Temperature expression patterns of genes and their coexpression with LncRNAs revealed by RNA-Seq in non-heading Chinese cabbage

Abstract

BackgroundNon-heading Chinese cabbage (NHCC, Brassica rapa ssp. chinensis) is an important leaf vegetable grown worldwide. However, little is known about the molecular mechanisms underlying tolerance for extreme temperature in NHCC. The limited availability of NHCC genomic information has greatly hindered functional analysis and molecular breeding.ResultsHere, we conduct comprehensive analyses of cold and heat treatments in NHCC using RNA-seq. Approximately 790 million paired-end reads representing 136,189 unigenes with N50 length of 1705 bp were obtained. Totally, 14,329 differentially expressed genes (DEGs) were detected. Among which, 10 DEGs were detected in all treatments, including 7 up-regulated and 3 down-regulated. The enrichment analyses showed 25 and 33 genes were enriched under cold and heat treatments, respectively. Additionally, 10,001 LncRNAs were identified, and 9,687 belonged to novel LncRNAs. The expression of miRNAs were more than that of pri-miRNAs and LncRNAs. Furthermore, we constructed a coexpression network for LncRNAs and miRNAs. It showed 67 and 192 genes were regulated by LncRNAs under cold and heat treatments, respectively. We constructed the flowchart for identifying LncRNAs of NHCC using transcriptome. Except conducting the de novo transcriptome analyses, we also compared these unigenes with the Chinese cabbage proteins. We identified several most important genes, and discussed their regulatory networks and crosstalk in cold and heat stresses.ConclusionsWe presented the first comprehensive characterization for NHCC crops and constructed the flowchart for identifying LncRNAs using transcriptome. Therefore, this study represents a fully characterized NHCC transcriptome, and provides a valuable resource for genetic and genomic studies under abiotic stress.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2625-2) contains supplementary material, which is available to authorized users.

Systematic identification and analysis of heat‐stress‐responsive lncRNAs, circRNAs and miRNAs with associated co‐expression and ceRNA networks in cucumber (Cucumis sativus L.)

“…Previous studies have shown that plant–pathogen interactions were associated with plant hyperthermia (Chen et al ). In addition, Song et al () studied the co‐expression of lncRNAs with genes under different temperature treatments in non‐heading Chinese cabbage and found that plant hormone signal transduction pathways were enriched according to KEGG analysis. Moreover, plant hormones have been shown to induce abiotic stress tolerance through biosynthesis and signal transduction (Tran and Pal ).…”

Comparative transcriptome analysis between resistant and susceptible tomato allows the identification of lncRNA16397 conferring resistance to Phytophthora infestans by co‐expressing glutaredoxin

“…Generally, long non‐coding RNAs (lncRNAs) are transcripts of more than 200 nucleotides (nt) in length that possess no apparent coding sequence (CDS) or open reading frame (Fan et al ., ; Wang et al ., ). A number of lncRNAs have recently been identified in plant species due to rapid progress in omics sequencing technology (Li et al ., ; Zou et al ., ), including Arabidopsis (Ben Amor et al ., ; Liu et al ., ; Di et al ., ; Wang et al ., ), rice (Zhang et al ., ), maize (Li et al ., ; Fan et al ., ), wheat (Xin et al ., ), cotton (Wang et al ., ; Zou et al ., ), tomato (Wang et al ., , ; Zhu et al ., ), cucumber (Hao et al ., ), Chinese cabbage (Song et al ., ), Populus (Shuai et al ., ; Chen et al ., ) and others. In particular, studies on plant lncRNAs are far behind those in humans and animals (Liu et al ., ).…”

Research progress of long noncoding RNA in China

“…, Oryza sativa , Populus tomentosa , Fragaria vesca , Solanum lycopersicum , Panax ginseng , Medicago truncatula , Morus notabilis , Brassica rapa ssp. Chinensis and Gossypium arboreum . For instance, Chen's group at Sun Yat‐Sen University has identified a set of lncRNAs that are involved in the sexual reproduction of rice; one such lncRNA XLOC_057324 has the potential to regulate panicle development and fertility .…”

“…(50), Brassica rapa ssp. Chinensis (51) and Gossypium arboreum (52). For instance, Chen's group at Sun Yat-Sen University has identified a set of lncRNAs that are involved in the sexual reproduction of rice; one such lncRNA XLOC_057324 has the potential to regulate panicle development and fertility (44).…”