CN109411014A - A kind of cyclic method of plant chloroplast full-length genome assembling based on the sequencing of two generations - Google Patents
A kind of cyclic method of plant chloroplast full-length genome assembling based on the sequencing of two generations Download PDFInfo
- Publication number
- CN109411014A CN109411014A CN201811174710.0A CN201811174710A CN109411014A CN 109411014 A CN109411014 A CN 109411014A CN 201811174710 A CN201811174710 A CN 201811174710A CN 109411014 A CN109411014 A CN 109411014A
- Authority
- CN
- China
- Prior art keywords
- scaffolds
- sequence
- genome
- parse
- chloroplast
- Prior art date
- Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
- Granted
Links
Abstract
The present invention is that based on two generation sequencing datas (such as: Illumina platform) plant chloroplast full-length genome data are assembled and constructed with a kind of method of cyclization.Method provided by the present invention has used data filtering software Trimmomatic, composite software SPAdes and MASHMAP software first, then ChloroplastCircle kit is utilized, and realizes the data flow procedure of entire plant chloroplast full-length genome assembling, cyclization in conjunction with perl script Programming with Pascal Language.By the way that experimental results demonstrate method provided by the present invention can quick, accurate, batch, automatically complete assembling and the cyclization of plant chloroplast full-length genome.Currently, the present invention has been carried out in 10,000 plant chloroplast full-length genome projects, good effect is achieved.
Description
Technical field
The invention belongs to technical field of biological information, and in particular to the plant chloroplast full-length genome sequence based on the sequencing of two generations
Column assembling, a kind of cyclic method.
Background technique
Chloroplaset is the important organelle that green plants is converted into luminous energy chemical energy on the earth, is that progress is photosynthetic
Important place.In the 1960s, researcher has found chloroplast DNA (chloroplast DNA, cpDNA).Study table
Bright, Chloroplast gene size has between 120kb to 217kb than more conservative cyclic structure.Plant chloroplast complete sequence
Analysis, which discloses cpDNA genome, following characteristics: 1. genomes are by two inverted repeats (IR) and one short single copy sequence
Arrange (short single copy seguence, SSC) and single-copy sequence (long single copy one long
Seguence, LSC) composition；Each 10-24Kb of 2.IRA and IRB long, coding is identical, contrary；3. although each plant
CpDNA size is different, but gene composition is similar, and the number of all genes is almost identical.
(Sanger Sequencing) is sequenced relative to traditional mulberry lattice, two generation sequencing technologies have speed fast, accuracy rate
The features such as high (99.99%), flux is high, at low cost, it is especially the most famous with the microarray dataset of Illumina company.In recent years,
Using high throughput sequencing technologies, a large amount of plant chloroplast genome has been decrypted, and is widely used and leads in each research
Domain.Such as: the phylogenomics based on chloroplaset, biodiversity research etc., but most famous should be
DNABarcoding research.DNA bar code (DNA Barcode) is fellow of the Royal Society of Canada Paul Herbert in 2003
The concept that year puts forward: biological species are identified based on genetic fragment.The meaning of DNA bar code is can have to species
Effect, Rapid identification；It was found that hidden storage kind, promotes bio-diversity discovery；Research for other problem in science such as systematic growth.
DNA bar code is not only the strong supplement of traditional species identification, more since it uses digitized forms, makes sample qualification process
It can be realized automation, standardization and globalization, breach the transition to experience and rely on, and carried out using the relic of organism
It quickly and effectively identifies, the application system to be formed and be easy to utilize can be established within a short period of time.The maximum of DNA bar code technology
Advantage be using fubaritic known of biological vestiges (bloodstain, feather trace, fragment of tissue etc.) Lai Jianding morphology or
Unknown species.Therefore, DNA bar code technology is in biological species identification, national health quarantine, national important biomolecule strategic resource mirror
Fixed, discovery of new species resource etc. has a wide range of applications.
