Skip to main content
SpringerLink
Log in

Identification and characterization of long non-coding RNAs in response to early infection by Melampsora larici-populina using genome-wide high-throughput RNA sequencing

  • Short Communication
  • Published:
Tree Genetics & Genomes Aims and scope Submit manuscript

Abstract

Long non-coding RNAs (lncRNAs) were found to widely exist in eukaryotes and play important roles in most biological processes. Trees belonging to Populus spp. are economically important because of their fast-growing characteristics and wide use for wood, pulp, paper, and fuel. However, the prevalence of leaf rust disease caused by Melampsora spp. on some species of Populus severely affects their growth and decreases wood production. Therefore, the identification and characterization of lncRNAs involved in the defense of Melampsora spp. would not only help us to understand plant-pathogen interactions but also provide genetic elements for producing disease-resistant poplars. In the present study, an RNA-Seq transcriptome analysis was performed for poplar leaves in response to early infection by M. larici-populina. The hybrid variety “NL895” (P. × euramericana) was used as plant material. A total of 3994 lncRNAs were identified by mining the RNA-Seq data. The identified lncRNAs had lower abundance, fewer exons, and shorter lengths when compared to protein-coding genes. In addition, 53 lncRNAs were differentially expressed between treatments and controls. Two of these 53 lncRNAs were predicted to compete to be the target of miRNAs. Moreover, the differentially expressed lncRNAs were found to be preferentially located in close proximity to the protein-coding genes they co-expressed. In this study, we were able to show that lncRNAs may play important roles in plant-pathogen interactions in the poplar. This study also improves our understanding of how plants deploy their defense system when encountering biotic stresses.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Abbreviations

FPKM:

Fragments per kilobase million

lncRNA:

Long non-coding RNA

LPI:

Leaf plastochron index

incRNAs:

Intronic ncRNAs

lincRNAs:

Long intergenic ncRNAs

miRNA:

MicroRNA

NATs:

Natural antisense transcripts

piRNAs:

Piwi-interacting RNAs

RNA-Seq:

RNA sequencing

siRNAs:

Small interfering RNAs

ta-siRNAs:

Trans-acting siRNAs

References

  • Ben Amor B, Wirth S, Merchan F, Laporte P, d'Aubenton-Carafa Y, Hirsch J, Maizel A, Mallory A, Lucas A, Deragon JM, Vaucheret H, Thermes C, Crespi M (2009) Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses. Genome Res 19:57–69

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Boerner S, McGinnis KM (2012) Computational identification and functional predictions of long noncoding RNA in Zea mays. PLoS One 7:e43047

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Borodina T, Adjaye J, Sultan M (2011) A strand-specific library preparation protocol for RNA sequencing. Methods Enzymol 500:79–98

    Article  CAS  PubMed  Google Scholar 

  • Chen JH, Quan MY, Zhang DQ (2015) Genome-wide identification of novel long non-coding RNAs in Populus tomentosa tension wood, opposite wood and normal wood xylem by RNA-seq. Planta 241:125–143

    Article  CAS  PubMed  Google Scholar 

  • Chen X (2009) Small RNAs and their roles in plant development. Annu Rev Cell Dev Biol 25:21–44

    Article  PubMed  PubMed Central  Google Scholar 

  • Dai X, Zhao PX (2011) psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39:W155–W159

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Di C, Yuan J, Wu Y, Li J, Lin H, Hu L, Zhang T, Qi Y, Gerstein MB, Guo Y, Lu ZJ (2014) Characterization of stress-responsive lncRNAs in Arabidopsis thaliana by integrating expression, epigenetic and structural features. The Plant journal: for cell and molecular biology 80:848–861

    Article  CAS  Google Scholar 

  • Ding J, Lu Q, Ouyang Y, Mao H, Zhang P, Yao J, Xu C, Li X, Xiao J, Zhang Q (2012) A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice. Proc Natl Acad Sci U S A 109:2654–2659

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dixon RA (2001) Natural products and plant disease resistance. Nature 411:843–847

    Article  CAS  PubMed  Google Scholar 

  • Foster AJ, Pelletier G, Tanguay P, Seguin A (2015) Transcriptome analysis of poplar during leaf spot infection with Sphaerulina spp. PLoS One 10:e0138162.

    Article  PubMed  PubMed Central  Google Scholar 

  • Giorgi FM, Del Fabbro C, Licausi F (2013) Comparative study of RNA-seq- and microarray-derived coexpression networks in Arabidopsis thaliana. Bioinformatics 29:717–724

  • Kong L, Zhang Y, Ye ZQ, Liu XQ, Zhao SQ, Wei L, Gao G (2007) CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res 35:W345–W349

    Article  PubMed  PubMed Central  Google Scholar 

  • Kornienko AE, Guenzl PM, Barlow DP, Pauler FM (2013) Gene regulation by the act of long non-coding RNA transcription. BMC Biol 11:59

    Article  PubMed  PubMed Central  Google Scholar 

  • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing S (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079

    Article  PubMed  PubMed Central  Google Scholar 

  • Li L, Wang X, Sasidharan R, Stolc V, Deng W, He H, Korbel J, Chen X, Tongprasit W, Ronald P, Chen R, Gerstein M, Deng XW (2007) Global identification and characterization of transcriptionally active regions in the rice genome. PLoS One 2:e294

    Article  PubMed  PubMed Central  Google Scholar 

  • Liu J, Wang H, Chua NH (2015) Long noncoding RNA transcriptome of plants. Plant Biotechnol J 13:319–328

    Article  CAS  PubMed  Google Scholar 

  • Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(−Delta Delta C(T)) method. Methods 25:402–408

