Integrated small RNA and Degradome sequencing provide insights into salt tolerance in sesame (Sesamum indicum L.)

Zhang, Yujuan; Gong, Huihui; Li, Donghua; Zhou, Rong; Zhao, Fei; Zhang, Xiurong; You, Jun

doi:10.1186/s12864-020-06913-3

Cited by 22 publications

(23 citation statements)

References 65 publications

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“…Specific examples include the brassinosteroid response and the response to blue light in Arabidopsis, and pollen development and the heat stress response in Solanum lycopersicum. Other types of non-coding RNA include sesame, as well as in the cold response in grapevine, the drought response in mulberry, and the drought-responsive multi-tiered regulatory network in drought-tolerant rice [23,30,[51][52][53][54][55][56]. However, a role for miRNAs in regulating the MAPK cascade that operates downstream of the core ABA signaling pathway has not been confirmed in Arabidopsis.…”

Section: Discussionmentioning

confidence: 99%

Identification of Novel miRNAs and Their Target Genes in the Response to Abscisic Acid in Arabidopsis

Mehdi

Krishnamoorthy

Szcześniak

et al. 2021

IJMS

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miRNAs are involved in various biological processes, including adaptive responses to abiotic stress. To understand the role of miRNAs in the response to ABA, ABA-responsive miRNAs were identified by small RNA sequencing in wild-type Arabidopsis, as well as in abi1td, mkkk17, and mkkk18 mutants. We identified 10 novel miRNAs in WT after ABA treatment, while in abi1td, mkkk17, and mkkk18 mutants, three, seven, and nine known miRNAs, respectively, were differentially expressed after ABA treatment. One novel miRNA (miRn-8) was differentially expressed in the mkkk17 mutant. Potential target genes of the miRNA panel were identified using psRNATarget. Sequencing results were validated by quantitative RT-PCR of several known and novel miRNAs in all genotypes. Of the predicted targets of novel miRNAs, seven target genes of six novel miRNAs were further validated by 5′ RLM-RACE. Gene ontology analyses showed the potential target genes of ABA-responsive known and novel miRNAs to be involved in diverse cellular processes in plants, including development and stomatal movement. These outcomes suggest that a number of the identified miRNAs have crucial roles in plant responses to environmental stress, as well as in plant development, and might have common regulatory roles in the core ABA signaling pathway.

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Section: Discussionmentioning

confidence: 99%

Identification of Novel miRNAs and Their Target Genes in the Response to Abscisic Acid in Arabidopsis

Mehdi

Krishnamoorthy

Szcześniak

et al. 2021

IJMS

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“…SYBRPrimeScript TM miRNA RT-PCR Kit (TaKaRa, Dalian, China) was used for reverse transcription reactions for miRNAs, and PrimeScript RT Reagent Kit (TaKaRa, Dalian, China) was used for reverse transcription of cDNAs. U6 and beta-tubulin (TUB) were selected for normalization of miRNAs and target genes, respectively ( Zhang et al, 2020 ). The names of miRNAs and their target genes, sequences, and primers in RT-qPCR test experiment are given in Supplementary File 1 .…”

Section: Methodsmentioning

confidence: 99%

“…Sesame ( Sesamum indicum L.), as one of the oldest herbaceous diploid oilseed plants (2n = 26) in the Pedaliaceae family with a genome size of approximately 369 Mb, is mainly cultivated in tropical and subtropical regions of Asia, Africa, and South America ( Wei X. et al, 2016 ; Majdalawieh et al, 2020 ). Among the major cultivated oil crops worldwide, sesame as a commercial material contains the highest number of fatty acids (FAs) ( Wacal et al, 2019 ; Zhang et al, 2020 ), and among the FA types, linoleic, oleic, palmitic, and stearic acids are the main components that make up the total FA configuration of sesame oil ( Elleuch et al, 2007 ; Adebowale et al, 2011 ; Bhunia et al, 2015 ). In previous studies, unsaturated fatty acids (UFAs) are considered as a quality indicator of edible oils in the core area of research for the development of functional and industrial products ( Wang et al, 2016 ; Ahmed et al, 2020 ), which can prevent cardiovascular sclerosis and reduce blood pressure and blood lipids ( Li et al, 2015 ).…”

Section: Introductionmentioning

confidence: 99%

“…In banana fruits, 128 known miRNAs belonging to 42 miRNA families were determined, and 12 new miRNAs were identified; in olive, 135 conserved miRNAs were identified and 38 putative new miRNAs were discovered; in strawberry, a total of 88 known miRNAs and 103 targets cleaved by 19 known miRNAs families were discovered ( Xu et al, 2013 ; Yanik et al, 2013 ; Dan et al, 2018 ). Notably, from 18 sesame libraries, 351 known and 91 novel miRNAs, 116 miRNAs were reported to regulate salt stress response ( Zhang et al, 2020 ). Similarly, major miRNA-target pairs and the complex regulatory network responsible for terpenoid biosynthesis in tea leaves ( Zhao et al, 2018 ) and cadmium phytoremediation in hyperaccumulator Sedum alfredii were revealed by integrating small RNAs, degradome, and transcriptomics ( Han et al, 2016 ).…”

