Response of Downy Oak (Quercus pubescens Willd.) to Climate Change: Transcriptome Assembly, Differential Gene Analysis and Targeted Metabolomics

Mévy, Jean-Philippe; Loriod, Béatrice; Liu, Xi; Corre, Erwan; Torres, Magali; Büttner, Michael; Haguenauer, Anne; Reiter, Ilja M.; Fernandez, Catherine; Gauquelin, Thierry

doi:10.3390/plants9091149

Cited by 8 publications

(13 citation statements)

References 52 publications

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“…Additionally, about 71% and 57% of the unitranscripts and predicted proteins were successfully assigned to genes by BLASTx and BLASTp searches against the UniProtKB/Swiss-Prot database (Table S9) which is similar to previous mangrove study and higher than that of another tree species; Downy Oak (Quercus pubescens Willd.) [38].…”

Section: Discussionmentioning

confidence: 99%

De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree (Bruguiera gymnorhiza)

Miryeganeh

Saze

2021

IJMS

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Their high adaptability to difficult coastal conditions makes mangrove trees a valuable resource and an interesting model system for understanding the molecular mechanisms underlying stress tolerance and adaptation of plants to the stressful environmental conditions. In this study, we used RNA sequencing (RNA-Seq) for de novo assembling and characterizing the Bruguiera gymnorhiza (L.) Lamk leaf transcriptome. B. gymnorhiza is one of the most widely distributed mangrove species from the biggest family of mangroves; Rhizophoraceae. The de novo assembly was followed by functional annotations and identification of individual transcripts and gene families that are involved in abiotic stress response. We then compared the genome-wide expression profiles between two populations of B. gymnorhiza, growing under different levels of stress, in their natural habitats. One population living in high salinity environment, in the shore of the Pacific Ocean- Japan, and the other population living about one kilometre farther from the ocean, and next to the estuary of a river; in less saline and more brackish condition. Many genes involved in response to salt and osmotic stress, showed elevated expression levels in trees growing next to the ocean in high salinity condition. Validation of these genes may contribute to future salt-resistance research in mangroves and other woody plants. Furthermore, the sequences and transcriptome data provided in this study are valuable scientific resources for future comparative transcriptome research in plants growing under stressful conditions.

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Section: Discussionmentioning

confidence: 99%

De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree (Bruguiera gymnorhiza)

Miryeganeh

Saze

2021

IJMS

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“…The transcriptome assembly contained more than 90% of genes represented at the available orthologue groups ( Table 1 ). Furthermore, about 60% of the unitranscripts and 57.5% of the predicted proteins were assigned to genes, by searches through BLASTx and BLASTp against the UniProtKB/Swiss-Prot database ( Table S10 ) which is similar to the previous mangrove study [ 8 ] and higher than that of other tree species such as Downy Oak ( Quercus pubescens ) [ 29 ].…”

Section: Discussionmentioning

confidence: 69%

The First De Novo Transcriptome Assembly and Transcriptomic Dynamics of the Mangrove Tree Rhizophora stylosa Griff. (Rhizophoraceae)

Miryeganeh

Saze

2021

IJMS

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Mangroves are salt-tolerant plant species that grow in coastal saline water and are adapted to harsh environmental conditions. In this study, we de novo assembled and functionally annotated the transcriptome of Rhizophora stylosa, the widely distributed mangrove from the largest mangrove family (Rhizophoraceae). The final transcriptome consists of 200,491 unigenes with an average length, and N50 of 912.7 and 1334 base pair, respectively. We then compared the genome-wide expression profiles between the two morphologically distinct natural populations of this species growing under different levels of salinity depending on their distance from the ocean. Among the 200,491 unigenes, 40,253 were identified as differentially expressed between the two populations, while 15,741 and 24,512 were up- and down-regulated, respectively. Functional annotation assigned thousands of upregulated genes in saline environment to the categories related to abiotic stresses such as response to salt-, osmotic-, and oxidative-stress. Validation of those genes may contribute to a better understanding of adaptation in mangroves species. This study reported, for the first time, the transcriptome of R. stylosa, and the dynamic of it in response to salt stress and provided a valuable resource for elucidation of the molecular mechanism underlying the salt stress response in mangroves and other plants that live under stress.

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“…The priority in current research into Quercus spp. is the response to stresses and climate change conditions, and this has been approached using a comparative transcriptomic approach in different species [ 90 , 91 , 92 , 93 ]. A comparison of the least drought-tolerant deciduous Q. robur , quite tolerant deciduous Q. pubescens , and the most tolerant evergreen Q. ilex revealed common and species-specific responses [ 94 ].…”

Section: The “Omics” and Their Integration With Other Approaches (How)mentioning

confidence: 99%

“…A few studies have dealt with responses to drought and climate change conditions. In a four-year Q. pubescens drought trial, GC-MS metabolomics revealed that tolerance implicates the tricarboxylic acid cycle shunt through the glyoxylate pathway, and the galactose metabolism by reducing carbohydrate storage and increasing proteolytic activity [ 92 ]. Changes in the phenolic pattern in Q. suber during drought and recovery treatments have been reported [ 144 ], and the process of metabolite resorption from plant leaves during senescence has been evaluated under drought and warming conditions in Q. rubra [ 145 ].…”

Section: The “Omics” and Their Integration With Other Approaches (How)mentioning

confidence: 99%

Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How

Maldonado‐Alconada

Castillejo

Rey

et al. 2022

IJMS

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The holm oak (Quercus ilex L.) is the dominant tree species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem, “dehesa.” It has been, since the prehistoric period, an important part of the Iberian population from a social, cultural, and religious point of view, providing an ample variety of goods and services, and forming the basis of the economy in rural areas. Currently, there is renewed interest in its use for dietary diversification and sustainable food production. It is part of cultural richness, both economically (tangible) and environmentally (intangible), and must be preserved for future generations. However, a worrisome degradation of the species and associated ecosystems is occurring, observed in an increase in tree decline and mortality, which requires urgent action. Breeding programs based on the selection of elite genotypes by molecular markers is the only plausible biotechnological approach. To this end, the authors’ group started, in 2004, a research line aimed at characterizing the molecular biology of Q. ilex. It has been a challenging task due to its biological characteristics (long life cycle, allogamous, high phenotypic variability) and recalcitrant nature. The biology of this species has been characterized following the central dogma of molecular biology using the omics cascade. Molecular responses to biotic and abiotic stresses, as well as seed maturation and germination, are the two main objectives of our research. The contributions of the group to the knowledge of the species at the level of DNA-based markers, genomics, epigenomics, transcriptomics, proteomics, and metabolomics are discussed here. Moreover, data are compared with those reported for Quercus spp. All omics data generated, and the genome of Q. ilex available, will be integrated with morphological and physiological data in the systems biology direction. Thus, we will propose possible molecular markers related to resilient and productive genotypes to be used in reforestation programs. In addition, possible markers related to the nutritional value of acorn and derivate products, as well as bioactive compounds (peptides and phenolics) and allergens, will be suggested. Subsequently, the selected molecular markers will be validated by both genome-wide association and functional genomic analyses.

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Response of Downy Oak (Quercus pubescens Willd.) to Climate Change: Transcriptome Assembly, Differential Gene Analysis and Targeted Metabolomics

Cited by 8 publications

References 52 publications

De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree (Bruguiera gymnorhiza)

De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree (Bruguiera gymnorhiza)

The First De Novo Transcriptome Assembly and Transcriptomic Dynamics of the Mangrove Tree Rhizophora stylosa Griff. (Rhizophoraceae)

Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How

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