CN102277335A - Chinese Baoding isolate of sugarcane mosaic virus and complete sequence of genetic group thereof - Google Patents

Chinese Baoding isolate of sugarcane mosaic virus and complete sequence of genetic group thereof Download PDF

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CN102277335A
CN102277335A CN2011101172533A CN201110117253A CN102277335A CN 102277335 A CN102277335 A CN 102277335A CN 2011101172533 A CN2011101172533 A CN 2011101172533A CN 201110117253 A CN201110117253 A CN 201110117253A CN 102277335 A CN102277335 A CN 102277335A
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mosaic virus
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scmv
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CN102277335B (en
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李向东
高波
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Shandong Agricultural University
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Abstract

The invention belongs to the field of biotechnology. The inventor utilizes the nationally existed virus resource to obtain a Chinese Baoding isolate of sugarcane mosaic virus (SCMV) from infected plants and obtain a complete sequence of a genetic group. The biological collection number of the isolate is CGMCC No.4577; a detection primer can be designed by utilizing the sequence and the detection primer can be used for rapidly detecting SCMV; and a Ribonucleic Acid interference (RNAi) carrier also can be constructed by the sequence to convert corns to culture new disease-resistant species.

Description

Corn mosaic virus China's Baoding isolate and genom sequence thereof
Technical field
The present invention relates to microbial genome and plant protection field, particularly relate to a kind of genom sequence and application thereof of corn mosaic virus.
Background technology
The corn short mosaic disease is a kind of important worldwide disease.This disease was at first found at Ohio, USA in 1963 10, the corn main producing region of more than 20 countries discovery successively so far in the world.China's corn short mosaic disease is found in Xinxiang, Henan and Anyang early than nineteen sixty-eight, and each corn planting district that spread all over the country has at present caused loss in various degree for local Maize Production, and is wherein the heaviest with North China and northwest loss.
What cause having identified before the virales of corn short mosaic disease has: maize dwarf mosaic virus (Maize dwarf mosaic virus, MDMV), corn mosaic virus (Sugarcane mosaic virus, SCMV), Johnson grass mosaic virus (Johnsongrass mosaic virus, JGMV), Zea mosaic virus (Zea mosaic virus, ZeMV), white showy flowers of herbaceous plants mosaic virus (Pennisetum mosaic virus, PenMV) and sorghum mosaic virus (Sorghum mosaic virus, SrMV), above-mentioned 6 kinds of viruses have been formed corn mosaic virus (SCMV) subgroup that infects grass in the Potyvirus jointly.And the virus that causes China's corn short mosaic disease at present is mainly corn mosaic virus and white showy flowers of herbaceous plants mosaic virus.
The classification of virus is mainly based on serology, biology and molecular biology method, wherein virus is classified and become more and more important by molecular level, continuous improvement along with sequencing technologies, the reduction of cost, coming virus is classified by the sequence that records virus is one of current most important method.Present classification for Potyvirus virus is based on mostly analyzes and researches to the Nucleotide or the aminoacid sequence of certain gene, but because these genes can only be represented the complete genomic part of virus, therefore based on virus genome complete sequence virus being carried out sort research will be more reliable also more meaningful.In the 8th virus taxis report of up-to-date ICTV (ICTV), the criteria for classifying of Potyvirus inner virus kind is stipulated: CP consensus amino acid sequence rate<80%, full genome nucleotide sequence concordance rate<85%, and in an other research, show should be ORF and CP for Potyvirus viral species optimal dividing standard the nucleotide sequence concordance rate all<76%.It is just clear and definite just to be based on molecular biology evidence, causes the virus of China's corn short mosaic disease all to belong to corn mosaic virus, and is another strain system that is different from SCMV-MDB.
SCMV belongs to Potyvirus, it can be propagated in non-persistent mode by aphid, also can carry out long-distance communications by kind of a subband poison, therefore need be by determination and analysis to the SCMV complete sequence that causes the corn short mosaic disease, grasping its strain is the variation situation, makes up the rapid detection system, cultivates disease-resistant varieties, formulate positive prevention and control measure, thereby guarantee the safety of Maize Production.
