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).