scholarly journals De novo transcriptome of Gymnema sylvestre identified putative lncRNA and genes regulating terpenoid biosynthesis pathway

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Garima Ayachit ◽  
Inayatullah Shaikh ◽  
Preeti Sharma ◽  
Bhavika Jani ◽  
Labdhi Shukla ◽  
...  
Keyword(s):  
De Novo ◽  
Gymnema Sylvestre ◽  
Biological Processes ◽  
Gene Profile ◽  
Sequencing Technology ◽  
Genomic Studies ◽  
Non Coding Rnas ◽  
Methyl Erythritol Phosphate ◽  
Simple Sequence ◽  
Important Enzyme

Abstract Gymnema sylvestre is a highly valuable medicinal plant in traditional Indian system of medicine and used in many polyherbal formulations especially in treating diabetes. However, the lack of genomic resources has impeded its research at molecular level. The present study investigated functional gene profile of G. sylvestre via RNA sequencing technology. The de novo assembly of 88.9 million high quality reads yielded 23,126 unigenes, of which 18116 were annotated against databases such as NCBI nr database, gene ontology (GO), KEGG, Pfam, CDD, PlantTFcat, UniProt & GreeNC. Total 808 unigenes mapped to 78 different Transcription Factor families, whereas 39 unigenes assigned to CYP450 and 111 unigenes coding for enzymes involved in the biosynthesis of terpenoids including transcripts for synthesis of important compounds like Vitamin E, beta-amyrin and squalene. Among them, presence of six important enzyme coding transcripts were validated using qRT-PCR, which showed high expression of enzymes involved in methyl-erythritol phosphate (MEP) pathway. This study also revealed 1428 simple sequence repeats (SSRs), which may aid in molecular breeding studies. Besides this, 8 putative long non-coding RNAs (lncRNAs) were predicted from un-annotated sequences, which may hold key role in regulation of essential biological processes in G. sylvestre. The study provides an opportunity for future functional genomic studies and to uncover functions of the lncRNAs in G. sylvestre.

scholarly journals Identification of differentially expressed microRNAs under imidacloprid exposure in Sitobion avenae Fabricius

2020 ◽  
Author(s):  
Baizhong Zhang ◽  
Shouping Zhang ◽  
Xu Su ◽  
Lanfen Xie ◽  
Wen-Yang Dong ◽  
...  
Keyword(s):  
Target Genes ◽  
De Novo ◽  
Sitobion Avenae ◽  
Differentially Expressed ◽  
Control Analysis ◽  
Sequencing Technology ◽  
Short Read Sequencing ◽  
Kegg Pathway Analysis ◽  
Candidate Target ◽  
Non Coding Rnas

Abstract Background: MicroRNAs (miRNAs), which are short single-stranded non-coding RNAs, regulate the expression of target genes, especially those involved in the regulation or metabolism of endogenous or xenobiotic compounds. Results: De novo assemblies of the transcriptome of Sitobion avenae Fabricius under control conditions and under imidacloprid treatment were obtained using Illumina short-read sequencing technology. Fifty-seven miRNAs, of which 36 were known and 21 were novel, were identified. Quantitative analysis of miRNA levels showed that 5 miRNAs were significantly up-regulated, and 11 miRNAs were significantly down-regulated in the nymphs of S. avenae treated with imidacloprid in comparison with those of the control. Analysis of the candidate target genes in S. avenae that could be regulated by these miRNAs were also carried out. The functions of the miRNAs, which could potentially regulate target genes that participate in metabolism, regulatory or detoxification pathways in S. avenae, were clarified based on Gene Ontology and KEGG pathway analysis. The effects of the miRNAs api-miR-1000, api-miR-316, and api-miR-iab-4 on susceptibility of S. avenae to imidacloprid was determined. Modulation of the abundances of api-miR-1000, api-miR-316, and api-miR-iab-4 by the addition of the correspondign inhibitors to the artificial diet significantly changed the susceptibility of S. avenae to imidacloprid, which further demonstrated the effect of these miRNAs on the regulation or metabolism of insecticides.Conclusion: The results of this study suggested that miRNAs differentially expressed in response to imidacloprid could play a critical regulatory role in the resistance of S. avenae to imidacloprid.

scholarly journals Identification of differentially expressed microRNAs under imidacloprid exposure in Sitobion avenae Fabricius

