Holm Oak (Quercus ilex) Transcriptome. De novo Sequencing and Assembly Analysis

Guerrero‐Sanchez, Víctor M.; Maldonado‐Alconada, Ana M.; Amil-Ruíz, Francisco; Jorrín‐Novo, Jesús V.

doi:10.3389/fmolb.2017.00070

Cited by 33 publications

(42 citation statements)

References 27 publications

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“…The first transcriptome of Q. ilex has recently been reported. For that reason, the Illumina Hiseq 2500 platform was employed to analyze the tissue mix sample, resulting in 119889 contigs, and 31973 Blast2GO annotated transcripts ( Guerrero-Sanchez et al, 2017 ). The number of annotated sequences have been increased to 62628 after a UniRef90 database search through Sma3s software ( Muñoz-Mérida et al, 2014 ; Casimiro-Soriguer et al, 2017 ).…”

Section: Resultsmentioning

confidence: 99%

“…Total RNA was extracted from the frozen homogenized pool tissue following the procedure previously reported by ( Guerrero-Sanchez et al, 2017 ). 50 mg pooled fresh tissue according the procedures previously set up in our laboratory for Q. ilex samples was employed ( Echevarría-Zomeño et al, 2012 ).…”

Section: Methodsmentioning

confidence: 99%

“…Nevertheless, the work of our group and others, has contributed to acquiring the knowledge on this species, focusing on natural variability ( Valero-Galván et al, 2011 ; Akcan et al, 2017 ), seed germination and seedling growth ( Echevarría-Zomeño et al, 2009 ; Romero-Rodríguez et al, 2015 ), physiology ( Valero-Galván et al, 2012a ), and biotic and abiotic stress-responses ( Echevarría-Zomeño et al, 2009 ; Sghaier-Hammami et al, 2013 ; Sardans et al, 2014 ; Simova-Stoilova et al, 2015 ). The above publications, provide fragmented information, mostly derived from classical biochemical approaches and, to a much lesser extent, those of proteomics ( Valero-Galván et al, 2011 ; Romero-Rodríguez et al, 2014 , 2015 ) transcriptomics ( Guerrero-Sanchez et al, 2017 ), or metabolomics ( Rakić et al, 2006 ; Rabhi et al, 2016 ; Vinha et al, 2016a ; López-Hidalgo, 2017 ), but lacking a validation and effective integration of the different molecular multilevels.…”

Section: Introductionmentioning

confidence: 99%

“…In this direction, trying to fill this gap with the use of the available high-throughput – omics, its combination and also the implementation of required methodology, we hoped to gain knowledge on the chemical composition and metabolism of the Q. ilex tree species, its variability among and within populations, the effect on endogenous ones and their environmental factors, and the search for molecular markers to select elite genotypes. The lack of information available in public databases on the Holm oak genome, transcriptome ( Guerrero-Sanchez et al, 2017 ), or proteome ( Romero-Rodríguez et al, 2014 ) and the absence of standardized laboratory and analytical protocols make this approach a real challenge.…”

Section: Introductionmentioning

confidence: 99%

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A Multi-Omics Analysis Pipeline for the Metabolic Pathway Reconstruction in the Orphan Species Quercus ilex

et al. 2018

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Holm oak (Quercus ilex) is the most important and representative species of the Mediterranean forest and of the Spanish agrosilvo-pastoral “dehesa” ecosystem. Despite its environmental and economic interest, Holm oak is an orphan species whose biology is very little known, especially at the molecular level. In order to increase the knowledge on the chemical composition and metabolism of this tree species, the employment of a holistic and multi-omics approach, in the Systems Biology direction would be necessary. However, for orphan and recalcitrant plant species, specific analytical and bioinformatics tools have to be developed in order to obtain adequate quality and data-density before to coping with the study of its biology. By using a plant sample consisting of a pool generated by mixing equal amounts of homogenized tissue from acorn embryo, leaves, and roots, protocols for transcriptome (NGS-Illumina), proteome (shotgun LC-MS/MS), and metabolome (GC-MS) studies have been optimized. These analyses resulted in the identification of around 62629 transcripts, 2380 protein species, and 62 metabolites. Data are compared with those reported for model plant species, whose genome has been sequenced and is well annotated, including Arabidopsis, japonica rice, poplar, and eucalyptus. RNA and protein sequencing favored each other, increasing the number and confidence of the proteins identified and correcting erroneous RNA sequences. The integration of the large amount of data reported using bioinformatics tools allows the Holm oak metabolic network to be partially reconstructed: from the 127 metabolic pathways reported in KEGG pathway database, 123 metabolic pathways can be visualized when using the described methodology. They included: carbohydrate and energy metabolism, amino acid metabolism, lipid metabolism, nucleotide metabolism, and biosynthesis of secondary metabolites. The TCA cycle was the pathway most represented with 5 out of 10 metabolites, 6 out of 8 protein enzymes, and 8 out of 8 enzyme transcripts. On the other hand, gaps, missed pathways, included metabolism of terpenoids and polyketides and lipid metabolism. The multi-omics resource generated in this work will set the basis for ongoing and future studies, bringing the Holm oak closer to model species, to obtain a better understanding of the molecular mechanisms underlying phenotypes of interest (productive, tolerant to environmental cues, nutraceutical value) and to select elite genotypes to be used in restoration and reforestation programs, especially in a future climate change scenario.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A Multi-Omics Analysis Pipeline for the Metabolic Pathway Reconstruction in the Orphan Species Quercus ilex