The present inventor proposed that achievement was published in using ITS as the new standard of seed plant core bar code in 2011
PNAS upper (Li et al., 2011).Plant species generation type is different, and some species hybridizations take place frequently.In actual plant species
In identification, just with several genetic fragments, the qualification result of some species is still undesirable.In recent years, high-flux sequence skill
The fast development of art and further decreasing for sequencing cost, bring new chance.Therefore, the present inventor proposes to utilize plant again
Bar code of the chloroplaset whole genome sequence as species identification.Target is 30 China, a higher plant chloroplaset more than 000
Whole genome sequence is all sequenced, and builds up the maximum Barcoding database in the whole nation or even the whole world, is researcher and government's phase
Pass department provides technical support service.Currently, completion 10 has been sequenced in the present inventor, a species more than 000.Such big data situation
Under, if being assembled and being spelled by hand completely ring, that workload is hardly conceivable.Therefore, urgent need will be established a kind of fast
Speed, efficient, accurate, automation method.
Summary of the invention
In view of the drawbacks of the prior art, the present invention is intended to provide a kind of quick, efficient, accurate, automatic plant
The assembling of chloroplaset whole genome sequence and cyclic method.The present invention tests in 10,000 plant chloroplast Genome Projects
Its reliability is demonstrate,proved.
In order to realize above-mentioned purpose of the invention, and the defect of the prior art is solved, the present invention is especially by following technology
Scheme is implemented:
A kind of cyclic method of plant chloroplast full-length genome assembling based on the sequencing of two generations, this method comprises the following steps:
Total DNA (including core DNA, chloroplast DNA and mitochondrial DNA) sample is carried out with two generations sequencing Illumina platform
2G is sequenced in sequencing, each sample；
Initial data is handled with data filtering software Trimmomatic, removes connector and low-quality reads,
Obtain clean reads；
Multiple kmer are carried out to clean reads with SPAdes from the beginning to assemble, and construct Scaffolds；
Use the 4Kb sequence in arabidopsis Chloroplast gene as library, then use assembling after Scaffolds sequence as
Query does BLASTN operation；
BLASTN is parsed with the parse_blastnToScaffold.pl script in ChloroplastCircle kit
As a result, obtaining that Scaffolds sequence of bitscore maximum score value；
With the Scaffolds sequence of maximum score value some complete Chloroplast gene libraries BLAST again, these chloroplasets
Genome sequence can be downloaded from NCBI or user oneself provides；
With the parse_blastnToReference_Genome.pl script in ChloroplastCircle kit into
Row parsing, obtains the chloroplaset full-length genome reference sequences with some species of the nearest edge of target Scaffolds；
All Scaffolds sequences after assembling are referred on genome sequence to chloroplaset with MASHMAP software
Mapping is positioned on reference genome；
Finally using the parse_MashMap.pl script in ChloroplastCircle kit to mapping to ginseng
The Scaffolds for examining genome is attached and carries out filling-up hole with the Scaffolds on no mapping, final cyclization,
Reach the upload standard of ncbi database.