Therefore how to know the complete sequence of this main Causative virus, and use the prevention and control that this complete sequence carries out disease, just become one of present problem demanding prompt solution.
Summary of the invention
Based on above-mentioned reason, the contriver utilizes domestic existing viral resource, from ill plant, obtained a kind of genom sequence of viral isolates, the contriver is with its called after corn mosaic virus (SCMV) Baoding isolate (BD8) (being called for short SCMV-BD8), by this sequence and existing SCMV genom sequence being analyzed existence and the distribution situation that can be used for clear and definite China SCMV strain system, cultivate transgenosis disease-resistant maize new variety for design RT-PCR rapid detection primer with structure RNA silent carrier foundation is provided, also can be the corresponding Maize Production prevention and control measure of formulation theoretical foundation is provided.
Corn mosaic virus provided by the present invention China Baoding isolate gene group complete sequence, its genom sequence shown in SEQ IDNO.1, its protein sequence just the sequence of open reading frame amino acids coding shown in SEQ ID NO.2;
The measuring method of this virogene complete sequence is as follows: the total RNA of maize leaf that shows obvious flower leaf paresthesia from a strain extracts, according to the listed SCMV complete sequence of GenBank conservative region design primer (seeing Table 1), utilization RT-PCR method increases, the purified recovery of the gene fragment that obtains is connected to later in the pMD18/19-T carrier and forms recombinant plasmid, the method that transforms by heat shock is transformed into it in competence bacillus coli DH 5 alpha again, screening through penbritin, utilize alkaline process to extract plasmid in a small amount after the picking list spot enlarged culturing, after plasmid PCR is defined as positive strain, it is delivered to order-checking company target gene fragment is checked order.(5 ' UTR) utilize the terminal rapid amplifying method of cDNA 5 ', and (5 ' RACE) obtain 5 ' terminal non-translational region.(Lynnon BioSoft, ver.5.2.2) (DNASTAR Inc., USA) SeqMan in carries out sequence assembly to each fragment sequence that obtains, and finally obtains complete SCMV-BD8 complete nucleotide sequence with DNASTAR 5.00 software packages with the DNAMAN software package.
Table 1BD8 gene fragment amplification the primer
Figure BSA00000490396100021
▲ utilize the degenerate primer of the conservative section design of SCMV isolate Nucleotide
◆ the position of primer sequence in the final SCMV-BD8 complete nucleotide sequence that obtains
★ annexs site Y=T/C, R=A/G, N=A/C/G/T, H=A/C/T
☆ is used for the anchor primer of 5 ' RACE
The gene complete sequence that the present invention obtained, shown in SEQ ID NO.1, its maximum characteristics are: this sequence total length is 9576nt (nucleotide), based composition is: A:33.38%, G:21.99%, T:24.74%, C:19.89% is with other members' of Potyvirus based composition basically identical.The long 148nt of its 5 ' UTR nucleotide sequence, 3 ' UTR is long to be 236nt.Its ORF is by 9192 based compositions, and will encode one and contain 3063 amino acid, and molecular weight is the polyprotein of 345.97kDa.By with SCMV-BD8 and the conservative motif comparison in 13 each protease hydrolysis sites of SCMV isolate complete sequence coding region ORF having reported in addition, 9 protease cracking sites (table 2) have been determined 2,, under the hydrolytic action of HC-Pro and NI a-Pro polyprotein cut into 10 sophisticated albumen in the protease P 1 of encoding viral 8
Table 2SCMV-BD8 genome structure and functional protein cracking site sequence thereof
Font-weight illustrates this amino acid to be conservative site
The ORF Nucleotide and the consensus amino acid sequence rate scope of the complete nucleotide sequence of SCMV-BD8 disclosed in this invention and 13 SCMV isolate complete sequences having reported in addition and one MDMV isolate AJ 001691 complete sequence being carried out concordance rate comparison result shows itself and other 13 SCMV isolates are respectively 78.9%-80.7% and 89.7%-91.5%, and wherein Nucleotide and the consensus amino acid sequence rate with Guangdong isolate AJ 310105 is the highest; Full genome nucleotide sequence concordance rate scope is 79.1%-80.8%; The Nucleotide of CP and consensus amino acid sequence rate scope are respectively 76.9%-82.6% and 82.8%-86.9%.ORF Nucleotide and the consensus amino acid sequence rate of itself and MDMV are respectively 69.5% and 74.3%, and full genome nucleotide sequence concordance rate is 69.2%, and CP Nucleotide and consensus amino acid sequence rate are respectively 71.0% and 75.6%.Therefore gained isolate SCMV-BD8 of the present invention and other 13 SCMV isolates should belong to virus of the same race.
