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.

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

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.

Pengaruh Periode Kekeringan Terhadap Pertumbuhan dan Hasil Beberapa Genotipe Padi

Agrotek ◽  
2018 ◽  
Vol 3 (1) ◽  
Author(s):  
Herman W. Tubur ◽  
M. A. Chozin ◽  
Edi Santosa ◽  
Ahmad Junaedi
Keyword(s):  
Drought Stress ◽  
Growth And Yield ◽  
High Yield ◽  
Drought Treatment ◽  
Drought Period ◽  
Land Type ◽  
Pipe Line ◽  
Main Plot ◽  
Rice Genotypes ◽  
And Control

<em>The objective of this experiment was to identify the growth and production responses of rice genotypes to drought period. Rice plants were grown under plastic house in plots separated by a massive walls and water was suplied by inlet pipe line. Drought treatments were placed as main-plot, consisted of K3, K6, K9 (water was supplied till 3, 6, and 9 weeks after rice transplanting (WAT), respectively) and control (standard rice growing without drought treatment).� Rice genotypes were placed as sub-plot, consisted of IR-64 and Ciherang (low land type improved varieties), IPB-97 (new plant type), Menthik Wangi (an aromatic local low land rice), Rokan (a hybryd rice), Way Apo Buru (amphibian type), Jatiluhur and Silugonggo (up land type). The results showed that rice growth and yield were significantly affected by drought treatment, especially in K3 and K6. Low yield in K3 and K6 were mostly caused by increased of unfilled spikelet. Jatiluhur, Ciherang and Way Apo Buru still showed relatively high yield under drought stress indicated that those genotypes were relatively tolerant to drought stress; Silugonggo and IPB-97 showed relatively medium tolerant to drought stress; IR-64, Menthik wangi and Rokan showed the most sensitive one.</em>

scholarly journals Genome-wide analysis and expression profiles of the StR2R3-MYB transcription factor superfamily in Solanum Tuberosum

2019 ◽  
Author(s):  
Yuanming Li ◽  
Kui Lin-Wang ◽  
Zhen Liu ◽  
Andrew C. Allan ◽  
Junlian Zhang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Abiotic Stress ◽  
Solanum Tuberosum ◽  
Drought Stress ◽  
Anthocyanin Biosynthesis ◽  
Rna Seq ◽  
Genome Wide ◽  
Ear Motif ◽  
Myb Genes ◽  
Myb Proteins

Abstract Background: MYB transcription factors comprise one of the largest families in plant kingdom, which play a variety of functions in plant developmental processes and defence responses. However, it has not been systematically studied in Potato (Solanum tuberosum), which is the most important non-cereal crop world-wide. Results: In the present study, a total of 108 StR2R3-MYB transcription factors were identified and further phylogenetically classified into 28 subfamilies, as supported by highly conserved gene structures and motifs. Collinearity analysis showed that the segmental duplication events played a crucial role in the expansion of StR2R3-MYB gene family. Synteny analysis indicated that 37 and 13 StR2R3-MYB genes were orthologous to Arabidopsis and wheat, respectively, and these gene pairs have evolved under strong purifying selection. RNA-seq data from different tissues and abiotic stresses revealed tissue-preferential and abiotic stress-responsive StR2R3-MYB genes. We further analyzed StR2R3-MYB genes might be involved in anthocyanin biosynthesis and drought stress by using RNA-seq data of pigmented tetraploid potato cultivars and drought-sensitive and -tolerant tetraploid potato cultivars under drought stress, respectively. Moreover, EAR motifs were found in 21 StR2R3-MYB proteins and 446 pairs of proteins were predicted to interact with 21 EAR motif-containing StR2R3-MYB proteins by constructing the interaction network with medium confidence (0.4). Additionally, Gene Ontology (GO) analysis of the 21 EAR motif-containing StR2R3-MYB proteins was performed to further investigate their functions. Conclusions: In this work, we systematically identified StR2R3-MYB genes by analyzing the potato genome sequence using a set of bioinformatics approaches. Genome-wide comparative analysis of StR2R3-MYB genes and their expression analysis identified members of this superfamily may be involved in tissue-specific development, anthocyanin biosynthesis and abiotic stress responses.

