CN110438241A - A kind of opsariichthys bidens DNA bar code sequence and its application - Google Patents
A kind of opsariichthys bidens DNA bar code sequence and its application Download PDFInfo
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- CN110438241A CN110438241A CN201910647588.2A CN201910647588A CN110438241A CN 110438241 A CN110438241 A CN 110438241A CN 201910647588 A CN201910647588 A CN 201910647588A CN 110438241 A CN110438241 A CN 110438241A
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- 241001248031 Opsariichthys bidens Species 0.000 title claims abstract description 53
- 241000894007 species Species 0.000 claims abstract description 24
- 238000001514 detection method Methods 0.000 claims abstract description 10
- 102000015884 Cytochrome c oxidase subunit I Human genes 0.000 claims description 4
- 108050004212 Cytochrome c oxidase subunit I Proteins 0.000 claims description 4
- 108090000623 proteins and genes Proteins 0.000 claims description 3
- 101150087323 COI gene Proteins 0.000 abstract description 7
- 108020004414 DNA Proteins 0.000 description 31
- 238000000034 method Methods 0.000 description 8
- XLYOFNOQVPJJNP-UHFFFAOYSA-N water Substances O XLYOFNOQVPJJNP-UHFFFAOYSA-N 0.000 description 7
- 241000251468 Actinopterygii Species 0.000 description 4
- 102100030878 Cytochrome c oxidase subunit 1 Human genes 0.000 description 4
- 239000012634 fragment Substances 0.000 description 4
- 241000252206 Cypriniformes Species 0.000 description 3
- 241001531955 Opsariichthys Species 0.000 description 3
- 238000001962 electrophoresis Methods 0.000 description 3
- 230000002068 genetic effect Effects 0.000 description 3
- 235000013372 meat Nutrition 0.000 description 3
- 238000012163 sequencing technique Methods 0.000 description 3
- 241000252210 Cyprinidae Species 0.000 description 2
- LFQSCWFLJHTTHZ-UHFFFAOYSA-N Ethanol Chemical compound CCO LFQSCWFLJHTTHZ-UHFFFAOYSA-N 0.000 description 2
- 241001465754 Metazoa Species 0.000 description 2
- 238000012408 PCR amplification Methods 0.000 description 2
- 238000006243 chemical reaction Methods 0.000 description 2
- 230000007423 decrease Effects 0.000 description 2
- 238000004925 denaturation Methods 0.000 description 2
- 230000036425 denaturation Effects 0.000 description 2
- 238000005516 engineering process Methods 0.000 description 2
- 239000000499 gel Substances 0.000 description 2
- 229920000936 Agarose Polymers 0.000 description 1
- 241000208340 Araliaceae Species 0.000 description 1
- 241001269238 Data Species 0.000 description 1
- 241000238557 Decapoda Species 0.000 description 1
- 241000238631 Hexapoda Species 0.000 description 1
- 108020005196 Mitochondrial DNA Proteins 0.000 description 1
- 108091028043 Nucleic acid sequence Proteins 0.000 description 1
- 238000009004 PCR Kit Methods 0.000 description 1
- 235000005035 Panax pseudoginseng ssp. pseudoginseng Nutrition 0.000 description 1
- 235000003140 Panax quinquefolius Nutrition 0.000 description 1
- 238000000246 agarose gel electrophoresis Methods 0.000 description 1
- 230000003321 amplification Effects 0.000 description 1
- 238000000137 annealing Methods 0.000 description 1
- 230000002457 bidirectional effect Effects 0.000 description 1
- UDSAIICHUKSCKT-UHFFFAOYSA-N bromophenol blue Chemical compound C1=C(Br)C(O)=C(Br)C=C1C1(C=2C=C(Br)C(O)=C(Br)C=2)C2=CC=CC=C2S(=O)(=O)O1 UDSAIICHUKSCKT-UHFFFAOYSA-N 0.000 description 1
- 238000005119 centrifugation Methods 0.000 description 1
- 239000000470 constituent Substances 0.000 description 1
- 239000012153 distilled water Substances 0.000 description 1
- 238000004043 dyeing Methods 0.000 description 1
- 235000019441 ethanol Nutrition 0.000 description 1
- 238000000605 extraction Methods 0.000 description 1
- 235000013305 food Nutrition 0.000 description 1
- 238000013467 fragmentation Methods 0.000 description 1
- 238000006062 fragmentation reaction Methods 0.000 description 1
- 235000008434 ginseng Nutrition 0.000 description 1
- 239000004615 ingredient Substances 0.000 description 1
- 239000000203 mixture Substances 0.000 description 1
- 238000003199 nucleic acid amplification method Methods 0.000 description 1
- 239000002773 nucleotide Substances 0.000 description 1
- 125000003729 nucleotide group Chemical group 0.000 description 1
- 238000004321 preservation Methods 0.000 description 1
- 238000005086 pumping Methods 0.000 description 1
- 238000000746 purification Methods 0.000 description 1
- 239000000376 reactant Substances 0.000 description 1
- 238000011084 recovery Methods 0.000 description 1
- 239000000758 substrate Substances 0.000 description 1
- 238000011144 upstream manufacturing Methods 0.000 description 1
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- C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
- C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
- C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
- C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- C12Q2600/00—Oligonucleotides characterized by their use
- C12Q2600/166—Oligonucleotides used as internal standards, controls or normalisation probes
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Abstract
The invention discloses a kind of opsariichthys bidens DNA bar code sequence and its applications, belong to species identification technical field.The opsariichthys bidens DNA bar code is opsariichthys bidens COI gene, which can be used as the standard detection sequence of opsariichthys bidens DNA, effectively identify opsariichthys bidens endemic species.
