Genome-wide identification and functional prediction of cold and/or drought-responsive lncRNAs in cassava

Li, Shuxia; Yu, Xiang; Ning, Lei; Cheng, Zhihao; Zhao, Pingjuan; He, Yuqing; Wang, Wenquan; Peng, Ming

doi:10.1038/srep45981

Cited by 117 publications

(158 citation statements)

References 63 publications

(92 reference statements)

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“…Among 24,368 lncRNAs, 983 and 1288 were responsive to cold treatment in the leaves and roots. The cold-responsive lncRNAs found in our study are more than those identified in cassava, and this may result from the different sequencing methods and plant species, such as different genome sizes and sensitivities to low temperature stress [44].…”

Section: Discussionmentioning

confidence: 71%

Identification of tissue-specific and cold-responsive lncRNAs in Medicago truncatula by high-throughput RNA sequencing

et al. 2020

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Background: Long non-coding RNAs (lncRNAs) play important roles in the regulation of plant responses to environmental stress by acting as essential regulators of gene expression. However, whether and how lncRNAs are involved in cold acclimation-dependent freezing tolerance in plants remains largely unknown. Medicago truncatula is a prominent model for studies of legume genomics, and distinguished by its cold-acclimation characteristics. To determine the roles of lncRNAs in plant cold stress response, we conducted genome-wide high-throughput sequencing in the legume model plant M. truncatula. Results: RNA-seq data were generated from twelve samples for the four treatments, i.e., non-cold treated leaves and roots, cold-treated leaves and roots of M. truncatula Jemalong A17 seedlings. A total of 1204 million raw reads were generated. Of them, 1150 million filtered reads after quality control (QC) were subjected to downstream analysis. A large number of 24,368 unique lncRNAs were identified from the twelve samples. Among these lncRNAs, 983 and 1288 were responsive to cold treatment in the leaves and roots, respectively. We further found that the intronic-lncRNAs were most sensitive to the cold treatment. The cold-responsive lncRNAs were unevenly distributed across the eight chromosomes in M. truncatula seedlings with obvious preferences for locations. Further analyses revealed that the cold-responsive lncRNAs differed between leaves and roots. The putative target genes of the lncRNAs were predicted to mainly involve the processes of protein translation, transport, metabolism and nucleic acid transcription. Furthermore, the networks of a tandem array of CBF/DREB1 genes that were reported to be located in a major freezing tolerance QTL region on chromosome 6 and their related lncRNAs were dissected based on their gene expression and chromosome location. Conclusions:We identified a comprehensive set of lncRNAs that were responsive to cold treatment in M. truncatula seedlings, and discovered tissue-specific cold-responsive lncRNAs in leaves and roots. We further dissected potential regulatory networks of CBF Intergenic RNA (MtCIR1) and MtCBFs that play critical roles in response and adaptation of M. truncatula to cold stress.

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Section: Discussionmentioning

confidence: 71%

Identification of tissue-specific and cold-responsive lncRNAs in Medicago truncatula by high-throughput RNA sequencing

et al. 2020

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“…As previously described (Li et al, 2017), A total of 140 gigabase in-depth sequencing of library was performed initially on a HiSeq 2500 instrument that generated paired-end reads with 125 nucleotides. After filter out the adapter and low quality sequences, TopHat2 (Trapnell et al, 2012) was used to map the clean reads to cassava genome.…”

Section: Methodsmentioning

confidence: 99%

Global Gene Expression Analysis Reveals Crosstalk between Response Mechanisms to Cold and Drought Stresses in Cassava Seedlings

Cheng

et al. 2017

Front. Plant Sci.

