CN108642186A - Molecular labeling for being identified between Mans needleless, tiger spot and swordtip squid and application - Google Patents
Molecular labeling for being identified between Mans needleless, tiger spot and swordtip squid and application Download PDFInfo
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Abstract
It being used for Mans needleless, the molecular labeling of tiger spot and swordtip squid species identification and application the present invention relates to a kind of, belongs to sibling species identification technology, the method for the nearly edge species identification of specifically a kind of cuttlefish.Specially using Sepiella maindroni, tiger spot cuttlefish and East Sea point squid genomic DNA as template, PCR amplification, and then differentiation cuttlefish species different using Tm value difference of the amplified production in high-resolution melting curve (HRM) are carried out according to the sequence label design primer of Sepiella maindroni, tiger spot cuttlefish and East Sea swordtip squid species gene group;It is capable of the identification of quick, economy, simplicity carried out between species using the present invention, accuracy rate is 100% compared with sequence label sequencing result.
Description
Technical field
The invention belongs to cuttlefish species identification technical fields more particularly to one kind can be used for Sepiella maindroni, tiger spot crow
Molecular labeling and the application of thief and swordtip squid species identification.
Background technology
Sepiella maindroni (Sepiella maindroni) belongs to Cephalopoda, Sepiida, Sepiidae, sepiella maindroni de Rochebrune category,
It is distributed widely in Russian Far East sea, Japanese Seto Island Sea, Korea's southwest seashore and China's Adjacent Sea Area, cephalopodium is blazoned for wide temperature
Veriety has certain distribution in the four big marine sites in China;Tiger spot cuttlefish (Sepia pharaonis) is subordinate to Mollusca
(Mollusca), Sepiida (Sepioidea), Sepiidae (Sepiidae), Sepia (Sepia), are distributed in the India Pacific Ocean
Tropical Ocean Area, from offshore to being found in the waters of depth of water 100m;Swordtip squid (Loligo edulis) is commonly called as red squid
Fish, Cephalopoda, gun-shaped mesh, squid section, shallow sea property warm water species are distributed in the East Sea, the South Sea, Japanese archipelago In Southern Coastal Sea, Fei Lv
Guest archipelago to Australian northern marine site.The East Sea is mainly distributed on outer continental shelf marine site, is that early 1990s are newly developed
One of Resources of Cephalopods, annual output about (2~3) × 104T is important aquatic products.Three kinds of cuttlefishes belong to Cephalopoda, dwell
Breath marine site is also engaged in internal strife crosslinking, and three kinds of cuttlefishes are nutritious to enrich, is tasty, is widely appreciated by consumers.Currently, fishery market
On the cuttlefish sold mostly sold with processing method in a manner of the fresh dead cuttlefish product not freezed because have stress for cuttlefish
The habit of ink-jet and cause the cuttlefish sold in the market because band ink due to it is smudgy, and after death cuttlefish inter-species phenotypic difference contracting
Small, common Morphological Characteristics difference disappears;And it is processed after, limbs integrality is poor, can not carry out entirety according to part
Differentiate.In general, the typoiogical classification identification difficulty of species level is larger, and is also easy to produce many disagreements, depends merely on morphology hardly possible
To distinguish.Therefore, select effective method has important meaning to distinguish Sepiella maindroni, tiger spot cuttlefish and swordtip squid
Justice;In recent years, with the development of molecular biology, become to identify that species have been increasingly becoming one kind using molecular biology method
Gesture, and received by most of biologist.The third generation proposed from American scholar Lander after RFLP, SSR in 1996
New molecular marker technology --- since SNP, the detection of SNP and parting have become the key technology of genetics research, what SNP referred to
The polymorphism that single nucleotide acid point mutation generates in certain biological Different Individual DNA sequence dna, including displacement, transversion, insertion or
Polymorphism caused by missing.High-resolution melting curve method is the difference based on different nucleic acid physical properties, by fluorescent dye
PCR reaction systems are added, when the DNA solution supination containing fluorescent dye, fluorescence information can be collected and form melting curve.When DNA sequences
Some base changes in row, and melting curve will occur to change accordingly, can be divided hereditary information by software
Analysis has many advantages, such as efficient, accurate, high-throughput, low cost.Currently, HRM technologies have been applied to the mirror of known type
Fixed, Mutation Screening, DNA methylation analysis, the fields such as microbial molecular parting and identification and rna editing are in molecule diagnosis
Hot technology.