2019 ◽  
Author(s):  
Baizhong Zhang ◽  
Xu Su ◽  
Lanfen Xie ◽  
Wen-Yang Dong ◽  
Fan-Bin Kong ◽  
...  
Keyword(s):  
Target Genes ◽  
De Novo ◽  
Sitobion Avenae ◽  
Differentially Expressed ◽  
Control Analysis ◽  
Sequencing Technology ◽  
Short Read Sequencing ◽  
Kegg Pathway Analysis ◽  
Candidate Target ◽  
Non Coding Rnas

Abstract Background MicroRNAs (miRNAs), which are short single-stranded non-coding RNAs, regulate the expression of target genes, especially those involved in the regulation or metabolism of endogenous or xenobiotic compounds.Results De novo assemblies of the transcriptome of Sitobion avenae Fabricius under control conditions and under imidacloprid treatment were obtained using Illumina short-read sequencing technology. Fifty-seven miRNAs, of which 36 were known and 21 were novel, were identified. Quantitative analysis of miRNA levels showed that five miRNAs were significantly up-regulated, and 11 miRNAs were significantly down-regulated in the nymphs of S. avenae treated with imidacloprid in comparison with those of the control. Analysis of the candidate target genes in S. avenae that could be regulated by these miRNAs were also carried out. The functions of the miRNAs, which could potentially regulate target genes that participate in metabolism, regulatory or detoxification pathways in S. avenae , were clarified based on Gene Ontology and KEGG pathway analysis. The effects of the miRNAs api-miR-1000, api-miR-316, and api-miR-iab-4 on susceptibility of S. avenae to imidacloprid was determined. Modulation of the abundances of api-miR-1000, api-miR-316, and api-miR-iab-4 by the addition of the correspondign inhibitors to the artificial diet significantly changed the susceptibility of S. avenae to imidacloprid, which further demonstrated the effect of these miRNAs on the regulation or metabolism of insecticides.Conclusion The results of this study suggested that miRNAs differentially expressed in response to imidacloprid could play a critical regulatory role in the resistance of S. avenae to imidacloprid.

Structural Alignment of RNAs with Pseudoknots

2011 ◽  
pp. 550-571
Author(s):  
Thomas K. F. Wong ◽  
S. M. Yiu
Keyword(s):  
Secondary Structure ◽  
De Novo ◽  
State Of The Art ◽  
Structural Alignment ◽  
Structural Similarity ◽  
Secondary Structures ◽  
Biological Processes ◽  
Computational Approaches ◽  
Different Types ◽  
Non Coding Rnas

Non-coding RNAs (ncRNAs) are found to be critical for many biological processes. However, identifying these molecules is very difficult and challenging due to the lack of strong detectable signals such as opening read frames. Most computational approaches rely on the observation that the secondary structures of ncRNA molecules are conserved within the same family. Aligning a known ncRNA to a target candidate to determine the sequence and structural similarity helps in identifying de novo ncRNA molecules that are in the same family of the known ncRNA. However, the problem becomes more difficult if the secondary structure contains pseudoknots. Only until recently, many of the existing approaches could not handle structures with pseudoknots. This chapter reviews the state-of-the-art algorithms for different types of structures that contain pseudoknots including standard pseudoknot, simple non-standard pseudoknot, recursive standard pseudoknot, and recursive simple non-standard pseudoknot. Although none of the algorithms is designed for general pseudoknots, these algorithms already cover all known ncRNAs in both Rfam and PseudoBase databases. The evaluation of the algorithms also shows that the approach is useful in identifying ncRNA molecules in other species, which are in the same family of a known ncRNA.

scholarly journals Regulatory Potential of Long Non-Coding RNAs (lncRNAs) in Boar Spermatozoa with Good and Poor Freezability

Life ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 300
Author(s):  
Leyland Fraser ◽  
Łukasz Paukszto ◽  
Anna Mańkowska ◽  
Paweł Brym ◽  
Przemysław Gilun ◽  
...  
Keyword(s):  
Target Genes ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Biological Processes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Potential Target ◽  
Non Coding Rnas

