularis and Crassostrea sikamea. The method includes: extracting genome DNA of crassostrea rivularis and crassostrea sikamea; utilizing an upstream primer and a downstream primer to perform PCR (polymerase chain reaction) amplification on the genome DNA to obtain a PCR product of a target segment, wherein the upstream primer is 5'-GATTATTATGCTGGGATTAG-3, and the downstream primer is 5'-ACCCTCTTTCGCTTCA-3; directly performing gel electrophoresis on the PCR product of the target segment, and judging species type according to stripe size of the PCR product. By using the method, crassostrea rivularis and crassostrea sikamea can be identified economically, quickly, simply and conveniently, and results of sequencing verification show that identifying accuracy is 100%. The method is about to play an important role in aquaculture, resource investigation and environment protection.
Description
Technical field
The invention belongs to Aquatic product species identification field, particularly to a kind of molecular identificalion Crassostrea rivularis and the method for Kumamoto Concha Ostreae.
Background technology
Oyster bioherm is to be assembled by a large amount of Concha Ostreaes to be grown on a kind of organic reef system that hard substrate surface is formed, and it is distributed widely in temperature
Band river mouth and littoral area.Oyster bioherm recovers to be maintenance offshore fishery resources, the important means repairing offshore fisheries water ecosystem
One of.Coexisting is distributed in for Crassostrea rivularis (Crassostrea ariakensis) and Kumamoto Concha Ostreae (Crassostrea sikamea)
Entrance of Changjiang River, Hangzhou Wan and Jiangsu are littoral, be China East China Sea region mainly make reef Concha Ostreae species.But for special regional choice which
Seed oyster is carried out oyster bioherm and is recovered engineering and can reach more preferable ecological recovery effect and still belong to unknown.And both species differentiate, it is
Carry out the premise of restoration of the ecosystem.It addition, Concha Ostreae is that one of main economic shellfish, nutritive value and economic worth are the highest.
Oyster culture is the pillar industry in shellfishery.
Owing to the morphological plasticity of oyster shell is strong, the most affected by environment, therefore, only it is sometimes difficult to distinguish specifically with formalness
Kind, especially Concha Ostreae germling and juvenile mollusk are all the more so.This is a difficult problem on shellfish taxonomy, also to oyster culture, open country
It is unfavorable that outer protection of resources and Sustainable Development and Utilization and restoration of the ecosystem work.
Summary of the invention
The technical problem to be solved is to provide a kind of molecular identificalion Crassostrea rivularis and the method for Kumamoto Concha Ostreae, and the method is
A kind of easy and simple to handle, low cost, the Crassostrea rivularis that the shortest, accuracy rate is high and the molecular identification method of Kumamoto Concha Ostreae.
A kind of molecular identificalion Crassostrea rivularis of the present invention and the method for Kumamoto Concha Ostreae, including:
(1) Crassostrea rivularis and the genomic DNA of Kumamoto Concha Ostreae are extracted;
(2) utilize forward primer and downstream primer that the genomic DNA in step (1) is carried out PCR amplification, obtain purpose
The PCR primer of fragment;Wherein, forward primer is 5 '-GATTATTATGCTGGGATTAG-3 ', downstream primer is 5 '-
ACCCTCTTTCGCTTCA-3’;
(3) PCR primer of the purpose fragment in step (2) is directly carried out gel electrophoresis, according to PCR primer band
Size judges species classification.
In described step (1) genomic DNA be Crassostrea rivularis and Kumamoto Concha Ostreae muscular tissue in total genomic dna;Extract
Method is phenol-chloroform method.
Described phenol-chlorine method is classical phenol-chlorine method, and concrete operation step is as follows:
(1) process before digestion.
Blot the liquid in sample with filter paper, take appropriate back tissue and add in corresponding centrifuge tube, add the final concentration of 1000 μ L
The Tris-Cl (pH=8.0) of 1mol/L, in centrifuge tube, fully shreds with the operating scissors of sterilizing, and room temperature places 1h.4 DEG C,
12000rpm/min, centrifugal 10min.Remove supernatant.
(2) digestion.
Respectively in centrifuge tube, adding the Tris buffer of 600 μ L, the SDS of the 10% of 50 μ L, the E.C. 3.4.21.64 of 10 μ L, in shaker
Upper vibration mixing.It is placed in 56 DEG C of water-baths, the most manually mixes during water-bath, until digestion is to clarification.
(3) extracting of DNA and purification.
