CN110423823A - A kind of C. guichenoti DNA bar code sequence and its application - Google Patents

A kind of C. guichenoti DNA bar code sequence and its application Download PDF

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Publication number
CN110423823A
CN110423823A CN201910674536.4A CN201910674536A CN110423823A CN 110423823 A CN110423823 A CN 110423823A CN 201910674536 A CN201910674536 A CN 201910674536A CN 110423823 A CN110423823 A CN 110423823A
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CN
China
Prior art keywords
guichenoti
bar code
dna
dna bar
code sequence
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CN201910674536.4A
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Chinese (zh)
Inventor
熊飞
曹梦西
王莹
刘红艳
文涵宇
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Jianghan University
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Jianghan University
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Priority to CN201910674536.4A priority Critical patent/CN110423823A/en
Publication of CN110423823A publication Critical patent/CN110423823A/en
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    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q2600/00Oligonucleotides characterized by their use
    • C12Q2600/166Oligonucleotides used as internal standards, controls or normalisation probes

Abstract

The invention discloses a kind of C. guichenoti DNA bar code sequence and its applications, belong to species identification technical field.The C. guichenoti DNA bar code is C. guichenoti COI gene, which can be used as the standard detection sequence of C. guichenoti DNA, effectively identify C. guichenoti endemic species.

Description

A kind of C. guichenoti DNA bar code sequence and its application
Technical field
The invention belongs to species identification technical fields, and in particular to a kind of C. guichenoti 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.
C. guichenoti (Coreius guichenoti), be subordinate to Cyprinidae (Cyprinidae) , Minnow subfamily (Gobioninae), Copper fish category (Coreius).It is distributed mainly on the Endemic fish of Upper Yangtze River, Jinsha jiang River middle and lower reaches and Yalongjiang River downstream.On the Changjiang river The gradually construction and operation for swimming Heavenly Stems and Earthly Branches stream step hydropower station result in the migratory C. guichenoti habitat in river and are cut off, affect The completion of the history of life, and inhabit ground area and also largely reduce.In the assessment of Chinese Wild vertebrate Endangered status, circle Mouth copper fish is in pole danger grade and is therefore effectively identified C. guichenoti endemic species and species conservation has been very urgent.
In existing technology, without C. guichenoti DNA bar code standard detection sequence and C. guichenoti COI gene Record and report as C. guichenoti DNA bar code standard detection sequence.
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 C. guichenoti DNA, can be effectively to circle Mouth copper fish endemic species are identified.
The technical scheme adopted by the invention is that:
A kind of C. guichenoti DNA bar code sequence, sequence are SEQ ID NO.1, particular sequence are as follows:
Preferably, the C. guichenoti DNA bar code is C. guichenoti 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 C. guichenoti DNA, effectively peculiar to C. guichenoti Kind and its sample are identified.
The invention has the following advantages that
(1) the obtained C. guichenoti DNA bar code sequence of the present invention can be used as the standard detection sequence of C. guichenoti DNA Column, to the progress and classification of C. guichenoti endemic species efficiently and accurately, while using the DNA bar code sequence to C. guichenoti sample Product are identified that step is few, method is simple.
(2) in actual operation, which facilitates comparison convenient for saving.
(3) C. guichenoti is distributed mainly on the Endemic fish of Upper Yangtze River, Jinsha jiang River middle and lower reaches and Yalongjiang River downstream.The Changjiang river The gradually construction and operation of upstream Heavenly Stems and Earthly Branches stream step hydropower station result in the migratory C. guichenoti habitat in river and are cut off, influence The completion of the history of life, and inhabit ground area and also largely reduce.In the assessment of Chinese Wild vertebrate Endangered status, C. guichenoti is in pole danger grade.Technical solution of the present invention can effectively identify C. guichenoti species, to instruct it The protection of resource.
Specific embodiment
Embodiment 1
5 C. guichenoti samples of Jinsha jiang River downstream Burner zone reservoir area river Hui Xi 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 C. guichenoti in embodiment 1 are as follows:
It is 99.6% with C. guichenoti DNA bar code sequence similarity degree by comparison, it can judge the species for circle Mouth copper fish.
Embodiment 2
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 C. guichenoti in embodiment 2 are as follows:
It is 99.6% with C. guichenoti DNA bar code sequence similarity degree by comparison, it can judge the species for circle Mouth copper fish.
Embodiment 3
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 C. guichenoti in embodiment 3 are as follows:
It is 99.7% with C. guichenoti DNA bar code sequence similarity degree by comparison, it can judge the species for circle Mouth copper fish.
It measures in 5 samples simultaneously, in addition the COI genetic fragment Yu C. guichenoti DNA bar code of 2 C. guichenoti samples Standard detection sequence similarity is 100%, it can judges the species for C. guichenoti.
According to sequencing result, the nucleotide sequence of above 5 samples and C. guichenoti DNA bar code standard detection sequence Homology can determine whether that these species are C. guichenoti 98% or more.
Embodiment 1, embodiment 2 and embodiment 3PCR reaction system and PCR response procedures are all the same, in this way can be more The accuracy for the C. guichenoti DNA bar code sequence that objectively the confirmation present invention obtains.
The obtained C. guichenoti DNA bar code sequence of the present invention can be used as the standard detection sequence of C. guichenoti DNA, To the progress and classification of C. guichenoti endemic species efficiently and accurately, while using the DNA bar code sequence to C. guichenoti sample It is identified, step is few, method is simple.In actual operation, which facilitates comparison convenient for saving.Circle Mouth copper fish is distributed mainly on the Endemic fish of Upper Yangtze River, Jinsha jiang River middle and lower reaches and Yalongjiang River downstream.Hydro-electricity ladder The gradually construction and operation in grade power station result in the migratory C. guichenoti habitat in river and are cut off, affect the complete of the history of life At, and inhabit ground area and also largely reduce.In the assessment of Chinese Wild vertebrate Endangered status, C. guichenoti is in Pole danger grade.Technical solution of the present invention can effectively identify C. guichenoti species, to instruct the protection of its resource.
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 C. guichenoti DNA bar code sequence and its application
<160> 1
<170> SIPOSequenceListing 1.0
<210> 1
<211> 672
<212> DNA
<213>C. guichenoti (Coreius guichenotiDNA bar code sequence)
<400> 1
gacattggca ccctttatct tgtatttggt gcctgagccg gcatagtagg gactgcttta 60
agcctcctca ttcgagctga actaagccag cccggatcac tactaggtga tgatcaaatt 120
tacaatgtta tcgttactgc ccacgccttc gtaataattt tctttatagt aataccaatc 180
cttattggcg gatttggaaa ctgactcgta ccgctaataa ttggagcacc cgatatggca 240
ttcccacgaa taaataatat aagtttctga cttttgccac cctcattcct tctattacta 300
gcctcttccg gggttgaagc tggggctggg acaggatgaa cagtttaccc accacttgca 360
ggtaatcttg cccatgcagg agcatcagta gacctaacaa ttttttcact gcacctagca 420
ggtgtctcat caatcttagg ggcaattaac ttcatcacca caaccattaa tatgaaaccc 480
ccagctattt cccaatacca aacacccctc tttgtgtggg ccgtacttgt aacagctgta 540
cttctccttc tatcactacc agtcttagct gccggaatta caatgcttct tacagaccgt 600
aatcttaata ccacattctt tgacccagca gggggaggag acccaatttt gtatcaacac 660
ttattctgat tc 672

