Abstract
Long noncoding RNAs (lncRNAs) have been reported to play key regulatory roles in plant growth, development, and biotic and abiotic stress physiology. Revealing the mechanism of lncRNA regulation in the albino portions of leaves is important for understanding the development of chimeric leaves in Ananas comosus var. bracteatus. In this study, a total of 3,543 candidate lncRNAs were identified, among which 1,451 were differentially expressed between completely green (CGr) and completely white (CWh) leaves. LncRNAs tend to have shorter transcripts, lower expression levels, and greater expression specificity than protein-coding genes. Predicted lncRNA targets were functionally annotated by the Gene Ontology (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. A lncRNA-mRNA interaction network was constructed, and 36 target mRNAs related to chlorophyll metabolism were predicted to interact with 86 lncRNAs. Among these, 25 significantly differentially expressed lncRNAs putatively interacted with 16 target mRNAs. Based on an expression pattern analysis of the lncRNAs and their target mRNAs, the lncRNAs targeting magnesium chelatase subunit H (ChlH), protochlorophyllide oxidoreductase (POR), and heme o synthase (COX10) were suggested as key regulators of chlorophyll metabolism. This study provides the first lncRNA database for A. comosus var. bracteatus and contributes greatly to understanding the mechanism of epigenetic regulation of leaf albinism.
Highlights
Noncoding RNAs are RNA transcripts that do not encode a protein
To identify long noncoding RNAs (lncRNAs) in A. comosus var. bracteatus, high-throughput sequencing of six RNA deep sequencing (RNA-seq) libraries constructed from completely green (CGr) and completely white (CWh) leaves at three developmental stages was performed
We report the first genome-wide lncRNA profiling of A. comosus var. bracteatus
Summary
Noncoding RNAs (ncRNAs) are RNA transcripts that do not encode a protein. A great diversity of ncRNAs has been observed. General conventions divide ncRNAs into two main categories: small ncRNAs (200 bp) [1]. LncRNAs are defined as RNAs that are at least 200 nucleotides (nt) in length, are independently transcribed, and bear a molecular resemblance to mRNAs but do not have recognizable potential to encode functional proteins.
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