Tissue-specific analysis of Coffea arabica L. transcriptome revealed potential regulatory roles of lncRNAs

Abstract

Long non-coding RNAs (lncRNAs) play pivot roles in regulating mRNA expression in eukaryotic organisms without coding any proteins. In the current study, a comprehensive analysis of 260 published RNA-Seq datasets collected from different tissues (fruits, leaves, stems, and roots) of Coffea arabica L. was performed to discover potential lncRNAs. A total of 10,564 unique lncRNAs were identified. Our results showed that 77.14% of the lncRNAs were intergenic and 60.39% of them are located within 5 Kbp from the partner gene. In general, all the identified lncRNAs showed shorter lengths, fewer number of exons, and lower expression levels as compared to mRNAs in different studied tissues. Several lncRNAs were determined as differentially expressed (DE) in fruits as compared to leaves, stems, or roots. The functional characterization of the DE lncRNAs revealed their roles in regulating significant biological processes in different tissues of C. arabica. The current study provides a comprehensive analysis and dataset of lncRNAs in C. arabica that could be utilized in further studies concerning the roles of these molecules in plant cells.

Keywords: Caffeine; Coffee; Differential expression; Gene ontology; Non-coding RNA.

Fig. 1

Length distribution of the assembled transcripts (a) and distribution of number of exons in each assembled transcript (b).

Fig. 2

Characterization of lncRNAs identified in different tissues of Coffea arabica. (a) Type of lncRNAs identified by FEELnc as either genic (overlaps partner gene) or intergenic (does not overlap partner gene), (b) the proportion of lncRNAs located within 5 K bp either downstream or upstream the partner gene and those which located beyond 5 K bp of the partner gene, (c) percentage of lncRNAs according to their location relative to the partner gene, and (d) number of exons in the identified lncRNAs.

Fig. 3

The variation in FPKM values of all the expressed transcripts in fruits, stems, leaves, and roots was compared and visualized using boxplots (a) and density distribution profiles (b). The difference in the average expression levels between lncRNAs and mRNAs in all the studied tissues showed that mRNAs was expressed more than lncRNAs as depicted in the violin plots (c) and density distribution profiles (d).

Fig. 4

(a) Number of DE lncRNAs in fruits as compared to leaves, stems, and roots. The expression landscape of lncRNAs in different pairwise comparisons is depicted by the volcano plots between (b) fruits vs. leaves, (c) fruits vs. stems, and (d) fruits vs. roots.

Fig. 5

The most enriched GO terms in C. arabica fruit tissues as compared to (a) leaves, (b) stems, and (c) roots. BP: biological process, CC: cellular component, MF: molecular function.