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Identification and characterization of long non-coding RNAs involved in osmotic and salt stress in Medicago truncatula using genome-wide high-throughput sequencing.

Wang TZ, Liu M, Zhao MG, Chen R, Zhang WH - BMC Plant Biol. (2015)

Bottom Line: Enrichments in GO terms in biological processes such as signal transduction, energy synthesis, molecule metabolism, detoxification, transcription and translation were found.LncRNAs are likely involved in regulating plant's responses and adaptation to osmotic and salt stresses in complex regulatory networks with protein-coding genes.These findings are of importance for our understanding of the potential roles of lncRNAs in responses of plants in general and M. truncatula in particular to abiotic stresses.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, People's Republic of China. tzwang@ibcas.ac.cn.

ABSTRACT

Background: Long non-coding RNAs (lncRNAs) have been shown to play crucially regulatory roles in diverse biological processes involving complex mechanisms. However, information regarding the number, sequences, characteristics and potential functions of lncRNAs in plants is so far overly limited.

Results: Using high-throughput sequencing and bioinformatics analysis, we identified a total of 23,324 putative lncRNAs from control, osmotic stress- and salt stress-treated leaf and root samples of Medicago truncatula, a model legume species. Out of these lncRNAs, 7,863 and 5,561 lncRNAs were identified from osmotic stress-treated leaf and root samples, respectively. While, 7,361 and 7,874 lncRNAs were identified from salt stress-treated leaf and root samples, respectively. To reveal their potential functions, we analyzed Gene Ontology (GO) terms of genes that overlap with or are neighbors of the stress-responsive lncRNAs. Enrichments in GO terms in biological processes such as signal transduction, energy synthesis, molecule metabolism, detoxification, transcription and translation were found.

Conclusions: LncRNAs are likely involved in regulating plant's responses and adaptation to osmotic and salt stresses in complex regulatory networks with protein-coding genes. These findings are of importance for our understanding of the potential roles of lncRNAs in responses of plants in general and M. truncatula in particular to abiotic stresses.

No MeSH data available.


Related in: MedlinePlus

Venn diagram of common and specific lncRNAs. a The number of common/specific lncRNAs identified in leaves and roots under non-stressed, control conditions. b The number of common/specific lncRNAs between osmotic stress-responsive and salt stress-responsive lncRNAs
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Fig2: Venn diagram of common and specific lncRNAs. a The number of common/specific lncRNAs identified in leaves and roots under non-stressed, control conditions. b The number of common/specific lncRNAs between osmotic stress-responsive and salt stress-responsive lncRNAs

Mentions: From these analyses, we identified 11,501, 18,275, 8,571, 18,277, 10,458 and 19,186 unique lncRNAs from the six cDNA libraries, respectively (Table 2). In total, 23,324 unique lncRNAs were obtained in the present study (Additional file 2: Table S1). And this number was similar to that of lncRNAs in Arabidopsis and maize [30, 41]. We found that these lncRNAs were more evenly distributed across the 8 chromosomes in M. truncatula with no obvious preferences of locations (Fig. 1a). According to the locations of lncRNAs in the genome, 10,426 intronic, 5,794 intergenic, 3,558 sense and 3,546 antisense lncRNAs were identified (Fig. 1b and e). In terms of the lncRNAs’ length, the majority of lncRNAs was relatively short. For example, 84.1 % of them were shorter than 1,000 nt (Fig. 1c). Interestingly, lncRNAs and mRNAs were much more abundant in roots than in leaves, given that similar amounts of raw reads were obtained for both leaf and root samples. In all libraries, more lncRNAs were detected in roots than in leaves (Table 2). For example, 18,275 lncRNAs were identified in roots, while there were 11,501 lncRNAs in leaves under control condition (Fig. 2a). Furthermore, we found that the accumulative frequency of lncRNAs differed in leaves from that in roots. The proportion of lncRNAs with a high level of expression was more than mRNAs in leaves, but this expression pattern was in contrary in roots under the control conditions (Fig. 1d). Moreover, these patterns of expression were not altered by treatments with osmotic and salt stress (Additional file 1: Figure S2). The lack of chloroplast-derived RNAs in roots might be a possible reason for the difference between leaves and roots.Fig. 1


Identification and characterization of long non-coding RNAs involved in osmotic and salt stress in Medicago truncatula using genome-wide high-throughput sequencing.

