Abstract
BackgroundLong noncoding RNAs (lncRNAs) play an important role in diverse biological processes and have been widely studied in recent years. However, the roles of lncRNAs in leaf pigment formation in ginkgo (Ginkgo biloba L.) remain poorly understood.ResultsIn this study, lncRNA libraries for mutant yellow-leaf and normal green-leaf ginkgo trees were constructed via high-throughput sequencing. A total of 2044 lncRNAs were obtained with an average length of 702 nt and typically harbored 2 exons. We identified 238 differentially expressed lncRNAs (DELs), 32 DELs and 49 differentially expressed mRNAs (DEGs) that constituted coexpression networks. We also found that 48 cis-acting DELs regulated 72 target genes, and 31 trans-acting DELs regulated 31 different target genes, which provides a new perspective for the regulation of the leaf-color mutation. Due to the crucial regulatory roles of lncRNAs in a wide range of biological processes, we conducted in-depth studies on the DELs and their targets and found that the chloroplast thylakoid membrane subcategory and the photosynthesis pathways (ko00195) were most enriched, suggesting their potential roles in leaf coloration mechanisms. In addition, our correlation analysis indicates that eight DELs and 68 transcription factors (TFs) might be involved in interaction networks.ConclusionsThis study has enriched the knowledge concerning lncRNAs and provides new insights into the function of lncRNAs in leaf-color mutations, which will benefit future selective breeding of ginkgo.
Highlights
Long noncoding RNAs play an important role in diverse biological processes and have been widely studied in recent years
LncRNA is a class of RNA molecules that have lengths over 200 bp and no protein-coding ability
The candidate lncRNAs were further screened by using Coding Potential Calculator (CPC) analysis, Coding-Non-Coding Index (CNCI) analysis, Protein Families (Pfam) protein domain analysis and predictor of long noncoding RNAs and messenger RNAs based on an improved k-mer scheme (PLEK) analysis methods (Fig. 1a)
Summary
Long noncoding RNAs (lncRNAs) play an important role in diverse biological processes and have been widely studied in recent years. 1 to 2% of the total RNAs produced by eukaryotic cells during transcription are encoded to produce proteins, and the remaining RNAs are called noncoding RNAs (ncRNAs). NcRNAs play important roles in cells, such as rRNAs and tRNAs in protein synthesis, snRNAs in the splicing of nascent RNA, and microRNAs, siRNAs and piRNAs in inhibiting gene expression [1]. Among ncRNAs, there is a widely distributed class of ncRNA transcripts with lengths greater than 200 nucleotides and no protein-encoding function, named long noncoding RNAs (lncRNAs) [2,3,4,5]. LncRNA is universally transcribed in eukaryotic cells and distributed in the cytoplasm, organelles and nucleus but mainly in the nucleus. With the continuous improvement of bioinformatics technology, including high-throughput sequencing technology and
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