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Abiotic stress negatively impacts cassava (Manihot esculenta) growth and yield. Several molecular mechanisms of plant response to cold and drought have been identified and described in the literature, however, little is known about the crosstalk of the responses of cassava to these two stresses. To elucidate this question, transcriptome analysis of cassava seedlings under cold or PEG-simulated drought stress treatment was performed. Our results showed that 6103 and 7462 transcripts were significantly regulated by cold and drought stress, respectively. Gene Ontology annotation revealed that the abscisic and jasmonic acid signaling pathways shared between the two stresses responses. We further identified 2434 common differentially expressed genes (DEGs), including 1130 up-regulated and 841 down-regulated DEGs by the two stresses. These co-induced or co-suppressed genes are grouped as stress signal perception and transduction, transcription factors (TFs), metabolism as well as transport facilitation according to the function annotation. Furthermore, a large proportion of well characterized protein kinases, TF families and ubiquitin proteasome system related genes, such as RLKs, MAPKs, AP2/ERFBPs, WRKYs, MYBs, E2 enzymes and E3 ligases, including three complexes of interacting proteins were shown as key points of crosstalk between cold and drought stress signaling transduction pathways in a hierarchical manner. Our research provides valuable information and new insights for genetically improving the tolerance of crops to multiple abiotic stresses.

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“…With advances in next-generation sequencing technology, many investigations have shown that lncRNAs exert their regulatory effects on gene expression levels, including epigenetic regulation, transcriptional regulation, and post-transcriptional regulation in the form of RNA [19]. It is known that sequence-specific DNA binding transcription factor activity [42,58], response to stimulus [59], response to abiotic stimulus [58], biosynthetic process [58], structural constituent of ribosome [56], photosynthesis [60] and oxidoreductase activity [60], which are regulated by some lncRNAs, have been reported in response to abiotic stresses, and these GO terms were identified in this study. To determine the similarity and differences between the two genotypes, the significantly enriched GO terms were compared.…”

Section: Differentially Expressed Lncrnas Specifically Enriched In Gomentioning

confidence: 99%

“…We found that phosphoprotein phosphatase activity, protein metabolic process, and sequence-specific DNA binding were significantly and specially enriched in Q2, while single-organism metabolic process, photosynthesis, and oxidoreductase activity were significantly and specially enriched in Qinyou8. Additionally, lncRNAs have been recognized as powerful regulators of pathways in response to drought stress, including ribosome, photosynthesis [61], and plant hormone signal transduction [42,62]. The ribosome pathway was simultaneously significant in both genotypes, and the differential lncRNA target genes were up-regulated in this pathway.…”

Section: Differentially Expressed Lncrnas Specifically Enriched In Gomentioning

confidence: 99%

“…DRIR can be significantly activated by drought and salt stress as well as by abscisic acid (ABA) treatment. In addition, in cassava, 318 lncRNAs were identified, which were responsive to cold and/or drought stress, and which are associated with hormone signal transduction, biosynthesis of secondary metabolites, and the sucrose metabolism pathway [42].…”

Section: Introductionmentioning

confidence: 99%

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

Tan

et al. 2019

Preprint

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Background: Drought stress is a major abiotic factor that affects rapeseed ( Brassica napus L.) productivity. Though previous studies indicated that long non-coding RNAs (lncRNAs) play a key role in response to drought stress, a scheme for genome-wide identification and characterization of lncRNAs' response to drought stress is still lacking, especially in the case of B . napus . In order to further understand the molecular mechanism of the response of B . napus to drought stress, we compared changes in the transcriptome between Q2 (a drought-tolerant genotype) and Qinyou8 (a drought-sensitive genotype) in response to drought stress and rehydration treatment at the seedling stage.Results: A total of 5,546 down-regulated and 6,997 up-regulated mRNAs were detected in Q2 compared with 7,824 and 10,251 in Qinyou8, respectively; 369 down-regulated and 108 up-regulated lncRNAs were detected in Q2 compared with 449 and 257 in Qinyou8, respectively. We further Abbreviations

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Genome-wide identification and functional prediction of cold and/or drought-responsive lncRNAs in cassava

Cited by 117 publications

References 63 publications

Identification of tissue-specific and cold-responsive lncRNAs in Medicago truncatula by high-throughput RNA sequencing

Identification of tissue-specific and cold-responsive lncRNAs in Medicago truncatula by high-throughput RNA sequencing

Global Gene Expression Analysis Reveals Crosstalk between Response Mechanisms to Cold and Drought Stresses in Cassava Seedlings

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

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