CN107475449A - A kind of transcript profile sequence measurement spliced suitable for dwarf virus section and geminivirus infection coe virus genome - Google Patents
A kind of transcript profile sequence measurement spliced suitable for dwarf virus section and geminivirus infection coe virus genome Download PDFInfo
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Abstract
The invention provides a kind of transcript profile sequence measurement spliced suitable for dwarf virus section and geminivirus infection coe virus genome.The transcript profile that this method includes infection DNA virus sample is sequenced, the comparison and splicing of virus sequence, three steps such as virus genome sequence white space is filled up.The method of the present invention can not only obtain the whole genome sequence of abaca bunchy top virus, other dwarf viruses or geminivirus infection full-length genome can also be spliced by this method, so as to obtain viral whole genome sequence.The present invention at home and abroad reports the method using transcript profile high-flux sequence splicing DNA virus genome first, has filled up the blank in the domestic and international field.Present invention can also apply to DNA virus identification and detection.
Description
Technical field
The application belongs to gene order-checking and bioinformatics technique field, and in particular to one kind is applied to dwarf virus section
With the transcript profile sequence measurement of geminivirus infection coe virus genome splicing.
Background technology
DNA virus refers to a kind of biological virus containing DNA inhereditary material, is widely present in people, vertebra moves
In thing, insect, plant and microorganism.According to newest ICTV worlds virus taxis standard, DNA virus can be divided into by host types
Vertebrate DNA virus, plant DNA virus, invertebrate DNA virus, prokaryotic micro-organisms (bacterium and archeobacteria) DNA virus
With eukaryotic microorganisms DNA (algae, fungi and protozoan) viruses.Gene is divided into code area and noncoding region in structure.Compile
Code area is the part for referring to transcribe mRNA (mRNA), and it can instruct the protein that synthesis has certain function to act on, rather than
Code area be can not transcript mRNA DNA sequence dna (part non-coding can produce RNA, such as mRNA 5 ' UTR and 3 ' UTR),
Expression to gene mainly plays regulating and controlling effect, and such as promoter is located at the area.
Since target gene was sequenced with Sanger methods 1977, with the continuous development of sequencing technologies, go out
The high throughput method using second generation sequencing technologies as representative is showed, it make it that nucleic acid sequence data high pass quantifies and single base is sequenced
The drastically decline of expense, more new approaches and new are brought to researchs such as genomics, transcription group and tiny RNA deep sequencings
It was found that.Transcript profile is sequenced, and also known as RNA-seq or mRNA-seq, i.e., is enriched with out mRNA from biological total serum IgE, is obtained through reverse transcription
Double-strand cDNA, high-flux sequence analysis then is carried out to it.The deep sequencings of Illumina HiSeqTM 2000 are second generation sequencings
Technology, simultaneously hundreds thousand of or even millions of DNA can be sequenced simultaneously on a large scale.At present, the microarray dataset is at home
It is widely used, it is also commonly used in viruses indentification, detection and RNA virus whole genome sequence splicing etc..
Dwarf virus coe virus genome is made up of multiple single-stranded cyclic DNA components, and each component size is
1100nt, its it is virus genomic acquisition mainly by PCR (Polymerase Chain Reaction,
PCR) method.Rolling ring PCR (rolling circle amplification, RCA) is also gradually used for expanding ring-type disease in recent years
Malicious DNA, so as to obtain viral whole genome sequence.Geminivirus infection coe virus genome is loop-like by unimolecule or two molecules
SsDNA is formed, and per molecule DNA grows 2.5~3.0nt, and total gene is about 2.5~5.2nt, can also pass through PCR or RCA method
Obtain geminivirus infection whole genome sequence.However, due to not belonged to together with geminivirus infection section between dwarf virus section virus not of the same race
Homology difference between virus is larger, can not obtain the full genome of new virus well by way of designing degenerate primer
Group sequence；And traditional viruses indentification method, as time and effort consuming is sequenced in Virus purification, electron microscopic observation and viral genome.The present invention
By carrying out transcript profile high-flux sequence to infecting doubtful DNA virus sample, all non-coding area sequences of DNA virus are disclosed
It can be transcribed, so as to which DNA virus full-length genome can be spliced using transcript profile high-flux sequence, fill up the domestic and international field
Blank.In addition, using present invention can also apply to DNA virus identification and detection.
The content of the invention
It is applied to dwarf virus section object of the present invention is to provide one kind and geminivirus infection coe virus genome splices
Transcript profile sequence measurement, method is simple.
In order to achieve the above object, the present invention takes following technical measures：
Thinking of the present invention：Applicant has found first, all noncoding regions of dwarf virus section and geminivirus infection section DNA virus
RNA can also be produced, therefore by splicing the code area of virus and the high flux transcript profile of noncoding region, you can obtain the disease
The whole genome sequence of poison.
A kind of transcript profile sequence measurement spliced suitable for dwarf virus section and geminivirus infection coe virus genome, will infect
The blade total serum IgE reverse transcription of viral sample simultaneously carries out high-flux sequence into cDNA, construction cDNA library；By with all known institutes
The nucleotide sequence of ill seed culture of viruses is compared, and the transcript profile sequencing fragment of matched is filtered out, then by the normal of this area
Rule mode is compared and spliced；Described virus is dwarf virus section or geminivirus infection coe virus.