With isolate SCMV-BD8 of the present invention and other 13 SCMV isolate complete nucleotide sequences is that the other nationality grows tree by multisequencing comparison back constructing system with MDMV, the result shows that SCMV-BD8 and Australian A strain are that isolate AJ278405 all independently becomes one, and Sino-Spanish, Mexican corn isolate is poly-for cluster is called as corn group (Maize group), and the sugarcane isolate in Chinese Zhejiang and corn isolate are poly-to be called as corn or sugarcane group (Sugarcane﹠amp for cluster; Maize) 1Corn mosaic virus isolate SCMV-BD8 involved in the present invention in sum should belong to a new strain system of this virus, and we are at called after MDC (causing maize dwarf in China) strain.
With viral isolates involved in the present invention is toxogen, 12 commercially available corn varieties have been carried out the juice frictional inoculation in the greenhouse, each kind all shows as high sense to SCMV-BD8 as a result, illustrates that the new strain of gained of the present invention is that virulence is very strong, is a virulent strain department.Therefore should be new strain system virus probably become the Maize Production of next popular strain system threat China.In this case, the new strain of corn mosaic virus involved in the present invention is that isolate SCMV-BD8 complete sequence will provide important clue and theoretical foundation for effective prevention and control of detection, disease-resistant maize breed of variety and the corn disease viral disease of China's corn mosaic virus.
Preservation information
The preservation time: on February 18th, 2011
Depositary institution's title: the common micro-organisms center C GMCC of China Committee for Culture Collection of Microorganisms
Deposit number: CGMCC NO.4577
Depositary institution address: No. 3, Yard 1, BeiChen xi Road, Chaoyang District, Beijing City
Classification name: corn mosaic virus
Description of drawings
Fig. 1 SCMV-BD8 full length nucleotide sequence clone strategy synoptic diagram;
The full-length gene group of BD8 obtains by 4 RT-PCR and 5 '-RACE, and the used primer of reverse transcription generally all is special, and forward primer is the degenerated primer according to the sequences Design of SCMV;
The systematic evolution tree that Fig. 2 utilizes SCMV-BD8 and other 13 SCMV isolate complete nucleotide sequences to make up;
Each isolate is listed with accession number/title/host/source place form among the figure, the value of bootstrapping of the numeral on the branch;
From evolutionary tree, begin to find out, SCMV-BD8 form one independently with A, corn group, the sugarcane/parallel branch of corn group, illustrate that BD8 is that the new strain of SCMV is.
Embodiment
Embodiment 1: the acquisition of viral isolates
From the corn field of Baoding, Hebei province, gather the blade that is obvious flower leaf paresthesia in July, 2009, obtain viral isolates, called after BD8.Sample retention is numbered No.4577 at China Committee for Culture Collection of Microorganisms common micro-organisms center (CGMCC).With this virus strain be malicious source frictional inoculation on the healthy milpa so that virus under greenhouse experiment, duplicated.