Add saturated phenol (Phenol saturated) 350 μ L, 350 μ L chloroforms/isoamyl alcohol (25:24:1), overturn and shake up 10min.
4 DEG C, 12000rpm/min, centrifugal 10min.Take supernatant.Repeat the above steps, carries out second time and extracts.Take supernatant.
Add isopyknic chloroform/isoamyl alcohol, mix 10min.4 DEG C, 12000rpm/min, centrifugal 10min.Take supernatant.
(4) DNA precipitation and be dried.
In the supernatant that step 3 obtains, add the ice dehydrated alcohol of 2 times of volumes, under the conditions of-20 DEG C, after mixing, stand 2h.4 DEG C,
10000rpm/min, centrifugal 15min.Quickly remove supernatant, naturally dry in tilting to be put in superclean bench by centrifuge tube.(heavy
Form sediment by 70% washing with alcohol three times)
(5) DNA dissolves.
In the DNA that step 4 obtains, add the aseptic double-distilled water of 100 μ L, first put under the conditions of 4 DEG C, make DNA fully dissolve.
Save backup under the conditions of moving to-20 DEG C.
(6) DNA detection.
Take the DNA in 8 μ L steps 5, the extraction situation of electrophoresis detection DNA in 1.5% agarose gel.Remaining DNA
Save backup under the conditions of being still placed on-20 DEG C.
In described step (2), PCR reaction system includes following component: 100ngDNA template, dNTPs final concentration
0.2mmol/L, each 0.4umol/L of primer final concentration, MgCl2Final concentration 2.0mmol/L, 12.5uL 2 × reaction buffer,
1.25U Taq polymerase, then adds deionized water to final volume 25 μ L;PCR amplification program is as follows: 94 DEG C of denaturations 5min;
Next being 37 circulations, each circulation includes 94 DEG C of degeneration 45s, and 51 DEG C of annealing 45s, 72 DEG C extend 1min;Last 72 DEG C
Extend 8min.
In described step (3), in PCR belt strip, the purpose fragment of Crassostrea rivularis is 599 ± 2bp, and Kumamoto Concha Ostreae purpose fragment is
531 ± 2bp, both differences about 68 ± 4bp.
In described step (3), gel electrophoresis is the agarose gel electrophoresis of 1.4%.
Use the present invention can be economical, quick, easy carry out nearly river and the qualification of Kumamoto Concha Ostreae, the result of sequence verification shows
The accuracy rate differentiated is 100%;This authentication method will play important work in aquaculture, resource investigation, environmental conservation
With.
The molecular biology identification labelling related in the present invention, for solving Kumamoto Concha Ostreae and a difficult problem for Crassostrea rivularis species discriminating, carries
Supply an extraordinary scientific method.The present invention is the most pioneering, and not only the taxonomy to Concha Ostreae has Important Academic meaning
Justice, and provide basic technology to support for oyster culture, protection of resources and Sustainable Development and Utilization, restoration of the ecosystem etc., have
Important actual application value.
Beneficial effect
(1) the method economy, quick, easy of the present invention, accuracy rate is high, sends out in aquaculture, resource investigation, environmental conservation
Wave important function;
(2) the present invention solves the difficult problem that Kumamoto Concha Ostreae and Crassostrea rivularis species differentiate, it is provided that an extraordinary scientific method,
Not only the taxonomy to Concha Ostreae has an Important Academic meaning, and for oyster culture, protection of resources and Sustainable Development and Utilization,
Restorations of the ecosystem etc. provide basic technology to support, and have important actual application value.
Accompanying drawing explanation
Fig. 1 is to design primer by Primer Premier 5 in embodiment 1 to obtain forward primer;
Fig. 2 is to design primer by Primer Premier 5 in embodiment 1 to obtain downstream primer;
Fig. 3 is PCR primer electrophoresis result figure in embodiment 1;
Fig. 4 is the part variation situation in embodiment 1 after the comparison of PCR primer sequencing result.
Detailed description of the invention
Below in conjunction with specific embodiment, the present invention is expanded on further.Should be understood that these embodiments be merely to illustrate the present invention and not
For limiting the scope of the present invention.In addition, it is to be understood that after having read the content that the present invention lectures, those skilled in the art can
To make various changes or modifications the present invention, these equivalent form of values fall within the application appended claims limited range equally.
