Identification of novel small ncRNAs in pollen of tomato

Bokszczanin, K.; Krezdorn, Nicolas; Fragkostefanakis, Sotirios; Müller, Sören; Rycak, Lukas; Chen, Yuanyuan; Hoffmeier, Klaus; Kreutz, Jutta; Paupière, Marine J.; Chaturvedi, Palak; Iannacone, Rina; Müller, Florian; Bostan, Hamed; Chiusano, Maria Luisa; Scharf, Klaus‐Dieter; Rotter, Björn; Schleiff, Enrico; Winter, Peter

doi:10.1186/s12864-015-1901-x

Cited by 28 publications

(25 citation statements)

References 115 publications

(115 reference statements)

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“…RNA was extracted by miRVana small RNA extraction kit (Ambion Life technologies, Carlsbad, California, USA), from caryopses harvested 8 days after anthesis. After quality control (Bioanalyzer, Agilent, Santa Clara, California, USA), small RNA libraries (two biological replicates for each condition) were processed as described in [52] for sncRNA libraries with TrueQuant technology for elimination of PCR bias. The fraction of 140-160 bp was size-selected by preparative polyacrylamide gel electrophoresis for Illumina HiSeq2000 sequencing of the small RNA fraction of 17-40 bp including the miRNA.…”

Section: Small Rna Sequencingmentioning

confidence: 99%

Increase of DNA Methylation at the HvCKX2.1 Promoter by Terminal Drought Stress in Barley

Surdonja¹,

Eggert

Hajirezaei

et al. 2017

Epigenomes

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Terminal drought stress during grain filling is the major abiotic factor that limits crop yield in barley. The mother plant acclimates to the environment and perceives signals that result in a change of the physiological state within the grain and therefore affect the seed development and germination of the next generation. Small regulatory RNAs have been described to be involved in plant drought stress response by suppressing the respective target genes. Based on their origin and function, these small RNAs are classified as micro RNAs (miRNA), short interfering RNAs (siRNA) or heterochromatic small interfering RNA (hc-siRNA). In addition, 24mer sized hc-siRNAs are associated with RNA directed DNA methylation (RdDM) and transcriptional gene silencing (TGS). The analysis of hc-siRNA by small RNA sequencing in barley caryopses after imposition of terminal drought stress allowed the identification of stress specific 24mers. Based on the sequence homology of the siRNAs to the promoter region of CYTOKININ-OXIDASE 2.1 (HvCKX2.1), this putative target gene was selected for further investigation. Terminal drought stress leads to an increased level of DNA methylation at the HvCKX2.1 promoter and the seeds derived from drought stressed plants showed faster shoot emergence. Accumulation of cytokinin ribosides, which are the known substrates of cytokinin-oxidase, can explain the observed phenotype of faster shoot emergence from seeds of drought stressed mother plants. Analysis of transgenic plants with modulated levels of abscisic acid (ABA) in the grain confirmed the ABA/drought stress responsive ProHvCKX2.1 methylation and correlation with shoot emergence speed.

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Section: Small Rna Sequencingmentioning

confidence: 99%

Increase of DNA Methylation at the HvCKX2.1 Promoter by Terminal Drought Stress in Barley

Surdonja¹,

Eggert

Hajirezaei

et al. 2017

Epigenomes

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“…However, the miRNAs involved in this process in tomato plants remain poorly understood. Only four differentially expressed novel miRNAs have been identified from the pollen of tomato plants upon 38 °C treatment for 1 h [ 30 ]. No study has been performed to identify the heat-responsive miRNAs in stamens and pistils of tomato plants.…”

Section: Introductionmentioning

confidence: 99%

Identification and expression profiling of microRNAs involved in the stigma exsertion under high-temperature stress in tomato

