scholarly journals Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting soybean genotypes subjected to phosphate starvation

2021 ◽  
Author(s):  
jinyu zhang ◽  
Huanqing Xu ◽  
Yuming Yang ◽  
Xiangqian Zhang ◽  
Zhongwen Huang ◽  
...  
Keyword(s):  
Growth And Yield ◽  
Biological Processes ◽  
Rna Seq ◽  
Plant Growth And Development ◽  
P Deficiency ◽  
Genome Wide ◽  
Low Phosphorus ◽  
Soybean Genotypes ◽  
Non Coding Rnas ◽  
Sensitive Genotype

Abstract Background: Phosphorus (P) is essential for plant growth and development, and low-phosphorus (LP) stress is a major factor limiting the growth and yield of soybean. Long noncoding RNAs (lncRNAs) have recently been reported to be key regulators in the responses of plants to stress conditions, but the mechanism through which LP stress mediates the biogenesis of lncRNAs in soybean remains unclear.Results: In this study, to explore the response mechanisms of lncRNAs to LP stress, we used the roots of two representative soybean genotypes that present opposite responses to P deficiency, namely, a P-sensitive genotype (Bogao) and a P-tolerant genotype (NN94156), for the construction of RNA sequencing (RNA-seq) libraries. In total, 4,166 novel lncRNAs, including 525 differentially expressed (DE) lncRNAs, were identified from the two genotypes at different P levels. GO and KEGG analyses indicated that numerous DE lncRNAs might be involved in diverse biological processes related to phosphate, such as lipid metabolic processes, catalytic activity, cell membrane formation, signal transduction, and nitrogen fixation. Moreover, lncRNA-mRNA-miRNA and lncRNA-mRNA networks were constructed, and the results identified several promising lncRNAs that might be highly valuable for further analysis of the mechanism underlying the response of soybean to LP stress.Conclusions: These results revealed that LP stress can significantly alter the genome-wide profiles of lncRNAs, particularly those of the P-sensitive genotype Bogao. Our findings increase the understanding of and provide new insights into the function of lncRNAs in the responses of soybean to P stress.

scholarly journals Genome-wide analysis of long non-coding RNAs (lncRNAs) in two contrasting soybean genotypes subjected to phosphate starvation

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jinyu Zhang ◽  
Huanqing Xu ◽  
Yuming Yang ◽  
Xiangqian Zhang ◽  
Zhongwen Huang ◽  
...  
Keyword(s):  
Growth And Yield ◽  
Biological Processes ◽  
Rna Seq ◽  
Plant Growth And Development ◽  
P Deficiency ◽  
Genome Wide ◽  
Low Phosphorus ◽  
Soybean Genotypes ◽  
Non Coding Rnas ◽  
Sensitive Genotype

Abstract Background Phosphorus (P) is essential for plant growth and development, and low-phosphorus (LP) stress is a major factor limiting the growth and yield of soybean. Long noncoding RNAs (lncRNAs) have recently been reported to be key regulators in the responses of plants to stress conditions, but the mechanism through which LP stress mediates the biogenesis of lncRNAs in soybean remains unclear. Results In this study, to explore the response mechanisms of lncRNAs to LP stress, we used the roots of two representative soybean genotypes that present opposite responses to P deficiency, namely, a P-sensitive genotype (Bogao) and a P-tolerant genotype (NN94156), for the construction of RNA sequencing (RNA-seq) libraries. In total, 4,166 novel lncRNAs, including 525 differentially expressed (DE) lncRNAs, were identified from the two genotypes at different P levels. GO and KEGG analyses indicated that numerous DE lncRNAs might be involved in diverse biological processes related to phosphate, such as lipid metabolic processes, catalytic activity, cell membrane formation, signal transduction, and nitrogen fixation. Moreover, lncRNA-mRNA-miRNA and lncRNA-mRNA networks were constructed, and the results identified several promising lncRNAs that might be highly valuable for further analysis of the mechanism underlying the response of soybean to LP stress. Conclusions These results revealed that LP stress can significantly alter the genome-wide profiles of lncRNAs, particularly those of the P-sensitive genotype Bogao. Our findings increase the understanding of and provide new insights into the function of lncRNAs in the responses of soybean to P stress.

scholarly journals Genome-Wide Analysis of Long Non-Coding RNAs (lncRNAs) in Two Contrasting Soybean Genotypes Subjected to Phosphate Starvation

2020 ◽  
Author(s):  
jinyu zhang ◽  
Xiangqian Zhang ◽  
Yuming Yang ◽  
Huanqing Xu ◽  
Zhongwen Huang ◽  
...  
Keyword(s):  
Growth And Yield ◽  
Biological Processes ◽  
Rna Seq ◽  
P Deficiency ◽  
Genome Wide ◽  
Low Phosphorus ◽  
Soybean Genotypes ◽  
Response To Stress ◽  
Non Coding Rnas ◽  
Sensitive Genotype