Embodiment 1
1, experiment material is collected and DNA extraction
By Morphological Identification, gather Kumamoto Concha Ostreae and Crassostrea rivularis sample muscular tissue.Use classical phenol-chloroform method extracting two
Total genomic dna in seed oyster muscular tissue ,-20 DEG C save backup.
Wherein, the method for phenol-chloroform method extracting total genomic dna:
(1) process before digestion.
Blot the liquid in sample with filter paper, take back tissue and add in corresponding centrifuge tube, add the final concentration 1mol/L of 1000 μ L
Tris-Cl (pH=8.0) in centrifuge tube, fully shred with the operating scissors of sterilizing, room temperature place 1h.4 DEG C, 12000rpm/min,
Centrifugal 10min.Remove supernatant.
(2) digestion.
Respectively in centrifuge tube, adding the Tris buffer of 600 μ L, the SDS of the 10% of 50 μ L, the E.C. 3.4.21.64 of 10 μ L, in shaker
Upper vibration mixing.It is placed in 56 DEG C of water-baths, the most manually mixes during water-bath, until digestion is to clarification.
(3) extracting of DNA and purification.
Add saturated phenol (Phenol saturated) 350 μ L, 350 μ L chloroforms/isoamyl alcohol (25:24:1), overturn and shake up 10min.
4 DEG C, 12000rpm/min, centrifugal 10min.Take supernatant.Repeat the above steps, carries out second time and extracts.Take supernatant.
Add isopyknic chloroform/isoamyl alcohol, mix 10min.4 DEG C, 12000rpm/min, centrifugal 10min.Take supernatant.
(4) DNA precipitation and be dried.
In the supernatant that step 3 obtains, add the ice dehydrated alcohol of 2 times of volumes, under the conditions of-20 DEG C, after mixing, stand 2h.4 DEG C,
10000rpm/min, centrifugal 15min.Quickly remove supernatant, naturally dry in tilting to be put in superclean bench by centrifuge tube.(heavy
Form sediment by 70% washing with alcohol three times)
(5) DNA dissolves.
In the DNA that step 4 obtains, add the aseptic double-distilled water of 100 μ L, first put under the conditions of 4 DEG C, make DNA fully dissolve.
Save backup under the conditions of moving to-20 DEG C.
(6) DNA detection.
Take the DNA in 8 μ L steps 5, the extraction situation of electrophoresis detection DNA in 1.5% agarose gel.Remaining DNA
Save backup under the conditions of being still placed on-20 DEG C.
2, PCR primer design
From NCBI website, (http://www.ncbi.nlm.nih.gov) downloads Crassostrea rivularis and the mitochondrial genome of Kumamoto Concha Ostreae
Complete sequence;Adjusted, Clustal software comparison, according to both sequence differences, with Primer Premier 5 design primer (on
Downstream primer sequence is shown in Fig. 1 and Fig. 2 respectively).Result display forward primer is 5 '-GATTATTATGCTGGGATTAG-3 ',
Downstream primer is 5 '-ACCCTCTTTCGCTTCA-3 '.
3, PCR reaction
Purpose fragment with above-mentioned upstream and downstream primer amplification mitochondrial DNA.PCR reaction system includes following component:
100ngDNA template, dNTPs final concentration 0.2mmol/L, each 0.4umol/L of primer final concentration, MgCl2Final concentration 2.0mmol/L,
12.5uL 2 × reaction buffer, 1.25U Taq polymerase, then add deionized water to final volume 25 μ L.PCR amplification program
As follows: 94 DEG C of denaturations 5min;Next being 37 circulations, each circulation includes 94 DEG C of degeneration 45s, 51 DEG C of annealing 45s,
72 DEG C extend 1min;Last 72 DEG C extend 8min.
4, PCR primer electrophoresis
PCR primer is directly placed into electrophoresis in the agarose gel of 1.4%, and deposition condition is: voltage 130V, time 100min,
Buffer is TBE.Result display Kumamoto Concha Ostreae purpose fragment length is 531 ± 2bp;Crassostrea rivularis purpose fragment length 599 ±
(see Fig. 3, the most each swimming lane PCR primer is followed successively by: 1-4 Kumamoto Concha Ostreae for 2bp, both differences about 68 ± 4bp;5-6
Kumamoto Concha Ostreae and Crassostrea rivularis biased sample;7-10 Crassostrea rivularis;11 swimming lane molecular weight marker AL2000Marker).According to electricity
Swimming result can be clear and definite identify Crassostrea rivularis and Kumamoto Concha Ostreae.