scholarly journals Identification and functional deciphering suggested the regulatory roles of long intergenic ncRNAs (lincRNAs) in increasing grafting pepper resistance to Phytophthora capsici

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Junliang Yin ◽  
Jiahui Yan ◽  
Lu Hou ◽  
Liling Jiang ◽  
Wenrong Xian ◽  
...  
Keyword(s):  
Stress Responses ◽  
Phytophthora Capsici ◽  
Vegetable Production ◽  
Rna Seq ◽  
Resistance Level ◽  
Protein Coding ◽  
Genome Wide ◽  
And Function ◽  
And Control ◽  
Pepper Sample

Abstract Background As a popular and valuable technique, grafting is widely used to protect against soil-borne diseases and nematodes in vegetable production. Growing evidences have revealed that long intergenic ncRNAs (lincRNAs) are strictly regulated and play essential roles in plants development and stress responses. Nevertheless, genome-wide identification and function deciphering of pepper lincRNAs, especially for their roles in improving grafting pepper resistance to Phytophthora capsici is largely unknown. Results In this study, RNA-seq data of grafting and control pepper plants with or without P. capsici inoculation were used to identify lincRNAs. In total, 2,388 reliable lincRNAs were identified. They were relatively longer and contained few exons than protein-coding genes. Similar to coding genes, lincRNAs had higher densities in euchromatin regions; and longer chromosome transcribed more lincRNAs. Expression pattern profiling suggested that lincRNAs commonly had lower expression than mRNAs. Totally, 607 differentially expressed lincRNAs (DE-lincRANs) were identified, of which 172 were found between P. capsici resistance grafting pepper sample GR and susceptible sample LDS. The neighboring genes of DE-lincRNAs and miRNAs competitively sponged by DE-lincRNAs were identified. Subsequently, the expression level of DE-lincRNAs was further confirmed by qRT-PCR and regulation patterns between DE-lincRNAs and neighboring mRNAs were also validated. Function annotation revealed that DE-lincRNAs increased the resistance of grafting prepper to P. capsici by modulating the expression of disease-defense related genes through cis-regulating and/or lincRNA-miRNA-mRNA interaction networks. Conclusions This study identified pepper lincRNAs and suggested their potential roles in increasing the resistance level of grafting pepper to P. capsici.

scholarly journals APERO: a genome-wide approach for identifying bacterial small RNAs from RNA-Seq data

2019 ◽  
Vol 47 (15) ◽  
pp. e88-e88 ◽  
Author(s):  
Simon Leonard ◽  
Sam Meyer ◽  
Stephan Lacour ◽  
William Nasser ◽  
Florence Hommais ◽  
...  
Keyword(s):  
R Package ◽  
Rna Seq ◽  
Dickeya Dadantii ◽  
Cellular Processes ◽  
Bacterial Rna ◽  
Genome Wide ◽  
A Genome ◽  
Domains Of Life ◽  
Race Pcr ◽  
Genome Annotations

Abstract Small non-coding RNAs (sRNAs) regulate numerous cellular processes in all domains of life. Several approaches have been developed to identify them from RNA-seq data, which are efficient for eukaryotic sRNAs but remain inaccurate for the longer and highly structured bacterial sRNAs. We present APERO, a new algorithm to detect small transcripts from paired-end bacterial RNA-seq data. In contrast to previous approaches that start from the read coverage distribution, APERO analyzes boundaries of individual sequenced fragments to infer the 5′ and 3′ ends of all transcripts. Since sRNAs are about the same size as individual fragments (50–350 nucleotides), this algorithm provides a significantly higher accuracy and robustness, e.g., with respect to spontaneous internal breaking sites. To demonstrate this improvement, we develop a comparative assessment on datasets from Escherichia coli and Salmonella enterica, based on experimentally validated sRNAs. We also identify the small transcript repertoire of Dickeya dadantii including putative intergenic RNAs, 5′ UTR or 3′ UTR-derived RNA products and antisense RNAs. Comparisons to annotations as well as RACE-PCR experimental data confirm the precision of the detected transcripts. Altogether, APERO outperforms all existing methods in terms of sRNA detection and boundary precision, which is crucial for comprehensive genome annotations. It is freely available as an open source R package on https://github.com/Simon-Leonard/APERO

scholarly journals Genome-Wide DNA Methylation Dynamics During Drought Responsiveness in Tibetan Hulless Barley