Specifically include following step：
(1) the blade total serum IgE of virus infection sample is extracted；
(2) RNA reverse transcriptions are simultaneously subjected to high-flux sequence into cDNA, construction cDNA library
(3) Bowtie softwares (default parameters) are run, fragment and institute in GenBank is sequenced in the transcript profile in step (2)
The nucleotide sequences for having known all virus kinds are compared, and filter out matched (preferable, homology 95% and more than)
Transcript profile sequencing fragment；
(4) Velvet softwares are run, parameter is arranged to k-mer=17 and minimum coverage=5, with step (3)
The RNA fragments that screening obtains are input, are spliced into short Contig (contig)；
(5) Blast softwares (default parameters) are run, by the short Contig that step (4) obtains and Genbank data
Known viruse genome sequence in storehouse is compared, and homology is 95% and the above, with the source species of this speculated sequence；
(6) the full-length genome sequence of all suspect sources viruses is downloaded and using this data as base from Genbank databases
Plinth, establish and can be used for the virus database that Bowtie softwares carry out sequence alignment；
(7) Bowtie softwares (default parameters) are run, the fragment of step (2) kind transcript profile sequencing is built with step (6)
Vertical virus database is compared and (is compared with the genome sequence of specific virus species), filters out matched
(present invention preferably homology 95% and more than) transcript profile sequencing fragment；
(8) according to the comparison result of step (7), the virus strain for the fragment that can match most transcript profile sequencings is write from memory
Think most probable viral candidates；
(9) most possible viral candidates name is subjected to simple marking, the fragment of transcript profile sequencing is also marked；
(10) Velvet softwares are run, parameter is arranged to k-mer=17 and minimum coverage=5, with step (9)
The fragment of transcript profile sequencing after middle mark is input, is spliced into short Contig；
(11) Velvet softwares are run, parameter is arranged to k-mer=17 and minimum coverage=5, with step
(10) the short Contig obtained in is input, is spliced into longer Contig；
(12) Specific PCR primers are designed from white space (gap) both sides for failing to have spliced, passes through gene cloning and survey
Sequence obtains the nucleotide sequence in gap regions, filling gap regions；
The Contig of acquisition is finally finally connected into a complete nucleotide sequence, i.e., DNA virus base to be measured
Because of the full length nucleotide sequence of a certain component in group, other components obtain also by this method, and all components are the virus
Genome sequence.Identification and classification are determined to virus according to the genome sequence simultaneously.
The virus belongs to dwarf virus section or geminivirus infection section.
The process described above can be used for the identification and detection of virus.
Compared with prior art, the present invention has advantages below：
The present invention confirms that the sequencing of high flux transcript profile can be used for carrying out genome sequence splicing to DNA virus first, enters
And viral whole genome sequence is obtained, while virus causing disease identification and detection can also be carried out to doubtful viral sample；And RNA-Seq
Technology has many unique advantages in identification of dna virus and clonal virus genome, specifically：
(1) high flux：Hundreds of thousands or even the transcript profile sequence of millions of can be once obtained, can rapidly and accurately be reflected
Determine the whole transcript profile mRNA sequences contained in sample；
(2) fast and automatically change：As long as data volume is enough, without being pre-designed specific primer, you can pass through biological information
Learn software and splice viral whole genome sequence；
(3) it is reproducible：Repeated without technology, and initial sample wants much less than chip technology, is particularly suitable for use in and
The extremely limited biological sample analysis in source.
(4) applied widely, the virus of dwarf virus section or geminivirus infection section can all be carried out with technical scheme
Sequencing.
(5) the high flux transcript profile sequence measurement of DNA virus genome splicing provided by the invention, this method are applied to
The known or unknown DNA virus logged in GenBank even other unknown virus.Using when, for theoretical, as long as having enough
Transcript profile data, can not only obtain one with there is the viral whole genome sequence of matching in Genbank, can also according to weight
Folded group's sequence obtains unknown new virus whole genome sequence by gene clone technology.
(6) applicant has found that all noncoding regions of DNA virus can also produce RNA first, therefore high using transcript profile
Flux sequencing splicing can obtain DNA virus genome, fill up the blank in the domestic and international field.While to cause banana seriously sick
Exemplified by harmful abaca bunchy top virus, the method for DNA virus genome is spliced by using transcript profile high-flux sequence, obtains perfume (or spice)
The whole genome sequence of any of several broadleaf plants bunchy top virus, it was demonstrated that the reliability of this method, so as to the acquisition for related DNA virus genome and disease
The former identification of viral disease provides technical support.
Brief description of the drawings
Fig. 1 is that RT-PCR methods identify that abaca bunchy top virus and Cotton leaf curl Multan virus noncoding region transcribe schematic diagram；
Wherein, M：2000bp DNA marker；1, expand abaca bunchy top virus DNA-R noncoding regions；2, expand MULTAN
Cotton curve leaf disease virus DNA-A noncoding regions；3, water control.
Fig. 2 is to go out the fragment match being sequenced with the transcript profile of matched in Genbank using Bowtie software screening methods to unite
Count result.
Fig. 3 is is spliced into longer Contig using Velvet softwares, by taking DNA-M component total length schematic diagrames as an example.
Fig. 4 is the gel electrophoresis figure that PCR methods expand bbtv dna-N component Liang Ge gap areas；Wherein,
M：2000bp DNA marker；1, B2 Banana swatches；2, blank control.
Embodiment
Explanation is further explained to the application with reference to embodiment, before specific embodiment is introduced, with regard to following realities
Part Experimental Background situation in example is applied to be briefly discussed below.
