CN109504681A - A kind of banana Fusarium oxysporum milRNA - Google Patents
A kind of banana Fusarium oxysporum milRNA Download PDFInfo
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Abstract
The invention discloses a kind of banana Fusarium oxysporum encoding endogenous milRNA.The present invention obtains the endogenous milRNA of banana Fusarium oxysporum coding by Deep sequencing deep sequencing, provides previous work place mat for subsequent further exploitation, using mechanism of action of the tiny RNA in banana Fusarium oxysporum.
Description
The application is application number CN201810175831.0, the applying date 20180302, denomination of invention " banana Fusarium oxysporum
The divisional application of the Chinese invention patent application of the Validation in vitro method of milRNAs and low abundance milRNAs ".
Technical field
The present invention relates to field of biotechnology, and in particular to banana Fusarium oxysporum milRNA.
Background technique
1, the expression of plant endogenous miRNA negative regulation target gene in a manner of gene silencing after transcription, it is raw in plant
Long development, the degeneration-resistant many aspects such as disease-resistant play an important role
Eukaryotic tiny RNA is broadly divided into microRNAs (miRNAs), siRNAs and piRNAs.MiRNA and siRNA
Length is about 20~25nt, is processed and is generated by the endonuclease Dicer (or Dicer albuminoid) of similar RNase III,
Their formation was not only related but also had any different.SiRNA approach is by being external source invasion, such as virus, transposons and transgenosis etc.
Generate what variant dsRNA caused;And miRNA approach is induced by endogenous hpRNA.SiRNA and miRNA is by DCLs (or Dicer
Albuminoid) shearing formation, wherein the silencing complex (RNA-Induced that the chain combination RNA complementary with mRNA is induced
Silencing Complex, RISC), the homologous mRNA of acting sequences in a manner of PTGS passes through mRNA shearing, Translational repression
Or the expression of the modes controlling gene such as methylation.PiRNA relies on PiWi Protein processing maturation, and there is only zooblasts.
Plant endogenous miRNA is cut from the endogenous transcript containing loop-stem structure by III type RNase nuclease Dicer
The small molecule non-coding RNA for generating one kind 21-24nt length, through post-transcriptional level in a manner of mRNA shearing or Translational repression
The homologous mRNA target gene of silencing sequence.MiR-96 gene is distributed widely in Plant Genome, usually has in the genome
Independent gene locus (1ocus), transcription product itself are folded into the hairpin structure (hairpin) of incomplete pairing.Have
Largely report confirms that plant endogenous miRNAs participates in plant and the PTI and ETI of pathogen are immunized, and in plant growth and development, resists
It plays an important role against many aspects such as disease-resistant.
2, there is the tiny RNA s (microRNA- similar in structure, length, the mode of action with Mirnas of plant in fungi
Like RNAs, milRNAs).
MilRNAs most early in what is found in Neurospora crassa (Neurospora crassa), is being tied with plant microRNA
It is closely similar in structure, tiny RNA length and the mode of action, microRNA-likes is named because of similar with the miRNA of plant
(milRNAs).The milRNAs of Neurospora crassa is by Dicers, QDE-2, the QIP effect protein of exonuclease activity and
Mitochondrial ribosome large subunit MRPL3 albumen (mitochondrial ribosomal with type III RNase functional domain
Protein large subunit, MRPL3) various combination, generate there are four types of different biological forming features.Although four kinds
The RNA precursor sequence different length transcribed in approach from intergenic region, but all there is hairpin structure, the milRNAs of formation has
Have the Preference of the end 5' U, can specifically with Argonaute (AGO) protein binding;In addition, experiments have shown that milR-1 can lead to
The mode for crossing gene silencing, which acts on, adjusts target sequence (NCU07311) mRNA, is mainly carried out by way of inhibiting mRNA translation,
With plant microRNA in such a way that mRNA is sheared and inhibits transcription inconsistent (Lee et al., 2010).MilR-1 is structure
