Genome-wide screening for novel, drought stress-responsive long non-coding RNAs in drought-stressed leaf transcriptome of drought-tolerant and -susceptible banana (Musa spp) cultivars using Illumina high-throughput sequencing

Abstract Background: Drought stress is a major abiotic factor that affects rapeseed ( Brassica napus L.) productivity. Though previous studies indicated that long non-coding RNAs (lncRNAs) play a key role in response to drought stress, a scheme for genome-wide identification and characterization of lncRNAs’ response to drought stress is still lacking, especially in the case of B . napus . In order to further understand the molecular mechanism of the response of B . napus to drought stress, we compared changes in the transcriptome between Q2 (a drought-tolerant genotype) and Qinyou8 (a drought-sensitive genotype) in response to drought stress and rehydration treatment at the seedling stage. Results: A total of 5,546 down-regulated and 6,997 up-regulated mRNAs were detected in Q2 compared with 7,824 and 10,251 in Qinyou8, respectively; 369 down-regulated and 108 up-regulated lncRNAs were detected in Q2 compared with 449 and 257 in Qinyou8, respectively. We further identified 34 TFs corresponding to 126 differently expressed lncRNAs in Q2, and 45 TFs corresponding to 359 differently expressed lncRNAs in Qinyou8. Differential expression analysis of lncRNAs indicated that up- and down-regulated mRNAs co-expressed with lncRNAs participated in different metabolic pathways and were involved in different regulatory mechanisms in the two genotypes . Notably, some lncRNAs were co-expressed and co-located with BnaC07g44670D, which are associated with plant hormone signal transduction. Additionally, some mRNAs which were co-located with LNC_002535 (XLOC_052298), LNC_004924 (XLOC_094954) and LNC_000539 (XLOC_012868) were mainly categorized as signal transport and defense/stress response. Finally, co-expression network analysis indicated that the co-expression network of Q2 was composed of 145 network nodes and 5,175 connections, while the co-expression network of Qinyou8 was composed of 305 network nodes and 22,327 connections. Conclusions: The differentially expressed mRNAs and lncRNAs may play important roles in response to drought stress and rehydration treatments and could provide basic information for new ways to improve the drought resistance of Rapeseed Brassica napus .

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Genome wide identification and characterization of light-harvesting Chloro a/b binding (LHC) genes reveals their potential role in enhancing drought tolerance in Gossypium hirsutum

Journal of Cotton Research ◽

10.1186/s42397-021-00090-8 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Teame Gereziher MEHARI ◽

Yanchao XU ◽

Richard Odongo MAGWANGA ◽

Muhammad Jawad UMER ◽

Joy Nyangasi KIRUNGU ◽

...

Keyword(s):

Drought Stress ◽

Gossypium Hirsutum ◽

Abiotic Stresses ◽

Substitution Rate ◽

Synonymous Substitution ◽

Synonymous Substitution Rate ◽

Drought Tolerant ◽

Genome Wide ◽

Identification And Characterization

Abstract Background Cotton is an important commercial crop for being a valuable source of natural fiber. Its production has undergone a sharp decline because of abiotic stresses, etc. Drought is one of the major abiotic stress causing significant yield losses in cotton. However, plants have evolved self-defense mechanisms to cope abiotic factors like drought, salt, cold, etc. The evolution of stress responsive transcription factors such as the trihelix, a nodule-inception-like protein (NLP), and the late embryogenesis abundant proteins have shown positive response in the resistance improvement to several abiotic stresses. Results Genome wide identification and characterization of the effects of Light-Harvesting Chloro a/b binding (LHC) genes were carried out in cotton under drought stress conditions. A hundred and nine proteins encoded by the LHC genes were found in the cotton genome, with 55, 27, and 27 genes found to be distributed in Gossypium hirsutum, G. arboreum, and G. raimondii, respectively. The proteins encoded by the genes were unevenly distributed on various chromosomes. The Ka/Ks (Non-synonymous substitution rate/Synonymous substitution rate) values were less than one, an indication of negative selection of the gene family. Differential expressions of genes showed that majority of the genes are being highly upregulated in the roots as compared with leaves and stem tissues. Most genes were found to be highly expressed in MR-85, a relative drought tolerant germplasm. Conclusion The results provide proofs of the possible role of the LHC genes in improving drought stress tolerance, and can be explored by cotton breeders in releasing a more drought tolerant cotton varieties.