Invention content
A technical problem to be solved by this invention be for the prior art present situation provide one kind can be used for Mans without
The molecular labeling of Sepia andreana, tiger spot cuttlefish and swordtip squid species identification.
Another technical problem to be solved by this invention is a kind of above-mentioned point of utilization of present situation offer for the prior art
Son marks to distinguish the application of Sepiella maindroni, tiger spot cuttlefish and swordtip squid species identification.
Another technical problem to be solved by this invention is a kind of above-mentioned point of utilization of present situation offer for the prior art
The method that son marks to distinguish Sepiella maindroni, tiger spot cuttlefish and swordtip squid species identification.
Technical solution is used by the present invention solves above-mentioned technical problem:This can be used for Sepiella maindroni, tiger spot crow
The SNP marker of thief and swordtip squid species identification, it is characterised in that:The SNP marker
Forward primer F1 is 5'CAGGAACAGTTTCCACTACCCCTAC 3';
Reverse primer F2 is 5'CGCGTACATATCGCCCGTC 3'.
The present invention provides a kind of above-mentioned SNP marker of utilization molten based on high resolution to solve second technical problem
Solution curve identifies Sepiella maindroni, tiger spot cuttlefish and the application in swordtip squid.
Further, the SNP in the Sepiella maindroni target amplification segment is:
CGCGTACATATCGCCCGTCGCTCTTGTTGATAAAATAAGATAAGTCGTAACATAGTAGGGGTAGTGGAAACTGTTCC
TG。
Further, the SNP in the tiger spot cuttlefish target amplified fragments is:
CGCGTACATATCGCCCGTCGCTCTTGTTGGTAAAATAAGATAAGTCGTAACATAGTAGGGGTAGTGGAAACTGTTCC
TG。
Further, the SNP in the swordtip squid target amplification segment is:
CGCGTACATATCGCCCGTCGCTCTTGTTGGAAGATAAGATAAGTCGTAACATAGTAGGGGTAGTGGAAACTGTTCCT
G。
The present invention provides one kind based on high-resolution solubility curve identification Mans needleless crow to solve third technical problem
Crafty, tiger spot cuttlefish and swordtip squid method, it is characterised in that:With Sepiella maindroni, tiger spot cuttlefish and swordtip squid
Genomic DNA is template, is drawn according to the design of the sequence label of the genome of Sepiella maindroni, tiger spot cuttlefish and swordtip squid
Object carries out PCR amplification, and then differentiation different using Tm value difference of the amplified production in high-resolution melting curve;With cuttlefish to be identified
Genomic DNA is template, PCR amplification is carried out according to the gene order design primer of cuttlefish, using amplified production in high-resolution
Tm value differences in melting curve are different and then distinguish the close species of cuttlefish.
Further, the PCR product obtained by above-mentioned amplification is added denaturation treatment after nucleic acid saturable dye, is cooled to
Room temperature carries out HRM measurement.
Compared with prior art, the invention has the advantages that:
1, method is simple and practicable;It need not be sequenced, directly by the Tm values of amplified fragments come the difference in reaction dna level
And distinguish different plant species;
2, result is clearly intuitive;Without progress sequence alignment, the difference of DNA level is with intuitive between different plant species
Peak figure form show, easily distinguish distinguish;
3, accurate and effective;Identification method of the present invention is had using high-resolution melting curve (HRM) differentiates single nucleotide acid
The ability of difference can accurately reflect the difference on DNA level so that qualification result is accurate and reliable, compared with sequencing result
Accuracy rate is 100%;
4, application is extensive;It is different from sequencing, it need not be by all individual sequencing analysis one by one to be identified, in of the invention
One group of primer can carry out species identification without redesigning primer on infinitely how similar individual;The present invention passes through offer
Differentiate Sepiella maindroni, tiger spot cuttlefish and swordtip squid SNP primers, successfully three kinds of cuttlefishes are carried out by HRM technologies
Genotyping, the gene fragment order that Sepiella maindroni, tiger spot cuttlefish and swordtip squid are explored from molecular level are poor
It is different, establish Sepiella maindroni, tiger spot cuttlefish and swordtip squid molecular identification method, secondly, the present invention be one open
System is put, is had wide range of applications;The identification of the nearly edge species of specific several cuttlefishes is cannot be only used for, as long as based on DNA level
The cuttlefish species that can distinguish of difference can be identified using this method.