The highest miRNA-like RNAs of abundance in nest aspergillus, Xue et al. (2012) using milR-1 as research object construct according to
The biochemical research frame for relying the in vitro biology of the milR-1 of AGO to be formed, research shows that the processing maturation of milR-1 can be with
It is divided into 5 steps, it is different with the biosynthesis pathway of plant microRNA to be, in addition to QDE-2, the core proteins such as Dicer
Group is exceptionally, it is also necessary to which mature tiny RNA (Xue is processed into the common participation of the external complex of QIP and RNA (exosome)
et al.,2012)。
Then, the tiny RNA Developments of plant pathogenic fungi are rapid, at rice blast (Magnaporthe oryzae)
(Nunes et al., 2011) rape endophytic bacterial (Sclerotinia sclerotiorum) (Zhou et al., 2012) grape
Botrytis cinerea (Botrytis cinerea) (Weiberg et al., 2013;Wang et al., 2017a) phytophthora
(Phytophthora) (Fahlgren et al., 2013) Fusarium oxysporum tomato specialized form (Fusarium oxysporum
F.sp.lycopersici) (Chen et al., 2014) aspergillus flavus (Aspergillus flavus) (Bai et al.,
2015) wheat item rust (Puccinia striiformis f.sp.tritici) (Mueth et al., 2015;Wang et
Al., 2017b) in have been found that there are milRNAs successively.With advances in technology, deep sequencing can predict low abundance
The presence of milRNA and its frame sequence, but since milRNAs most in disease fungus expression background level is too low, often
The isotope of rule32The miRNA probe of p-ATP label can not detect low-abundance milRNAs, therefore, it is impossible to low-abundance
MilRNAs and its hairpin are verified.
3, there is MicroRNA gene silencing transboundary between plant pathogenic fungi and host, the immune response of host is inhibited to promote
Pathogen is infected.
Disease fungus, which is entered inside plant cell using tiny RNA as effector (effector), inhibits plant immune anti-
Defend reaction.The gray mold that botrytis cinerea causes can infect 200 various plants.Weiberg et al. (2013) researches show that ashes
Mould can convey Bc-sRNAs and enter host cell by specifically binding inhibition AGO1 function with AGO1, and silencing host's exempts from
Epidemic disease related gene promotes pathogen infection.The Δ ago1 deletion mutant of arabidopsis reduces pair due to losing AGO1 function
The sensibility of botrytis cinerea;On the contrary, the Δ dcl1dcl2 double-mutant of botrytis cinerea is complete due to that can not process generation Bc-sRNAs
Lose infectivity.Therefore, the nosomycosis original by transfer there is the tiny RNA effector of pathogenicity to enter host cell and pass through
The defense response of host is inhibited to promote infecting for pathogen, which illustrates this abiogenous RNAi silencing phenomenon transboundary
A kind of more advanced pathogenic mechanism (Weiberg et al., 2013) as disease fungus.In addition, in grape botrytis cinerea
It has also been found that the Bc-siR37 of a low abundance expression in (Botrytis cinerea), up-regulated expression when only infecting, and Bc-
3 determining action targets of siR37 are all that host immunity is relevant (Wang et al., 2017).Bc-DCL1 and DCL2 are
The main component of Bc-sRNAs is generated, silencing DCLs can substantially reduce the pathogenicity of pathogen.There are environment RNAi for pathogen
External RNA can be absorbed, can pass through in the dsRNA and sRNA of water fruits and vegetables and the surface applied of fresh flower targeting DCLs
Regulate and control Bc-sRNAs expression to substantially reduced gray mold symptom (Wang et al., 2016;Wang et al.,2017a).
Tiny RNA is a kind of important virulence factor of disease fungus.The Pst-milR1 of stripe rust of wheat coding is only infecting
When inducing expression, in Pst by BSMV gene silencing inhibit Pst-milR1 expression obviously reduce stripe rust cause a disease
Property, meanwhile, its target wheat pathogenesis related gene PR2 (SM638) is knocked out in wheat then enhances wheat to avirulent strains
Susceptibility, positive and negative experiment confirm that Pst-milR1 targets host immunity related gene PR2 (SM638) in a manner of trans-kingdom gene silencing
To inhibit the immune response of host to promote pathogen infection (Wang et al., 2017b).