The extraction of embodiment 2:RNA and RT-PCR
The amplification of BD8 genomic fragment is carried out according to strategy shown in Figure 1.Genome divides earlier A, B, C, D to increase for 4 sections, and per two intersegmentally have the overlapping of 100-200 base.5 '-UTR increases by RACE.
1.RNA extract
(Beijing TransGen Biotech Co., the method that Ltd) provides are extracted total RNA from susceptible maize leaf according to the TransZol test kit.
2. reverse transcription-PCR (RT-PCR) reaction
With the viral RNA that contains among the total RNA of plant is that template is carried out reverse transcription.
Gene fragment A
The reverse transcription system
Figure BSA00000490396100051
Hatch 50min for 42 ℃ behind the above composition mixing, hatch the 15min stopped reaction for 70 ℃.The gained reverse transcription product is used for the PCR reaction.
The PCR system
Figure BSA00000490396100052
Above component mixes to be placed in the PCR instrument and increases.Response procedures is: 94 ℃ of pre-sex change 3min; 94 ℃ of sex change 30s, 50 ℃ of annealing 30s, 72 ℃ are extended 2.5min, totally 35 circulations; 72 ℃ are extended 10min.
Gene fragment B
The reverse transcription system
Hatch 50min for 42 ℃ behind the above composition mixing, hatch the 15min stopped reaction for 70 ℃.The gained reverse transcription product is used for the PCR reaction.
The PCR system is
Above component mixes to be placed in the PCR instrument and increases.Response procedures is: 94 ℃ of pre-sex change 3min; 94 ℃ of sex change 30s, 50 ℃ of annealing 30s, 72 ℃ are extended 2.5min, totally 35 circulations; 72 ℃ are extended 10min.
Gene fragment C
Hatch 50min for 42 ℃ behind the mixing, hatch 15mi n stopped reaction for 70 ℃.The gained reverse transcription product is used for the PCR reaction.
Figure BSA00000490396100062
Mix to be placed in the PCR instrument and increase.Response procedures is: 94 ℃ of pre-sex change 3min; 94 ℃ of sex change 30s, 50 ℃ of annealing 30s, 72 ℃ are extended 2.5min, totally 35 circulations; 72 ℃ are extended 10min.
Gene fragment D
The reverse transcription system is:
Figure BSA00000490396100063
Hatch 50min for 42 ℃ behind the mixing, hatch the 15min stopped reaction for 70 ℃.The gained reverse transcription product is used for the PCR reaction.
The PCR reaction system is:
Figure BSA00000490396100064
Each component mixes to be placed in the PCR instrument and increases.Response procedures is: 94 ℃ of pre-sex change 3min; 94 ℃ of sex change 30s, 55 ℃ of annealing 30s, 72 ℃ are extended 2.5min, totally 35 circulations; 72 ℃ are extended 10min.
3.cDNA terminal rapid amplifying method (RACE) acquisition 5 '-the UTR sequence
Adopt the method purification SCMV virus of beam new talent.Get 100 μ l purified virus liquid and add 1ml Trizol, method is extracted with the total RNA of plant afterwards.The viral RNA that obtains is used for next step 5 ' RACE method, amplification 5 '-the UTR fragment.
(1) cDNA first chain is synthetic
On ice following composition is joined in the Eppendorf pipe:
Figure BSA00000490396100071
In the another one pipe, add 1 μ l reverse transcription special primer GSP456 (10 μ M) and 11 μ l RNA, totally 12 μ l, 80 ℃ of sex change 3min, place rapidly after the cooled on ice wink from.
Will be behind the mixed solution mixing in two pipes add 1 μ l (200U) SuperScript II RT,, hatch 1h in 42 ℃, hatch 10min for 50 ℃ afterwards with rifle head mixing gently.Form DNA-RNA heterozygote in the pipe this moment.Hatch 15min for 70 ℃ and make enzyme deactivation.
(2) degraded of RNA in the DNA-RNA heterozygote
The RNase H that uses TaKaRa company to produce, the RNA in degradation of dna-RNA heterozygote.