Claims (3)

1. a kind of C. guichenoti DNA bar code sequence, which is characterized in that sequence is SEQ ID NO.1.
2. C. guichenoti DNA bar code sequence according to claim 1, which is characterized in that the C. guichenoti DNA bar shaped Code is C. guichenoti COI (cytochrome c oxidase subunit I, cytochrome c oxidase subunit I) gene.
3. a kind of application of C. guichenoti DNA bar code sequence, which is characterized in that the DNA bar code sequence can be used as round mouth The standard detection sequence of copper fish DNA, effectively identifies C. guichenoti endemic species and its sample.
CN201910674536.4A 2019-07-25 2019-07-25 A kind of C. guichenoti DNA bar code sequence and its application Pending CN110423823A (en)

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Cited By (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN114941034A (en) * 2022-05-27 2022-08-26 中国长江三峡集团有限公司中华鲟研究所 COI primer pair, kit and identification method for identifying cupfish and cupfish

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN105063031A (en) * 2015-08-05 2015-11-18 中国长江三峡集团公司 Coreius guichenoti microsatellite markers and use thereof
CN108998547A (en) * 2018-09-18 2018-12-14 中国水产科学研究院长江水产研究所 A kind of microsatellite marking method for C. guichenoti paternity test

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN105063031A (en) * 2015-08-05 2015-11-18 中国长江三峡集团公司 Coreius guichenoti microsatellite markers and use thereof
CN108998547A (en) * 2018-09-18 2018-12-14 中国水产科学研究院长江水产研究所 A kind of microsatellite marking method for C. guichenoti paternity test

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
FEI CHENG等: "Population genetic structure and its implication for conservation of Coreius guichenoti in the upper Yangtze River", 《ENVIRONMENTAL BIOLOGY OF FISHES》 *
黄燕: "长江上游特有鱼类DNA条形码研究", 《中国优秀硕士学位论文全文数据库 农业科技辑》 *

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN114941034A (en) * 2022-05-27 2022-08-26 中国长江三峡集团有限公司中华鲟研究所 COI primer pair, kit and identification method for identifying cupfish and cupfish
CN114941034B (en) * 2022-05-27 2023-10-13 中国长江三峡集团有限公司中华鲟研究所 COI primer pair, kit and identification method for identifying copper fish with round mouth

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Application publication date: 20191108