Long non-coding RNAs (lncRNAs) are suggested to play an important role in the sperm biological processes. We performed de novo transcriptome assembly to characterize lncRNAs in spermatozoa, and to investigate the role of the potential target genes of the differentially expressed lncRNAs (DElncRNAs) in sperm freezability. We detected approximately 4007 DElncRNAs, which were differentially expressed in spermatozoa from boars classified as having good and poor semen freezability (GSF and PSF, respectively). Most of the DElncRNAs were upregulated in boars of the PSF group and appeared to significantly affect the sperm’s response to the cryopreservation conditions. Furthermore, we predicted that the potential target genes were regulated by DElncRNAs in cis or trans. It was found that DElncRNAs of both freezability groups had potential cis- and trans-regulatory effects on different protein-coding genes, such as COX7A2L, TXNDC8 and SOX-7. Gene Ontology (GO) enrichment revealed that the DElncRNA target genes are associated with numerous biological processes, including signal transduction, response to stress, cell death (apoptosis), motility and embryo development. Significant differences in the de novo assembled transcriptome expression profiles of the DElncRNAs between the freezability groups were confirmed by quantitative real-time PCR analysis. This study reveals the potential effects of protein-coding genes of DElncRNAs on sperm functions, which could contribute to further research on their relevance in semen freezability.

scholarly journals Differentially expressed microRNAs under imidacloprid exposure and identification in Sitobion avenae

2019 ◽  
Author(s):  
Baizhong Zhang ◽  
Jun-Jie Liu ◽  
Liu-yang Lu ◽  
Lan-Fen Xie ◽  
Xi-Ling Chen ◽  
...  
Keyword(s):  
Target Genes ◽  
De Novo ◽  
Sitobion Avenae ◽  
Differentially Expressed ◽  
Regulatory Role ◽  
Sequencing Technology ◽  
Quantitative Expression ◽  
Non Coding Rnas ◽  
Putative Transcript

Abstract BACKGROUD MicroRNAs (miRNAs) are short single-stranded non-coding RNAs that regulate the expression of target genes, especially regulation or metabolism of endogenous or xenobiotic compounds. RESULTS The de novo assembly of the transcriptomes was obtained through Illumina short-read sequencing technology in Sitobion avenae. 57 miRNAs, of which 36 were known and 21 were novel were identified. Quantitative expression levels of miRNA showed that the expression of 5 miRNAs were significant up-regulation, and the expression of 11 miRNAs were significant down-regulation in the nymph of S. avenae treated by imidacloprid compared to the control, respectively. The putative transcript target genes in S. avenae that could be regulated by these miRNAs were also carried out. The potential functions of these miRNAs in the regulation of genes involved in the metabolism, regulatory or detoxification of S. avenae were clarified based on Gene Ontology and KEGG pathway. The effects of these miRNAs identified api-miR-1000, api-miR-316, and api-miR-iab-4 on susceptibility of S. avenae to imidacloprid was determined. Modulation of the abundance of api-miR-1000, api-miR-316, and api-miR-iab-4 through the addition of inhibitors of api-miR-1000, api-miR-316, and api-miR-iab-4 to the artificial diet significantly altered the susceptibility of S. avenae to imidacloprid, which further proved that the regulatory role of these miRNAs in regulation or metabolism of insecticides. CONCLUSION It suggested that differentially expressed microRNAs under the stress of imidacloprid could play critical regulatory role in the resistance of S. avenae to imidacloprid.

scholarly journals Differentially expressed microRNAs under imidacloprid exposure and identification in Sitobion avenae

2019 ◽  
Author(s):  
Xi-Ling Chen ◽  
Baizhong Zhang ◽  
Junjie Liu ◽  
Liuyang Lu ◽  
Lanfen Xie ◽  
...  
Keyword(s):  
Target Genes ◽  
De Novo ◽  
Kegg Pathway ◽  
Sitobion Avenae ◽  
Differentially Expressed ◽  
Sequencing Technology ◽  
Short Read Sequencing ◽  
Quantitative Expression ◽  
Non Coding Rnas ◽  
Candidate Transcript