Description of the drawings
Fig. 1 be the nearly edge species identification high-resolution melting curve figure of Sepia cuttlefish provided in an embodiment of the present invention (wherein
Abscissa is temperature DEG C), ordinate is the logarithm of fluorescence intensity;Abscissa corresponding to the peak of every curve is should
The Tm values of the corresponding PCR product of curve);
Fig. 2 is that the standardization that the nearly edge species identification high-resolution of Sepia cuttlefish provided in an embodiment of the present invention melts is bent
Line;
Fig. 3 is the nearly edge species of Sepia cuttlefish provided in an embodiment of the present invention in the molten of standardization and different temperatures
Solution curve peak.
Specific implementation mode
Below by way of accompanying drawings and embodiments are combined, the invention will be further described.
The present invention introduces high-resolution melting curve side during being distinguished by nucleic acid sequence and carry out species identification
Difference of the different plant species on DNA level is only converted to more intuitive melting curve by method with one couple of PCR primers.
Its step is:
A, DNA is extracted
Genomic DNA is extracted using traditional phenol chloroform-isoamyl alcohol method, agarose gel electrophoresis detects DNA sample
Quality, NANODROP 2000 (Thermo Scientific, USA) measures DNA stock solution qualities and concentration, and is diluted to 50ng/
The concentration of ul is for use.
B, acquisition and sequence alignment analysis of the species identification according to sequence
It is soft using AlignX by obtaining the mtDNA sequence overall length of tiger spot cuttlefish and quasi- mesh cuttlefish from ncbi database
Part carries out sequence alignment, finds base difference present in two kinds of cuttlefishes;From containing SNP site sequence, selection meets primer
The sequence of design carries out SNP primer design using Premier5.0;
C, design of primers and screening
Design of primers should meet the following conditions:Target amplification sequence is between 50bp-150bp, to keep melting temperature different,
There are the differences of GC base contents between sequence;Annealing temperature (Tm) should be between 50 DEG C -60 DEG C;It should be as possible between positive anti-primer
Avoid mispairing, hairpin structure and primer dimer;Primer is synthesized by Shanghai Sheng Gong engineering finites responsible company.Random selection 5
Corresponding cuttlefish DNA sample is template, using using agarose gel electrophoresis technology to carry out preliminary screening to primer, selects energy
Amplify bright, the primer progress HRM analyses of single band.
D, PCR amplification and high-resolution melting curve (HRM) analysis
Using the genomic DNA of target cuttlefishes to be identified as template, PCR amplification is carried out using above-mentioned primer;PCR system is
Using cuttlefish genomic DNA as template, DNA concentration is adjusted to 50ng/ μ l, the primer after screening is used for HRM points of target fragment
Analysis.In LightThe molten of PCR amplification and product is carried out on 480 real-time quantitative analysis instrument (Roche Diagnostics)
Solution curve is analyzed.Reaction uses Light480HRM kits,
PCR system:20μL 1×Light480HRM Master Mix with Resodye
(Roche Diagnostics), positive each 1 μ L of anti-primer, the DNA profiling of 1 μ L 100ng/ μ L, 2.8 μ L MgCl2, moisturizing to 20 μ
L。
PCR amplification program is:95 DEG C (pre-degeneration 10min), 95 DEG C (denaturation 30sec), Tm (renaturation 30sec), 72 DEG C (are prolonged
Stretch 30sec) denaturation, renaturation, extend after three steps recycle 45 times altogether, solubility curve fluorescent collecting:95 DEG C denaturation 30seconds, 65
DEG C annealing 30seconds, 95 DEG C heating 30seconds.
After PCR amplification, product is directly in Light480 real-time quantitative analysis instrument (Roche
Diagnostics the operation of HRM is carried out on) automatically, 1 DEG C is often increased and acquires fluorescence 25 times.Use LightOn 480 certainly
1.5 softwares of Tm Calling and Gene Scanning Software of band carry out the analysis of Tm values and Genotyping.In addition, with
It can be directed to the optimal canonical sequence of different plant species by unrestricted choice as needed in the foundation sequence of species identification, can be COI
Gene order or other meet the sequence of biomarker feature.