The following reaction solution of preparation in Eppendorf tube:
Figure BSA00000490396100072
30 ℃ were reacted 1 hour.
(3) cDNA purifying
EasyPure rapid DNA gel with Beijing Quan Shi King Company reclaims test kit, provides method purification cDNA by it, with 30 μ l H 2O returns molten.
(4) 5 ' add end reaction
The terminal enzyme (DNA) (TdT) that uses TaKaRa company to produce, the following reaction solution of preparation in Eppendorf tube, cumulative volume 50 μ l.
Figure BSA00000490396100073
37 ℃ of reaction 15min, EDTA (pH 8.0) termination reaction that adds NaCl and the 1 μ l 0.5M of 5 μ l 5M, after using phenol/chloroform/primary isoamyl alcohol (25: 24: 1) 50 μ l extractings then, carry out 125 μ l (2.5 times of consumptions) dehydrated alcohol precipitation, place 30-60min for-20 ℃, the gained precipitation is dissolved in 10 μ l ddH after centrifugal 2Be used for pcr amplification (using after diluting 10 times) subsequently among the O.
(5) pcr amplification
The high-fidelity LA Taq archaeal dna polymerase that uses TaKaRa company to produce adds following reaction solution in Eppendorf tube:
Figure BSA00000490396100074
Figure BSA00000490396100081
Increase on the PCR instrument, program is: 94 ℃ of 3min, 48 ℃ of 2min, 72 ℃ of 40min; 94 ℃ of 30s, 60 ℃ of 30s, 72 ℃ of 1min carry out 30 circulations; 72 ℃ are extended 10min.
Take turns nest-type PRC with carrying out second after 20 times of the first round PCR product dilutions, reaction solution is:
Figure BSA00000490396100082
The pcr amplification program is 94 ℃ of 3min; 94 ℃ of 30s, 60 ℃ of 30s, 72 ℃ of 1min carry out 30 circulations; 72 ℃ are extended 10min.
Embodiment 3:PCR product purification reclaims and the clone
Pcr amplification product downcuts the purpose band behind 1% agarose gel electrophoresis, reclaims the method purifying recovery DNA of test kit (centrifugal column type) (Beijing Bioteke Corporation) by its specification sheets with the multifunctional dna purifying.
Method on the by specification, the DNA that purifying is reclaimed is connected to pMD18/19-T, and (TaKaRa Biotechnology Dalian Co is Ltd) on the carrier.The recombinant plasmid that connects heat shock method Transformed E .coli DH5 α, alkaline process extracts recombinant plasmid, PCR evaluation and screening positive colony.
Embodiment 4: sequencing and analysis
Each segment is got 3 positive colonies and is sent to Nanjing Genscript Biotechnology Co., Ltd. and checks order.5 ' RACE is obtained the sequence that segmental positive colony will be measured 6 clones at least.
(Lynnon BioSoft, ver.5.2.2) (DNASTAR Inc., USA) SeqMan in splices each fragment sequence that records, and carries out the comparison of sequence concordance rate with the MegAlign among the DNASTAR with DNASTAR 5.00 with DNAMAN.Use the CLUSTAL W in MEGA 4.0 softwares to carry out the multisequencing comparison, and then with adjacent method (neighbor-joining, NJ) constructing system evolutionary tree.
BD8 genome total length is 9576 Nucleotide (nt), with the full genome nucleotide sequence concordance rate scope of other 13 SCMV isolates be 79.1%-80.8%, ORF Nucleotide and consensus amino acid sequence rate scope are respectively 78.9%-80.7% and 89.7%-91.5%, and wherein Nucleotide and the consensus amino acid sequence rate with Guangdong isolate (AJ310105) is the highest; The Nucleotide of CP and consensus amino acid sequence rate scope are respectively 76.9%-82.6% and 82.8%-86.9%.The full genome nucleotide sequence concordance rate of SCMV-BD8 and MDMV is 69.2%, and ORF Nucleotide and consensus amino acid sequence rate are respectively 69.5% and 74.3%, and CP Nucleotide and consensus amino acid sequence rate are respectively 71.0% and 75.6%.According to the criteria for classification of ICTV (ICTV), gained isolate BD8 of the present invention with should belong to corn mosaic virus (SCMV).