Abstract Backgroud: MicroRNAs (miRNAs), which are as short single-stranded non-coding RNAs, coudl regulate the expression of target genes, especially regulation or metabolism of endogenous or xenobiotic compounds. Results: The de novo assembly of the transcriptomes was obtained through Illumina short-read sequencing technology in Sitobion avenae. 57 miRNAs, of which 36 were known and 21 were novel were identified. Quantitative expression levels of miRNA showed that the expression of 5 miRNAs were significant up-regulation, and the expression of 11 miRNAs were significant down-regulation in the nymph of S. avenae treated by imidacloprid in comparison with the control, respectively. The candidate transcript target genes in S. avenae that could be regulated by these miRNAs were also carried out. The functions of the miRNAs, which could potentially regulate the target genes participated in the metabolism, regulatory or detoxification of S. avenae were clarified based on Gene Ontology and KEGG pathway. The effects of the miRNAs identified api-miR-1000, api-miR-316, and api-miR-iab-4 on susceptibility of S. avenae to imidacloprid was determined. The abundance of api-miR-1000, api-miR-316, and api-miR-iab-4 modulated by the addition of their own inhibitors to the artificial diet could change significantly the susceptibility of S. avenae to imidacloprid, which further proved that the regulatory affect of these miRNAs on regulation or metabolism of insecticides. Conclusion: It suggested that differentially expressed microRNAs under the stress of imidacloprid could play critical regulatory role in the resistance of S. avenae to imidacloprid.

LncRNAs a New Target for Post-Stroke Recovery

2020 ◽  
Vol 26 (26) ◽  
pp. 3115-3121
Author(s):  
Jun Yang ◽  
Jingjing Zhao ◽  
Xu Liu ◽  
Ruixia Zhu
Keyword(s):  
Ischemic Stroke ◽  
Microglial Activation ◽  
Vital Role ◽  
Stroke Recovery ◽  
Biological Processes ◽  
Current Development ◽  
Post Stroke ◽  
Cascade Processes ◽  
Non Coding Rnas ◽  
Neuron Injury

LncRNAs (long non-coding RNAs) are endogenous molecules, involved in complicated biological processes. Increasing evidence has shown that lncRNAs play a vital role in the post-stroke pathophysiology. Furthermore, several lncRNAs were reported to mediate ischemia cascade processes include apoptosis, bloodbrain barier breakdown, angiogenesis, microglial activation induced neuroinflammation which can cause neuron injury and influence neuron recovery after ischemic stroke. In our study, we first summarize current development about lncRNAs and post-stroke, focus on the regulatory roles of lncRNAs on pathophysiology after stroke. We also reviewed genetic variation in lncRNA associated with functional outcome after ischemic stroke. Additionally, lncRNA-based therapeutics offer promising strategies to decrease brain damage and promote neurological recovery following ischemic stroke. We believe that lncRNAs will become promising for the frontier strategies for IS and can open up a new path for the treatment of IS in the future.

Abiotic Stress Tolerance in Soybean : Regulated by ncRNA

2016 ◽  
Vol 3 (1) ◽  
Author(s):  
YASIN JESHIMA KHAN ◽  
HUSNARA Tyagi ◽  
Anil kumar Singh ◽  
Santosh kumar. Magadum
Keyword(s):  
Abiotic Stresses ◽  
Target Genes ◽  
Abiotic Stress Tolerance ◽  
Crop Improvement ◽  
Vital Role ◽  
Grain Legume ◽  
Biological Processes ◽  
Small Interfering Rnas ◽  
Cellular Environment ◽  
Non Coding Rnas

Plants respond through a cascade of reactions resulting in varied cellular environment leading to alterations in the patterns of protein expression resulting in phonotypic changes. Single cell genomics and global proteomics came out to be powerful tools and efficient techniques in studying stress tolerant plants. Non-coding RNAs are a distinct class of regulatory RNAs in plants and animals that control a variety of biological processes. Small ncRNAs play a vital role in post transcriptional gene regulation by either translational repression or by inducing mRNA cleavage. The major classes of small RNAs include microRNAs (miRNAs) and small interfering RNAs (siRNAs), which differ in their biogenesis. miRNAs control the expression of cognate target genes by binding to complementary sequences, resulting in cleavage or translational inhibition of the target RNAs. siRNAs too have a similar structure, function, and biogenesis like miRNAs but are derived from long double-stranded RNAs and can often direct DNA methylation at target sequences.In this review, we focus on the involvement of ncRNAs in comabting abiotic stresses of soybean. This review emphasis on previously known miRNAs as they play important role in several abiotic stresses like drought, salinity, chilling and heat stress by their diverse roles in mediating biological processes like gene expression, chromatin formation, defense of genome against invading viruses. This review attempts to elucidate the various kinds of non-coding RNAs explored, their discovery, biogenesis, functions, and response for different type of abiotic stresses and future aspects for crop improvement in the context of soybean, a representative grain legume.