    Article  CAS  PubMed  Google Scholar 

  • Ponjavic J, Oliver PL, Lunter G, Ponting CP (2009) Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain. PLoS Genet 5:e1000617

    Article  PubMed  PubMed Central  Google Scholar 

  • Ponting CP, Oliver PL, Reik W (2009) Evolution and functions of long noncoding RNAs. Cell 136:629–641

    Article  CAS  PubMed  Google Scholar 

  • Rinaldi C, Kohler A, Frey P, Duchaussoy F, Ningre N, Couloux A, Wincker P, Le Thiec D, Fluch S, Martin F, Duplessis S (2007) Transcript profiling of poplar leaves upon infection with compatible and incompatible strains of the foliar rust Melampsora larici-populina. Plant Physiol 144:347–366

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139–140

    Article  CAS  PubMed  Google Scholar 

  • Shuai P, Liang D, Tang S, Zhang Z, Ye CY, Su Y, Xia X, Yin W (2014) Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa. J Exp Bot 65:4975–4983

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105–1111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7:562–578

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wakasa Y, Oono Y, Yazawa T, Hayashi S, Ozawa K, Handa H, Matsumoto T, Takaiwa F (2014) RNA sequencing-mediated transcriptome analysis of rice plants in endoplasmic reticulum stress conditions. BMC Plant Biol 14:101

  • Wang H, Niu QW, Wu HW, Liu J, Ye J, Yu N, Chua NH (2015a) Analysis of non-coding transcriptome in rice and maize uncovers roles of conserved lncRNAs associated with agriculture traits. The Plant journal: for cell and molecular biology 84:404–416

    Article  CAS  Google Scholar 

  • Wang J, Yu W, Yang Y, Li X, Chen T, Liu T, Ma N, Yang X, Liu R, Zhang B (2015b) Genome-wide analysis of tomato long non-coding RNAs and identification as endogenous target mimic for microRNA in response to TYLCV infection. Sci Rep 5:16946

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang TZ, Liu M, Zhao MG, Chen R, Zhang WH (2015c) Identification and characterization of long non-coding RNAs involved in osmotic and salt stress in Medicago truncatula using genome-wide high-throughput sequencing. BMC Plant Biol 15:131

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang X, Ai G, Zhang CL, Cui L, Wang JF, Li HX, Zhang JH, Ye ZBA (2016) Expression and diversification analysis reveals transposable elements play important roles in the origin of Lycopersicon-specific lncRNAs in tomato. New Phytol 209:1442–1455

    Article  CAS  PubMed  Google Scholar 

  • Wen J, Parker BJ, Weiller GF (2007) In silico identification and characterization of mRNA-like noncoding transcripts in Medicago truncatula. In silico biology 7:485–505

    CAS  PubMed  Google Scholar 

  • Widin KD, Schipper AL (1981) Effect of Melampsora medusae leaf rust infection on yield of hybrid poplars. Eur J Forest Pathol 11:438–448

  • Young MD, Wakefield MJ, Smyth GK, Oshlack A (2010) Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol 11:R14

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang H, Hu W, Hao J, Lv S, Wang C, Tong W, Wang Y, Wang Y, Liu X, Ji W (2016) Genome-wide identification and functional prediction of novel and fungi-responsive lincRNAs in Triticum aestivum. BMC Genomics 17:238

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhang YC, Liao JY, Li ZY, Yu Y, Zhang JP, Li QF, Qu LH, Shu WS, Chen YQ (2014) Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice. Genome Biol 15:512

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

This study was financed by project 31670651 supported by the National Natural Science Foundation of China (NSFC No. 31670651) and the Fundamental Research Funds for the Central Universities (No. 52902-0900202801). The authors are grateful to AJE (American Journal Experts) for improving the English in this paper.

Author information

Authors and Affiliations

  1. College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China

    Nian Wang, Pei Cao, Wenxiu Xia & Hongyan Yu

  2. Institute of Fruit and Forest Tree, Wuhan Academy of Agricultural Science and Technology, Wuhan, 430070, China

    Linchuan Fang

Authors
  1. Nian Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Pei Cao
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Wenxiu Xia
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Linchuan Fang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Hongyan Yu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Nian Wang.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Data archiving statement

All of these raw data have been deposited in the National Center for Biotechnology Information (NCBI) Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra/) under Bioproject accession PRJNA354475 and 6 Biosamples were included in this Bioproject. Accessions for these 6 Biosamples are SAMN06046477, SAMN06046496, SAMN06046497, SAMN06046498, SAMN06046499 and SAMN06046500 and they refer to samples of PI1 to 3 and PN1 to 3 in this study, respectively.

Additional information

Communicated by A. Brunner

Electronic supplementary material

Table S1

Primer sequences used in the qRT-PCR assay (XLSX 9 kb)

Table S2

Full information for all identified lncRNAs (XLSX 492 kb)

Table S3

Prediction lncRNA as miRNA targets (XLSX 19 kb)

Table S4

Target genes of ptc-miR396 and ptcmiR530 families and their expression profiles in response to infection by leaf rust disease (XLSX 4870 kb)

Supplementary file 1

Sequence file for all 3994 lncRNAs (FA 1549 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wang, N., Cao, P., Xia, W. et al. Identification and characterization of long non-coding RNAs in response to early infection by Melampsora larici-populina using genome-wide high-throughput RNA sequencing. Tree Genetics & Genomes 13, 34 (2017). https://doi.org/10.1007/s11295-017-1116-1

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s11295-017-1116-1

Keywords

Search

Navigation