[논문]Transcriptome profiling of abiotic responses to heat, cold, salt, and osmotic stress of Capsicum annuum L.

Kang, Won-Hee; Sim, Young Mi; Koo, Namjin; Nam, Jae-Young; Lee, Junesung; Kim, Nayoung; Jang, Hakgi; Kim, Yong-Min; Yeom, Seon-In

doi:10.1038/s41597-020-0352-7

[해외논문] Transcriptome profiling of abiotic responses to heat, cold, salt, and osmotic stress of Capsicum annuum L. 원문보기

Scientific data, v.7 = v.7 no.1, 2020년, pp.17 -

Kang, Won-Hee (Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828 Republic of Korea) , Sim, Young Mi (Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141 Republic of Korea) , Koo, Namjin (Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141 Republic of Korea) , Nam, Jae-Young (Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828 Republic of Korea) , Lee, Junesung (Department of Agricultural Plant Science, Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju, 52828 Republic of Korea) , Kim, Nayoung (Department of Agricultural Plant Science, Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju, 52828 Republic of Korea) , Jang, Hakgi (Department of Agricultural Plant Science, Division of Applied Life Science (BK21 Plus Program), Gyeongsang National University, Jinju, 52828 Republic of Korea) , Kim, Yong-Min (Korean Bioinformation Center, Korea Research Institute of B) , Yeom, Seon-In

Abstract ▼ AI-Helper

Peppers (Capsicum annuum L.), belonging to the Solanaceae family, are one of the most economically important crops globally. Like other crops, peppers are threatened by diverse environmental conditions due to different pathogens and abiotic stresses. High-quality reference genomes with massive datasets of transcriptomes from various conditions can provide clues to preferred agronomic traits for breeding. However, few global gene expression profiling datasets have been published to examine the environmental stress-resistant mechanisms in peppers. In this study, we report the RNA-seq analyses of peppers treated with heat, cold, salinity, and osmotic stress at six different time points. RNA-seq libraries from 78 RNA samples containing three biological replicates per time point for each of the abiotic stresses and a mock control were constructed. A total of 204.68 Gb of transcriptome data were verified by differentially expressed genes and gene ontology enrichment analysis. Analyses of the transcriptome data in this study will provide useful information for basic studies of various stimuli to facilitate the development of stress-resistant pepper cultivars.Measurement(s)RNA • transcriptomeTechnology Type(s)RNA sequencingFactor Type(s)time point measurementSample Characteristic - OrganismCapsicum annuumMachine-accessible metadata file describing the reported data: 10.6084/m9.figshare.11440659

참고문헌 (30)

1. Zhu JK Abiotic stress signaling and responses in plants Cell 2016 167 313 324 27716505

상세보기
2. Coolen S Transcriptome dynamics of Arabidopsis during sequential biotic and abiotic stresses Plant J. 2016 86 249 267 10.1111/tpj.13167 26991768

상세보기
3. Rasmussen S Transcriptome responses to combinations of stresses in Arabidopsis Plant Physiol. 2013 161 1783 1794 10.1104/pp.112.210773 23447525

상세보기
4. Cohen SP Leach JE Abiotic and biotic stresses induce a core transcriptome response in rice Sci. Rep. 2019 9 6273 10.1038/s41598-019-42731-8 31000746

상세보기
5. Ma J Transcriptomics analyses reveal wheat responses to drought stress during reproductive stages under field conditions Front. Plant Sci. 2017 8 592 10.3389/fpls.2017.00592 28484474

상세보기
6. Liu Z Temporal transcriptome profiling reveals expression partitioning of homeologous genes contributing to heat and drought acclimation in wheat ( Triticum aestivum L.) BMC Plant Biol. 2015 15 152 10.1186/s12870-015-0511-8 26092253

상세보기
7. Gong L Transcriptome profiling of the potato ( Solanum tuberosum L.) plant under drought stress and water-stimulus conditions PLoS One 2015 10 e0128041 10.1371/journal.pone.0128041 26010543

상세보기
8. Kang WH Yeom SI Genome-wide Identification, classification, and expression analysis of the receptor-like protein family in tomato Plant Pathol. J. 2018 34 435 444 30369853
9. Kim S New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication Genome Biol. 2017 18 210 10.1186/s13059-017-1341-9 29089032

상세보기
10. Kim MS Global gene expression profiling for fruit organs and pathogen infections in the pepper Capsicum annuum L. Sci. Data 2018 5 180103 10.1038/sdata.2018.103 29870035

상세보기
11. Kang WH Kim S Lee HA Choi D Yeom SI Genome-wide analysis of Dof transcription factors reveals functional characteristics during development and response to biotic stresses in pepper Sci. Rep. 2016 6 33332 10.1038/srep33332 27653666

상세보기
12. Dang FF CaWRKY40, a WRKY protein of pepper, plays an important role in the regulation of tolerance to heat stress and resistance to Ralstonia solanacearum infection Plant Cell Environ. 2013 36 757 774 10.1111/pce.12011 22994555

상세보기
13. Kim SY Identification of a CaRAV1 possessing an AP2/ERF and B3 DNA-binding domain from pepper leaves infected with Xanthomonas axonopodis pv. glycines 8ra by differential display Biochim. Biophys. Acta 2005 1729 141 146 10.1016/j.bbaexp.2005.04.009 15978683

상세보기
14. Park CJ Pathogenesis-related protein 10 isolated from hot pepper functions as a ribonuclease in an antiviral pathway Plant J. 2004 37 186 198 10.1046/j.1365-313X.2003.01951.x 14690503

