Differential Expression of Maize and Teosinte microRNAs under Submergence, Drought, and Alternated Stress

Submergence and drought stresses are the main constraints to crop production worldwide. MicroRNAs (miRNAs) are known to play a major role in plant response to various stresses. In this study, we analyzed the expression of maize and teosinte miRNAs by high-throughput sequencing of small RNA libraries in maize and its ancestor teosinte (Zea mays ssp. parviglumis), under submergence, drought, and alternated stress. We found that the expression patterns of 67 miRNA sequences representing 23 miRNA families in maize and other plants were regulated by submergence or drought. miR159a, miR166b, miR167c, and miR169c were downregulated by submergence in both plants but more severely in maize. miR156k and miR164e were upregulated by drought in teosinte but downregulated in maize. Small RNA profiling of teosinte subject to alternate treatments with drought and submergence revealed that submergence as the first stress attenuated the response to drought, while drought being the first stress did not alter the response to submergence. The miRNAs identified herein, and their potential targets, indicate that control of development, growth, and response to oxidative stress could be crucial for adaptation and that there exists evolutionary divergence between these two subspecies in miRNA response to abiotic stresses.

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Computational and analytical framework for small RNA profiling by high-throughput sequencing

RNA ◽

10.1261/rna.1473809 ◽

2009 ◽

Vol 15 (5) ◽

pp. 992-1002 ◽

Cited By ~ 93

Author(s):

N. Fahlgren ◽

C. M. Sullivan ◽

K. D. Kasschau ◽

E. J. Chapman ◽

J. S. Cumbie ◽

...

Keyword(s):

High Throughput ◽

Small Rna ◽

High Throughput Sequencing ◽

Analytical Framework ◽

Rna Profiling

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Identification of microRNAs Responding to Aluminium, Cadmium and Salt Stresses in Barley Roots

Plants ◽

10.3390/plants10122754 ◽

2021 ◽

Vol 10 (12) ◽

pp. 2754

Author(s):

Liuhui Kuang ◽

Jiahua Yu ◽

Qiufang Shen ◽

Liangbo Fu ◽

Liyuan Wu

Keyword(s):

Genetic Diversity ◽

Gene Ontology ◽

Salt Stress ◽

Small Rna ◽

Abiotic Stresses ◽

Molecular Mechanisms ◽

High Throughput Sequencing ◽

Expression Patterns ◽

Barley Cultivar ◽

Golden Promise

Plants are frequently exposed to various abiotic stresses, including aluminum, cadmium and salinity stress. Barley (Hordeum vulgare) displays wide genetic diversity in its tolerance to various abiotic stresses. In this study, small RNA and degradome libraries from the roots of a barley cultivar, Golden Promise, treated with aluminum, cadmium and salt or controls were constructed to understand the molecular mechanisms of microRNAs in regulating tolerance to these stresses. A total of 525 microRNAs including 198 known and 327 novel members were identified through high-throughput sequencing. Among these, 31 microRNAs in 17 families were responsive to these stresses, and Gene Ontology (GO) analysis revealed that their targeting genes were mostly highlighted as transcription factors. Furthermore, five (miR166a, miR166a-3p, miR167b-5p, miR172b-3p and miR390), four (MIR159a, miR160a, miR172b-5p and miR393) and three (miR156a, miR156d and miR171a-3p) microRNAs were specifically responsive to aluminum, cadmium and salt stress, respectively. Six miRNAs, i.e., miR156b, miR166a-5p, miR169a, miR171a-5p, miR394 and miR396e, were involved in the responses to the three stresses, with different expression patterns. A model of microRNAs responding to aluminum, cadmium and salt stresses was proposed, which may be helpful in comprehensively understanding the mechanisms of microRNAs in regulating stress tolerance in barley.

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Identification and Characterization of Known and Novel MicroRNAs in Five Tissues of Wax Gourd (Benincasa hispida) Based on High-Throughput Sequencing

Applied Sciences ◽

10.3390/app112110068 ◽

2021 ◽

Vol 11 (21) ◽

pp. 10068

Author(s):

Jinqiang Yan ◽

Min Wang ◽

Wenrui Liu ◽

Dasen Xie ◽

Xiaoming He ◽

...