Specifically, this method comprises the following steps:
(1) with two generations sequencing Illumina microarray dataset to plant genomic DNA (including core DNA, chloroplast DNA and mitochondria
DNA) sample is sequenced, and is obtained initial data (raw data), and about 2G or so is sequenced in each sample；
(2) it is handled with the initial data that data filtering software Trimmomatic obtains step (1), removes connector
With low-quality reads, clean reads is obtained；
(3) multiple kmer are carried out with the clean reads that SPAdes obtains step (2) from the beginning to assemble, is constructed
Scaffolds；
(4) use the 4Kb sequence in arabidopsis Chloroplast gene as library, it is then assembled with step (3)
Scaffolds sequence does BLASTN operation as query；
(5) with parse_blastnToScaffold.pl script analyzing step in ChloroplastCircle kit
(4) BLASTN obtained is as a result, obtain that Scaffolds sequence of bitscore maximum score value, wherein parse_
BlastnToScaffold.pl the Script section main code is as follows:
(6) the Scaffolds sequence some complete chloroplaset bases of BLAST again of the maximum score value obtained with step (5)
Because of a group library, these Chloroplast gene sequences can be downloaded from NCBI (https: //www.ncbi.nlm.nih.gov), or be used
Family oneself provides；
(7) with parse_blastnToReference_Genome.pl script in ChloroplastCircle kit into
The file that row analyzing step (6) obtains obtains joining with the chloroplaset full-length genome of some species of the nearest edge of target Scaffolds
Sequence is examined, wherein parse_blastnToReference_Genome.pl the Script section main code is as follows:
(8) the leaf assembled all Scaffolds sequences of step (1) obtained to step (7) with MASHMAP software is green
Body positions on reference genome with reference to mapping on genome sequence；
(9) finally using parse_MashMap.pl script in ChloroplastCircle kit to step (8)
The Scaffolds of mapping to reference genome is attached and is mended with the Scaffolds on no mapping
Hole, final cyclization, wherein the main pseudocode of parse_blastnToReference_Genome.pl script algorithm is as follows:
Detailed description of the invention
Following drawings is not intended to limit the present invention range for illustrating specific embodiments of the present invention；
Fig. 1 shows the flow chart of a technical solution of the invention；
Fig. 2 shows the algorithm idea schematic diagram of parse_MashMap.pl in the present invention；
Fig. 3 shows that the present invention assembles certain plant chloroplast full-length genome, and after cyclization, in Geneious8.0
Schematic diagram.
Specific embodiment
Property content is described further son for the essence of the present invention with reference to the accompanying drawings and examples, as described below, but
The present invention is not limited with this.Any person skilled in the art is become possibly also with the technology contents of above-mentioned description
More equivalent embodiment.It is all without departing from the contents of the present invention, following embodiment is done according to the technical essence of the invention
Any simple modification or the variation of program language, fall within the scope of protection of the present invention.
The present invention is to chloroplast number according to assembling cyclization, but to mitochondria data assembling cyclization, the present invention is equally also fitted
With.Therefore, it for mitochondria data assembling cyclization, all falls in restriction protection scope of the invention.
Embodiment 1
LHT120202 total DNA sample is completed by the Hiseq2500 microarray dataset of Illumina company, using pair-end
Build library sequencing, sequencing reading length 150bp, initial data about 2.2G.
It is filtered with data filtering software Trimmomatic initial data, removes connector and low-quality reads, obtain
To clean reads, order are as follows: nohup java~/Trimmomatic-0.32/trimmomatic-0.32.jar PE-
threads 2-phred33LHT120202_R1.fastq LHT120202_R2.fastq LHT120202_R1.trim
LHT120202_R1.unpaired LHT120202_R2.trim LHT120202_R2.unpaired ILLUMINACLIP:
~/Trimmomatic-0.32/adapters/TruSeq2-PE.fa:2:30:10 LEADING:5 TRAILING:5
SLIDINGWINDOW:4:15MINLEN:80&；
Multiple kmer are carried out to clean reads with SPAdes from the beginning to assemble, and construct Scaffolds, order are as follows:
Nohup python spades.py--careful-k 21,33,55,77,99,127-o~/outsamplename--pe1-1
~/cpgenome/samplename--pe1-2~/cpgenome/samplename&；
Use the 4Kb sequence in arabidopsis Chloroplast gene as library, then with assembled Scaffolds sequence above
As query, BLASTN operation is done, is ordered are as follows: nohup makeblastdb-in~/Arabidopsis_thaliana_
4K.fasta-out~/Arabidopsis_thaliana_4K-dbtype nucl&nohup blastn-query~/
LHT120202_scaffolds.fasta-db~/Arabidopsis_thaliana_4K-out~/scaffolds_AT_
4K.xls-num_threads 4-outfmt"6 qseqid sseqid length sstart send qstart qend
bitscore qcovs pident evalue mismatch"&；
It is obtained above with the parse_blastnToScaffold.pl script parsing in ChloroplastCircle kit
BLASTN as a result, obtain that Scaffolds sequence of bitscore maximum score value, order are as follows: nohup perl
parse_blastnToScaffold.pl scaffolds_BLASTN_AT_4K.xls LHT120202_
scaffolds.fasta scaffolds_Filtered.fa bitscore_max_scaffold.fa&；
(6) the Scaffolds sequence some complete chloroplaset bases of BLAST again of the maximum score value obtained with step (5)
Because of a group library, these Chloroplast gene sequences can be downloaded from NCBI (https: //www.ncbi.nlm.nih.gov), or be used
Family oneself provides, order are as follows: nohup makeblastdb-in~/plastid_genomic.fna-out~/plastid_
genomic-dbtype nucl&
Nohup blastn-query~/bitscore_max_scaffold.fa-db~/plastid_genomic-
Out~/bitscore_max_scaffold_Ref.xls-num_threads 4-outfmt " 6qseqid sseqid
length sstart send qstart qend bitscore qcovs pident evalue mismatch"&；
(7) with the parse_blastnToReference_Genome.pl script in ChloroplastCircle kit
The file that analyzing step (6) obtain is carried out, the chloroplaset full-length genome with some species of the nearest edge of target Scaffolds is obtained
Reference sequences, order are as follows: nohup perl parse_blastnToReference_Genome.pl bitscore_max_
scaffold_Ref.xlsplastid_genomic.fna reference_genome.fa&；
(8) the leaf assembled all Scaffolds sequences of step (1) obtained to step (7) with MASHMAP software is green
Body positions on reference genome with reference to mapping on genome sequence, orders are as follows: nohup mashmap-
rreference_genome.fa-q scaffolds.fa-s 300-f none-o test-t 10&；
(9) finally using the parse_MashMap.pl script in ChloroplastCircle kit to step (8)
The Scaffolds of mapping to reference genome is attached and is mended with the Scaffolds on no mapping
Hole, final cyclization, order are as follows: nohup perl parse_MashMap.pl-m mashmap_test-s
scaffolds.fa-k 127-dbitscore_max_scaffold.fa-t MashMap_site_sort.xls-a
scaffolds_all.fasta-p mapped_seq.fa-olinked_each_contigs.fa&。
The main software used in 1 present invention of table
Claims (2)
1. a kind of plant chloroplast full-length genome based on the sequencing of two generations assembles cyclic method, it is characterised in that this method includes such as
Lower step:
Total DNA (including core DNA, chloroplast DNA and mitochondrial DNA) sample is surveyed with two generations sequencing Illumina platform
2G is sequenced in sequence, each sample；
Initial data is handled with data filtering software Trimmomatic, connector and low-quality reads is removed, obtains
clean reads；
Multiple kmer are carried out to clean reads with SPAdes from the beginning to assemble, and construct Scaffolds；
Use the 4Kb sequence in arabidopsis Chloroplast gene as library, then use assembling after Scaffolds sequence as
Query does BLASTN operation；
With in ChloroplastCircle kit parse_blastnToScaffold.pl script parsing BLASTN as a result,
Obtain that Scaffolds sequence of bitscore maximum score value；
With the Scaffolds sequence of maximum score value some complete Chloroplast gene libraries BLAST again, these chloroplast genes
Group sequence can be downloaded from NCBI or user oneself provides；
It is solved with the parse_blastnToReference_Genome.pl script in ChloroplastCircle kit
Analysis, obtains the chloroplaset full-length genome reference sequences with some species of the nearest edge of target Scaffolds；
All Scaffolds sequences after assembling are referred to mapping on genome sequence to chloroplaset with MASHMAP software,
It is positioned on reference genome；
Finally utilize the parse_MashMap.pl script in ChloroplastCircle kit to mapping to reference to base
It is attached because of the Scaffolds of group and carries out filling-up hole with the Scaffolds on no mapping, final cyclization reaches
The upload standard of ncbi database.