Biological material specimens：
The big leaf of Flos Carthami piece of infection BBTV Leaf of banana (B2) and infection Cotton leaf curl Multan virus picks up from Hainan Province；
PMD18-T carriers, DNase I, Reverse Transcriptase M-MLV reverse transcription reagent box are purchased from precious bioengineering
(Dalian) Co., Ltd；Upstream and downstream primer synthesizes and sequencing, is completed by Invitrogen (Shanghai) Trading Co., Ltd.；Illumina
The high throughput sequencing technologies platforms of HiSeqTM 2000, Nuo Hezhi sources company；
The experimental method of unreceipted actual conditions in following examples, generally according to normal condition such as《Molecular Cloning: A Laboratory
Guide》Condition described in reference books commonly used in the art such as (third editions, Science Press, 2005), or by reagent manufacturer
Proposed condition is carried out.
Embodiment 1：
The noncoding region of dwarf virus section and geminivirus infection section DNA virus can produce RNA：
Dwarf virus section：
Abaca bunchy top virus (Banana bunchy top virus, BBTV) is used as banana bunchy top disease (Banana
Bunchy top virus, BBTD) pathogen, genome at least by 6 sizes 1.0~1.1kb ring-type ssDNA components
Formed.International Commission on Virus Classification belongs to it dwarf virus section (Nanaviridae) banana bunchy top disease within 2015
In poison category (Babuvirus), turn into the line-up of delegates of the category.The present embodiment is by taking abaca bunchy top virus as an example, it was demonstrated that dwarf virus
The noncoding region of section member can produce RNA, and step is as follows：
(1) using the B2 samples total serum IgE of extraction as template, after DNase I processing, Reverse is utilized
Transcriptase M-MLV reverse transcription reagent box synthesizes the first chain cDNA；
(2) and then according to DNA-R noncoding regions (SEQ ID NO.1) following primer sequence is designed：
Forward primer DNA-R 967F：5’-CACGCTATGCCAATCGTACAC-3’；
Reverse primer DNA-R 102R：5’-CTGTCGACGATGATGATCTTG-3’.
(3) performing PCR identification is entered using DNA-R 967F/DNA-R 102R, electrophoretic analysis result is as shown in Figure 1.From figure
As can be seen that amplified fragments size about 250bp, is consistent with actual size, it was demonstrated that abaca bunchy top virus noncoding region produces RNA.
Geminivirus infection section：
Cotton leaf curl Multan virus (Cotton leaf curl Multan virus, CLCuMV) is to cause cotton, big
The pathogen of the plant serious plant disease such as safflower, genome are made up of unimolecule or the loop-like ssDNA of two molecules, per molecule
DNA grows 2.5~3.0nt, and total gene is about 2.5~5.2nt.It is belonged to twin disease by International Commission on Virus Classification in 2015
In the Begomovirus (Begomovirus) of malicious section (Geminiviridae), turn into the important member of the category.This
Embodiment is by taking Cotton leaf curl Multan virus as an example, it was demonstrated that the noncoding region of geminivirus infection section member can produce RNA, and step is such as
Under：
(1) the big leaf of Flos Carthami piece total serum IgE of extraction infection Cotton leaf curl Multan virus is template, after DNase I processing,
The first chain cDNA is synthesized using Reverse Transcriptase M-MLV reverse transcription reagent box；
(2) and then according to DNA-A noncoding regions (JQ424826.1) following primer sequence is designed：
Forward primer DNA-A 2430F：5’-CTTCGTGTAACTCTCTGCAGAC-3’；
Reverse primer DNA-A 2730R：5’-ACGGATGGCCGCTTTTTGG-3’.
(3) performing PCR identification is entered using DNA-A 2430F/DNA-A 2730R, electrophoretic analysis result is as shown in Figure 1.From figure
In as can be seen that amplified fragments size about 300bp, be consistent with actual size, it was demonstrated that infect the MULTAN cotton Qu Ye of big safflower
Viral noncoding region produces RNA.
Embodiment 2：
A kind of sequence measurement for being applied to dwarf virus section and geminivirus infection coe virus genome, comprises the steps (this
Embodiment illustrates by taking the Banana swatches that BBTV infects as an example to this method)：
(1) commercialization TRIzol Reagent kits are used, the extraction total serum IgE from infection BBTV Leaf of banana (B2)；
(2) commercialization is usedUltraTM RNA Library Prep Kit for(NEB,USA)
Kit：First by the enrichment with magnetic bead mRNA with Oligo (dT), mRNA is broken into short-movie section；Then with short-movie section
MRNA is template, and reverse transcription is into the first chain cDNA；Again by the further synthetic double chain cDNA of kit, i.e. cDNA library, can use
Yu Shangji carries out high-flux sequence (the high throughput sequencing technologies platforms of Illumina HiSeqTM 2000).
(3) Bowtie softwares (default parameters) are run, fragment and institute in GenBank is sequenced in the transcript profile in step (2)
The nucleotide sequence for having known viruse sequence is compared, filter out matched (the homologous Sexual behavior mode of the present embodiment 95 with
Upper %) transcript profile sequencing fragment；
(4) Velvet softwares are run, parameter is arranged to k-mer=17 and minimum coverage=5, with step (3)
The RNA fragments that screening obtains are input, are spliced into short Contig；
(5) Blast softwares (default parameters) are run, by the short Contig that step (4) obtains and Genbank data
Known viruse genome sequence in storehouse is compared, and homology is more than 95%, with the source species of this speculated sequence；
(6) the full-length genome sequence of all suspect sources species is downloaded and using this data as base from Genbank databases
Plinth, establish and can be used for the virus database that Bowtie softwares carry out sequence alignment；
(7) Bowtie softwares (default parameters) are run, the fragment of step (2) kind transcript profile sequencing is built with step (6)
Vertical virus database be compared (genome sequence i.e. with specific virus species is compared, in this embodiment it is believed that
Belong to abaca bunchy top virus, therefore concentrate on the comparative analysis of abaca bunchy top virus in GenBank), filter out matched (this
The homologous Sexual behavior mode of embodiment % more than 95) transcript profile sequencing fragment.