Description
Technical field
The invention belongs to species identification technical fields, and in particular to a kind of opsariichthys bidens DNA bar code sequence and its application.
Background technique
Species identification is always the vital basic steps of research on taxology or even almost all creatures field.Cause
This, accurately just seems to species identification and classification and is even more important.Currently, various countries researcher has carried out from lake to ocean
The fish DNA bar code project of different geographic regions efficiently may be used research shows that DNA bar code has in terms of species identification
Row.A large amount of result of study, which is shown, accurately can carry out species to all kinds of animals with the DNA bar code that COI gene is label
Identification, can select COI gene as the standard bar code in various animal bar code datas library.
DNA bar code refer to can be represented in organism the species, it is having enough variations, standard, easily amplification and
Relatively short DNA fragmentation.DNA bar code technology is just as the commodity bar code used in retail business, by species
One or more genes be scanned, it is established that mutual corresponding relationship between DNA sequence dna and biological species, so as to fast
Speed accurately carries out species identification.The COI gene of mitochondrial DNA have moderate length, evolutionary rate it is moderate and rich in system into
The features such as row development information.Under study for action, can the COI genetic fragment preferably to species effectively expanded.Therefore, dynamic
In object species taxonomy and identification, COI gene has very big potentiality as bar code applications.
There is certain limitation using traditional form identification method, for example will receive species gender, stage of development, phenotype
The influence of the factors such as plasticity and cause it is incorrect identification etc..In actual operation, it can also encounter that specimen amount is less and sample
The problems such as this preservation is imperfect leads to incorrect identification.Traditional taxology method is combined using DNA bar code, to species
The identification and classification of efficiently and accurately play an important role.
Opsariichthys bidens (Opsariichthys bidens), are subordinate to Cypriniformes (Cypriniformes), Cyprinidae
(Cyprinidae), subfamily (Danioninae), Opsariichthy (Opsariichthys).Opsariichthys bidens move in streams and water more
In the limpid water body such as library, the cluster life in the more anxious shoal of water flow, the brook and rivers tributary that substrate is sandstone is especially liked, with
Small fish, shrimp, aquatic insect etc. are food, and opsariichthys bidens meat and taste are all good, popular among consumers.In recent years, opsariichthys bidens from
Right resource fails because of the reasons such as excessive use and habitat water environment pollution, therefore the protection of germ plasm resource causes attention,
It is necessary to accurately and effectively be identified its germplasm.
In existing technology, without opsariichthys bidens DNA bar code standard detection sequence and opsariichthys bidens COI gene conduct
The record of opsariichthys bidens DNA bar code standard detection sequence and report.
Summary of the invention
It is an object of the present invention to provide a kind of standard detection sequences that can be used as opsariichthys bidens DNA, can be effectively to Ma Kou
Fish endemic species are identified.
The technical scheme adopted by the invention is that:
A kind of opsariichthys bidens DNA bar code sequence, sequence are SEQ ID NO.1, particular sequence are as follows:
Preferably, the opsariichthys bidens DNA bar code be opsariichthys bidens COI (cytochrome c oxidase subunit I,
Cytochrome c oxidase subunit I) gene.
The DNA bar code sequence can be used as the standard detection sequence of opsariichthys bidens DNA, effectively to opsariichthys bidens endemic species and
Its sample is identified.
The invention has the following advantages that
(1) the obtained opsariichthys bidens DNA bar code sequence of the present invention can be used as the standard detection sequence of opsariichthys bidens DNA,
Opsariichthys bidens sample is carried out to the progress and classification of opsariichthys bidens endemic species efficiently and accurately, while using the DNA bar code sequence
Identification, step is few, method is simple.
