Genome-wide identification, functional prediction and expression profiling of long non-coding RNAs in Camelina sativa

Subburaj, Saminathan; Jeon, Yongsam; Tu, Luhua; Jin, Yong-Tae; Kumari, Shipra; Lee, Geung–Joo

doi:10.1007/s10725-018-0410-8

Cited by 10 publications

(4 citation statements)

References 82 publications

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“…All of these putative lncRNAs play various roles in response to different biotic stresses such as tomato yellow leaf curl virus (TYLCV), infection by Sclerotinia sclerotiorum, Fusarium oxysporum, and Puccinia striiformis, as well as to abiotic or environmental stresses like drought, low and high temperatures, osmotic or hypoxic stress, and nitrogen or phosphate deficiency [ 11 ]. In Camelina (Camelina sativa L.), through drought-stress specific transcriptome analysis, 5390 putative lncRNAs were identified, including 1347 intergenic, 69 antisense, 670 sense, and 2681 intronic lncRNAs [ 31 ]. Mining more than 200 transcriptome datasets for Arabidopsis [ 32 ] revealed that 70% of lncRNAs (~40,000 candidate lncRNAs; >30,000 natural antisense transcripts (NATs); >6000 long intergenic ncRNAs (lincRNAs)) were transcribed from coding loci to be associated with antisense transcripts [ 33 , 34 ].…”

Section: Introductionmentioning

confidence: 99%

Long Non-Coding RNAs, the Dark Matter: An Emerging Regulatory Component in Plants

Waseem

Liu

Xia

2020

IJMS

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Long non-coding RNAs (lncRNAs) are pervasive transcripts of longer than 200 nucleotides and indiscernible coding potential. lncRNAs are implicated as key regulatory molecules in various fundamental biological processes at transcriptional, post-transcriptional, and epigenetic levels. Advances in computational and experimental approaches have identified numerous lncRNAs in plants. lncRNAs have been found to act as prime mediators in plant growth, development, and tolerance to stresses. This review summarizes the current research status of lncRNAs in planta, their classification based on genomic context, their mechanism of action, and specific bioinformatics tools and resources for their identification and characterization. Our overarching goal is to summarize recent progress on understanding the regulatory role of lncRNAs in plant developmental processes such as flowering time, reproductive growth, and abiotic stresses. We also review the role of lncRNA in nutrient stress and the ability to improve biotic stress tolerance in plants. Given the pivotal role of lncRNAs in various biological processes, their functional characterization in agriculturally essential crop plants is crucial for bridging the gap between phenotype and genotype.

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Section: Introductionmentioning

confidence: 99%

Long Non-Coding RNAs, the Dark Matter: An Emerging Regulatory Component in Plants

Waseem

Liu

Xia

2020

IJMS

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“…Further investigations on lncRNAs have supported their roles in a variety of key biological processes of plants similar to mammalian lncRNAs. In recent years, numerous lncRNAs responsive to biotic and abiotic stresses have been identified in many plant species [27,31,32,33,34]. For instance, a large number of lncRNAs responsive to nitrogen stresses, phosphate deficiency, osmotic and salt stress, cold stress, and drought stress etc., were mined in many plants via high-throughput sequencing technology [1,26,32,35,36], while many lncRNAs might be related to plant defense against fungi, bacteria, and virus pathogens [31,37,38,39,40,41].…”

Section: Introductionmentioning

confidence: 99%

Identification of Long Non-Coding RNAs and the Regulatory Network Responsive to Arbuscular Mycorrhizal Fungi Colonization in Maize Roots

Han

Cheng

Zheng

et al. 2019

IJMS

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Recently, long noncoding RNAs (lncRNAs) have emerged as vital regulators of many biological processes in animals and plants. However, to our knowledge no investigations on plant lncRNAs which respond to arbuscular mycorrhizal (AM) fungi have been reported thus far. In this study, maize roots colonized with AM fungus were analyzed by strand-specific RNA-Seq to identify AM fungi-responsive lncRNAs and construct an associated regulatory network. A total of 1837 differentially expressed protein coding genes (DEGs) were identified from maize roots with Rhizophagus irregularis inoculation. Many AM fungi-responsive genes were homologs to MtPt4, STR, STR2, MtFatM, and enriched pathways such as fatty acid biosynthesis, response to phosphate starvation, and nitrogen metabolism are consistent with previous studies. In total, 5941 lncRNAs were identified, of which more than 3000 were new. Of those, 63 lncRNAs were differentially expressed. The putative target genes of differentially expressed lncRNAs (DELs) were mainly related to phosphate ion transmembrane transport, cellular response to potassium ion starvation, and lipid catabolic processes. Regulatory network analysis showed that DELs might be involved in the regulation of bidirectional nutrient exchange between plant and AM fungi as mimicry of microRNA targets. The results of this study can broaden our knowledge on the interaction between plant and AM fungi.

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“…With the goal to elucidate the function of lncRNAs, distinct approaches have been utilized. One approach is to analyze the biological functions of coding genes in the vicinity of lncRNAs, under the assumption that they may be regulated in cis, and their functions might reflect that of the lncRNA (Wang et al, 2015a;Subburaj et al, 2018). In this approach, coding genes are searched 100 kb upstream or downstream to the genome location of the lncRNA of interest.…”

Section: Elucidating Of Lncrna Physiological Functions In Plantsmentioning

confidence: 99%

Plant long non-coding RNAs: identification and analysis to unveil their physiological functions

Domínguez-Rosas,

Hernández-Oñate,

Fernandez-Valverde

et al. 2023

Front. Plant Sci.

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Eukaryotic genomes encode thousands of RNA molecules; however, only a minimal fraction is translated into proteins. Among the non-coding elements, long non-coding RNAs (lncRNAs) play important roles in diverse biological processes. LncRNAs are associated mainly with the regulation of the expression of the genome; nonetheless, their study has just scratched the surface. This is somewhat due to the lack of widespread conservation at the sequence level, in addition to their relatively low and highly tissue-specific expression patterns, which makes their exploration challenging, especially in plant genomes where only a few of these molecules have been described completely. Recently published high-quality genomes of crop plants, along with new computational tools, are considered promising resources for studying these molecules in plants. This review briefly summarizes the characteristics of plant lncRNAs, their presence and conservation, the different protocols to find these elements, and the limitations of these protocols. Likewise, it describes their roles in different plant physiological phenomena. We believe that the study of lncRNAs can help to design strategies to reduce the negative effect of biotic and abiotic stresses on the yield of crop plants and, in the future, help create fruits and vegetables with improved nutritional content, higher amounts of compounds with positive effects on human health, better organoleptic characteristics, and fruits with a longer postharvest shelf life.

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Genome-wide identification, functional prediction and expression profiling of long non-coding RNAs in Camelina sativa

Cited by 10 publications

References 82 publications

Long Non-Coding RNAs, the Dark Matter: An Emerging Regulatory Component in Plants

Long Non-Coding RNAs, the Dark Matter: An Emerging Regulatory Component in Plants

Identification of Long Non-Coding RNAs and the Regulatory Network Responsive to Arbuscular Mycorrhizal Fungi Colonization in Maize Roots

Plant long non-coding RNAs: identification and analysis to unveil their physiological functions

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