Embodiment 1
The identification of Sepiella maindroni, tiger spot cuttlefish and swordtip squid:
A, acquisition of the species identification according to sequence:It is complete by obtaining above-mentioned cuttlefish mtDNA sequence from ncbi database
It is long, carry out sequence alignment using AlignX softwares, find base difference segment present in three kinds of cuttlefishes, as species identification according to
According to sequence;
B, design of primers:Selection can obviously distinguish the sequence of target species in above-mentioned Sepia mitochondria full length sequence
PCR amplification primer is designed in region in the area using Primer Premier5 softwares, and primer extension product is in different plant species
Between should have apparent Tm value differences different, be mainly reflected in that C, T content is different.
Forward primer F1 is:5'CAGGAACAGTTTCCACTACCCCTAC 3';
Reverse primer F2 is:5'CGCGTACATATCGCCCGTC 3'.
C, PCR amplification:Using the genomic DNA of cuttlefish sample to be identified as template, PCR amplification is carried out using above-mentioned primer.
PCR amplification program according to:94 DEG C (pre-degeneration 10min), 94 DEG C (denaturation 15sec), 53 DEG C of Tm (renaturation 15sec), 72 DEG C (extend
Extend 5min after 72 DEG C after 30sec) denaturation, renaturation, three steps of extension recycle 35 times altogether, 4 DEG C (cooling) terminates.
D, high-resolution melting curve (HRM) is analyzed:Above-mentioned product is directly in LightIt is run on 480 platforms
HRM collects the fluorescent signal data between 55 DEG C -95 DEG C.After using the analysis software carried on platform by fluorescence signal
It is converted to melting curve peak figure;The nearly edge object of different Sepias is distinguished according to the difference of the corresponding Tm values of the peak value of different curves
Kind (referring to Fig. 1).
Experimental result is as follows:
As seen from Figure 1:Melting curve is polymerized to 3 beams respectively, and 3 kinds of different Tm values are presented respectively, wild in counter sample
Graceful formula sepiella maindroni de Rochebrune, tiger spot cuttlefish and East Sea swordtip squid;Type A is Sepiella maindroni, and Tm values are 80.67 DEG C, class
Type B is tiger spot cuttlefish, and Tm values are 81.48 DEG C, and Type C is East Sea swordtip squid, and Tm values are 82.45 DEG C, different type
Melting curve between distinguish clear, apparent, the clear Tm values shown between tiger spot cuttlefish and East Sea swordtip squid are micro-
Small difference, relatively far apart with Sepiella maindroni, this is with Wang Wanchao about three kinds of cuttlefish relationships in the development of cuttlefish phyletic evolution
Result of study in the correlative study of relationship is consistent, also embodies the sensitivity and accuracy of HRM analyses.
Fig. 2 is through LightGene Scanning resume modules are analyzed on 480, obtain standardization melting curve
View can preferably reflect that Sepiella maindroni, tiger spot cuttlefish and the different caused peak figure of East Sea swordtip squid Tm value differences become
Change;
Fig. 3 be in the case of standardization and different temperatures both melting curve peak figures with East Sea point squid be with reference to baseline,
Sepiella maindroni is distributed in East Sea swordtip squid both sides with tiger spot cuttlefish, and Fig. 2 Fig. 3 is for preferably reflecting Mans
Sepiella maindroni de Rochebrune, tiger spot cuttlefish and the different caused peak figure variation of East Sea swordtip squid Tm value differences.
E, sequence verification
For the SNP site of the apparent parting of energy, randomly chooses each corresponding PCR product of genotype curve and is sequenced,
The sequencing result of various genotype is compared, the base composition difference between observing, such as the following table 1.
1 sequence of table and comparison result:Show be present in Sepiella maindroni in three kinds of Sepias, tiger spot cuttlefish with
SNPs in the swordtip squid target amplification segment of the East Sea, respectively SEQ1, SEQ2 and SEQ3, such as following table.
Table 1
Meanwhile the base composition difference between observing, such as the following table 2, it shows and is present in Sepiella maindroni and tiger
SNPs in spot cuttlefish target amplified fragments detects 1 SNP site altogether in the differential fragment of this 79bp, is base transition
Site.
Table 2
Meanwhile the base composition difference between observing, such as the following table 3, it shows and is present in Sepiella maindroni and tiger
SNPs in spot cuttlefish target amplified fragments detects 3 SNP sites altogether in the differential fragment of this 79bp, and 2 are base
Convert site, 1 SNP site missing.