As a result it is as shown in Figure 2.What is matched is abaca bunchy top virus sequence, and wherein DNA-R components reads is 1022
Bar, DNA-U3 components reads are 4164, and DNA-S components reads is 8956, and DNA-M components reads is 1085, DNA-
Component C reads is 44, and DNA-N components reads is 10953, and S2 satellite components reads is 398, Sat4 satellite components
Reads is 1007.
(8) according to the comparison result of step (7), the virus strain for the fragment that can match most transcript profile sequencings is write from memory
Think most probable viral candidates；
As a result as shown in table 1, DNA-R, DNA-U3, DNA-S, DNA-M, DNA-C, DNA-N this 6 must component with
BBTV HK strains matcheds (more than 97%).And nonessential component S2 and Sat4 respectively with from Taiwan strain (88%) and
The satellite component matched of Vietnam's strain (97%).
The abaca bunchy top virus that table 1. matches with B2 height of specimen
(9) the most possible viral candidates name of above-mentioned steps (8) is subjected to simple marking, to the fragment of transcript profile sequencing
Also it is marked；
(10) Velvet softwares are run, parameter is arranged to k-mer=17 and minimum coverage=5, with step (9)
The fragment of transcript profile sequencing after middle mark is input, is spliced into short Contig；
(11) Velvet softwares are run, parameter is arranged to k-mer=17 and minimum coverage=5, with step
(10) the short Contig obtained in is input, is spliced into longer Contig；
As a result it is as shown in Figure 3.Result in B2 samples after BBTV viruses each component sequence assembly.
(12) according to the abaca bunchy top virus transcript profile Contig (sharing 8 components) spliced in step (11), profit
Checked with BioEdit, find two gap regions that DNA-N components fail to have spliced.
Final 7 total length components for obtaining infection B2 sample abaca bunchy top viruses, respectively DNA-R (SEQ ID NO.1),
DNA-U3 (SEQ ID NO.2), DNA-S (SEQ ID NO.3), DNA-M (SEQ ID NO.4), DNA-C (SEQ ID NO.5),
DNA-S2 (SEQ ID NO.7), DNA-Sat4 (SEQ ID NO.8)；And DNA-N components have two to fail to splice Hao gap areas
Domain, size are respectively 74nt and 27nt.
Embodiment 3：
The supplement in gap regions：
The present embodiment enters performing PCR supplement to two white spaces of DNA-N components, and step is as follows：
(1) using the B2 samples total serum IgE of extraction as template, tried using Reverse Transcriptase M-MLV reverse transcriptions
Agent box synthesizes the first chain cDNA, then designs following primer sequence and enters performing PCR amplification：
Forward primer DNA-N 23F：5’-CCAGCGCTCGGGACGGG-3’；
Reverse primer DNA-N 878R：5’-GCCCAATCAACCCCCGATTCTTC-3’.
(2) performing PCR amplification is entered using DNA-N 23F/DNA-N 878R, electrophoretic analysis result is as shown in Figure 4.Can from figure
To find out, amplified fragments size about 850bp, it is consistent with actual size；
(3) after pcr amplification product is reclaimed, it is attached with pMD18T carriers；
(4) connection product conversion Escherichia coli, picking positive colony carry out bacterium solution PCR Preliminary Identifications；
(5) clone bacterium for being initially identified as the positive is sent to Guangzhou Invitrogen companies and carries out sequencing analysis；
(6) gained sequence contains above-mentioned two gap regional sequences, and then can be spliced to DNA-N components (SEQ ID
NO.6 full length sequence) is obtained.
Further analysis shows, the genome of abaca bunchy top virus (BBTV) includes 8 components, specific base in the sample
Sequence is as shown in SEQ ID NO.1~8.At present, the viral genome is obtained mainly to expand by PCR and obtained, but to same
The poor nonessential component of source property, it is impossible to which amplification obtains well.The present invention utilizes full-length genome after transcript profile high-flux sequence
The method of splicing, the necessary component of all abaca bunchy top viruses and nonessential component can be obtained.The mode expanded using PCR is right
Virus in above-mentioned B2 samples is expanded, completely the same with the result of the present invention.
In summary, inventor disclose abaca bunchy top virus transcript can total length Corticovirus genome, transcribe simultaneously
Group sequencing result shows the peak value that several high coverage rates be present, is all located at the code area of abaca bunchy top virus each component.It is in addition, fragrant
Any of several broadleaf plants bunchy top virus rna transcription sheet is overlapped, overlapping region is assembled into abaca bunchy top virus whole genome sequence.
The present processes, which are once analyzed, can obtain hundreds of thousands or even the transcript profile sequence of millions of, can be quickly accurate
Really identify the whole transcript profile mRNA sequences contained in sample.Meanwhile with reference to bioinformatics software analysis and data
Processing, can carry out assembling splicing to the virus transcription group sequence in infection plant's sample, finally successfully obtain viral in the sample
Whole genome sequence, the application the Leaf of banana of virus infection is carried out the sequencing of high flux transcript profile for abaca bunchy top virus or
Other DNA virus genomic clones or new virus identification etc. research have important scientific basis.