4, the research of banana Fusarium oxysporum
Banana blight (Fusarium oxysporum f.sp.cubense, Foc) is to destroy banana vascular bundles to cause to plant
The dead crushing soil-borne disease of strain, germ is saprophytic very capable, in the soil can long-term surviving, belong to typical resting form
It infects.The performance of early stage external symptom is unobvious, and the middle and later periods just shows symptom, therefore, causes to banana industry and banana planting person
Huge economic loss.The area Zhi Jiao, the world has found that it has 4 biological strains (there is likely to be other microspecies), and wherein physiology is small
Kind 1 infects dwarf banana (ABB group), Musa AAB (AAB group) class and part AAA group kind;Biological strain No. 2 are only infected three times of hybridization
Body rib banana (ABB) is smaller to the harm of banana cultivar;Biological strain No. 3 are infected wild castrated ram's tail any of several broadleaf plants category, to banana cultivation
Training kind does not cause damages, and has been reported that in many areas;Biological strain No. 4 are infected fragrant tooth any of several broadleaf plants, Musa AAB, plantain, host
Range is greater than biological strain No. 1.No. 4 biological strains are divided into subtropical zone 4 (Subtropical Race4, SR4) and the torrid zone 4 again
Number microspecies (Tropical Race4, TR4) are mainly No. 1 and No. 4 biological strains in China, wherein the microspecies harm of the torrid zone 4 is most
Seriously.
Currently, banana does not have effective resistance germ plasm resource, without effective chemical prevention and control method in production, therefore, training
Educating resistant strain is one of the fundamental way for solving banana blight.Tiny RNA is in mediating pathogen-host's interaction process
It plays an important role, there is the great potential for promoting Genes For Plant Tolerance disease ability.Whether banana Fusarium oxysporum encodes tiny RNA, is
It is no using tiny RNA promotion infect equal correlative studys do not have at present it has been reported that for this purpose, we to have carried out banana Fusarium oxysporum endogenous
Tiny RNA identification and detection verifying work.
Summary of the invention
In place of the above the deficiencies in the prior art, the present invention provides a kind of banana Fusarium oxysporum milRNA.
The technical solution adopted by the present invention is as follows:
A kind of banana Fusarium oxysporum milRNA, the gene order of the banana Fusarium oxysporum milRNA is as shown in SEQ ID NO:1.
The invention further relates to a kind of carrier, the carrier contains milRNA described in claim 1.
The invention further relates to a kind of competent cell, the competent cell contains milRNA as described in claim 1
Or contain carrier as claimed in claim 2.
Compared with prior art, the beneficial effects of the present invention are:
Banana Fusarium oxysporum milRNA is obtained by deep sequencing, is subsequent further exploitation, withered in banana using tiny RNA
The mechanism of action to wither in bacterium provides previous work place mat.
Detailed description of the invention
Fig. 1: tiny RNA sequencing result statistical chart;
In figure, the length statistical result of tiny RNA in the four tiny RNA libraries (A);(B) four tiny RNA database tiny RNA sequences
The Venn of column schemes;(C) the 5 terminal bases Preference of tiny RNA obtained analyzes result;(D) normal chain in four tiny RNA databases, negative
The tiny RNA in chain source counts;
Fig. 2: the isotope of high abundance milRNAs32The reverse complemental DNA probe results of hybridization of P-ATP label;
In figure ,-: spore;+: mycelia;M: *: mixing sample indicates the adjoint chain tiny RNA of milRNA;
Fig. 3: the outer transient expression assay of this life of agroinfiltration smoke verifies low abundance milRNAs result;
In figure, soaked in (A) banana Fusarium oxysporum Foc containing 21nt, 5'-U structure feature candidate milRNAs this life tobacco grower bacillus
It is corresponding after profit32The DNA probe hybridization check result of P-ATP label;(B) other different lengths in banana Fusarium oxysporum Foc, no
It is corresponding after the milRNA of 5' terminal bases this life cigarette agroinfiltration32The DNA probe hybridization check result of P-ATP label.
Specific embodiment
Below by specific embodiment combination attached drawing, invention is further described in detail.
The main agents being related in the embodiment of the present invention:
Trizol(TRNzol Reagent,Tiangen,Cat#DP405-02)
8000 precipitation buffering liquid of PEG: 20% (w/v) PEG 8000,1M NaCl.
EDC cross-linking buffer (12ml): 122.5 μ l 12.5M 1- methylimidazoles (pH8.0), 0.373g 1- ethyl -3-
(3- dimethylaminopropyl) phosphinylidyne diimmonium salt hydrochlorate (EDC).