상세보기
15. Zhong S High-throughput illumina strand-specific RNA sequencing library preparation Cold Spring Harb. Protoc. 2011 2011 940 949 10.1101/pdb.prot5652 21807852

상세보기
16. Martin M Cutadapt removes adapter sequences From high-throughput sequencing reads. EMBnet Journal 2011 17 10 12
17. Patel RK Jain M NGS QC Toolkit: a toolkit for quality control of next generation sequencing data PLoS One 2012 7 e30619 10.1371/journal.pone.0030619 22312429

상세보기
18. Ewels P Magnusson M Lundin S Kaller M MultiQC: summarize analysis results for multiple tools and samples in a single report Bioinformatics 2016 32 3047 3048 10.1093/bioinformatics/btw354 27312411

상세보기
19. Kim S 2017 Capsicum annuum cultivar CM334, whole genome shotgun sequencing project GenBank AYRZ00000000
20. Kim D Langmead B Salzberg SL HISAT: a fast spliced aligner with low memory requirements Nat. Methods 2015 12 357 360 10.1038/nmeth.3317 25751142

상세보기
21. Liao Y Smyth GK Shi W featureCounts: an efficient general purpose program for assigning sequence reads to genomic features Bioinformatics 2014 30 923 930 10.1093/bioinformatics/btt656 24227677

상세보기
22. Robinson MD Oshlack A A scaling normalization method for differential expression analysis of RNA-seq data Genome Biol. 2010 11 R25 10.1186/gb-2010-11-3-r25 20196867

상세보기
23. Sollner JF An RNA-Seq atlas of gene expression in mouse and rat normal tissues Sci. Data 2017 4 170185 10.1038/sdata.2017.185 29231921

상세보기
24. Robinson MD McCarthy DJ Smyth GK edgeR: a Bioconductor package for differential expression analysis of digital gene expression data Bioinformatics 2010 26 139 140 10.1093/bioinformatics/btp616 19910308

상세보기
25. Kolde, R. pheatmap: Pretty Heatmaps , https://CRAN.R-project.org/package=pheatmap (2015).
26. Yu, G., Wang, L. G., Han, Y. & He, Q. Y. ClusterProfiler: an R package for comparing biological themes among gene clusters. OMICS 16 , 284？287？(2012).
27. Kang WH 2019 Transcriptome profiling of abiotic responses to heat, cold, salt, and osmotic stress of Capsicum annuum L figshare 10.6084/m9.figshare.10264832.v5
28. Wickham, H. ggplot2: elegant graphics for data analysis. Springer-Verlag New York (2009).
29. 2019 NCBI Sequence Read Archive SRP187794
30. 2019 NCBI Gene Expression Omnibus GSE132824

LOADING...

활용도 분석정보

상세보기

다운로드

내보내기

활용도 Top5 논문

해당 논문의 주제분야에서 활용도가 높은 상위 5개 콘텐츠를 보여줍니다.
더보기 버튼을 클릭하시면 더 많은 관련자료를 살펴볼 수 있습니다.

원문 보기

AccessON 원문보기

원문 URL 링크

DOI : 10.1038/s41597-020-0352-7 [무료]
PubMed Central : 저널 > 논문 [무료]
Nature Publishing : 저널
AccessON : 저널

*원문 PDF 파일 및 링크정보가 존재하지 않을 경우 KISTI DDS 시스템에서 제공하는 원문복사서비스를 사용할 수 있습니다.

오픈액세스(OA) 유형

GOLD

오픈액세스 학술지에 출판된 논문

저작권 관리 안내

내보내기 메뉴

내보내기 구분

파일저장
인쇄
메일전송

구성항목

기본정보
상세정보

관리번호, 논문명, 저널/프로시딩명, 저자 , 발행년, 권, 호, 시작페이지, 끝페이지, 발행기관

저장형식

Text(ASCII format)
Excel format
RefWorks Direct Export
RIS format (for Reference Manager, ProCite, EndNote), Scholar's Aids, Mendeley

메일정보

받는사람 (필수): @
보내는사람 (선택): @
제목
내용: KISTI 검색결과 이메일 서비스

안내

총 건의 자료가 검색되었습니다.

다운받으실 자료의 인덱스를 입력하세요. (1-10,000)

검색결과의 순서대로 최대 10,000건 까지 다운로드가 가능합니다.

데이타가 많을 경우 속도가 느려질 수 있습니다.(최대 2~3분 소요)

다운로드 파일은 UTF-8 형태로 저장됩니다.
파일의 내용이 제대로 보이지 않을실 때는 웹브라우저 상단의 보기 -> 인코딩 -> 자동선택 여부를 확인하십시오.

Text(ASCII format)
Excel format

표제어: PCR

동의어: Packet Collision Rate

용어 설명 출처 목록 (6)

용어 설명: PCR은 세균 특이성이 있는 primer를 이용하여 적은 수의 세균이 있을지라도 쉽게 검출할 수 있는 유용한 방법이며, 이를 이용하여 구강 내 치면세균막이나 타액에서 직접 세균을 검출할 수 있게 되었다[8].

AI-Helper ※ AI-Helper는 을 사용합니다.

AI-Helper

안녕하세요, AI-Helper입니다. 좌측 "선택된 텍스트"에서 텍스트를 선택하여 요약, 번역, 용어설명을 실행하세요.
※ AI-Helper는 부적절한 답변을 할 수 있습니다.

연합인증