Table 3
Sequence table
<110>University Of Ningbo
<120>Molecular labeling for being identified between Mans needleless, tiger spot and swordtip squid and application
<130> Not published yet
<160> 3
<170> SIPOSequenceListing 1.0
<210> 1
<211> 79
<212> DNA
<213> Sepiella maindroni
<400> 1
cgcgtacata tcgcccgtcg ctcttgttga taaaataaga taagtcgtaa catagtaggg 60
gtagtggaaa ctgttcctg 79
<210> 2
<211> 79
<212> DNA
<213> Sepia pharaonis
<400> 2
cgcgtacata tcgcccgtcg ctcttgttgg taaaataaga taagtcgtaa catagtaggg 60
gtagtggaaa ctgttcctg 79
<210> 3
<211> 78
<212> DNA
<213> Loligo edulis
<400> 3
cgcgtacata tcgcccgtcg ctcttgttgg aagataagat aagtcgtaac atagtagggg 60
tagtggaaac tgttcctg 80
Claims (6)
1. a kind of SNP marker for Mans needleless, tiger spot and swordtip squid species identification, it is characterised in that:
The forward primer F1 of the SNP marker is 5'CAGGAACAGTTTCCACTACCCCTAC 3';Reverse primer F2 is
5'CGCGTACATATCGCCCGTC 3'。
2. a kind of SNP marker according to claim 1 is based on high resolution solubility curve identification Mans needleless crow
Thief, tiger spot cuttlefish and the application in swordtip squid.
3. SNP marker according to claim 2 is based on high resolution solubility curve identification Sepiella maindroni, tiger
Spot cuttlefish and the application in swordtip squid, it is characterised in that:SNP in the Sepiella maindroni target amplification segment is:
CGCGTACATATCGCCCGTCGCTCTTGTTGATAAAATAAGATAAGTCGTAACATAGTAGGGGTAGTGGAAACTG
TTCCTG。
4. SNP marker according to claim 2 is based on high resolution solubility curve identification Sepiella maindroni, tiger
Spot cuttlefish and the application in swordtip squid, it is characterised in that:SNP in the tiger spot cuttlefish target amplified fragments is:
CGCGTACATATCGCCCGTCGCTCTTGTTGGTAAAATAAGATAAGTCGTAACATAGTAGGGGTAGTGGAAACTG
TTCCTG。
5. SNP marker according to claim 2 is based on high resolution solubility curve identification Sepiella maindroni, tiger
Spot cuttlefish and the application in swordtip squid, it is characterised in that:SNP in the swordtip squid target amplification segment is:
CGCGTACATATCGCCCGTCGCTCTTGTTGGAAGATAAGATAAGTCGTAACATAGTAGGGGTAGTGGAAACTGT
TCCTG。
6. a kind of method based on high-resolution solubility curve identification Sepiella maindroni, tiger spot cuttlefish and swordtip squid,
It is characterized in that:Using Sepiella maindroni, tiger spot cuttlefish and swordtip squid genomic DNA as template, according to Sepiella maindroni,
The sequence label design primer of the genome of tiger spot cuttlefish and swordtip squid carries out PCR amplification, using amplified production in high score
Tm value differences in resolution melting curve are different and then distinguish;Using cuttlefish genomic DNA to be identified as template, according to the gene sequence of cuttlefish
Row design primer carries out PCR amplification, and then differentiation cuttlefish different using Tm value difference of the amplified production in high-resolution melting curve
Close species.
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Citations (2)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
CN102758009A (en) * | 2012-06-08 | 2012-10-31 | 中国科学院海洋研究所 | Method for identifying related species of oyster |
CN104046683B (en) * | 2013-03-13 | 2015-06-10 | 中国科学院海洋研究所 | Method for discriminating two closely-related species of shellfish or identifying their hybrid generation |
-
2018
- 2018-03-29 CN CN201810272245.8A patent/CN108642186A/en active Pending
Patent Citations (2)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
CN102758009A (en) * | 2012-06-08 | 2012-10-31 | 中国科学院海洋研究所 | Method for identifying related species of oyster |
CN104046683B (en) * | 2013-03-13 | 2015-06-10 | 中国科学院海洋研究所 | Method for discriminating two closely-related species of shellfish or identifying their hybrid generation |
Non-Patent Citations (2)
Title |
---|
LAURE BONNAUD等: ""Morphological character evolution and molecular trees in sepiids (Mollusca: Cephalopoda): is the cuttlebone a robust phylogenetic marker?"", 《BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY》 * |
温旺荣: "《临床分子诊断学》", 31 May 2015 * |
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