Genome-wide analysis of long non-coding RNAs affecting roots development at an early stage in the rice response to cadmium stress

Abstract

BackgroundLong non-coding RNAs (lncRNAs) have been found to play a vital role in several gene regulatory networks involved in the various biological processes in plants related to stress response. However, systematic analyses of lncRNAs expressed in rice Cadmium (Cd) stress are seldom studied. Thus, we presented the characterization and expression of lncRNAs in rice root development at an early stage in response to Cd stress.ResultsThe lncRNA deep sequencing revealed differentially expressed lncRNAs among Cd stress and normal condition. In the Cd stress group, 69 lncRNAs were up-regulated and 75 lncRNAs were down-regulated. Furthermore, 386 matched lncRNA-mRNA pairs were detected for 120 differentially expressed lncRNAs and 362 differentially expressed genes in cis, and target gene-related pathway analyses exhibited significant variations in cysteine and methionine metabolism pathway-related genes. For the genes in trans, overall, 28,276 interaction relationships for 144 lncRNAs and differentially expressed protein-coding genes were detected. The pathway analyses found that secondary metabolites, such as phenylpropanoids and phenylalanine, and photosynthesis pathway-related genes were significantly altered by Cd stress. All of these results indicate that lncRNAs may regulate genes of cysteine-rich peptide metabolism in cis, as well as secondary metabolites and photosynthesis in trans, to activate various physiological and biochemical reactions to respond to excessive Cd.ConclusionThe present study could provide a valuable resource for lncRNA studies in response to Cd treatment in rice. It also expands our knowledge about lncRNA biological function and contributes to the annotation of the rice genome.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4807-6) contains supplementary material, which is available to authorized users.

Genome-Wide Identification of lncRNAs During Rice Seed Development

“…Although plant lncRNA research is still in its infancy, the rapid development and application of transcriptome technology has led to the identification of a large number of lncRNAs in plants [23][24][25][26]. Many lncRNAs have been found to be involved in the regulation of important agronomic traits [11], cadmium stress response in root [27], female reproduction [28], male reproduction [23] and other stress responses [29] in rice. In addition, 578 lncRNAs related to high-temperature-induced grain chalkiness development were identified in rice spikelets harvested at 10 DAP exposed to high-temperature stress, and expression levels of some of them were verified by RT-PCR [30].…”

Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting rapeseed (Brassica napus L.) genotypes subjected to drought stress and re-watering

“…Altered splicing is one of the mechanisms for lncRNA transcripts to affect gene expression in many physiological processes [67][68][69]. In Q2, 477 lncRNA transcripts from 469 lncRNA genes were identified, in which 8 lncRNA coding genes were alternatively spliced.…”

Integrative Analysis of the lncRNA and mRNA Transcriptome Revealed Genes and Pathways Potentially Involved in the Anther Abortion of Cotton (Gossypium hirsutum L.)

“…LncRNA16397 is resistant to Phytophthora infestans by co-expressing glutaredoxin in tomato [16]. LncRNAs affect the root development response to cadmium stress at an early stage of rice [17]. Phosphate deficiency-induced lncRNAs (PDILs) involved in Pi-deficiency signaling and Pi transport have shown that lncRNAs regulate the responses of plants to phosphate starvation [18,19].…”