Maritime Pine Genomics in Focus

Sterck, Lieven; María, Nuria de; Cañas, Rafael A.; Miguel, Marina de; Perdiguero, Pedro; Raffin, Annie; Budde, Katharina B.; López-Hinojosa, Miriam; Cantón, Francisco R.; Rodrigues, Andreia S.; Morcillo, Marian; Hurel, Agathe; Vélez, María Dolores; Torre, Fernando N. de la; Modesto, Inês; Manjarrez, Lorenzo Federico; Pascual, María Belén; Alves, Ana; Mendoza-Poudereux, Isabel; Díaz, Marta Callejas; Pizarro, Alberto; El-Azaz, Jorge; Hernandez‐Escribano, Laura; Guevara, M. Ángeles; Majada, Juan; Salse, Jérôme; Grivet, Delphine; Bouffier, Laurent; Raposo, Rosa; Torre, Amanda R. De La; Zas, Rafael; Cabezas, José Antonio; Ávila, Concepción; Trontin, Jean-François; Sanchez, Léopoldo; Alı́a, Ricardo; Arrillaga, Isabel; González‐Martínez, Santiago C.; Miguel, Celia María Gonzalo; Cánovas, Francisco M.; Plomion, Christophe; Dı́az-Sala, Carmen; Cervera, María Teresa

doi:10.1007/978-3-030-93390-6_5

Cited by 4 publications

(6 citation statements)

References 330 publications

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“…DNA methylation (5mC) is currently the epigenetic modification, which can most easily be monitored at both gene and genome levels during memory formation. In the context of climate change, the possibility for early temperature priming during embryogenesis to stimulate plant phenotypic plasticity (e.g., increased tolerance to drought and heat stress) through epigenetic stress memory has great potential in plants, especially in trees with long life cycle and delayed reproductive maturity (Liu et al 2021, 2022, Sterck et al 2022, Zhu et al 2023). If transgenerational stress memory currently appears to be out of reach for trees in an acceptable time frame, intergenerational stress memory can be considered for (epi)genetic breeding applications, including in conifers (Liu and He 2020).…”

Section: Discussionmentioning

confidence: 99%

“…Global changes were also observed in pine following temperature sensing during SE initiation or maturation suggesting that DNA methylation could contribute to the establishment of an epigenetic stress memory (Castander-Olarieta et al 2020, Pereira et al 2021. Despite increasing availability of genomic resources in trees (Plomion et al 2016, Sterck et al 2022, evidence for temperature effect on genes involved in DNA methylation (Yakovlev et al 2016), and the possibility for bisulfite sequencing, it is still unknown what is the extent of 5mC imprinting during conifer embryogenesis as a result of both developmental transition and temperature sensing effects.…”

Section: Introductionmentioning

confidence: 99%

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Epigenetic memory of temperature sensed during somatic embryo maturation in 2-year-old maritime pine trees

Trontin,

Sow,

Delaunay

et al. 2024

Preprint

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Embryogenesis is a brief but potentially critical phase in the tree life cycle for adaptive phenotypic plasticity. Using somatic embryogenesis in maritime pine, we found that temperature during the maturation phase affects embryo development and post-embryonic tree growth for up to three years. We examined whether this somatic stress memory could stem from temperature- and/or development-induced changes in DNA methylation. To do this, we developed a 200 Mb custom sequence capture bisulfite analysis of genes and promoters to identify differentially methylated cytosines (DMCs) between temperature treatments (18, 23, and 28°C) and developmental stages (immature and cotyledonary embryos, shoot apical meristem of 2-year-old plants) and investigate if these differences can be mitotically transmitted from embryonic to post-embryonic development (epigenetic memory). We revealed a high prevalence of temperature-induced DMCs in genes (8-14%) compared to promoters (less than 1%) in all 3 cytosine contexts. Developmental DMCs showed a comparable pattern but only in the CG context, and with a high trend towards hypo-methylation, particularly in the promoters. A high percentage of DMCs induced by developmental transitions were found memorized in genes (up to 45-50%) and promoters (up to 90%). In contrast, temperature-induced memory was lower and confined to genes after both embryonic (up to 14%) and post-embryonic development (up to 8%). Using stringent criteria, we identified ten genes involved in defense responses and adaptation, embryo development and chromatin regulation that are candidates for the establishment of a persistent epigenetic memory of temperature sensed during embryo maturation in maritime pine.Graphical abstract

