Identification of Stress Associated microRNAs in Solanum lycopersicum by High-Throughput Sequencing

Tomato (Solanum lycopersicum) is one of the most important crops around the world and also a model plant to study response to stress. High-throughput sequencing was used to analyse the microRNA (miRNA) profile of tomato plants undergoing five biotic and abiotic stress conditions (drought, heat, P. syringae infection, B. cinerea infection, and herbivore insect attack with Leptinotarsa decemlineata larvae) and one chemical treatment with a plant defence inducer, hexanoic acid. We identified 104 conserved miRNAs belonging to 37 families and we predicted 61 novel tomato miRNAs. Among those 165 miRNAs, 41 were stress-responsive. Reverse transcription quantitative PCR (RT-qPCR) was used to validate high-throughput expression analysis data, confirming the expression profiles of 10 out of 11 randomly selected miRNAs. Most of the differentially expressed miRNAs were stress-specific, except for sly-miR167c-3p upregulated in B. cinerea and P. syringae infection, sly-newmiR26-3p upregulated in drought and Hx treatment samples, and sly-newmiR33-3p, sly-newmiR6-3p and sly-newmiR8-3p differentially expressed both in biotic and abiotic stresses. From mature miRNAs sequences of the 41 stress-responsive miRNAs 279 targets were predicted. An inverse correlation between the expression profiles of 4 selected miRNAs (sly-miR171a, sly-miR172c, sly-newmiR22-3p and sly-miR167c-3p) and their target genes (Kinesin, PPR, GRAS40, ABC transporter, GDP and RLP1) was confirmed by RT-qPCR. Altogether, our analysis of miRNAs in different biotic and abiotic stress conditions highlight the interest to understand the functional role of miRNAs in tomato stress response as well as their putative targets which could help to elucidate plants molecular and physiological adaptation to stress.

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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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High-throughput sequencing of circRNAs reveals novel insights into mechanisms of nigericin in pancreatic cancer

BMC Genomics ◽

10.1186/s12864-019-6032-3 ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 1

Author(s):

Zhihua Xu ◽

Jiaqing Shen ◽

Shangbo Hua ◽

Daiwei Wan ◽

Qian Chen ◽

...

Keyword(s):

Pancreatic Cancer ◽

High Throughput ◽

High Throughput Sequencing ◽

Expression Profiles ◽

Potential Functions ◽

Differentially Expressed ◽

Pcr Analysis ◽

Signal Pathways ◽

Sequencing Data ◽

Anti Cancer

Abstract Background Our previous study had proved that nigericin could reduce colorectal cancer cell proliferation in dose- and time-dependent manners by targeting Wnt/β-catenin signaling. To better elucidate its potential anti-cancer mechanism, two pancreatic cancer (PC) cell lines were exposed to increasing concentrations of nigericin for different time periods, and the high-throughput sequencing was performed to explore the circRNA expression profiles after nigericin exposure on pancreatic cancer (PC) cells. Results In this study, a total of 183 common differentially expressed circRNAs were identified, and the reliability and validity of the sequencing data were verified by the PCR analysis. According to the parental genes of circRNAs, the GO analysis was performed to predict the most enriched terms in the biological process, cellular components and molecular functions. The KEGG analysis and pathway-pathway network exhibited the potential signal pathways and their regulatory relationships. Meanwhile, a potential competing endogenous RNA (ceRNA) mechanism through a circRNA-miRNA-mRNA network was applied to annotate potential functions of these common differentially expressed circRNAs, and these predicted miRNAs or mRNAs might be involved in nigericin damage. Conclusions By the bioinformatics method, our data will facilitate the understanding of nigericin in PC cells, and provide new insight into the molecular mechanism of nigericin toward cancer cells. This is the first report that discusses the potential functions of nigericin in cancers through the bioinformatics method. Our data will facilitate the understanding of nigericin-mediated anti-cancer mechanisms in PC.

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Identification of Differentially Expressed Circular RNAs in Keloid and Normal Skin Tissue by High‐throughput Sequencing

Dermatologic Therapy ◽

10.1111/dth.14745 ◽

2021 ◽

Author(s):

Jing Zhang ◽

Ninghua Liu ◽

Xiufa Wu ◽

Peixuan Wu ◽

Nan Song ◽

...

Keyword(s):

High Throughput ◽

High Throughput Sequencing ◽

Normal Skin ◽

Differentially Expressed ◽

Skin Tissue ◽

Circular Rnas

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Towards the validation of high-throughput sequencing (HTS) for routine plant virus diagnostics: measurement of variation linked to HTS detection of citrus viruses and viroids

Virology Journal ◽

10.1186/s12985-021-01523-1 ◽

2021 ◽

Vol 18 (1) ◽

Author(s):

Rachelle Bester ◽

Glynnis Cook ◽

Johannes H. J. Breytenbach ◽

Chanel Steyn ◽

Rochelle De Bruyn ◽

...

