Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening

Minghui Wang,Weihua Zhao,Lei Gao,Lingxia Zhao

doi:10.1186/s12870-018-1300-y

Minghui Wang, Weihua Zhao + Show 2 more

Open Access

https://doi.org/10.1186/s12870-018-1300-y

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Abstract

BackgroundLong non-coding RNAs (lncRNAs) are involved in multiple biological processes in both mammals and plants. There is growing evidence that they are associated with development; but their expression and regulation during fruit ripening in the model plant tomato (Solanum lycopersicum) has yet to be described.ResultsFollowing integration of 134 RNA-seq data sets, we identified 79,322 putative lncRNAs, consisting of 70,635 lincRNAs, 8085 antisense non-coding RNAs (ancRNAs) and 602 sense lncRNAs (slncRNAs). lncRNAs had specific features that are distinct from mRNAs, including tissue-specificity, and shorter and fewer exons. Notably, more than 5000 of the novel lincRNAs were found to be expressed across the mature green (MG), breaker (BR) and breaker plus 7 days (BR + 7) developmental stages. The differently expressed lincRNAs had different DNA methylation profiles from the mRNAs.ConclusionsIntegrating transcriptome datasets and genome-wide screening enabled the identification of a comprehensive set of tomato lncRNAs. Here, we found that the lncRNAs DNA methylation profiles were different from those of mRNAs. This will help future investigation of lncRNA function, especially for the dissection of the molecular mechanisms involved in the regulation of fruit development.

Highlights

Long non-coding RNAs are involved in multiple biological processes in both mammals and plants
We found that the transcripts overlapping with known mRNAs from the complementary DNA, namely antisense non-coding RNAs (ncRNAs) (ancRNAs), corresponded to approximately 32% of the total 127,724 Fig. 1d)
6895 potential Long non-coding RNAs (lncRNAs) overlapped with the sense strand and no intron located lncRNAs were recovered from our pipeline

Summary

Introduction

Long non-coding RNAs (lncRNAs) are involved in multiple biological processes in both mammals and plants. Tomato development is a complex biological process, involving tightly regulated cell division and differentiation, cell expansion, and ripening [7]. During this ripening phase, the coordinated activation of multiple genes and regulatory pathways result in changes in color, flavor, aroma, texture and nutritional attributes [8, 9]. Non-coding RNAs (ncRNAs), which do not encode proteins, comprise a substantial portion of eukaryotic transcripts [20, 21] They can be divided into various classes, including microRNAs (miRNAs), piwiinteracting RNAs (piRNAs), lncRNAs, and others with a length of more than 200 nucleotides [22].

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