2. a kind of plant chloroplast full-length genome based on the sequencing of two generations assembles cyclic method, it is characterised in that this method includes such as
Lower step:
(1) with two generations sequencing Illumina microarray dataset to plant genomic DNA (including core DNA, chloroplast DNA and mitochondrial DNA)
Sample is sequenced, and is obtained initial data (raw data), and about 2G is sequenced in each sample；
(2) it is handled with the initial data that data filtering software Trimmomatic obtains step (1), removes connector and low
The reads of quality obtains clean reads；
(3) multiple kmer are carried out with the clean reads that SPAdes obtains step (2) from the beginning to assemble, constructs Scaffolds；
(4) it uses the 4Kb sequence in arabidopsis Chloroplast gene as library, then uses step (3) assembled Scaffolds sequence
Column are used as query, do BLASTN operation；
(5) it is obtained with parse_blastnToScaffold.pl script analyzing step (4) in ChloroplastCircle kit
BLASTN as a result, obtain that Scaffolds sequence of bitscore maximum score value, wherein parse_
BlastnToScaffold.pl the Script section main code is as follows:
(6) the Scaffolds sequence some complete Chloroplast genes of BLAST again of the maximum score value obtained with step (5)
Library, these Chloroplast gene sequences are downloaded from NCBI (https: //www.ncbi.nlm.nih.gov) or user oneself
It provides；
(7) it is solved with parse_blastnToReference_Genome.pl script in ChloroplastCircle kit
The file that step (6) obtain is analysed, is obtained with the chloroplaset full-length genome of some species of the nearest edge of target Scaffolds with reference to sequence
Column, wherein parse_blastnToReference_Genome.pl the Script section main code is as follows:
(8) joined with the chloroplaset that MASHMAP software obtains the assembled all Scaffolds sequences of step (1) to step (7)
Mapping on genome sequence is examined, is positioned on reference genome；
(9) finally using parse_MashMap.pl script in ChloroplastCircle kit to step (8) mapping
Scaffolds to reference genome is attached and carries out filling-up hole with the Scaffolds on no mapping, finally at
Ring, wherein the main pseudocode of parse_blastnToReference_Genome.pl script algorithm is as follows:
Priority Applications (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| CN201811174710.0A CN109411014B (en) | 2018-10-09 | 2018-10-09 | Plant chloroplast whole genome assembly cyclization method based on second-generation sequencing |
Applications Claiming Priority (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| CN201811174710.0A CN109411014B (en) | 2018-10-09 | 2018-10-09 | Plant chloroplast whole genome assembly cyclization method based on second-generation sequencing |
Publications (2)
| Publication Number | Publication Date |
|---|---|
| CN109411014A true CN109411014A (en) | 2019-03-01 |
| CN109411014B CN109411014B (en) | 2021-11-09 |
Family
ID=65466913
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| CN201811174710.0A Active CN109411014B (en) | 2018-10-09 | 2018-10-09 | Plant chloroplast whole genome assembly cyclization method based on second-generation sequencing |
Country Status (1)
| Country | Link |
|---|---|
| CN (1) | CN109411014B (en) |