(2) in actual operation, which facilitates comparison convenient for saving.
(3) opsariichthys bidens meat and taste are all good, popular among consumers, but because natural resources is because of excessive use and habitat
The decline of the reasons opsariichthys bidens species such as water environment pollution, technical solution of the present invention can be effectively protected opsariichthys bidens species.
Specific embodiment
Embodiment 1
5 opsariichthys bidens samples of Jinsha jiang River downstream Burner zone reservoir area Suijiang river section are taken to be verified.
The extraction of 1.DNA
The fish musculature of clip 5mg or so, shreds as far as possible, is placed in the centrifuge tube of 1.5ml, places at room temperature,
The pumping of genomic DNA is carried out using the cell/tissue genomic kit of GENEray company after ethyl alcohol volatilizees completely completely
It mentions.
2.PCR amplification
PCR primer uses COI gene in the universal primer of Cypriniformes fish, and upstream and downstream primer sequence is respectively as follows:
CypFCOI:tctcaaccaaccacaaagacattgg, CypRCOI:gacttctgggtggccaaagaatca.PCR reactant
Be total volume it is 50 μ l, PCR amplification is carried out using PCR kit, specific ingredient is shown in Table 1, PCR response procedures and is shown in Table 2.
1 PCR reaction system of table
Reacted constituent | Volume (μ l) |
Sterilize distilled water | 22 |
CypFCOI | 1(10Μm/μl) |
CypRCOI | 1(10Μm/μl) |
Genomic DNA template | 1(20ng/μl) |
2ⅹPCR mix | 25 |
2 PCR response procedures of table
Step | Temperature | Time |
1. initial denaturation | 94℃ | 5min |
2. denaturation | 94℃ | 30s |
3. annealing | 52℃ | 30s |
4. extending | 72℃ | 1min |
5. 4to2 | Circulation 30 times | |
6. extending eventually | 72℃ | 10min |
3. agarose gel electrophoresis detects
It carries out carrying out electrophoresis to PCR product with the standard of constant pressure 5V/cm, when bromophenol blue is moved on to away from Ago-Gel forward position about
When 5cm, stop electrophoresis.Gel is taken out, is placed in EB dyeing liquor and impregnates 15min, then observed with ultraviolet transilluminator.
4. sequencing
Through agarose electrophoresis testing goal band clearly PCR product, carried out with centrifugation pillar PCR product purification kit
After the recovery purifying of target fragment, send to one Hui Yuan Biotechnology Co., Ltd of Wuhan Tian and carry out bidirectional sequencing.
The COI genetic fragment of 1 opsariichthys bidens in embodiment 1 are as follows:
It is 99.9% with opsariichthys bidens DNA bar code sequence similarity degree, it can judge the species for Ma Kou by comparison
Fish.
It measures in 5 templates simultaneously, in addition the COI genetic fragment of 4 opsariichthys bidens samples and opsariichthys bidens DNA bar code standard
Detection sequence similitude is 100%, it can judges the species for opsariichthys bidens.
According to sequencing result, above 5 samples are same with the nucleotide sequence of opsariichthys bidens DNA bar code standard detection sequence
Source property can determine whether that these species are opsariichthys bidens 98% or more.
The above PCR reaction system and PCR response procedures are all the same, can more objectively confirm what the present invention obtained in this way
The accuracy of opsariichthys bidens DNA bar code sequence.
The obtained opsariichthys bidens DNA bar code sequence of the present invention can be used as the standard detection sequence of opsariichthys bidens DNA, to horse
The progress and classification of mouth fish endemic species efficiently and accurately, while opsariichthys bidens sample is identified using the DNA bar code sequence,
Step is few, method is simple.In actual operation, which facilitates comparison convenient for saving.Opsariichthys bidens meat with
Sample it is all good, it is popular among consumers, but because natural resources is because of the reasons opsariichthys bidens such as excessive use and habitat water environment pollution
Species decline, technical solution of the present invention can be effectively protected opsariichthys bidens species.
It should be noted last that the above examples are only used to illustrate the technical scheme of the present invention and are not limiting, although ginseng
It is described the invention in detail according to preferred embodiment, those skilled in the art should understand that, it can be to the present invention
Technical solution be modified or replaced equivalently, without departing from the spirit and scope of the technical solution of the present invention, should all cover
In the scope of the claims of the present invention.
