Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection
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Date
Authors
Kwenda, Stanford
Birch, P.R.J. (Paul)
Moleleki, Lucy Novungayo
Journal Title
Journal ISSN
Volume Title
Publisher
BioMed Central
Abstract
BACKGROUND : Long noncoding RNAs (lncRNAs) represent a class of RNA molecules that are implicated in regulation
of gene expression in both mammals and plants. While much progress has been made in determining the biological
functions of lncRNAs in mammals, the functional roles of lncRNAs in plants are still poorly understood. Specifically, the
roles of long intergenic nocoding RNAs (lincRNAs) in plant defence responses are yet to be fully explored.
RESULTS : In this study, we used strand-specific RNA sequencing to identify 1113 lincRNAs in potato (Solanum
tuberosum) from stem tissues. The lincRNAs are expressed from all 12 potato chromosomes and generally smaller
in size compared to protein-coding genes. Like in other plants, most potato lincRNAs possess single exons. A
time-course RNA-seq analysis between a tolerant and a susceptible potato cultivar showed that 559 lincRNAs are
responsive to Pectobacterium carotovorum subsp. brasiliense challenge compared to mock-inoculated controls. Moreover,
coexpression analysis revealed that 17 of these lincRNAs are highly associated with 12 potato defence-related genes.
CONCLUSIONS : Together, these results suggest that lincRNAs have potential functional roles in potato defence responses.
Furthermore, this work provides the first library of potato lincRNAs and a set of novel lincRNAs implicated in potato
defences against P. carotovorum subsp. brasiliense, a member of the soft rot Enterobacteriaceae phytopathogens.
Description
The datasets supporting the conclusions of this article are available in
the NCBI’s Gene Expression Omnibus (GEO) repository [GEO accession
number, GSE74871; http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=
czatweashdgvdyl&acc=GSE74871].
Additional file 1: Table S5. List of RT-qPCR primers used in this study.
Additional file 2: Table S6. List of RT-PCR primers used in this study.
Additional file 3: Table S1. List of the identified 1113 lincRNA
Additional file 4: Figure S1. A) Comparison of the genomic distribution of lincRNAs and protein-coding genes across the 12 potato chromosomes. The outer grey track represents the 12 potato chromosomes, with a scale (Mb) showing the length of each chromosome. The red histograms (second track with an outer orientation) and blue histograms (third track with inner orientation) represent the abundance and distribution of mRNA and lincRNAs, respectively, throughout the potato genome. The bin size (histogram width) = 5 Mbp). B) Comparison of LincRNA lengths to protein-coding mRNA transcripts in potato (PGSC_DM_v4.03 genome assembly).
Additional file 5: Table S2. LincRNA conservation analysis.
Additional file 6: Figure S2. Comparison of the 1113 lincRNA transcripts identified in the present study with potato lncRNAs available in the GreenC database.
Additional file 7: Table S3. Differentially expressed lincRNA transcripts.
Additional file 8: Table S4. LincRNAs targeted by potato miRNAs.
Additional file 9: Figure S3. RT-qPCR confirmation of five potato defense-related miRNAs in S. tuberosum cv BP1, computationally predicted to target some of the lincRNA transcripts. U6 snRNA was used as the reference gene. The fold changes of miRNAs at each time point were calculated relative to calibrator (control sample; 0 hpi). The experiments were done in triplicate. Error bars represent the fold change range calculated by 2-(ΔΔCt±SD).
Additional file 1: Table S5. List of RT-qPCR primers used in this study.
Additional file 2: Table S6. List of RT-PCR primers used in this study.
Additional file 3: Table S1. List of the identified 1113 lincRNA
Additional file 4: Figure S1. A) Comparison of the genomic distribution of lincRNAs and protein-coding genes across the 12 potato chromosomes. The outer grey track represents the 12 potato chromosomes, with a scale (Mb) showing the length of each chromosome. The red histograms (second track with an outer orientation) and blue histograms (third track with inner orientation) represent the abundance and distribution of mRNA and lincRNAs, respectively, throughout the potato genome. The bin size (histogram width) = 5 Mbp). B) Comparison of LincRNA lengths to protein-coding mRNA transcripts in potato (PGSC_DM_v4.03 genome assembly).
Additional file 5: Table S2. LincRNA conservation analysis.
Additional file 6: Figure S2. Comparison of the 1113 lincRNA transcripts identified in the present study with potato lncRNAs available in the GreenC database.
Additional file 7: Table S3. Differentially expressed lincRNA transcripts.
Additional file 8: Table S4. LincRNAs targeted by potato miRNAs.
Additional file 9: Figure S3. RT-qPCR confirmation of five potato defense-related miRNAs in S. tuberosum cv BP1, computationally predicted to target some of the lincRNA transcripts. U6 snRNA was used as the reference gene. The fold changes of miRNAs at each time point were calculated relative to calibrator (control sample; 0 hpi). The experiments were done in triplicate. Error bars represent the fold change range calculated by 2-(ΔΔCt±SD).
Keywords
Noncoding RNA, Potato, Pectobacterium, lincRNA, Plant defence, Soft rot bacteria, Solanum tuberosum, Entereobacteria
Sustainable Development Goals
Citation
Kwenda, S, Birch, PRJ & Moleleki, LN 2016, 'Genome-wide identification of potato long intergenic noncoding RNAs responsive to Pectobacterium carotovorum subspecies brasiliense infection', BMC Genomics, vol. 17, art. #614, pp. 1-14.