Wang TZ, Liu M, Zhao MG, Chen R, Zhang WH - BMC Plant Biol. (2015)

Venn diagram of common and specific lncRNAs. a The number of common/specific lncRNAs identified in leaves and roots under non-stressed, control conditions. b The number of common/specific lncRNAs between osmotic stress-responsive and salt stress-responsive lncRNAs
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4457090&req=5

Fig2: Venn diagram of common and specific lncRNAs. a The number of common/specific lncRNAs identified in leaves and roots under non-stressed, control conditions. b The number of common/specific lncRNAs between osmotic stress-responsive and salt stress-responsive lncRNAs
Mentions: From these analyses, we identified 11,501, 18,275, 8,571, 18,277, 10,458 and 19,186 unique lncRNAs from the six cDNA libraries, respectively (Table 2). In total, 23,324 unique lncRNAs were obtained in the present study (Additional file 2: Table S1). And this number was similar to that of lncRNAs in Arabidopsis and maize [30, 41]. We found that these lncRNAs were more evenly distributed across the 8 chromosomes in M. truncatula with no obvious preferences of locations (Fig. 1a). According to the locations of lncRNAs in the genome, 10,426 intronic, 5,794 intergenic, 3,558 sense and 3,546 antisense lncRNAs were identified (Fig. 1b and e). In terms of the lncRNAs’ length, the majority of lncRNAs was relatively short. For example, 84.1 % of them were shorter than 1,000 nt (Fig. 1c). Interestingly, lncRNAs and mRNAs were much more abundant in roots than in leaves, given that similar amounts of raw reads were obtained for both leaf and root samples. In all libraries, more lncRNAs were detected in roots than in leaves (Table 2). For example, 18,275 lncRNAs were identified in roots, while there were 11,501 lncRNAs in leaves under control condition (Fig. 2a). Furthermore, we found that the accumulative frequency of lncRNAs differed in leaves from that in roots. The proportion of lncRNAs with a high level of expression was more than mRNAs in leaves, but this expression pattern was in contrary in roots under the control conditions (Fig. 1d). Moreover, these patterns of expression were not altered by treatments with osmotic and salt stress (Additional file 1: Figure S2). The lack of chloroplast-derived RNAs in roots might be a possible reason for the difference between leaves and roots.Fig. 1

Bottom Line: Enrichments in GO terms in biological processes such as signal transduction, energy synthesis, molecule metabolism, detoxification, transcription and translation were found.LncRNAs are likely involved in regulating plant's responses and adaptation to osmotic and salt stresses in complex regulatory networks with protein-coding genes.These findings are of importance for our understanding of the potential roles of lncRNAs in responses of plants in general and M. truncatula in particular to abiotic stresses.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093, People's Republic of China. tzwang@ibcas.ac.cn.

ABSTRACT

Background: Long non-coding RNAs (lncRNAs) have been shown to play crucially regulatory roles in diverse biological processes involving complex mechanisms. However, information regarding the number, sequences, characteristics and potential functions of lncRNAs in plants is so far overly limited.

Results: Using high-throughput sequencing and bioinformatics analysis, we identified a total of 23,324 putative lncRNAs from control, osmotic stress- and salt stress-treated leaf and root samples of Medicago truncatula, a model legume species. Out of these lncRNAs, 7,863 and 5,561 lncRNAs were identified from osmotic stress-treated leaf and root samples, respectively. While, 7,361 and 7,874 lncRNAs were identified from salt stress-treated leaf and root samples, respectively. To reveal their potential functions, we analyzed Gene Ontology (GO) terms of genes that overlap with or are neighbors of the stress-responsive lncRNAs. Enrichments in GO terms in biological processes such as signal transduction, energy synthesis, molecule metabolism, detoxification, transcription and translation were found.

Conclusions: LncRNAs are likely involved in regulating plant's responses and adaptation to osmotic and salt stresses in complex regulatory networks with protein-coding genes. These findings are of importance for our understanding of the potential roles of lncRNAs in responses of plants in general and M. truncatula in particular to abiotic stresses.

No MeSH data available.


Related in: MedlinePlus