Cited By (6)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN110379462A (en) * | 2019-06-21 | 2019-10-25 | 中南民族大学 | A method of based on the golden waist Chloroplast gene sequence of Illumina Technical form China |
| CN111424076A (en) * | 2020-05-08 | 2020-07-17 | 中国科学院昆明植物研究所 | Method for identifying poppy by using chloroplast genome |
| CN112259169A (en) * | 2020-11-18 | 2021-01-22 | 东北农业大学 | Method for rapidly acquiring chloroplast genome from transcriptome data |
| CN112481413A (en) * | 2021-01-13 | 2021-03-12 | 南京集思慧远生物科技有限公司 | Plant mitochondrial genome assembly method based on second-generation and third-generation sequencing technologies |
| CN112802554A (en) * | 2021-01-28 | 2021-05-14 | 中国科学院成都生物研究所 | Animal mitochondrial genome assembly method based on second-generation data |
| CN117106875A (en) * | 2023-10-23 | 2023-11-24 | 中国科学院昆明植物研究所 | Method for estimating plant genome size and/or repeatability based on low-depth sequencing |
Citations (9)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US20030054370A1 (en) * | 2001-02-27 | 2003-03-20 | Qiandong Zeng | Systematic discovery of new genes and genes discovered thereby |
| CN103849687A (en) * | 2014-02-25 | 2014-06-11 | 广州白云山潘高寿药业股份有限公司 | Molecular biological identification method of fritillaria taipaiensis |
| CN104450682A (en) * | 2014-12-16 | 2015-03-25 | 西南大学 | Method for assembling chloroplast genome sequence |
| CN106868116A (en) * | 2017-01-24 | 2017-06-20 | 华南农业大学 | A kind of mulberry tree pathogen high throughput identification and kind sorting technique and its application |
| CN107784199A (en) * | 2017-10-18 | 2018-03-09 | 中国科学院昆明植物研究所 | A kind of organelle gene group screening technique based on STb gene sequencing result |
| CN108165617A (en) * | 2017-12-03 | 2018-06-15 | 浙江大学 | Chloroplast genomic dna separation, sequencing new method, kit and its application |
| CN108251504A (en) * | 2018-01-17 | 2018-07-06 | 翌圣生物科技（上海）有限公司 | A kind of method and kit of supper-fast structure genomic DNA sequencing library |
| CN108250288A (en) * | 2018-01-17 | 2018-07-06 | 吉林省农业科学院 | A kind of brain-derived neurotrophic factor hBDNFb albumen of chloroplast expression and preparation method thereof |
| CN108486266A (en) * | 2018-02-06 | 2018-09-04 | 北京市农林科学院 | The molecular labeling of DCIPThe chloroplast of maize genome and the application in cultivar identification |
-
2018
- 2018-10-09 CN CN201811174710.0A patent/CN109411014B/en active Active
Patent Citations (9)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| US20030054370A1 (en) * | 2001-02-27 | 2003-03-20 | Qiandong Zeng | Systematic discovery of new genes and genes discovered thereby |
| CN103849687A (en) * | 2014-02-25 | 2014-06-11 | 广州白云山潘高寿药业股份有限公司 | Molecular biological identification method of fritillaria taipaiensis |
| CN104450682A (en) * | 2014-12-16 | 2015-03-25 | 西南大学 | Method for assembling chloroplast genome sequence |
| CN106868116A (en) * | 2017-01-24 | 2017-06-20 | 华南农业大学 | A kind of mulberry tree pathogen high throughput identification and kind sorting technique and its application |
| CN107784199A (en) * | 2017-10-18 | 2018-03-09 | 中国科学院昆明植物研究所 | A kind of organelle gene group screening technique based on STb gene sequencing result |
| CN108165617A (en) * | 2017-12-03 | 2018-06-15 | 浙江大学 | Chloroplast genomic dna separation, sequencing new method, kit and its application |
| CN108251504A (en) * | 2018-01-17 | 2018-07-06 | 翌圣生物科技（上海）有限公司 | A kind of method and kit of supper-fast structure genomic DNA sequencing library |