Pan

Zheng

et al. 2017

BMC Genomics

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BackgroundAutogamy in cultivated tomato varieties is a derived trait from wild type tomato plants, which are mostly allogamous. However, environmental stresses can cause morphological defects in tomato flowers and hinder autogamy. Under elevated temperatures, tomato plants usually exhibit the phenotype of stigma exsertion, with severely hindered self-pollination and fruit setting, whereas the inherent mechanism of stigma exsertion have been hitherto unknown. Numerous small RNAs (sRNAs) have been shown to play significant roles in plant development and stress responses, however, none of them have been studied with respect to stamen and pistil development under high-temperature conditions. We investigated the associations between stigma exsertion and small RNAs using high-throughput sequencing technology and molecular biology approaches.ResultsSixteen sRNA libraries of Micro-Tom were constructed from plants stamen and pistil samples and sequenced after 2 d and 12 d of exposure to heat stress, respectively, from which a total of 110 known and 84 novel miRNAs were identified. Under heat stress conditions, 34 known and 35 novel miRNAs were differentially expressed in stamens, and 20 known and 10 novel miRNAs were differentially expressed in pistils. GO and KEGG pathway analysis showed that the predicted target genes of differentially expressed miRNAs were significantly enriched in metabolic pathways in both stamen and pistil libraries. Potential miRNA-target cleavage cascades that correlated with the regulation of stigma exsertion under heat stress conditions were found and validated through qRT-PCR and RLM-5′ RACE.ConclusionOverall, a global spectrum of known and novel miRNAs involved in tomato stigma exsertion and induced by high temperatures were identified using high-throughput sequencing and molecular biology approaches, laying a foundation for revealing the miRNA-mediated regulatory network involved in the development of tomato stamens and pistils under high-temperature conditions.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4238-9) contains supplementary material, which is available to authorized users.

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“…Indeed, gene expression studies by RNA-seq permitted to identify around 150 different pollen-expressed genes in different plant species associated with a range of different functions, including cell wall metabolism, cytoskeleton and signaling (Honys and Twell 2003;Palanivelu and Tsukamoto 2012;Rutley and Twell 2015). Moreover, RNA-seq also shed light on the composition and expression profile of pollen small RNAs (Bokszczanin et al 2015;Borges et al 2011;GrantDownton et al 2009;Li et al 2013;Lu et al 2015;Slotkin et al 2009;Zhang et al 2009). …”

Section: Next Generation Sequencing (Ngs) Datamentioning

confidence: 96%

“…In Bokszczanin et al (2015), novel small nuclear RNAs (sncRNAs) from tomato tetrads, post-meiotic and mature pollen, expressed under control or heat stress conditions were detected. A specific reference Web site that describes this collection is available at http://www.cab.unina.it/mirna-pollen.…”

Section: Next Generation Sequencing (Ngs) Datamentioning

confidence: 98%

Bioinformatics resources for pollen

et al. 2016

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Bioinformatics for Pollen. Pollen plays a key role in crop production, and its development is the most delicate phase in reproduction. Different metabolic pathways are involved in pollen development, and changes in the level of some metabolites, as well as responses to stress, are correlated with the reduction in pollen viability, leading consequently to a decrease in the fruit production. However, studies on pollen may be hard because gamete development and fertilization are complex processes that occur during a short window of time. The rise of the so-called -omics sciences provided key strategies to promote molecular research in pollen tissues, starting from model organisms and moving to increasing number of species. An integrated multi-level approach based on investigations from genomics, transcriptomics, proteomics and metabolomics appears now feasible to clarify key molecular processes in pollen development and viability. To this aim, bioinformatics has a fundamental role for data production and analysis, contributing varied and ad hoc methodologies, endowed with different sensitivity and specificity, necessary for extracting added-value information from the large amount of molecular data achievable. Bioinformatics is also essential for data management, organization, distribution and integration in suitable resources. This is necessary to catch the biological features of the pollen tissues and to design effective approaches to identifying structural or functional properties, enabling the modeling of the major involved processes in normal or in stress conditions. In this review, we provide an overview of the available bioinformatics resources for pollen, ranging from raw data collections to complete databases or platforms, when available, which include data and/or results from -omics efforts on the male gametophyte. Perspectives in the fields will also be described.

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Identification of novel small ncRNAs in pollen of tomato

Cited by 28 publications

References 115 publications

Increase of DNA Methylation at the HvCKX2.1 Promoter by Terminal Drought Stress in Barley

Increase of DNA Methylation at the HvCKX2.1 Promoter by Terminal Drought Stress in Barley

Identification and expression profiling of microRNAs involved in the stigma exsertion under high-temperature stress in tomato

Bioinformatics resources for pollen

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