Recent transcriptomics advances and emerging applications in food science

Valdés, Alberto; Ibáñez, Clara; Simó, Carolina; García‐Cañas, Virginia

doi:10.1016/j.trac.2013.06.014

Cited by 58 publications

(32 citation statements)

References 131 publications

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“…Despite their value, these approaches have several important limitations. In fact, EST technology has been hampered by its low coverage, high error rate and high cost while the microarray-based analysis faces the constraints of specific probe design and RNA-variants detection (Valdés et al, 2013). As an alternative, current RNA sequencing (RNA-seq) technologies offer increased specificity and sensitivity for the enhanced detection of genes, transcripts, and differential expression profiling, which has permitted gene function to be monitored at the level of the entire genome (Wang et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Transcriptional Responses in Root and Leaf of Prunus persica under Drought Stress Using RNA Sequencing

et al. 2016

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Prunus persica L. Batsch, or peach, is one of the most important crops and it is widely established in irrigated arid and semi-arid regions. However, due to variations in the climate and the increased aridity, drought has become a major constraint, causing crop losses worldwide. The use of drought-tolerant rootstocks in modern fruit production appears to be a useful method of alleviating water deficit problems. However, the transcriptomic variation and the major molecular mechanisms that underlie the adaptation of drought-tolerant rootstocks to water shortage remain unclear. Hence, in this study, high-throughput sequencing (RNA-seq) was performed to assess the transcriptomic changes and the key genes involved in the response to drought in root tissues (GF677 rootstock) and leaf tissues (graft, var. Catherina) subjected to 16 days of drought stress. In total, 12 RNA libraries were constructed and sequenced. This generated a total of 315 M raw reads from both tissues, which allowed the assembly of 22,079 and 17,854 genes associated with the root and leaf tissues, respectively. Subsets of 500 differentially expressed genes (DEGs) in roots and 236 in leaves were identified and functionally annotated with 56 gene ontology (GO) terms and 99 metabolic pathways, which were mostly associated with aminobenzoate degradation and phenylpropanoid biosynthesis. The GO analysis highlighted the biological functions that were exclusive to the root tissue, such as “locomotion,” “hormone metabolic process,” and “detection of stimulus,” indicating the stress-buffering role of the GF677 rootstock. Furthermore, the complex regulatory network involved in the drought response was revealed, involving proteins that are associated with signaling transduction, transcription and hormone regulation, redox homeostasis, and frontline barriers. We identified two poorly characterized genes in P. persica: growth-regulating factor 5 (GRF5), which may be involved in cellular expansion, and AtHB12, which may be involved in root elongation. The reliability of the RNA-seq experiment was validated by analyzing the expression patterns of 34 DEGs potentially involved in drought tolerance using quantitative reverse transcription polymerase chain reaction. The transcriptomic resources generated in this study provide a broad characterization of the acclimation of P. persica to drought, shedding light on the major molecular responses to the most important environmental stressor.

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Section: Introductionmentioning

confidence: 99%

Transcriptional Responses in Root and Leaf of Prunus persica under Drought Stress Using RNA Sequencing

et al. 2016

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“…The cDNA is then stained by fluorescent compounds, usually Cy3 and Cy5 cyanines (one for the controls and one for evaluated samples), and hybridization occurs with the complementary probe, followed by substrate washing and photography by a high‐resolution scanner (Valdés et al . ). The gene expression is measured by the fluorescent intensity of the two dye‐labelled targets, that emit signals proportional to their concentrations (Storhoff et al .…”

Section: Molecular Biology Identification Techniques and Their Applicmentioning

confidence: 97%

“…This technique can be used to measure the relative abundance of transcripts from two or more samples to thousands of genes simultaneously (Valdés et al . ). Among the advantages of this technique are good sensitivity, reproducibility and high yield, which allow a large number of samples to be screened at the same time.…”

Section: Molecular Biology Identification Techniques and Their Applicmentioning

confidence: 97%

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Application of molecular tools to elucidate the microbiota of seafood

2018

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The aim of this review is to present the methodologies currently applied to identify microbiota and pathogens transmitted to humans through seafood consumption, focusing on molecular techniques and pointing out their importance, advantages, disadvantages and applicability. Knowledge of available techniques allows researchers to identify which technique best fits their expectations. With such discernment, it will be possible to infer which disadvantages will be present and, therefore, not interfering with the final result. Two methodologies can be employed for this purpose, dependent and independent cultures. However, the dependent culture has certain limitations that can be solved through the independent cultivation techniques, such as PCR, PFGE and NGS, especially through the sequencing of the 16S rRNA region, providing a complete view of microbial diversity. These have revolutionized microbiological knowledge, mainly because they allow for the identification of uncultivable micro-organisms, which represent a substantial portion of total micro-organisms, making it possible to elucidate not yet described taxa which may display pathogenic potential, besides quantifying microbial communities, microbiota genetics, translated proteins and produced metabolites. In addition, transcriptomic and metabolomic techniques also allow for the evaluation of possible impacts that microbial communities may create in their environment, as well as the determination of potential pathogenicity to humans.

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“…limitation and the increasing requirements from administrative authorities for control of food safety and quality with scientifically based guarantees, the development of novel and complementary non-targeted analytical methodologies is highly advisable. Non-targeted methods combined with suitable chemometric tools have the potential to improve the breadth of traditional targeted analysis and open up new prospects for novel applications, providing the opportunity to explore formerly unanswered problems relevant to food science [2][3][4]. A good example of this revolutionary view of food analysis is the emerging discipline of foodomics.…”

Section: Introductionmentioning

confidence: 99%

The role of direct high-resolution mass spectrometry in foodomics

et al. 2015

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Foodomics has been defined as a global discipline in which advanced analytical techniques and bioinformatics are combined to address different questions in food science and nutrition. There is a growing number of works on the development and application of non-targeted omics methods in foodomics, which reflects that this emerging discipline is already considered by the scientific community to be a valuable approach to assess food safety, quality, and traceability as well as for the study of the links between food and health. As a result, there is a clear need for more rapid, high-throughput MS approaches for developing and applying non-targeted studies. Nowadays, direct MS analysis is one of the main choices to achieve high throughput, generating a set of information from the largest possible number of samples in a fast and straightforward way. The use of high- and ultrahigh-resolution MS greatly improves the analytical performance and offers a good combination of selectivity and sensitivity. By using a range of methods for direct sample introduction/desorption/ionization, high-throughput and non-target analysis of a variety of samples can be obtained in a few seconds by HRMS analysis. In this review, a general overview is presented of the main characteristics of direct HRMS-based approaches and their principal applications in foodomics.

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Recent transcriptomics advances and emerging applications in food science

Cited by 58 publications

References 131 publications

Transcriptional Responses in Root and Leaf of Prunus persica under Drought Stress Using RNA Sequencing

Transcriptional Responses in Root and Leaf of Prunus persica under Drought Stress Using RNA Sequencing

Application of molecular tools to elucidate the microbiota of seafood

The role of direct high-resolution mass spectrometry in foodomics

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