| CN108250288A (en) * | 2018-01-17 | 2018-07-06 | 吉林省农业科学院 | A kind of brain-derived neurotrophic factor hBDNFb albumen of chloroplast expression and preparation method thereof |
| CN108486266A (en) * | 2018-02-06 | 2018-09-04 | 北京市农林科学院 | The molecular labeling of DCIPThe chloroplast of maize genome and the application in cultivar identification |
Non-Patent Citations (9)
| Title |
|---|
| NAM V. HOANG等: "Next generation sequencing of total DNA from sugarcane provides no evidence for chloroplast heteroplasmy", 《NEW NEGATIVES IN PLANT SCIENCE》 * |
| ZHONGJIEWANG: "MashMap：快速近似的长序列匹配软件", 《HTTP://BLOG.SINA.COM.CN/S/BLOG_6C0267490102WKQQ.HTML》 * |
| 刘晶星: "宁夏枸杞和黑果枸杞叶绿体全基因组测序及基因注释分析", 《中国优秀博硕士学位论文全文数据库(硕士) 基础科学辑》 * |
| 毕桂萁: "海水红毛菜(Bangia fuscopurpurea OUCPT-01)与暗紫红毛菜(Bangia atropurpurea)细胞器基因组测序及系统发育分析", 《中国优秀博硕士学位论文全文数据库(硕士) 基础科学辑》 * |
| 白雪菲: "基于混合样品高通量测序数据的植物叶绿体基因组拼接和分析", 《中国优秀硕士学位论文全文数据库(硕士)基础科学辑》 * |
| 管锐: "太湖蓝藻藻块宏基因组及微生物在其聚集过程中作用机制研究", 《中国优秀博硕士学位论文全文数据库(硕士) 基础科学辑》 * |
| 聂小军: "基于高通测序技术的小麦和紫茎泽兰基因组学初步研究", 《中国优秀博硕士学位论文全文数据库(博士) 基础科学辑》 * |
| 胡志刚: "菊科药用植物DNA条形码及叶绿体基因组研究", 《中国优秀博硕士学位论文全文数据库(博士) 农业科技辑》 * |
| 陈琴怡: "两种五加科植物的叶绿体全基因组研究及其系统发育分析", 《中国优秀博硕士学位论文全文数据库(硕士) 基础科学辑》 * |
Cited By (11)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN110379462A (en) * | 2019-06-21 | 2019-10-25 | 中南民族大学 | A method of based on the golden waist Chloroplast gene sequence of Illumina Technical form China |
| CN110379462B (en) * | 2019-06-21 | 2021-11-26 | 中南民族大学 | Method for assembling Chinese Jinyao chloroplast genome sequence based on Illumina technology |
| CN111424076A (en) * | 2020-05-08 | 2020-07-17 | 中国科学院昆明植物研究所 | Method for identifying poppy by using chloroplast genome |
| CN112259169A (en) * | 2020-11-18 | 2021-01-22 | 东北农业大学 | Method for rapidly acquiring chloroplast genome from transcriptome data |
| CN112259169B (en) * | 2020-11-18 | 2024-01-30 | 东北农业大学 | Method for rapidly obtaining chloroplast genome from transcriptome data |
| CN112481413A (en) * | 2021-01-13 | 2021-03-12 | 南京集思慧远生物科技有限公司 | Plant mitochondrial genome assembly method based on second-generation and third-generation sequencing technologies |
| CN112481413B (en) * | 2021-01-13 | 2022-02-15 | 南京集思慧远生物科技有限公司 | Plant mitochondrial genome assembly method based on second-generation and third-generation sequencing technologies |
| CN112802554A (en) * | 2021-01-28 | 2021-05-14 | 中国科学院成都生物研究所 | Animal mitochondrial genome assembly method based on second-generation data |
| CN112802554B (en) * | 2021-01-28 | 2023-09-22 | 中国科学院成都生物研究所 | Animal mitochondrial genome assembly method based on second-generation data |
| CN117106875A (en) * | 2023-10-23 | 2023-11-24 | 中国科学院昆明植物研究所 | Method for estimating plant genome size and/or repeatability based on low-depth sequencing |
| CN117106875B (en) * | 2023-10-23 | 2024-02-06 | 中国科学院昆明植物研究所 | Method for estimating plant genome size and/or repeatability based on low-depth sequencing |
Also Published As
| Publication number | Publication date |
|---|---|
| CN109411014B (en) | 2021-11-09 |
Similar Documents
| Publication | Publication Date | Title |
|---|---|---|
| CN109411014A (en) | A kind of cyclic method of plant chloroplast full-length genome assembling based on the sequencing of two generations | |
| Carpenter et al. | Access to RNA-sequencing data from 1,173 plant species: The 1000 Plant transcriptomes initiative (1KP) | |