Sequence table
<110>China tropic Agriculture Academy Sciences tropic Biotechnology Research Institute
<120>A kind of transcript profile sequence measurement spliced suitable for dwarf virus section and geminivirus infection coe virus genome
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atgctggatg ttcaccatca acaatcccgc ttcacttcca gtgatgcggg atgagtttaa 180
atatatggta tatcaagtgg agaggggaca ggagggtact cgtcatgtgc aaggatacgt 240
cgagatgaag agacgaagtt ctctgaagca gatgagaggc ttcttcccag gcgcacacct 300
tgagaaacga aaggggagcc aagaagaagc acgggcgtac tgtatgaagg aagatacaag 360
aatcgaaggt cccttcgagt ttggtgcttt taaattgtca tgtaatgata atttatttga 420
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cagatgcaaa gaggaatatt taaactacgg tttattagaa gaatttaaaa atggaattat 840
tcaaagcggg aaatatgaac ccgttttgaa aattgtagaa tatgttgaag tcattgtaat 900
ggctaacttc cttccgaagg aaggaatctt ttctgaagat cgaataaagc tagttgcttg 960
ttgaacacgc tatgccaatc gtacactatg acaaaagggg aaaagcaaag attcgggggt 1020
tgattgtgct atcctaacga ttaagggccg caggcccgtc aagatggacg acgcgatcat 1080
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agaacgtgtt caaaatctgg gtttgaccga aggtcaaggt agatggtcaa caatattctg 180
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aatacttccg atctctataa atagcctaaa tctgttattg ataatagctc tcgctcttct 300
gtcaaagttg ttgtgctgag gaggaagatc gccaccggcg atcatcggac ggaaagcgtc 360
aagagagacg gagaatcatg ctgcgaagcg tatatcgggt atttatagac ttctagcgca 420
gctagaagtt tcgttgtatt tgatattgta ttttgtaaat tacgaagaaa ttcgtataat 480
gatattaata aaacaactgg gattgttcat gtttacatta actagtatca aaaaatgcac 540
aatttaaata ttgtataagg aacttataca atatatatta cactatgttg agcgtagcgt 600
gataaacagg tgtttaggta taattaaaat aattatgtca tgtaaagata atactgaaca 660
tgttaaagta tgaggtgaaa gaggaggtat tagaatatta aaaacccaat tatattatgt 720
atcatgacaa gcgtacgcta tgacaaaaag ggaaaaatga aaaatcaggg gttgattgtg 780
ctatcctaac gattaagggc cgcaggcccg tcaagttgga tgaacggtta gatttgattg 840
cttagccacg aaggaaggaa tctttttggg accacagaca agacagctgt cattgtttta 900
aaaataatat aataactaat tgacaattgt acccctcact aacaagataa taacgatagt 960
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accaaaaaca ggcgggaacc gtccaaattt caaacataga ttgcttgccc tgcaagccat 180
ctagaagtct atatatacca gtgtcgacat attgtctaga tatgaaatgg cgaggtatcc 240
gaagaaatcg atcaagaaga ggcgggttgg caggaggaag tatggaagca aggcggcaac 300
aagccacgac tactcgtcgt taggatcaat attggttcct gaaaataccg tcaaggtatt 360
taggattgag cctactgata aaacattacc cagatatttt atctggaaaa tgtttatgct 420
gttggtgtgc aaggtgaagc ccggaagaat acttcactgg gctatgatta aaagttcttg 480
ggaaatcaac cagccgacta catgtctgga agcaccaggt ttatttataa aacctgaaca 540
tagccatctg gttaaactgg tatgcagtgg ggaacttgaa gcaggagtcg caacagggac 600
atcagatgtt gaatgtcttc ttaggaagac aaccgtgttg aggaagaatg taacagaggt 660
ggattacttg tatttggcat tttattgtag tgctggagtt agtattaact accagaacag 720
aattacatat catgtatgat atgtttatgt aaacataaac ctttgtaagg aataatgtcc 780
aaataacata caacacgcta tgacaaaagg ggaaaaatga agaatcgggg gttgattggt 840
ctatcgtatc gcttaagggc cgcaggcccg ttgaaatgat tctttattaa acaaatatac 900
atgatacgga tagttgaata tataaacaac tatgtataaa tacaacagaa tgttgaaaat 960
aattaatata atgagaagga aggtatattt gtgacggata aggatgagaa ccaccacttt 1020
agtggtgggt catatgtccc gagttagtgc gccacgta 1058
<210> 4
<211> 1041
<212> DNA
<213>Artificial sequence (Artificial Sequence)
<400> 4
agcgctgggg cttattatta cccccagcgc tcgggacggg acatcacgtg caacttaaaa 60
atgcacgtga ctgatatata tgataaaacg gtttattgaa ccgttatgtt gagatataac 120
gaaaagtcac gtatgaaaga gacatgaacg tgacggagtc aaatgtattg aataaacatt 180
tgacgtccgg aaacttccga aggaagccat gattgcttcg aggcgaagca aatcatttat 240
atattggtct gaactgctgc ctataaataa gaggcaggga aatggcattg acaacagagc 300
gggtgaaaca attctttgaa tggtttctgt ttattggagc aatattcgtt gcgataacaa 360
tattatatat attgttggca ttgctctttg aggttcccaa gtatattaag gaggttgtta 420
ggtatctcgt agaatacctg accagacgac gtgtatggat gcagaagacg cagttgacgg 480
aggcaaccgg agatgtagag ctcgtcagag gtagtgtgga agacagacgc gatcaacaac 540
cggctgtcat accacatgcg agtcatgtta tccattctca accaagaagg gatgaacaag 600
caagacgagg aaacgccggc cctatgtttt aatacactgt atcataatat acgaaatata 660
aatggttaag gatatctagt gtcaaacata tataagtgaa acataatata tgttgtataa 720
gaaacatatt gtaatatgtg acttgtatac gagtgttgta tttataaact atacaacacg 780
ctatgacaaa aggggaaaaa tgaagaatcg ggggttgatt ggtctatcgt atcgcttaag 840
ggccgcaggc ccgttgaaat gattctttat taaacaaata tacatgatac ggatagttga 900