Keyword(s):

High Throughput ◽

Extraction Method ◽

Pathogen Detection ◽

High Throughput Sequencing ◽

Expression Profiles ◽

Rna Extraction ◽

Healthy Plant ◽

Ion Torrent ◽

Extraction Protocol ◽

Zymo Research

Abstract Background High-throughput sequencing (HTS) has been applied successfully for virus and viroid discovery in many agricultural crops leading to the current drive to apply this technology in routine pathogen detection. The validation of HTS-based pathogen detection is therefore paramount. Methods Plant infections were established by graft inoculating a suite of viruses and viroids from established sources for further study. Four plants (one healthy plant and three infected) were sampled in triplicate and total RNA was extracted using two different methods (CTAB extraction protocol and the Zymo Research Quick-RNA Plant Miniprep Kit) and sent for Illumina HTS. One replicate sample of each plant for each RNA extraction method was also sent for HTS on an Ion Torrent platform. The data were evaluated for biological and technical variation focussing on RNA extraction method, platform used and bioinformatic analysis. Results The study evaluated the influence of different HTS protocols on the sensitivity, specificity and repeatability of HTS as a detection tool. Both extraction methods and sequencing platforms resulted in significant differences between the data sets. Using a de novo assembly approach, complemented with read mapping, the Illumina data allowed a greater proportion of the expected pathogen scaffolds to be inferred, and an accurate virome profile was constructed. The complete virome profile was also constructed using the Ion Torrent data but analyses showed that more sequencing depth is required to be comparative to the Illumina protocol and produce consistent results. The CTAB extraction protocol lowered the proportion of viroid sequences recovered with HTS, and the Zymo Research kit resulted in more variation in the read counts obtained per pathogen sequence. The expression profiles of reference genes were also investigated to assess the suitability of these genes as internal controls to allow for the comparison between samples across different protocols. Conclusions This study highlights the need to measure the level of variation that can arise from the different variables of an HTS protocol, from sample preparation to data analysis. HTS is more comprehensive than any assay previously used, but with the necessary validations and standard operating procedures, the implementation of HTS as part of routine pathogen screening practices is possible.

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Mapping and candidate gene screening of Cladosporium fulvum resistance gene Cf‐12 in tomato ( Solanum lycopersicum ) by high‐throughput sequencing

Plant Breeding ◽

10.1111/pbr.12852 ◽

2020 ◽

Vol 139 (5) ◽

pp. 977-987

Author(s):

Xinfeng Chai ◽

Xiangyang XU ◽

Dong Wang ◽

Dongqi Xue ◽

Jingfu Li

Keyword(s):

Candidate Gene ◽

Solanum Lycopersicum ◽

Resistance Gene ◽

High Throughput ◽

High Throughput Sequencing ◽

Cladosporium Fulvum ◽

Gene Screening

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Comprehensive analysis of miRNA-mRNA/lncRNA during gonadal development of triploid female rainbow trout (Oncorhynchus mykiss)

10.21203/rs.3.rs-31357/v2 ◽

2020 ◽

Author(s):

Tianqing Huang ◽

Wei Gu ◽

Enhui Liu ◽

Xiulan Shi ◽

Bingqian Wang ◽

...

Keyword(s):

Rainbow Trout ◽

High Throughput Sequencing ◽

Developmental Stages ◽

Expression Profiles ◽

Noncoding Rnas ◽

Gonadal Development ◽

Differentially Expressed ◽

Rainbow Trout Oncorhynchus Mykiss ◽

Oocyte Meiosis ◽

Non Coding Rna

Abstract Background: Chromosomal ploidy manipulation is one of the means to create excellent germplasm. Triploid fish could provide an ideal sterile model for the mechanism research of abnormality in meiosis. The complete understanding of the coding and noncoding RNAs regulating sterility caused by meiosis abnormality is still not well understood.Results: By high-throughput sequencing, we compared the expression profiles of gonadal mRNA, long non-coding RNA (lncRNA), and microRNA (miRNA) at different developmental stages [65 days post fertilisation (dpf), 180 dpf, and 600 dpf] between the diploid (XX) and triploid (XXX) female rainbow trout. A majority of differentially expressed (DE) RNAs were identified, and 22 DE mRNAs related to oocyte meiosis and homologous recombination were characterized. The predicted miRNA-mRNA/lncRNA networks of 3 developmental stages were constructed based on the target pairs of DE lncRNA-miRNA and DE mRNA-miRNA. According to the networks, meiosis-related gene of ccne1 was targeted by dre-miR-15a-5p_R+1, and 6 targeted DE lncRNAs were identified. Also, RT-qPCR was performed to validate the credibility of the network.Conclusions: This study explored the potential interplay between coding and noncoding RNAs during the gonadal development of polyploid fish. It provides full insights into polyploidy-associated effects on fertility of fish. These differentially expressed coding and noncoding RNAs provide a novel resource for studying genome diversity of polyploid induction.