| Koch et al. | BrassiBase: Tools and biological resources to study characters and traits in the Brassicaceae—version 1.1 | |
| Tice et al. | PhyloFisher: a phylogenomic package for resolving eukaryotic relationships | |
| CN104450682B (en) | A kind of method for assembling Chloroplast gene sequence | |
| Tao et al. | Transcriptome profiling and digital gene expression by deep sequencing in early somatic embryogenesis of endangered medicinal Eleutherococcus senticosus Maxim. | |
| CN105112518B (en) | A kind of HLA classifying method based on Pacbio RS II microarray dataset | |
| CN110951911B (en) | Tilia EST-SSR primer based on transcriptome as well as screening method and application thereof | |
| CN113151542B (en) | Development method and application of Huashansong genome SNP | |
| AU2021101596A4 (en) | SSR molecular marker primer set for identifying Rhynchostylis and use thereof | |
| KR101426466B1 (en) | Complete sequencing of Chloroplast genomes of Panax ginseng-derived Maker, DNA primer sets and Kits for discrimination of Panax ginseng cultivars and Panax species and uses thereof | |
| CN112695124B (en) | Phalaenopsis SSR molecular marker primer composition and application thereof | |
| KR102298751B1 (en) | Molecular marker based on chloroplast genome sequence for discriminating Codonopsis sp. and uses thereof | |
| CN111235303B (en) | Method for identifying cord-grass and spartina alterniflora | |
| Riaño-Pachón et al. | Surveying the complex polyploid sugarcane genome sequence using synthetic long reads | |
| KR20170068093A (en) | Complete sequencing of chloroplast genome and nrDNA of Ledebouriella seseloides, Peucedanum japonicum and Glehnia littoralis-derived barcoding marker, DNA primer set for discrimination of origin and species and uses thereof | |
| CN112259169A (en) | Method for rapidly acquiring chloroplast genome from transcriptome data | |
| Calcino et al. | Heteroplasmy and repeat expansion in the plant-like mitochondrial genome of a bivalve mollusc | |
| Wang et al. | How to survive in the world’s third poplar: Insights from the genome of the highest altitude woody plant, Hippophae tibetana (Elaeagnaceae) | |
| CN110890134A (en) | Method for identifying dendrobium candidum base source by using chloroplast genome large single copy area | |
| CN111172312B (en) | PCR amplification primer for chloroplast genomes of bamboo cypress and long-leaf bamboo cypress and application of PCR amplification primer | |
| CN108642166A (en) | Utilize the unicellular method for carrying out genome haplotype assembling of pear pollen | |
| CN112391491B (en) | DNA probe for identifying specific chloroplast gene mutation sites of Oleacea sinensis species and identification method thereof | |
| CN115323060B (en) | Fish nuclear gene molecular marker primer, molecular marker and molecular marker database | |
| CN116121437B (en) | SNP (single nucleotide polymorphism) marker combination of mangiferin fruit variety and application of SNP marker combination in mangiferin fruit breeding |
Legal Events
| Date | Code | Title | Description |
|---|---|---|---|
| PB01 | Publication | ||
| PB01 | Publication | ||
| SE01 | Entry into force of request for substantive examination | ||
| SE01 | Entry into force of request for substantive examination | ||
| GR01 | Patent grant | ||
| GR01 | Patent grant |