atatataaac aactatgtat aaatacaaca gaatgttgaa aataattaat ataatgagaa 960
gataagtata tttgtacggg atagtgatca caaacaccac tttagtggtg ggtcatatgt 1020
cccgagttag tgcgccacgt a 1041
<210> 5
<211> 1013
<212> DNA
<213>Artificial sequence (Artificial Sequence)
<400> 5
agcgctgggg cttattatta cccccagcgc tcaggacggg acatcacgtg catttaacaa 60
atgcacgtga gaaggcagtt gcttgcagcg aaagataact atcaacatca aaaaagaaga 120
gggcatattc gttgcttcga gacgaagcaa cggtgataga taaatgttcg agattcgata 180
atggaggcta tttaaacctg atggtgttgt gatttccgaa atcactcatc ggaggagaat 240
ggaattctgg gaatcgtctg ccatgccaga cgatgtgaag agagtgatca aggaaatata 300
ttgggaagat cggattaaac ttctgttttg tcagaagttg aagtgctgtg tcagaaggat 360
tcttgtatat ggagatcaag atgatgctct agctgcagtg aaggatatga agacttctat 420
cattcgttat agcgaatatc tgaagaaacc atgtgtggta atatgttgtt tgactaataa 480
gtctattgtt cataggttaa acacaatggt gttcttttat catgaatata tggaagacct 540
aggtggtgac tactcggtat atcaagagtt gtattgtgat gaggaacttc ctgcttcctt 600
gacagaggaa gaagatgaag aagtaatata caggaatgtt attatgtcat cgacagaaga 660
gaagatctct tggagtgaat gtcagaagat agtcatatcg gattatgatg taacattact 720
gtaatgtaat atccattatc ataaataaaa taatggtatg atgattatgt atttaaacta 780
aatacataat ggtgtacgta tagcataaaa tacattaaca tacatacaac acactatgac 840
aaaaagggaa aaaagaagaa tcgggggttg attgggctat cttaacgatt aagggccgaa 900
ggcccgttta aatatgtgtt ggacgaagtc caaaacacat aaaagtcatc agaacagtgg 960
aatataatga gctggcagtg gcgggtccat gtcccgagtt agtgcgccac gtg 1013
<210> 6
<211> 1082
<212> DNA
<213>Artificial sequence (Artificial Sequence)
<400> 6
agcacggggg actattatta ccccccgtgc tcgggacggg acatgacgta agcatagatt 60
ataatgggct ttttaaagcc catataaggg aagtgggccg ggtttgagac atatttcgaa 120
agcccggctt ggaaaaggat aaagtcacgt tccgaataat aggttgcttc gccgcgaagc 180
aacctaataa attgttgcgt attcaatacg caactaaaag tctattaata tgcctgtctc 240
tgccgaataa atcagagcgt atgcgaagca gaagcgatgg attgggcaga atcacaattc 300
aagacatgta cccatggctg tgattggaag acgatatcat cggattcatc ggaaaatcgg 360
caatatgtac cttgcgtcga ctctggtgtt ggaagaaaga cgcctcgcaa ggtacttctt 420
cgatctatcg aagttgtatt caatggaagt tttaaaggga ataatcggaa tgttcgtggc 480
ttcttatacg tatcaatccg agacgatgat ggaacaatgc gtccagtact tatagtacca 540
tttggaggat atggatatca taatgatttt tattatttcg aagggaaggg gaaagttgaa 600
tgtgatatat catcagatta tgttgcgcca gaagtagatt ggagcagaga catggaagtt 660
agtattagta acagcaacaa ctgtaatgaa tcatgtgatc tgaagtgtta tgttatttgt 720
tcgttaagaa taaaggaata acagatgtgc tgtaatgaat attaataaat cttattttta 780
atgtaagtga aagttgtata aaacatacaa cacgctatga caaaagggga aaaatgaaaa 840
ataaggggtt gattgttcta tagtatcgct taagggccgc aggcccgttg aaaaataata 900
atcgaattat atacgattga taataatcag agatagatga tcaaggatat ataaacatag 960
acgaagtata tggctgtata atataaaaga agcatataat ataaaatatg tatactattc 1020
tctgattggt gcagaaagta gacccactaa ctttaagtta gtggaaatgt cccgatgacg 1080
tg 1082
<210> 7
<211> 1091
<212> DNA
<213>Artificial sequence (Artificial Sequence)
<400> 7
tatataaagg cagagggcat agtattaccc ctctgcctta cacctctgcc ttacacctga 60
cgtcatcata tggcgtcctc taaatggtgc ttcactctga attattcctc cgcagccgag 120
agagaagact ttctctcgcg tctgaaggag gaggatgttc actacgcggt ggtcggcgac 180
gaagtcgctc cgagctccgg ccagaagcac ctacagggat atctatccct gaaaaaagga 240
atccgtttag gcggattgaa gaagaggtac tcttcgaagg ctcactggga gatcgcgaga 300
ggaacagacg aacagaatcg tggatactgt tcgaaggaaa ccctagttct tgaactgggt 360
acgcctgtag ttcctaggtc taataagcgt aagctaatgg agcgttatag agaagaccct 420
gaagaattga agatggatga tccttccaag tatcgcagat gcttggcagc ggattcaatc 480
gagaaagcca gaaataattc taaatgggtt cacgaactaa gagaatggca gaatcaatta 540
attcaacaca tcgaaggtgt tcctgatgat cgaagtatca tctgggtcta cggtccagcc 600
ggaggcgaag gtaagtcaac cttcgcgaga tatttatcat taaaacccgg atggggatat 660
atcaatgggg gaaagacctc ggatatgatg cacatcataa cgatggatgc ggataatcat 720
tggattatag atattcccag aagtaattca gagtatctga attacggcgt tatagaacag 780
attaagaata gagttttaat aaatacgaag tatgaaccat gtgtgattag aaaagacgga 840
cagaatgtcc atgtaattgt gatggcaaat gtgttgcctg attattgtaa aatatcagaa 900
gatagaataa aaataattaa ttgttgaaat acattacttc ttcgccaagc aaccgcgtga 960
agaaaccgcg tggaccccac cactacaata acacgctatg ccgtacaacg aagtcatcaa 1020
tatatttatt attaaaatat tgggccgaag gcccaataag gatgtcggtg gcactgttgc 1080
ctgccacaca c 1091
<210> 8
<211> 1102
<212> DNA
<213>Artificial sequence (Artificial Sequence)
<400> 8
tgggctagta ttacccacct ccgcgcacta cctccgcgca cctataaaat gtctgcctct 60
cgatggacat ttacgcttca ctattccgac gcaacggagc gaggcaaatt cctcgcgact 120