scholarly journals Full-Length Transcriptome of Thalassiosira weissflogii as a Reference Resource and Mining of Chitin-Related Genes

Marine Drugs ◽  
2021 ◽  
Vol 19 (7) ◽  
pp. 392
Author(s):  
Haomiao Cheng ◽  
Chris Bowler ◽  
Xiaohui Xing ◽  
Vincent Bulone ◽  
Zhanru Shao ◽  
...  
Keyword(s):  
Cell Wall ◽  
Full Length ◽  
Biosynthetic Pathways ◽  
Glycosidic Linkage ◽  
Thalassiosira Weissflogii ◽  
Ecological Value ◽  
Pacbio Sequencing ◽  
Non Coding Rnas ◽  
Chitin And Chitosan ◽  
Simple Sequence

β-Chitin produced by diatoms is expected to have significant economic and ecological value due to its structure, which consists of parallel chains of chitin, its properties and the high abundance of diatoms. Nevertheless, few studies have functionally characterised chitin-related genes in diatoms owing to the lack of omics-based information. In this study, we first compared the chitin content of three representative Thalassiosira species. Cell wall glycosidic linkage analysis and chitin/chitosan staining assays showed that Thalassiosira weissflogii was an appropriate candidate chitin producer. A full-length (FL) transcriptome of T. weissflogii was obtained via PacBio sequencing. In total, the FL transcriptome comprised 23,362 annotated unigenes, 710 long non-coding RNAs (lncRNAs), 363 transcription factors (TFs), 3113 alternative splicing (AS) events and 3295 simple sequence repeats (SSRs). More specifically, 234 genes related to chitin metabolism were identified and the complete biosynthetic pathways of chitin and chitosan were explored. The information presented here will facilitate T. weissflogii molecular research and the exploitation of β-chitin-derived high-value enzymes and products.

scholarly journals Transcriptome analysis reveals potential function of long non-coding RNAs in 20-hydroxyecdysone regulated autophagy in Bombyx mori

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Huili Qiao ◽  
Jingya Wang ◽  
Yuanzhuo Wang ◽  
Juanjuan Yang ◽  
Bofan Wei ◽  
...  
Keyword(s):  
Bombyx Mori ◽  
Target Gene ◽  
Fat Body ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Differentially Expressed ◽  
Post Injection ◽  
Biological Processes ◽  
Potential Target ◽  
Non Coding Rnas

Abstract Background 20-hydroxyecdysone (20E) plays important roles in insect molting and metamorphosis. 20E-induced autophagy has been detected during the larval–pupal transition in different insects. In Bombyx mori, autophagy is induced by 20E in the larval fat body. Long non-coding RNAs (lncRNAs) function in various biological processes in many organisms, including insects. Many lncRNAs have been reported to be potential for autophagy occurrence in mammals, but it has not been investigated in insects. Results RNA libraries from the fat body of B. mori dissected at 2 and 6 h post-injection with 20E were constructed and sequenced, and comprehensive analysis of lncRNAs and mRNAs was performed. A total of 1035 lncRNAs were identified, including 905 lincRNAs and 130 antisense lncRNAs. Compared with mRNAs, lncRNAs had longer transcript length and fewer exons. 132 lncRNAs were found differentially expressed at 2 h post injection, compared with 64 lncRNAs at 6 h post injection. Thirty differentially expressed lncRNAs were common at 2 and 6 h post-injection, and were hypothesized to be associated with the 20E response. Target gene analysis predicted 6493 lncRNA-mRNA cis pairs and 42,797 lncRNA-mRNA trans pairs. The expression profiles of LNC_000560 were highly consistent with its potential target genes, Atg4B, and RNAi of LNC_000560 significantly decreased the expression of LNC_000560 and Atg4B. These results indicated that LNC_000560 was potentially involved in the 20E-induced autophagy of the fat body by regulating Atg4B. Conclusions This study provides the genome-wide identification and functional characterization of lncRNAs associated with 20E-induced autophagy in the fat body of B. mori. LNC_000560 and its potential target gene were identified to be related to 20-regulated autophagy in B. mori. These results will be helpful for further studying the regulatory mechanisms of lncRNAs in autophagy and other biological processes in this insect model.

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