MiRNA Northern blotting hybridization buffer: 5 × SSC, 20mM NaHPO4 (pH7.2), 7%SDS, 3
× Denhardt`s solution.
17%dPAGE: urea 12.6g, water 1.25ml, 10 × TBE 1.5ml, Acr/Bis (30%) 17ml, in micro-wave oven
Or dissolved urea in hot water, 240 μ l 10%AP are added after cooling, 10 μ l TEMED are added after mixing.
Washing Buffer:2 × SSC, 0.1%SDS.
1M MES (pH5.6,10ml): it weighs 2.132g MES and is dissolved in sterile water, with KOH tune pH to 5.6, be settled to
10ml, filtration sterilization are dispensed into centrifuge tube, -20 DEG C of preservations.
100mM AS (10ml): it weighs 0.1962g AS and is dissolved in DMSO, be settled to 10ml, be dispensed into 1.5ml centrifuge tube
In, -20 DEG C of preservations.
Embodiment 1: tiny RNA sequencing and bioinformatic analysis
Foc1, the mycelia of Foc4 and the tiny RNA library of spore are constructed respectively, send Beijing Hua Da gene sequencing, and sequencing obtains
Data as shown in figure 1 and table 1.
1 tiny RNA sequencing data list of table
By bioinformatic analysis, identify 88 have complete hair clip (stem-loop structure) and two
End generates the milRNAs of tiny RNA, (2 are shown in Table, table 2 gives one of milRNA, it is named as milRNA8, and
The adjoint chain tiny RNA of milRNA8).
MiRNA-likes (milRNAs) list that 2 Foc of table sequencing obtains
Embodiment 2: the hybridization check of high abundance milRNAs
1, the extraction of tiny RNA:
The acquisition of 1.1 samples
It is cultivated 5-7 days for 28 DEG C after bacterial strain PDA inoculation, beats bacteria cake (diameter 0.5cm) at the edge of PDA plate with punch,
The access of picking 5-6 ferfas cake is equipped in the 250mL triangular flask of 100mL PDB culture solution, in 28 DEG C, 180rpm shake culture 5-7d
It is filtered afterwards with three layers of filter paper, obtains spore respectively and mycelia carries out subsequent tiny RNA extraction.
1.2, Trizol is extracted
Under protection of liquid nitrogen, the sample that step 1.1 is obtained is transferred to centrifuge tube after pulverizing, and isometric Trizol is added
Reagent is placed at room temperature for 5-10min after sufficient vortex.The chloroform of 1/5 volume: isoamyl alcohol (24:1) is added, is stood on ice after vortex
3-5min is centrifuged after AUTOMATIC ZONING, 12000g, is centrifuged 10min under the conditions of 4 DEG C.
1.3, fractional precipitation high molecular weight RNA
After centrifugation, supernatant is transferred to new centrifuge tube, and the PEG8000 precipitation buffering of 65 DEG C of isometric incubations is then added
Liquid is stored at room temperature until being cooled to room temperature after being mixed by inversion, and then centrifugation 10min precipitates high molecular weight after ice bath 30-45min
RNA。
1.4, tiny RNA is precipitated
The isopropanol of 3M NaAc (pH5.2) and isometric pre-cooling of supernatant 1/10 volume of addition after centrifugation, -20
DEG C precipitating 1-2hr, 12000g, 4 DEG C of centrifugation 20min, for precipitating with ethanol washing 1-2 times of 80%, DEPC water is put into -80 after dissolving
It is DEG C spare.
2, the hybridization check of tiny RNA:
2.1,17%dPAGE is separated
The tiny RNA that step 1 is extracted dissolves in isometric milRNAs Loading buffer (ABI, cat.AM8547),
After 100 DEG C of denaturation 5min, ice bath 5min is denaturalized RNA sample completely immediately.MilRNAs sample after denaturation is in 17%dPAGE
Loading, 0.5 × TBE electrophoretic buffer, 300V electrophoresis 3-6h.