ttgaaggagg aagatgtgca ctacgccgtc gtcggcgacg aaactgctcc gaatactggt 180
cggaaacatc ttcaaggata tctttccttg aagaaacgtt ttcgtattag cggaataaag 240
aagaaatatt cgtcgagagc gcattgggag aaagctcgag gatcagatta cgacaacaag 300
gcgtactgtt ctaaagaagc cctaattctt gaattagggg ttccttgcca aacaggttcg 360
aataagcgta aattagcaga tatggttaca agatcgccgg aacgaatgaa aatcgaacag 420
ccggagatat ttcaccgata cgaatcggtg aagaagatga aagaattcaa agaaaggtat 480
gtctatccta tcctcgatag gccatggcag gtacaattaa cggagttaat tgaagcagaa 540
cctgatgatc gaacgatcat ctgggtattc ggaccaaaag ggaatgaagg caaatcaacg 600
tatgcgaagt cattaatcca aaaggattgg ttctacacaa ggggaggaaa gaaggagaac 660
atattgttcg cctacgtaga tgaaggttcg acaaaaaacg ttgtatttga tcttccgcgt 720
acagtacaag aatttattaa ttatgatgtt atcgaggcac tgaaagatag agtaatcgag 780
agtacaaaat acaagcctgt gaagtattta gagttgaatt ctgtacatgt aatagttatg 840
gctaattttc tgcctgatat gtgtaaaata tctgaagatc gaataaagat agttgcttgc 900
tgaacacgct atgacaatcg tacgctatga caaaagggga aaaatgaaga atcgggggtt 960
gattgggcta tcctaacgaa taagggccgc aggcccgtta agatggatcc ttataacccg 1020
ttaagaagct aaacgggtct aaaacgattg cttcgcccgc aagcaacacc tttaacctct 1080
gcgcacctat atatagcgga gg 1102
Claims (4)
1. a kind of transcript profile sequence measurement spliced suitable for dwarf virus section and geminivirus infection coe virus genome, including it is following
Step：
The blade total serum IgE reverse transcription of virus infection sample is simultaneously subjected to high-flux sequence into cDNA, construction cDNA library；By with
The nucleotide sequence of all known all virus kinds is compared, and filters out the transcript profile sequencing fragment of matched, then presses
The usual manner of this area is screened and spliced；Described virus is dwarf virus section or geminivirus infection coe virus.
2. according to the method for claim 1, it is characterised in that：
（1）Extract the blade total serum IgE of virus infection sample；
（2）RNA reverse transcriptions are simultaneously subjected to high-flux sequence into cDNA, construction cDNA library；
（3）Bowtie softwares are run, by step（2）In transcript profile sequencing fragment and GenBank in all known all viruses
The nucleotide sequence of kind is compared, and filters out the transcript profile sequencing fragment of matched；
（4）Velvet softwares are run, parameter is arranged to k-mer=17 and minimum coverage=5, with step（3）Screening obtains
The RNA fragments obtained are input, are spliced into short Contig；
（5）Blast softwares are run, by step（4）The short Contig obtained and the known viruse in Genbank databases
Genome sequence is compared, and homology is 95% and the above, with the source species of this speculated sequence；
（6）The full-length genome sequence of all suspect sources viruses is downloaded from Genbank databases and based on this data, is built
The vertical virus database that can be used for Bowtie softwares and carry out sequence alignment；
（7）Bowtie softwares are run, by step（2）The fragment and step of kind transcript profile sequencing（6）The virus database established
It is compared, filters out the fragment of the transcript profile sequencing of matched；
（8）According to step（7）Comparison result, the virus strain for the fragment that can match the sequencing of most transcript profiles is defaulted as
Most probable viral candidates；
（9）Most possible viral candidates name is subjected to simple marking, the fragment of transcript profile sequencing is also marked；
（10）Velvet softwares are run, parameter is arranged to k-mer=17 and minimum coverage=5, with step（9）Middle mark
The fragment of transcript profile sequencing afterwards is input, is spliced into short Contig；
（11）Velvet softwares are run, parameter is arranged to k-mer=17 and minimum coverage=5, with step（10）In obtain
The short Contig obtained is input, is spliced into longer Contig；
（12）Specific PCR primers are designed from the white space both sides for failing to have spliced, gap is obtained by cloning and sequencing gene
The nucleotide sequence in region, filling gap regions；
The Contig of acquisition is finally finally connected into a complete nucleotide sequence, i.e., DNA virus genome to be measured
In a certain component full length nucleotide sequence, other components obtain also by this method, and all components are the viral gene
Group sequence；The virus belongs to dwarf virus section or geminivirus infection section.