et al. 2018

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“…They also help forest pathologists to detect, identify, and monitor forest pathogens and sequence their entire genome, examine global distributions of forest pathogens and their hosts, assess the diversity and structure of host and pathogen populations, and evaluate the structure and function of genes as well as their levels of expression within species and within communities (Kaul et al 2016;Plomion et al 2016;Ross-Davis et al 2013). Recently, these new technologies, such as NGS, have been applied for oak species to evaluate their phylogeny and evolutionary relationships (e.g., Alexander and Woeste 2014;Fitz-Gibbon et al 2017;Schroeder et al 2016;Sork et al 2016a;San Jose-Maldia et al 2017), explore structure of different populations (Degner 2014), study their molecular and physiological mechanisms for biotic and abiotic stress tolerance (e.g., Magalhães 2015;Guerrero-Sanchez et al 2017;Plomion et al 2016;Rellstab et al 2016;Sork et al 2016b;Usié et al 2017), characterize chloroplast genomes of oaks , and to examine plant-microbe interactions in these trees (e.g., Caravaca et al 2015;Fernandes et al 2014;Moore et al 2015;He et al 2016;Koide et al 2017).…”

Section: Introductionmentioning

confidence: 99%

Rapid and economical protocols for genomic and metagenomic DNA extraction from oak (Quercus brantii Lindl.)

Ahmadi

Kowsari

Azadfar

et al. 2018

Annals of Forest Science

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& Key message Two new efficient, fast and low-cost metagenomic DNA extraction methods were developed for different Persian oak tissues (leaf, stem, root, and rhizospheric) and soil samples. & Context The new "omics" studies on the genus Quercus are of importance to help finding efficient strategies for overcoming environmental challenges, and to do this, presence of efficient DNA extraction protocols for different Quercus species are very critical. & Aims The objective of the present study was to develop new efficient methods for extraction of metagenomic DNA (mDNA) from of Persian oak (Quercus brantii Lindl.) tissues. & Methods The efficiency of two newly developed mDNA extraction methods, including indirect SDS-based (ISB or concentrate method) and one spin column-based method (SCB) were compared to that of two classical direct methods, including CTABbased and SDS-based methods, and two commercial mDNA extraction kits. & Results The maximum average yield of mDNA for all samples (leaf, stem, root, bulk, and rhizospheric soils) was obtained by SCB (258 ng/μl) and ISB (189 ng/μl) methods, respectively. Successful PCR amplification for 16SrRNA and ITS sequence was consistently observed for ISB, SCB, and kit-extracted mDNAs, which confirmed the high purity of mDNA extracted by these methods. The new methods showed more than 96% quantitative PCR efficiency, and partial restriction digestion and metagenomic library construction confirmed the high efficiency of the newly developed methods. & Conclusion It could be concluded that two new protocols enhanced efficiency (yield, purity, and cost) of mDNA extraction from different tissues of Persian oak.

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Mass spectrometry‐based forest tree metabolomics

Rodrigues

Miguel

Chaves

et al. 2019

Mass Spectrometry Reviews

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Research in forest tree species has advanced slowly when compared with other agricultural crops and model organisms, mainly due to the long‐life cycles, large genome sizes, and lack of genomic tools. Additionally, trees are complex matrices, and the presence of interferents (e.g., oleoresins and cellulose) challenges the analysis of tree tissues with mass spectrometry (MS)‐based analytical platforms. In this review, advances in MS‐based forest tree metabolomics are discussed. Given their economic and ecological significance, particular focus is given to Pinus, Quercus, and Eucalyptus forest tree species to better understand their metabolite responses to abiotic and biotic stresses in the current climate change scenario. Furthermore, MS‐based metabolomics technologies produce large and complex datasets that require expertize to adequately manage, process, analyze, and store the data in dedicated repositories. To ensure that the full potential of forest tree metabolomics data are translated into new knowledge, these data should comply with the FAIR principles (i.e., Findable, Accessible, Interoperable, and Re‐usable). It is essential that adequate standards are implemented to annotate metadata from forest tree metabolomics studies as is already required by many science and governmental agencies and some major scientific publishers. © 2019 John Wiley & Sons Ltd. Mass Spec Rev 40:126–157, 2021.

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Holm Oak (Quercus ilex) Transcriptome. De novo Sequencing and Assembly Analysis

Cited by 33 publications

References 27 publications

A Multi-Omics Analysis Pipeline for the Metabolic Pathway Reconstruction in the Orphan Species Quercus ilex

A Multi-Omics Analysis Pipeline for the Metabolic Pathway Reconstruction in the Orphan Species Quercus ilex

Rapid and economical protocols for genomic and metagenomic DNA extraction from oak (Quercus brantii Lindl.)

Mass spectrometry‐based forest tree metabolomics

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