5, the sequence verification to PCR primer
PCR primer is checked order by the dideoxy chain termination utilizing Sanger, and then with Clustal software comparison, result shows
Show Crassostrea rivularis and the Fragment Differential of Kumamoto Concha Ostreae about 68 ± 4bp, be to cause by the insertion/deletion of sequence that (excalation fragment is shown in
Fig. 4, the most each sequence is followed successively by: AA5-AD5 is Crassostrea rivularis;SE5-SG5 is Kumamoto Concha Ostreae).
Claims (6)
1. molecular identificalion Crassostrea rivularis and a method for Kumamoto Concha Ostreae, including:
(1) Crassostrea rivularis and the genomic DNA of Kumamoto Concha Ostreae are extracted;
(2) utilize forward primer and downstream primer that the genomic DNA in step (1) is carried out PCR amplification, obtain purpose sheet
The PCR primer of section;Wherein, forward primer is 5 '-GATTATTATGCTGGGATTAG-3 ', downstream primer is 5 '-
ACCCTCTTTCGCTTCA-3’;
(3) PCR primer of the purpose fragment in step (2) is directly carried out gel electrophoresis, big according to PCR primer band
Little judgement species classification.
A kind of molecular identificalion Crassostrea rivularis the most according to claim 1 and the method for Kumamoto Concha Ostreae, it is characterised in that described step
Suddenly in (1) genomic DNA be Crassostrea rivularis and Kumamoto Concha Ostreae muscular tissue in total genomic dna;Extracting method be phenol-
Chloroform method.
A kind of molecular identificalion Crassostrea rivularis the most according to claim 1 and the method for Kumamoto Concha Ostreae, it is characterised in that described step
Suddenly in (2), PCR reaction system includes following component: 100ngDNA template, dNTPs final concentration 0.2mmol/L, primer is eventually
The each 0.4umol/L of concentration, MgCl2Final concentration 2.0mmol/L, 12.5uL 2 × reaction buffer, 1.25U Taq polymerase,
Then deionized water is added to final volume 25 μ L.
A kind of molecular identificalion Crassostrea rivularis the most according to claim 1 and the method for Kumamoto Concha Ostreae, it is characterised in that described step
Suddenly in (2), PCR amplification program is as follows: 94 DEG C of denaturations 5min;Next being 37 circulations, each circulation includes 94 DEG C
Degeneration 45s, 51 DEG C of annealing 45s, 72 DEG C extend 1min;Last 72 DEG C extend 8min.
A kind of molecular identificalion Crassostrea rivularis the most according to claim 1 and the method for Kumamoto Concha Ostreae, it is characterised in that described step
Suddenly in (3), gel electrophoresis is the agarose gel electrophoresis of 1.4%.
A kind of molecular identificalion Crassostrea rivularis the most according to claim 1 and the method for Kumamoto Concha Ostreae, it is characterised in that described step
Suddenly in (3), in PCR belt strip, the purpose fragment of Crassostrea rivularis is 599 ± 2bp, and Kumamoto Concha Ostreae purpose fragment is 531 ± 2bp,
Both difference about 68 ± 4bp.
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Cited By (3)
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CN107557484A (en) * | 2017-10-30 | 2018-01-09 | 中国水产科学研究院东海水产研究所 | A kind of Kumamoto oyster based on DNA specific fragments(Crassostreasikamea)Authentication method |
CN107723345A (en) * | 2017-11-10 | 2018-02-23 | 中国水产科学研究院东海水产研究所 | Crassostrea rivularis discrimination method based on DNA specific fragments |
CN112626238A (en) * | 2021-01-19 | 2021-04-09 | 浙江万里学院宁海海洋生物种业研究院 | Characteristic sequence for identifying crassostrea sikamea, specificity identification primer and identification method |
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Cited By (4)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
CN107557484A (en) * | 2017-10-30 | 2018-01-09 | 中国水产科学研究院东海水产研究所 | A kind of Kumamoto oyster based on DNA specific fragments(Crassostreasikamea)Authentication method |
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CN112626238A (en) * | 2021-01-19 | 2021-04-09 | 浙江万里学院宁海海洋生物种业研究院 | Characteristic sequence for identifying crassostrea sikamea, specificity identification primer and identification method |
CN112626238B (en) * | 2021-01-19 | 2022-02-22 | 浙江万里学院宁海海洋生物种业研究院 | Characteristic sequence for identifying crassostrea sikamea, specificity identification primer and identification method |
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