3. application of the method described in claim 1 in viruses indentification.
4. application of the method described in claim 1 in Viral diagnosis.
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Cited By (5)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN108334750A (en) * | 2018-04-19 | 2018-07-27 | 江苏先声医学诊断有限公司 | A kind of macro genomic data analysis method and system |
| CN110129339A (en) * | 2019-05-10 | 2019-08-16 | 中国计量大学 | Black nightshade curly top poison whole genome sequence and its detection method |
| CN111598181A (en) * | 2020-05-21 | 2020-08-28 | 中国热带农业科学院热带生物技术研究所 | Banana flower and leaf heart rot APP identification method and system |
| CN116072222A (en) * | 2023-02-16 | 2023-05-05 | 湖南大学 | Method for identifying and splicing viral genome and application thereof |
| CN117198409A (en) * | 2023-09-15 | 2023-12-08 | 云南省农业科学院农业环境资源研究所 | microRNA prediction method and system based on transcriptome data |
Citations (5)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN1285406A (en) * | 1999-08-20 | 2001-02-28 | 中国科学院微生物研究所 | Complete sequence of Chinese Zhangzhou isolate gene group 1 and group 4 of banana top bundling virus |
| CN1344797A (en) * | 2001-11-09 | 2002-04-17 | 北京大学 | No.6 gene segment of rice dwarfing virus |
| WO2005119640A2 (en) * | 2004-06-02 | 2005-12-15 | Combimatrix Corporation | Interfering stem-loop sequences and method for identifying |
| CN102899335A (en) * | 2012-09-14 | 2013-01-30 | 中国热带农业科学院热带生物技术研究所 | Method for obtaining genome sequence of papaya ringspot virus through high-throughput small RNA sequencing |
| CN107119146A (en) * | 2017-04-25 | 2017-09-01 | 郑州云基因数据科技有限公司 | The method and its application of high throughput identification plant virus |
-
2017
- 2017-09-12 CN CN201710818934.XA patent/CN107475449A/en active Pending
Patent Citations (5)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN1285406A (en) * | 1999-08-20 | 2001-02-28 | 中国科学院微生物研究所 | Complete sequence of Chinese Zhangzhou isolate gene group 1 and group 4 of banana top bundling virus |
| CN1344797A (en) * | 2001-11-09 | 2002-04-17 | 北京大学 | No.6 gene segment of rice dwarfing virus |
| WO2005119640A2 (en) * | 2004-06-02 | 2005-12-15 | Combimatrix Corporation | Interfering stem-loop sequences and method for identifying |
| CN102899335A (en) * | 2012-09-14 | 2013-01-30 | 中国热带农业科学院热带生物技术研究所 | Method for obtaining genome sequence of papaya ringspot virus through high-throughput small RNA sequencing |
| CN107119146A (en) * | 2017-04-25 | 2017-09-01 | 郑州云基因数据科技有限公司 | The method and its application of high throughput identification plant virus |
Non-Patent Citations (6)
| Title |
|---|
| AHMED HADIDI ET AL.: "Next-Generation Sequencing and Genome Editing in Plant Virology", 《FRONT MICROBIOL》 * |
| GIULIANA LOCONSOLE ET AL.: "《Identification of a Single-Stranded DNA Virus Associated With Citrus Chlorotic Dwarf Disease, a New Member in the Family Geminiviridae》", 《VIROLOGY》 * |
| 周朋: "香蕉束顶病毒（BBTV）DNA-U3序列多态性及转录特征", 《中国优秀硕士学位论文全文数据库 农业科技辑（月刊）》 * |
| 崔艳华主编: "《高等微生物学》", 31 October 2015, 哈尔滨工业大学出版社 * |
| 李伟佳: "利用高通量测序技术快速解析草莓病毒基因组序列", 《沈阳农业大学学报》 * |
| 百度文库: "RNA-seq数据的处理与分析", 《HTTPS://WENKU.BAIDU.COM/VIEW/4836AD46453610661ED9F478.HTML》 * |
Cited By (7)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN108334750A (en) * | 2018-04-19 | 2018-07-27 | 江苏先声医学诊断有限公司 | A kind of macro genomic data analysis method and system |
| CN110129339A (en) * | 2019-05-10 | 2019-08-16 | 中国计量大学 | Black nightshade curly top poison whole genome sequence and its detection method |
| CN111598181A (en) * | 2020-05-21 | 2020-08-28 | 中国热带农业科学院热带生物技术研究所 | Banana flower and leaf heart rot APP identification method and system |
| CN111598181B (en) * | 2020-05-21 | 2023-04-07 | 中国热带农业科学院热带生物技术研究所 | Banana flower and leaf heart rot APP identification method and system |
| CN116072222A (en) * | 2023-02-16 | 2023-05-05 | 湖南大学 | Method for identifying and splicing viral genome and application thereof |
| CN116072222B (en) * | 2023-02-16 | 2024-02-06 | 湖南大学 | Method for identifying and splicing viral genome and application thereof |
| CN117198409A (en) * | 2023-09-15 | 2023-12-08 | 云南省农业科学院农业环境资源研究所 | microRNA prediction method and system based on transcriptome data |
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