Abstract Background: Phosphorus (P) is essential for plant growth and development, and low-phosphorus (LP) stress is a major factor limiting the growth and yield of soybean. Recently, long noncoding RNAs (lncRNAs) have been reported to be key regulators in response to stress conditions in plants. In soybean, however, how LP stress mediates biogenesis of lncRNAs remains unclear. Results: In this study, to explore the response mechanisms of lncRNAs to LP stress, we used the roots of two representative soybean genotypes with opposite P deficiency responsiveness, a P-sensitive genotype (Bogao) and a P-tolerant genotype (NN94156), to construct RNA sequencing (RNA-seq) libraries. In total, 4,166 novel lncRNAs including 525 differently expressed (DE) lncRNAs were identified across two genotypes at different P levels. GO and KEGG analyses indicated that numerous DE lncRNAs might be involved in diverse biological processes of phosphate, such as lipid metabolic process, catalytic activity, cell membrane formation, signal transduction, nitrogen fixation. Moreover, lncRNA-mRNA-miRNA and lncRNA-mRNA networks were constructed and several promising lncRNAs were identified, which may have highly valuable for further analysis the mechanism in response to LP stress in soybean.Conclusions: These results revealed that LP stress can significantly alter the genome-wide profiles of lncRNAs, especially for P sensitive genotype Bogao. Our findings increase the understanding and provides new insights into the function of lncNRAs responses to P stress in soybean.

scholarly journals Genome-Wide Identification of Long Non-coding RNAs Responsive to Lasiodiplodia theobromae Infection in Grapevine

2019 ◽  
Vol 15 ◽  
pp. 117693431984136 ◽  
Author(s):  
Qikai Xing ◽  
Wei Zhang ◽  
Mei Liu ◽  
Lingxian Li ◽  
Xinghong Li ◽  
...  
Keyword(s):  
Biological Processes ◽  
Rna Seq ◽  
Lasiodiplodia Theobromae ◽  
Rna Molecules ◽  
Grapevine Trunk Diseases ◽  
Genome Wide ◽  
Botryosphaeria Dieback ◽  
Trunk Diseases ◽  
Non Coding Rnas ◽  
Insight Into

Long non-coding RNAs (lncRNAs) refer to a class of RNA molecules that are longer than 200 nucleotides and do not encode proteins. Numerous lncRNAs have recently emerged as important regulators of many biological processes in animals and plants, including responses to environmental stress and pathogens. Botryosphaeria dieback is one of the more severe grapevine trunk diseases worldwide. However, how lncRNAs function during Botryosphaeriaceae infection is largely unknown. We performed high-throughput RNA-sequencing (RNA-seq) of susceptible and more tolerant grapevine cultivars infected with Lasiodiplodia theobromae. Overall, we predicted 1826 novel candidate lncRNAs, including long intergenic non-coding RNAs (lincRNAs) and natural antisense transcripts (lncNATs). The data reveal the functions of a set of lncRNAs that were differentially expressed between the resistant cultivar Merlot and the susceptible cultivar Cabernet Franc. Several lncRNAs were predicted to be precursors for grape microRNAs involved in the L theobromae infection. These results provide new insight into the lncRNAs of grapevine that are involved in the response to L theobromae infection.

scholarly journals Genome-wide identification and characterization of long non-coding RNAs involved in flag leaf senescence of rice

2021 ◽  
Author(s):  
Xiaoping Huang ◽  
Hongyu Zhang ◽  
Qiang Wang ◽  
Rong Guo ◽  
Lingxia Wei ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Leaf Senescence ◽  
Flag Leaf ◽  
Reduction Process ◽  
Sequencing Analysis ◽  
Biological Processes ◽  
Genome Wide ◽  
A Genome ◽  
Non Coding Rnas ◽  
Systematic Identification