2021 ◽  
Author(s):  
Dunzhu Jabu ◽  
Zhaiming Yu ◽  
Qijun Xu ◽  
Haizhen Yang ◽  
Wang Mu ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Transcription Factors ◽  
Drought Stress ◽  
Antioxidant Activities ◽  
Differentially Methylated Region ◽  
Hulless Barley ◽  
Drought Tolerant ◽  
Genome Wide ◽  
Tibetan Hulless Barley ◽  
And Control

Abstract Differences in drought stress tolerance within diverse grass genotypes have been attributed to epigenetic modifications. DNA methylation is an important epigenetic alteration regulating responses to drought-stress. However, its effects on drought-tolerance are poorly understood in Tibetan hulless barley. Here, bisulfite sequencing was conducted to profile the DNA methylation patterns of drought-tolerant variety XL and drought-sensitive one DQ under drought and control conditions. A total of 5843 million reads were generated. We found the significant genome-wide changes in CHH methylation rates between XL and DQ, while CG or CHG methylation rates did not. Besides that, the two contrasting varieties do reveal distinct responses to drought-stress in differentially methylated region (DMR) numbers and antioxidant activities. Genes in drought-tolerant varieties XL are rapidly and significantly methylated to alleviate the drought stress. DMR related genes in XL might involve in defense response and response to stimuli, which are confirmed by gene ontology analysis. Then, we focused on 1003 transcription factors and identified 15 specific DMR related transcription factors exhibiting specific methylation changes under drought stimuli. Finally, we identified three DMR related TFs (HVUL6H08680.2, HVUL4 h39100.2, and HVUL2H41931.2) where Arabidopsis homologues involve in responses to drought conditions. Altogether, DNA methylation regulate responsiveness to environmental stimuli, which could be mediated by methylation of transcription factors in hulless barely.

scholarly journals Genome-wide identification and characterization of lncRNAs responding to iron deficiency in Oryza sativa

2020 ◽  
Author(s):  
Shoudong Wang ◽  
Shuo Sun ◽  
Huixia Shou
Keyword(s):  
Chlorophyll Biosynthesis ◽  
Vital Role ◽  
Fe Deficiency ◽  
Systematic Screening ◽  
Cellular Processes ◽  
Yield And Quality ◽  
Genome Wide ◽  
Non Coding Rnas ◽  
Identification And Characterization

Abstract Background: Iron (Fe) plays a vital role in various cellular processes in plants, including chlorophyll biosynthesis, photosynthesis and respiration. Fe deficiency directly affects crop growth and development, ultimately resulting in reduced crop yield and quality. Long non-coding RNAs (lncRNAs) have recently been demonstrated to play critical regulatory roles in a multitude of pathways across numerous species. However, systematic screening of lncRNAs responding to Fe deficiency in plants has not been reported. In this work, genome-wide identification and characterization of lncRNAs responsive to Fe deficiency were performed by strand-specific RNA sequencing in rice. Results: In total, 6477 lncRNAs were identified. In Fe-deficient conditions, 47 lncRNAs were up-regulated and 33 lncRNAs were down-regulated in shoots, while 89 lncRNAs were up-regulated and 32 lncRNAs were down-regulated in roots compared to normal conditions. The lncRNAs that were differentially expressed under Fe-sufficient and -deficient conditions appear to be clustered in the genome. Among five monocotyledon species, 88 lncRNAs were conserved, but only 3 lncRNAs responded to Fe deficiency in shoots. Two lncRNAs were identified as putative target mimics of miRNAs that respond to Fe deficiency. Conclusions: Our results provide evidence that lncRNAs are involved in Fe-deficiency signaling pathway in plants, providing a new pathway for further investigation into Fe-regulatory and response mechanisms.

scholarly journals Genome-Wide Identification and Analysis of NAC Transcription Factor Family in Two Diploid Wild Relatives of Cultivated Sweet Potato Uncovers Potential NAC Genes Related to Drought Tolerance