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Reactive Oxygen Species (ROS) Metabolism and Signaling in Plant-Mycorrhizal Association Under Biotic and Abiotic Stress Conditions

Mycorrhiza - Eco-Physiology, Secondary Metabolites, Nanomaterials ◽

10.1007/978-3-319-57849-1_12 ◽

2017 ◽

pp. 223-232 ◽

Cited By ~ 10

Author(s):

Manoj Nath ◽

Deepesh Bhatt ◽

Ram Prasad ◽

Narendra Tuteja

Keyword(s):

Reactive Oxygen Species ◽

Abiotic Stress ◽

Reactive Oxygen ◽

Stress Conditions ◽

Oxygen Species ◽

Biotic And Abiotic Stress ◽

Ros Metabolism ◽

Mycorrhizal Association

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CCCH Zinc Finger Genes in Barley: Genome-Wide Identification, Evolution, Expression and Haplotype Analysis

10.21203/rs.3.rs-1114922/v1 ◽

2021 ◽

Author(s):

Qi Ai ◽

Wenqiu Pan ◽

Yan Zeng ◽

Yihan Li ◽

Licao Cui

Keyword(s):

Transcription Factors ◽

Abiotic Stress ◽

Zinc Finger ◽

Molecular Breeding ◽

Animal Feed ◽

Expression Profiles ◽

Exome Capture ◽

Biotic And Abiotic Stress ◽

Motif Analysis ◽

Developmental Processes

Abstract Background: CCCH transcription factors are important zinc finger transcription factors involved in the response to biotic and abiotic stress and physiological and developmental processes. Barley (Hordeum vulgare) is an agriculturally important cereal crop with multiple uses, such as brewing production, animal feed, and human food. The identification and assessment of new functional genes are important for the molecular breeding of barley. Results: In this study, a total of 35 protein-encoding CCCH genes unevenly dispersed on seven different chromosomes were identified in barley. Phylogenetic analysis categorized the barley CCCH genes (HvC3Hs) into seven subfamilies according to their distinct features, and this classification was supported by intron–exon structure and conserved motif analysis. Despite the large genome size of barley, the lower number of CCCH genes in barley might be attributed to the low frequency of segmental and tandem duplication events. Furthermore, the HvC3H genes displayed distinct expression profiles for different developmental processes and in response to various types of stresses. The expression of HvC3H9 was significantly induced by multiple types of abiotic stress and/or phytohormone treatment, which might make it an excellent target for the molecular breeding of barley. Genetic variation of HvC3Hs was characterized using publicly available exome-capture sequencing datasets. Clear genetic divergence was observed between wild and landrace barley populations in HvC3H genes. For most HvC3Hs, nucleotide diversity and the number of haplotype polymorphisms decreased during barley domestication. Conclusion: Overall, our study provides a comprehensive characterization of barley CCCH transcription factors, their diversity, and their biological functions.

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Identification of conserved and novel miRNAs responsive to heat stress in flowering Chinese cabbage using high-throughput sequencing

Scientific Reports ◽

10.1038/s41598-019-51443-y ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Waqas Ahmed ◽

Yanshi Xia ◽

Hua Zhang ◽

Ronghua Li ◽

Guihua Bai ◽

...

Keyword(s):

Heat Stress ◽

Abiotic Stress ◽

High Throughput ◽

Chinese Cabbage ◽

Stress Responses ◽

High Throughput Sequencing ◽

Differential Expression Analysis ◽

Plant Responses ◽

Limited Information ◽

Flowering Chinese Cabbage

Abstract Plant microRNAs (miRNAs) are noncoding and endogenous key regulators that play significant functions in regulating plant responses to stress, and plant growth and development. Heat stress is a critical abiotic stress that reduces the yield and quality of flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee). However, limited information is available on whether miRNAs are involved in the regulation of heat stress in B. campestris. A high-throughput sequencing approach was used to identify novel and conserved heat-responsive miRNAs in four small RNA libraries of flowering Chinese cabbage using leaves collected at 0 h, 1 h, 6 h and 12 h after a 38 °C heat-stress treatment. The analysis identified 41 conserved miRNAs (belonging to 19 MIR families), of which MIR156, MIR159, MIR168, MIR171 and MIR1885 had the most abundant molecules. Prediction and evaluation of novel miRNAs using the unannotated reads resulted in 18 candidate miRNAs. Differential expression analysis showed that most of the identified miRNAs were downregulated in heat-treated groups. To better understand functional importance, bioinformatic analysis predicted 432 unique putative target miRNAs involved in cells, cell parts, catalytic activity, cellular processes and abiotic stress responses. Furthermore, the Kyoto Encyclopedia of Genes and Genomes maps of flowering Chinese cabbage identified the significant role of miRNAs in stress adaptation and stress tolerance, and in several mitogen-activated protein kinases signaling pathways including cell death. This work presents a comprehensive study of the miRNAs for understanding the regulatory mechanisms and their participation in the heat stress of flowering Chinese cabbage.

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