2.2, transferring film and crosslinking
Gel containing RNA is cut, first infiltrates 30s in 1 × TBE transferring film buffer, while getting out the neutral electricity of NX
Lotus nylon membrane (GE) and transferring film filter paper, according to illustrating to carry out transferring film.Sequence from top to bottom is successively: filter
Paper-gel-NX nylon membrane-filter paper.It drives away and carries out transferring film with the half-dried transferring film instrument of GE TE77 PWR after bubble, with 400mA transferring film 1h
?.Turn to be placed on film after film on the filter paper of EDC cross-linking buffer infiltration, the one side of contact RNA upward, avoids handing over when transferring film
Connection buffer is dipped on RNA, and after 60 DEG C of baking 2h, remaining EDC cross-linking buffer on clear water flushing membrane, -20 DEG C are saved backup.
2.3, tiny RNA hybridizes
MiRNA hybridization uses miRNA Northern blotting hybridization buffer, eitherCompanyHybridization buffer (Cat#AM8663) hybridization buffer.Film after crosslinking is put into
Hybrid pipe, the one side for contacting RNA contact hybridization buffer inwardly, are added and use32P-ATP label with tiny RNA sequence reverse mutual
The first prehybridization 1hr of 40-42 DEG C of the DNA probe of benefit, then 37 DEG C of hybridized overnights.
2.4 exposures and signal detection
The hybridization solution with isotope is outwelled after hybridization, washes film 2 times with washing buffer, each 15-
20min.Signal is detected with monitor after washing, the signal of positive region should be stronger than the signal in film edge place, and by signal
Control, if overflow, continues to wash film within 5 μ Ci.Film is loaded on preservative film or stretched film after washing film, is placed on
30min-3h or so is exposed in phosphorus screen, is put into Typoon scanning and is saved picture.As a result see Fig. 2.
Embodiment 3: the gene transient expression of the outer mediated by agriculture bacillus of this life smoke of low abundance milRNAs
1, the preparation of this life cigarette
This life cigarette Seed storage is in Research Institute of Environment and Plant Protection, Chinese Academy of Tropi laboratory, this life cigarette
(N.benthamiana) in 23-25 DEG C, the photoperiod of 14h illumination/10h dark (about 75 μm of ol/m2.s) is grown, 6-8
Agroinfiltration is carried out when piece leaf.After infiltrating 48-72hr, the region not infiltrated by Agrobacterium bacterium solution is wiped out with scissors, is taken
Freeze immediately afterwards into liquid nitrogen, -80 DEG C save until using.
2, candidate's milRNA expression vector establishment
According to the prediction of bioinformatics, design primer amplification contains candidate's milRNA skeleton in the genomic DNA of Foc
DNA sequence dna, be connected on T-vector be sequenced after compared with reference genome sequence, determine amplification sequence do not contain
Then code area and exon region are connected to expression vector pSuper1300 by Xba I-Kpn I or Xba I-Sac I
In (improved carrier of pCambia1300), the correctness of digestion verification or PCR verifying sequence.Details are shown in Table 3.
3, this life of agroinfiltration cigarette
(1) the electroporated method of clone built is imported into Agrobacterium competent cell, be coated on additional corresponding
On the LB solid plate of antibiotic, 28 DEG C dark culture two days.
(2) the picking single colonie after growing bacterium colony on LB plate is inoculated into the LB Liquid Culture that 2ml adds corresponding antibiotic
In base, 28 DEG C, 250rpm shaken cultivation r for 24 hours.
(3) 2ml bacterium solution is inoculated into 20ml to add in the LB liquid medium of corresponding antibiotic, 200 μ l 1M MES is added
(pH5.6) and 8 μ l 100mM AS, 28 DEG C, 250rpm shaken cultivation 12hr.
(4) bacterium solution is centrifuged 15min in 4000rpm, is precipitated with 10mM MgCl2 suspension thalline, adjust OD600=1.0.
(5) 100mM AS is added, added volume and uses MgCl2Bacterium solution volume relationship after suspension are as follows: VAS(μ l)=VMgCl2
(ml) × 2, oscillation mixes, and is stored at room temperature no less than 3hr.
(6) preparation of vegetable material: injection the previous day should place a plant under dim light, and be watered with water, be more suitable for plant
Injection.