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High-throughput sequencing profile of laryngeal cancers: analysis of co-expression and competing endogenous RNA networks of circular RNAs, long non-coding RNAs, and messenger RNAs

Annals of Translational Medicine ◽

10.21037/atm-21-584 ◽

2021 ◽

Vol 9 (6) ◽

pp. 483-483

Author(s):

Zheng Wang ◽

Jia Gu ◽

Tao Han ◽

Kai Li

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Circular Rnas ◽

Messenger Rnas ◽

Competing Endogenous Rna ◽

Non Coding Rnas

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PRIME-3D2D is a 3D2D model to predict binding sites of protein–RNA interaction

Communications Biology ◽

10.1038/s42003-020-1114-y ◽

2020 ◽

Vol 3 (1) ◽

Author(s):

Juan Xie ◽

Jinfang Zheng ◽

Xu Hong ◽

Xiaoxue Tong ◽

Shiyong Liu

Keyword(s):

Full Advantage ◽

High Throughput ◽

Binding Sites ◽

High Throughput Sequencing ◽

Secondary Structures ◽

Biological Processes ◽

Genome Wide ◽

Rna Interaction ◽

Rna Complexes ◽

Better Than

AbstractProtein-RNA interaction participates in many biological processes. So, studying protein–RNA interaction can help us to understand the function of protein and RNA. Although the protein–RNA 3D3D model, like PRIME, was useful in building 3D structural complexes, it can’t be used genome-wide, due to lacking RNA 3D structures. To take full advantage of RNA secondary structures revealed from high-throughput sequencing, we present PRIME-3D2D to predict binding sites of protein–RNA interaction. PRIME-3D2D is almost as good as PRIME at modeling protein–RNA complexes. PRIME-3D2D can be used to predict binding sites on PDB data (MCC = 0.75/0.70 for binding sites in protein/RNA) and transcription-wide (MCC = 0.285 for binding sites in RNA). Testing on PDB and yeast transcription-wide data show that PRIME-3D2D performs better than other binding sites predictor. So, PRIME-3D2D can be used to predict the binding sites both on PDB and genome-wide, and it’s freely available.

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Identification of Exogenous Nitric Oxide-Responsive miRNAs from Alfalfa (Medicago sativa L.) under Drought Stress by High-Throughput Sequencing

Genes ◽

10.3390/genes11010030 ◽

2019 ◽

Vol 11 (1) ◽

pp. 30

Author(s):

Yaodong Zhao ◽

Wenjing Ma ◽

Xiaohong Wei ◽

Yu Long ◽

Ying Zhao ◽

...

Keyword(s):

Nitric Oxide ◽

Drought Stress ◽

Medicago Sativa ◽

High Throughput ◽

Drought Resistance ◽

High Throughput Sequencing ◽

Target Genes ◽

Expression Profiles ◽

Differentially Expressed ◽

Medicago Sativa L

Alfalfa (Medicago sativa L.) is a high quality leguminous forage. Drought stress is one of the main factors that restrict the development of the alfalfa industry. High-throughput sequencing was used to analyze the microRNA (miRNA) profiles of alfalfa plants treated with CK (normal water), PEG (polyethylene glycol-6000; drought stress), and PEG + SNP (sodium nitroprusside; nitric oxide (NO) sprayed externally under drought stress). We identified 90 known miRNAs belonging to 46 families and predicted 177 new miRNAs. Real-time quantitative fluorescent PCR (qRT-PCR) was used to validate high-throughput expression analysis data. A total of 32 (14 known miRNAs and 18 new miRNAs) and 55 (24 known miRNAs and 31 new miRNAs) differentially expressed miRNAs were identified in PEG and PEG + SNP samples. This suggested that exogenous NO can induce more new miRNAs. The differentially expressed miRNA maturation sequences in the two treatment groups were targeted by 86 and 157 potential target genes, separately. The function of target genes was annotated by gene ontology (GO) enrichment and kyoto encyclopedia of genes and genomes (KEGG) analysis. The expression profiles of nine selected miRNAs and their target genes verified that their expression patterns were opposite. This study has documented that analysis of miRNA under PEG and PEG + SNP conditions provides important insights into the improvement of drought resistance of alfalfa by exogenous NO at the molecular level. This has important scientific value and practical significance for the improvement of plant drought resistance by exogenous NO.

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