In systematic evolution tree, SCMV can be divided into four groups, and one of all independent one-tenth of wherein Australian isolate (AJ278405) is called the A group; China, Spain and Mexican corn isolate are poly-for cluster, are called corn group (Maize group); The sugarcane isolate in China Zhejiang and corn isolate are poly-to be cluster, is called corn or sugarcane group (Sugarcane﹠amp; Maize); Corn mosaic virus Baoding isolate SCMV-BD8 involved in the present invention forms an independently group in evolution is stated, be a new strain system (MDC) of this virus.
Embodiment 5: the biology test
With greenhouse morbidity strain is 12 kinds of common corn varieties on the frictional inoculation market, fresh malicious source: north, Tianjin 288, and Five Sacred Mountins 97-1, Five Sacred Mountins 21, black beautiful No. 2, the former list 22 in Shandong is chatted jade 19, Shandong list 850, Zheng Dan 958, agricultural university 108, Shandong list 981, Lu Yu 15, No. 7, safe jade; 9-12 of every kind inoculation do not wait, and cultivates under 22~25 ℃ of conditions in greenhouse, observes and the record incidence result such as following table after 15 days:
The sickness rate of table 3 inoculation 12 corn varieties after SCMV-BD815 days
Experimental results show that, 12 corn varieties of test all show high sense to SCMV-BD8, illustrate that the new strain of gained of the present invention system virus is virulent strain department, this new strain system probably becomes the Maize Production that next popular strain system threatens China, in this case, the new strain of corn mosaic virus involved in the present invention is that isolate SCMV-BD8 complete sequence will be the detection of China's corn mosaic virus, and the corn disease-resistant variety is cultivated and the formulation of Maize Production prevention and control measure provides the important theory foundation.
Figure ISA00000490396300011
Figure ISA00000490396300021
Figure ISA00000490396300031
Figure ISA00000490396300041
Figure ISA00000490396300051
Figure ISA00000490396300061
Figure ISA00000490396300071
Figure ISA00000490396300081
Figure ISA00000490396300091
Figure ISA00000490396300101
Figure ISA00000490396300111
Figure ISA00000490396300131
Figure ISA00000490396300141
Figure ISA00000490396300161
Figure ISA00000490396300171
Figure ISA00000490396300181
Figure ISA00000490396300201
Figure ISA00000490396300211
Figure ISA00000490396300221
Figure ISA00000490396300231
Figure ISA00000490396300241
Figure ISA00000490396300251

Claims (4)

1. corn mosaic virus China Baoding isolate, its biological preserving number is: CGMCC NO.4577.
2. according to the described corn mosaic virus of claim China Baoding isolate, it is characterized in that: its genom sequence is shown in SEQ ID NO.1, and the sequence of its open reading frame amino acids coding is shown in SEQ IDNO.2.
3. the corn mosaic virus China Baoding isolate gene group complete sequence of gene order shown in SEQ ID NO.1, its forward and inverse kernel nucleotide sequence and deutero-recombinant plasmid or transgenic plant thus are in the application that improves aspect the anti-SCMV ability of corn.
4. nucleotide sequence and the complementary sequence thereof of all or part of gene preface shown in open reading frame coded amino acid among corn mosaic virus China Baoding isolate gene group complete sequence SEQ ID NO.1 as described in the claim 2, the application in the PCR of corn mosaic virus quick diagnosis.
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CN108728581B (en) * 2018-06-26 2021-02-05 广西大学 Multiple RT-PCR method for simultaneously detecting 5 sugarcane viruses, primers and kit thereof

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