Abstract Key message This study showed the systematic identification of long non-coding RNAs (lncRNAs) involving in flag leaf senescence of rice, providing the possible lncRNA-mRNA regulatory relationships and lncRNA-miRNA-mRNA ceRNA networks during leaf senescence. Abstract LncRNAs have been reported to play crucial roles in diverse biological processes. However, no systematic identification of lncRNAs associated with leaf senescence in plants has been studied. In this study, a genome-wide high throughput sequencing analysis was performed using rice flag leaves developing from normal to senescence. A total of 3953 lncRNAs and 38757 mRNAs were identified, of which 343 lncRNAs and 9412 mRNAs were differentially expressed. Through weighted gene co-expression network analysis (WGCNA), 22 continuously down-expressed lncRNAs targeting 812 co-expressed mRNAs and 48 continuously up-expressed lncRNAs targeting 1209 co-expressed mRNAs were considered to be significantly associated with flag leaf senescence. Gene Ontology results suggested that the senescence-associated lncRNAs targeted mRNAs involving in many biological processes, including transcription, hormone response, oxidation–reduction process and substance metabolism. Additionally, 43 senescence-associated lncRNAs were predicted to target 111 co-expressed transcription factors. Interestingly, 8 down-expressed lncRNAs and 29 up-expressed lncRNAs were found to separately target 12 and 20 well-studied senescence-associated genes (SAGs). Furthermore, analysis on the competing endogenous RNA (CeRNA) network revealed that 6 down-expressed lncRNAs possibly regulated 51 co-expressed mRNAs through 15 miRNAs, and 14 up-expressed lncRNAs possibly regulated 117 co-expressed mRNAs through 21 miRNAs. Importantly, by expression validation, a conserved miR164-NAC regulatory pathway was found to be possibly involved in leaf senescence, where lncRNA MSTRG.62092.1 may serve as a ceRNA binding with miR164a and miR164e to regulate three transcription factors. And two key lncRNAs MSTRG.31014.21 and MSTRG.31014.36 also could regulate the abscisic-acid biosynthetic gene BGIOSGA025169 (OsNCED4) and BGIOSGA016313 (NAC family) through osa-miR5809. The possible regulation networks of lncRNAs involving in leaf senescence were discussed, and several candidate lncRNAs were recommended for prior transgenic analysis. These findings will extend the understanding on the regulatory roles of lncRNAs in leaf senescence, and lay a foundation for functional research on candidate lncRNAs.

Genome-wide identification of low phosphorus responsive microRNAs in two soybean genotypes by high-throughput sequencing

2020 ◽  
Vol 20 (6) ◽  
pp. 825-838
Author(s):  
Xiaoqian Liu ◽  
Shanshan Chu ◽  
Chongyuan Sun ◽  
Huanqing Xu ◽  
Jinyu Zhang ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Genome Wide ◽  
Low Phosphorus ◽  
Soybean Genotypes

scholarly journals Emerging Roles of Estrogen-Regulated Enhancer and Long Non-Coding RNAs

2020 ◽  
Vol 21 (10) ◽  
pp. 3711
Author(s):  
Melina J. Sedano ◽  
Alana L. Harrison ◽  
Mina Zilaie ◽  
Chandrima Das ◽  
Ramesh Choudhari ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Expression Patterns ◽  
Biological Significance ◽  
Rna Seq ◽  
Biological Functions ◽  
Protein Coding ◽  
Rna Molecules ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Non Coding Rnas

Genome-wide RNA sequencing has shown that only a small fraction of the human genome is transcribed into protein-coding mRNAs. While once thought to be “junk” DNA, recent findings indicate that the rest of the genome encodes many types of non-coding RNA molecules with a myriad of functions still being determined. Among the non-coding RNAs, long non-coding RNAs (lncRNA) and enhancer RNAs (eRNA) are found to be most copious. While their exact biological functions and mechanisms of action are currently unknown, technologies such as next-generation RNA sequencing (RNA-seq) and global nuclear run-on sequencing (GRO-seq) have begun deciphering their expression patterns and biological significance. In addition to their identification, it has been shown that the expression of long non-coding RNAs and enhancer RNAs can vary due to spatial, temporal, developmental, or hormonal variations. In this review, we explore newly reported information on estrogen-regulated eRNAs and lncRNAs and their associated biological functions to help outline their markedly prominent roles in estrogen-dependent signaling.

scholarly journals Genome-wide identification of novel long non-coding RNAs and their possible roles in hypoxic zebrafish brain

2020 ◽  
Author(s):  
Bodhisattwa Banerjee ◽  
Debaprasad Koner ◽  
David Karasik ◽  
Nirmalendu Saha
Keyword(s):  
Target Genes ◽  
Neuronal Development ◽  
Rna Seq ◽  
Master Regulators ◽  
Expression Studies ◽  
Genome Wide ◽  
Development And Differentiation ◽  
Non Coding Rnas ◽  
Differentiation Pathways ◽  
Syntenic Regions

AbstractLong non-coding RNAs (lncRNAs) are the master regulators of numerous biological processes. Hypoxia causes oxidative stress with severe and detrimental effects on brain function and acts as a critical initiating factor in the pathogenesis of Alzheimer’s disease (AD). From the RNA-Seq in the forebrain (Fb), midbrain (Mb), and hindbrain (Hb) regions of hypoxic and normoxic zebrafish, we identified novel lncRNAs, whose potential cis targets showed involvement in neuronal development and differentiation pathways. Under hypoxia, several lncRNAs and mRNAs were differentially expressed. Co-expression studies indicated that the Fb and Hb regions’ potential lncRNA target genes were involved in the AD pathogenesis. In contrast, those in Mb (cry1b, per1a, cipca) were responsible for regulating circadian rhythm. We identified specific lncRNAs present in the syntenic regions between zebrafish and humans, possibly functionally conserved. We thus identified several conserved lncRNAs as the probable regulators of AD genes (adrb3b, cav1, stat3, bace2, apoeb, psen1, s100b).