Sequence table
<110>Jianghan University
<120>a kind of opsariichthys bidens DNA bar code sequence and its application
<160> 1
<170> SIPOSequenceListing 1.0
<210> 1
<211> 672
<212> DNA
<213>opsariichthys bidens (Opsariichthys bidensDNA bar code sequence)
<400> 1
gacattggca ccctttatct tgtattcggt gcctgagctg gaatagtagg aaccgcacta 60
agcctcctta ttcgagccga actgagccaa cccggatcac ttctaggcga cgatcaaatt 120
tataatgtta ttgttactgc ccatgccttt gttataattt tctttatagt aataccaatt 180
cttattggag ggtttggaaa ctgacttgtg ccgctaatga ttggggcacc tgacatggca 240
tttcctcgaa taaataacat aagcttttga cttctccctc cctctttcct cctgttatta 300
gcctcttctg gtgttgaggc cggggctggg acagggtgaa cagtctaccc gccacttgca 360
ggcaatctcg ctcacgcagg cgcatctgta gacctaacaa ttttctcact ccacctagca 420
ggtgtttcat caattttagg agcaattaat tttattacta caactattaa tatgaaaccc 480
ccagccatct ctcagtatca gacacccctg tttgtttgag ccgtacttgt gacagctgtg 540
cttcttcttc tatccctgcc cgtattggcc gccgggatta caatgctcct tacggatcga 600
aatcttaaca ccacattctt cgaccctgcg ggaggaggag acccaattct atatcaacac 660
ctattctgat tc 672
Claims (3)
1. a kind of opsariichthys bidens DNA bar code sequence, which is characterized in that sequence is SEQ ID NO.1.
2. opsariichthys bidens DNA bar code sequence according to claim 1, which is characterized in that the opsariichthys bidens DNA bar code is
Opsariichthys bidens COI (cytochrome c oxidase subunit I, cytochrome c oxidase subunit I) gene.
3. a kind of application of opsariichthys bidens DNA bar code sequence, which is characterized in that the DNA bar code sequence can be used as opsariichthys bidens
The standard detection sequence of DNA, effectively identifies opsariichthys bidens endemic species and its sample.
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Cited By (1)
Publication number | Priority date | Publication date | Assignee | Title |
---|---|---|---|---|
CN113699256A (en) * | 2021-09-26 | 2021-11-26 | 浙江省农业科学院 | Functional marker for rapidly identifying gynogenesis progeny of opsariichthys bidens and fancy carps and application of functional marker |
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CN107988382A (en) * | 2017-11-28 | 2018-05-04 | 江汉大学 | The long thin loach DNA bar code sequence of one kind and its application |
CN108441564A (en) * | 2017-11-28 | 2018-08-24 | 江汉大学 | A kind of middle Warsaw loach DNA bar code sequence and its application |
CN108611424A (en) * | 2018-01-04 | 2018-10-02 | 中国水产科学研究院南海水产研究所 | Cyprinid fish mitochondrial genome complete sequence amplimer and amplification method |
CN109022457A (en) * | 2018-07-25 | 2018-12-18 | 江汉大学 | A kind of * DNA bar code sequence and its application |
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2019
- 2019-07-17 CN CN201910647588.2A patent/CN110438241A/en active Pending
Patent Citations (4)
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CN107988382A (en) * | 2017-11-28 | 2018-05-04 | 江汉大学 | The long thin loach DNA bar code sequence of one kind and its application |
CN108441564A (en) * | 2017-11-28 | 2018-08-24 | 江汉大学 | A kind of middle Warsaw loach DNA bar code sequence and its application |
CN108611424A (en) * | 2018-01-04 | 2018-10-02 | 中国水产科学研究院南海水产研究所 | Cyprinid fish mitochondrial genome complete sequence amplimer and amplification method |
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Non-Patent Citations (4)
Title |
---|
SHEN,Y.等: "Opsariichthys bidens isolate 003 from China cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial,GenBank: MF122593.1" * |
SHEN,Y.等: "Opsariichthys bidens isolate 003 from China cytochrome oxidase subunit 1 (COI) gene, partial cds; mitochondrial,GenBank: MF122593.1", 《GENBANK》 * |
Y SHEN等: "DNA barcoding and evaluation of genetic diversity in Cyprinidae fish in the midstream of the Yangtze River" * |
Y SHEN等: "DNA barcoding and evaluation of genetic diversity in Cyprinidae fish in the midstream of the Yangtze River", 《ECOLOGY AND EVOLUTION》 * |
Cited By (1)
Publication number | Priority date | Publication date | Assignee | Title |
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CN113699256A (en) * | 2021-09-26 | 2021-11-26 | 浙江省农业科学院 | Functional marker for rapidly identifying gynogenesis progeny of opsariichthys bidens and fancy carps and application of functional marker |
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