Keyword(s):

High Throughput ◽

Small Rna ◽

High Throughput Sequencing ◽

Target Genes ◽

Expression Patterns ◽

Small Rna Sequencing ◽

Specific Expression ◽

Nac Transcription Factors ◽

Benincasa Hispida ◽

Wax Gourd

MicroRNAs (miRNAs) are endogenous single-stranded non-coding small RNAs of 20-24 nucleotides and play important roles in many plant biological and metabolic processes. Wax gourd is an important vegetable of Cucurbitacea family, with great economic and medicinal value. Although miRNAs have been extensively studied in model plant species, less is known in wax gourd (Benincasa hispida). In this study, in order to identify miRNAs in wax groud, five independent small RNA libraries were constructed using leaf, root, stem, flower, and fruit of B227. Based on high-throughput Illumina deep sequencing. In total, 422 known and 409 novel miRNAs were identified from five libraries. Comparative analysis revealed that many miRNAs were differentially expressed among different tissues, indicating tissue-specific expression of some miRNAs. qRT-PCR verified the reliability of small RNA sequencing results. Furthermore, miRNAs with similar expression patterns among five tissues were clustered into the same profile, among which many miRNAs were found with relatively high expression in the fruit of wax gourd. MiR164-x had the highest expression in fruit than in other tissues and many NAC transcription factors were predicted as its target genes. We propose that miR164 might regulate fruit development by forming miR164-NAC module in wax gourd. Taken together, this study provides the first global miRNAs profiling of wax gourd, and lays the foundation for understanding the regulatory roles of miRNAs in the growth and development processes of wax gourd.

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Small RNA Library Construction for High-Throughput Sequencing

Methods in Molecular Biology - PIWI-Interacting RNAs ◽

10.1007/978-1-62703-694-8_16 ◽

2013 ◽

pp. 195-208 ◽

Cited By ~ 10

Author(s):

Jon McGinn ◽

Benjamin Czech

Keyword(s):

High Throughput ◽

Small Rna ◽

High Throughput Sequencing ◽

Library Construction ◽

Small Rna Library

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Millet Could Be both a Weed and Serve as a Virus Reservoir in Crop Fields

Plants ◽

10.3390/plants9080954 ◽

2020 ◽

Vol 9 (8) ◽

pp. 954

Author(s):

György Pasztor ◽

Zsuzsanna Galbacs N. ◽

Tamas Kossuth ◽

Emese Demian ◽

Erzsebet Nadasy ◽

...

Keyword(s):

Mosaic Virus ◽

Seed Dormancy ◽

High Throughput ◽

Small Rna ◽

Diagnostic Method ◽

High Throughput Sequencing ◽

Infection Risk ◽

Viral Diseases ◽

Crop Fields ◽

Special Control

Millet is a dangerous weed in crop fields. A lack of seed dormancy helps it to spread easily and be present in maize, wheat, and other crop fields. Our previous report revealed the possibility that millet can also play a role as a virus reservoir. In that study, we focused on visual symptoms and detected the presence of several viruses in millet using serological methods, which can only detect the presence of the investigated pathogen. In this current work, we used small RNA high-throughput sequencing as an unbiased virus diagnostic method to uncover presenting viruses in randomly sampled millet grown as a volunteer weed in two maize fields, showing stunting, chlorosis, and striped leaves. Our results confirmed the widespread presence of wheat streak mosaic virus at both locations. Moreover, barley yellow striate mosaic virus and barley virus G, neither of which had been previously described in Hungary, were also identified. As these viruses can cause severe diseases in wheat and other cereals, their presence in a weed implies a potential infection risk. Our study indicates that the presence of millet in fields requires special control to prevent the emergence of new viral diseases in crop fields.

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Technological advancements and their importance for nematode identification

SOIL ◽

10.5194/soil-2-257-2016 ◽

2016 ◽

Vol 2 (2) ◽

pp. 257-270 ◽

Cited By ~ 6

Author(s):

Mohammed Ahmed ◽

Melanie Sapp ◽

Thomas Prior ◽

Gerrit Karssen ◽

Matthew Alan Back

Keyword(s):

High Throughput ◽

Crop Production ◽

Large Scale ◽

High Throughput Sequencing ◽

Biological Indicators ◽

Rapid Identification ◽

Community Studies ◽

Terrestrial Environments ◽

Traditional Taxonomy ◽

Sequencing Platforms

Abstract. Nematodes represent a species-rich and morphologically diverse group of metazoans known to inhabit both aquatic and terrestrial environments. Their role as biological indicators and as key players in nutrient cycling has been well documented. Some plant-parasitic species are also known to cause significant losses to crop production. In spite of this, there still exists a huge gap in our knowledge of their diversity due to the enormity of time and expertise often involved in characterising species using phenotypic features. Molecular methodology provides useful means of complementing the limited number of reliable diagnostic characters available for morphology-based identification. We discuss herein some of the limitations of traditional taxonomy and how molecular methodologies, especially the use of high-throughput sequencing, have assisted in carrying out large-scale nematode community studies and characterisation of phytonematodes through rapid identification of multiple taxa. We also provide brief descriptions of some the current and almost-outdated high-throughput sequencing platforms and their applications in both plant nematology and soil ecology.

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