scholarly journals Genome-wide identification and expression analysis of the 14-3-3 gene family in soybean (Glycine max)

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7950 ◽  
Author(s):  
Yongbin Wang ◽  
Lei Ling ◽  
Zhenfeng Jiang ◽  
Weiwei Tan ◽  
Zhaojun Liu ◽  
...  
Keyword(s):  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Growth And Development ◽  
Genomic Data ◽  
Evolutionary Analysis ◽  
Rna Seq ◽  
Plant Growth And Development ◽  
Genome Wide ◽  
Gene Structures

In eukaryotes, proteins encoded by the 14-3-3 genes are ubiquitously involved in the plant growth and development. The 14-3-3 gene family has been identified in several plants. In the present study, we identified 22 GmGF14 genes in the soybean genomic data. On the basis of the evolutionary analysis, they were clustered into ε and non-ε groups. The GmGF14s of two groups were highly conserved in motifs and gene structures. RNA-seq analysis suggested that GmGF14 genes were the major regulator of soybean morphogenesis. Moreover, the expression level of most GmGF14s changed obviously in multiple stress responses (drought, salt and cold), suggesting that they have the abilities of responding to multiple stresses. Taken together, this study shows that soybean 14-3-3s participate in plant growth and can response to various environmental stresses. These results provide important information for further understanding of the functions of 14-3-3 genes in soybean.

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

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Shuxia Li ◽  
Xiang Yu ◽  
Ning Lei ◽  
Zhihao Cheng ◽  
Pingjuan Zhao ◽  
...  
Keyword(s):  
Drought Stress ◽  
Experimental Studies ◽  
Growth And Yield ◽  
Rna Seq ◽  
Functional Prediction ◽  
Systematic Screening ◽  
Cellular Processes ◽  
Genome Wide ◽  
Young Leaves ◽  
And Control

Abstract Cold and drought stresses seriously affect cassava (Manihot esculenta) plant growth and yield. Recently, long noncoding RNAs (lncRNAs) have emerged as key regulators of diverse cellular processes in mammals and plants. To date, no systematic screening of lncRNAs under abiotic stress and their regulatory roles in cassava has been reported. In this study, we present the first reference catalog of 682 high-confidence lncRNAs based on analysis of strand-specific RNA-seq data from cassava shoot apices and young leaves under cold, drought stress and control conditions. Among them, 16 lncRNAs were identified as putative target mimics of cassava known miRNAs. Additionally, by comparing with small RNA-seq data, we found 42 lncNATs and sense gene pairs can generate nat-siRNAs. We identified 318 lncRNAs responsive to cold and/or drought stress, which were typically co-expressed concordantly or discordantly with their neighboring genes. Trans-regulatory network analysis suggested that many lncRNAs were associated with hormone signal transduction, secondary metabolites biosynthesis, and sucrose metabolism pathway. The study provides an opportunity for future computational and experimental studies to uncover the functions of lncRNAs in cassava.

Computational methods for annotation of plant regulatory non-coding RNAs using RNA-seq

2020 ◽  
Author(s):  
A T Vivek ◽  
Shailesh Kumar
Keyword(s):  
Computational Methods ◽  
High Throughput ◽  
Rna Seq ◽  
Physiological Mechanisms ◽  
Software Packages ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Plant Transcriptome ◽  
Non Coding Rnas

Abstract Plant transcriptome encompasses numerous endogenous, regulatory non-coding RNAs (ncRNAs) that play a major biological role in regulating key physiological mechanisms. While studies have shown that ncRNAs are extremely diverse and ubiquitous, the functions of the vast majority of ncRNAs are still unknown. With ever-increasing ncRNAs under study, it is essential to identify, categorize and annotate these ncRNAs on a genome-wide scale. The use of high-throughput RNA sequencing (RNA-seq) technologies provides a broader picture of the non-coding component of transcriptome, enabling the comprehensive identification and annotation of all major ncRNAs across samples. However, the detection of known and emerging class of ncRNAs from RNA-seq data demands complex computational methods owing to their unique as well as similar characteristics. Here, we discuss major plant endogenous, regulatory ncRNAs in an RNA sample followed by computational strategies applied to discover each class of ncRNAs using RNA-seq. We also provide a collection of relevant software packages and databases to present a comprehensive bioinformatics toolbox for plant ncRNA researchers. We assume that the discussions in this review will provide a rationale for the discovery of all major categories of plant ncRNAs.

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