2021 ◽  
Vol 12 ◽  
Author(s):  
Haifeng Yan ◽  
Guohua Ma ◽  
Jaime A. Teixeira da Silva ◽  
Lihang Qiu ◽  
Juan Xu ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Sweet Potato ◽  
Abiotic Stresses ◽  
Tandem Duplication ◽  
Wild Relatives ◽  
Potential Candidate ◽  
Rna Seq ◽  
Genome Wide ◽  
Nac Family

NAC (NAM, ATAF1/2, and CUC2) proteins play a pivotal role in modulating plant development and offer protection against biotic and abiotic stresses. Until now, no systematic knowledge of NAC family genes is available for the food security crop, sweet potato. Here, a comprehensive genome-wide survey of NAC domain-containing proteins identified 130 ItbNAC and 144 ItfNAC genes with full length sequences in the genomes of two diploid wild relatives of cultivated sweet potato, Ipomoea triloba and Ipomoea trifida, respectively. These genes were physically mapped onto 15 I. triloba and 16 I. trifida chromosomes, respectively. Phylogenetic analysis divided all 274 NAC proteins into 20 subgroups together with NAC transcription factors (TFs) from Arabidopsis. There were 9 and 15 tandem duplication events in the I. triloba and I. trifida genomes, respectively, indicating an important role of tandem duplication in sweet potato gene expansion and evolution. Moreover, synteny analysis suggested that most NAC genes in the two diploid sweet potato species had a similar origin and evolutionary process. Gene expression patterns based on RNA-Seq data in different tissues and in response to various hormone, biotic or abiotic treatments revealed their possible involvement in organ development and response to various biotic/abiotic stresses. The expression of 36 NAC TFs, which were upregulated in the five tissues and in response to mannitol treatment, was also determined by real-time quantitative polymerase chain reaction (RT-qPCR) in hexaploid cultivated sweet potato exposed to drought stress. Those results largely corroborated the expression profile of mannitol treatment uncovered by the RNA-Seq data. Some significantly up-regulated genes related to drought stress, such as ItbNAC110, ItbNAC114, ItfNAC15, ItfNAC28, and especially ItfNAC62, which had a conservative spatial conformation with a closely related paralogous gene, ANAC019, may be potential candidate genes for a sweet potato drought tolerance breeding program. This analysis provides comprehensive and systematic information about NAC family genes in two diploid wild relatives of cultivated sweet potato, and will provide a blueprint for their functional characterization and exploitation to improve the tolerance of sweet potato to abiotic stresses.

scholarly journals Genome-Wide Expression Profiles of Hemp (Cannabis sativa L.) in Response to Drought Stress

2018 ◽  
Vol 2018 ◽  
pp. 1-13 ◽  
Author(s):  
Chunsheng Gao ◽  
Chaohua Cheng ◽  
Lining Zhao ◽  
Yongting Yu ◽  
Qing Tang ◽  
...  
Keyword(s):  
Drought Stress ◽  
Differentially Expressed Genes ◽  
Cannabis Sativa ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Signal Transduction Pathway ◽  
Differentially Expressed ◽  
Growth And Yield ◽  
Rna Seq ◽  
Kegg Pathways

Drought is the main environmental factor impairing hemp growth and yield. In order to decipher the molecular responses of hemp to drought stress, transcriptome changes of drought-stressed hemp (DS1 and DS2), compared to well-watered control hemp (CK1 and CK2), were studied with RNA-Seq technology. RNA-Seq generated 9.83, 11.30, 11.66, and 11.31 M clean reads in the CK1, CK2, DS1, and DS2 libraries, respectively. A total of 1292 differentially expressed genes (DEGs), including 409 (31.66%) upregulated and 883 (68.34%) downregulated genes, were identified. The expression patterns of 12 selected genes were validated by qRT-PCR, and the results were accordant with Illumina analysis. Gene Ontology (GO) and KEGG analysis illuminated particular important biological processes and pathways, which enriched many candidate genes such as NAC, B3, peroxidase, expansin, and inositol oxygenase that may play important roles in hemp tolerance to drought. Eleven KEGG pathways were significantly influenced, the most influenced being the plant hormone signal transduction pathway with 15 differentially expressed genes. A similar expression pattern of genes involved in the abscisic acid (ABA) pathway under drought, and ABA induction, suggested that ABA is important in the drought stress response of hemp. These findings provide useful insights into the drought stress regulatory mechanism in hemp.

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