Section: Introductionmentioning

confidence: 99%

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Integration of miRNAs, Degradome, and Transcriptome Omics Uncovers a Complex Regulatory Network and Provides Insights Into Lipid and Fatty Acid Synthesis During Sesame Seed Development

Zhang

Thakur

et al. 2021

Front. Plant Sci.

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Sesame (Sesamum indicum L.) has always been known as a health-promoting oilseed crop because of its nutrient-rich oil. In recent years, studies have focused on lipid and fatty acid (FA) biosynthesis in various plants by high-throughput sequencing. Here, we integrated transcriptomics, small RNAs, and the degradome to establish a comprehensive reserve intensive on key regulatory micro RNA (miRNA)-targeting circuits to better understand the transcriptional and translational regulation of the oil biosynthesis mechanism in sesame seed development. Deep sequencing was performed to differentially express 220 miRNAs, including 65 novel miRNAs, in different developmental periods of seeds. GO and integrated KEGG analysis revealed 32 pairs of miRNA targets with negatively correlated expression profiles, of which 12 miRNA-target pairs were further confirmed by RT-PCR. In addition, a regulatory co-expression network was constructed based on the differentially expressed gene (DEG) profiles. The FAD2, LOC10515945, LOC105161564, and LOC105162196 genes were clustered into groups that regulate the accumulation of unsaturated fatty acid (UFA) biosynthesis. The results provide a unique advanced molecular platform for the study of lipid and FA biosynthesis, and this study may serve as a new theoretical reference to obtain increased levels of UFA from higher-quality sesame seed cultivars and other plants.

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“…Degradome sequencing enabled researchers to dispose of the limitations of bioinformatics prediction of false positive, and really found the target gene of miRNA splicing from the experiment. Therefore, a large number of miRNA target genes have been identified in many plants by degradome sequencing technology, such as rice [ 18 ], wheat [ 19 ], sesame [ 20 ], and cotton [ 21 ], etc.…”

Section: Introductionmentioning

confidence: 99%

Integration of Small RNA and Degradome Sequencing Reveals the Regulatory Network of Al-Induced Programmed Cell Death in Peanut

Tong

Shi

Ntambiyukuri

et al. 2021

IJMS

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Peanut is one of the most important oil crops in the world. In China, the peanut is highly produced in its southern part, in which the arable land is dominated by acid soil. At present, miRNAs have been identified in stress response, but their roles and mechanisms are not clear, and no miRNA studies have been found related to aluminum (Al)-induced programmed cell death (PCD). In the present study, transcriptomics, sRNAs, and degradome analysis in the root tips of two peanut cultivars ZH2 (Al-sensitive, S) and 99-1507 (Al-tolerant, T) were carried out. Here, we generated a comprehensive resource focused on identifying key regulatory miRNA-target circuits that regulate PCD under Al stress. Through deep sequencing, 2284 miRNAs were identified and 147 miRNAs were differentially expressed under Al stress. Furthermore, 19237 target genes of 749 miRNAs were validated by degradome sequencing. GO and KEGG analyses of differential miRNA targets showed that the pathways of synthesis and degradation of ketone bodies, citrate cycle (TCA cycle), and peroxisome were responded to Al stress. The combined analysis of the degradome data sets revealed 89 miRNA-mRNA interactions that may regulate PCD under Al stress. Ubiquitination may be involved in Al-induced PCD in peanut. The regulatory networks were constructed based on the differentially expressed miRNAs and their targets related to PCD. Our results will provide a useful platform to research on PCD induced by Al and new insights into the genetic engineering for plant stress response.

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Integrated small RNA and Degradome sequencing provide insights into salt tolerance in sesame (Sesamum indicum L.)

Cited by 22 publications

References 65 publications

Identification of Novel miRNAs and Their Target Genes in the Response to Abscisic Acid in Arabidopsis

Identification of Novel miRNAs and Their Target Genes in the Response to Abscisic Acid in Arabidopsis

Integration of miRNAs, Degradome, and Transcriptome Omics Uncovers a Complex Regulatory Network and Provides Insights Into Lipid and Fatty Acid Synthesis During Sesame Seed Development

Integration of Small RNA and Degradome Sequencing Reveals the Regulatory Network of Al-Induced Programmed Cell Death in Peanut

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