(7) several apertures (being careful not to tear in blade) is pricked on blade with white pipette tips when injecting, then with removing
The disposable 2ml syringe of syringe needle draws bacterium solution, and a hand index finger resists at blade back aperture, and another hand resists leaf with syringe
Face aperture, touching syringe piston makes bacterium solution inject blade along aperture.
(8) it places a plant under low light condition and cultivates one day after injecting, be then put under light and normally cultivate, taken after 2-3 days
Sample.
4, the detection of tiny RNA.
Inventor has carried out this life cigarette agroinfiltration Validation in vitro analysis (result is shown in Fig. 3-B) for milRNA8, is adopted
DNA sequence dna is expanded from Foc genomic DNA, and specific sequence information is shown in Table 2 and table 3, the results show that can be with
It is processed into mature milRNA.
Sequence list used in 3 candidate's milRNA transient expression of table
Note: the sequence that single underscore indicates is forward primer sequence, and what wave indicated is reverse primer sequences, double lower strokes
What line indicated is skeleton (precursor) sequence of the milRNA of prediction.
The above content is specific embodiment is combined, further detailed description of the invention, and it cannot be said that this hair
Bright specific implementation is only limited to these instructions.For those of ordinary skill in the art to which the present invention belongs, it is not taking off
Under the premise of from present inventive concept, a number of simple deductions or replacements can also be made.
Sequence table
<110>Research Institute of Environment and Plant Protection, Chinese Academy of Tropi
<120>a kind of banana Fusarium oxysporum milRNA
<160> 3
<170> SIPOSequenceListing 1.0
<210> 1
<211> 20
<212> DNA/RNA
<213>banana Fusarium oxysporum (Fusarium oxysporum)
<400> 1
gctgtgttgc ggtggtaggt 20
<210> 2
<211> 21
<212> DNA/RNA
<213>banana Fusarium oxysporum (Fusarium oxysporum)
<400> 2
ctaccgcatg cacctcggca g 21
<210> 3
<211> 667
<212> DNA/RNA
<213>banana Fusarium oxysporum (Fusarium oxysporum)
<400> 3
ccaggagagt atcgggaaaa cgaagagagg gttggtgaga cgaattaatg gatcaacatc 60
atctaatgac cacatcgagg gatgccacga aacgggcgca tagttatatt tcccactttt 120
tctttttgag atcacggagg cagcaggatg ggagatggat ggtaatggag ttcaactggg 180
agtggttgga cctcactgtc gcttttgtat caaacatgcc ggcgttccga gggagtccga 240
actatacgga ctaatatctg ctgtgttgcg gtggtaggtt gccgagtcgg acaacataca 300
gccatacaat cacatgcgtg tacgaatcgt gcacacatgc atatggttgg cttgtcgtgt 360
caacattggg agccaagaga gcttcattca aatgaggcag tcgaaatgtc tttcgacgaa 420
ctcgtcaagc cattttggaa aagggggttc ctcacttata tgtgcaacac tctcgctggc 480
ctcaaatcaa cctaccgcat gcacctcggc agtacaccat ctccctcggg ccatgtattc 540
aagcacctat atcttcttgt acaatcacgc ttgccactat ctatttcgaa cacacttaat 600
aatactacca ccttgacgct cgctacctct accccccgac ccgcgtgcta ttcacactcc 660
tagcccc 667
Claims (3)
1. a kind of banana Fusarium oxysporum milRNA, which is characterized in that the gene order such as SEQ ID of the banana Fusarium oxysporum milRNA
Shown in NO:1.
2. a kind of carrier, which is characterized in that the carrier contains milRNA described in claim 1.
3. a kind of competent cell, which is characterized in that the competent cell contains milRNA as described in claim 1 or contains
Carrier described in having the right to require 2.
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CN104611451A (en) * | 2015-02-16 | 2015-05-13 | 中国热带农业科学院环境与植物保护研究所 | Complete set primers for identification or assisted identification of fusarium oxysporum f.sp.cubense and application of complete set primers |
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Title |
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RUI CHEN等: "Exploring MicroRNA-Like Small RNAs in the Filamentous Fungus Fusarium oxysporum", 《PLOS ONE》 * |
XUEFEI JIANG等: "MicroRNA-like RNAs in plant pathogenic fungus Fusarium oxysporum f. sp. niveum are involved in toxin gene expression fine tuning", 《3 BIOTECH》 * |
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