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Epigenetic memory of temperature sensed during somatic embryo maturation in 2-year-old maritime pine trees

Trontin,

Sow,

Delaunay

et al. 2024

Preprint

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“…Promoter region analysis of PpGS1b.1 and PpGS1b.2 . For promoter comparison, 1916 and 2408 nucleotides upstream of start codon of PpGS1b.1 and PpGS1b.2 were recovered from genomic data, respectively (Sterck et al, 2022). A. Sequences alignment of the promoter region.…”

Section: Short Legends For Supporting Informationmentioning

confidence: 99%

A new gene encoding a cytosolic glutamine synthetase in pine is linked to developing tissues

Valderrama‐Martín

Ortigosa

Aledo

et al. 2022

Preprint

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The enzyme glutamine synthetase (EC 6.3.1.2) is mainly responsible for the incorporation of inorganic nitrogen into organic molecules in plants. In the present work, a new pineGS1(PpGS1b.2) gene was identified, showing a high sequence identity with theGS1b.1gene previously characterized in conifers. Phylogenetic analysis revealed that the presence ofPpGS1b.2is restricted to the generaPinusandPiceaand is not found in other conifers. Gene expression data suggest a putative role ofPpGS1b.2in plant development, similar to other GS1b genes from angiosperms, suggesting evolutionary convergence. The characterization of GS1b.1 and GS1b.2 at the structural, physicochemical, and kinetic levels has shown differences even though they have high sequence homology. Alterations in the kinetic characteristics produced by the site-directed mutagenesis approach carried out in this work strongly suggest an implication of amino acids at positions 264 and 267 in the active center of pine GS1b.1 and GS1b.2. Therefore, the amino acid differences between GS1b.1 and GS1b.2 would support the functioning of both enzymes to meet distinct plant needs.

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“…In these areas maritime pine constitutes extensive forests being mainly located in Portugal, Spain, and France where it has been used for raw material obtention such as timber, pulp, and resin. This tree is a model species for research on functional genomics, drought resistance or nitrogen nutrition and metabolism in conifers ( Sterck et al., 2022 ; Ávila et al., 2022 ). Maritime pine is a plant with a preference for ammonium over nitrate nutrition, which promotes an increase in biomass accumulation, especially in the roots where a higher number of lateral roots has been observed ( Ortigosa et al., 2020 ; Ortigosa et al., 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Epitranscriptome changes triggered by ammonium nutrition regulate the proteome response of maritime pine roots

et al. 2022

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Epitranscriptome constitutes a gene expression checkpoint in all living organisms. Nitrogen is an essential element for plant growth and development that influences gene expression at different levels such as epigenome, transcriptome, proteome, and metabolome. Therefore, our hypothesis is that changes in the epitranscriptome may regulate nitrogen metabolism. In this study, epitranscriptomic modifications caused by ammonium nutrition were monitored in maritime pine roots using Oxford Nanopore Technology. Transcriptomic responses mainly affected transcripts involved in nitrogen and carbon metabolism, defense, hormone synthesis/signaling, and translation. Global detection of epitranscriptomic marks was performed to evaluate this posttranscriptional mechanism in un/treated seedlings. Increased N6-methyladenosine (m6A) deposition in the 3’-UTR was observed in response to ammonium, which seems to be correlated with poly(A) lengths and changes in the relative abundance of the corresponding proteins. The results showed that m6A deposition and its dynamics seem to be important regulators of translation under ammonium nutrition. These findings suggest that protein translation is finely regulated through epitranscriptomic marks likely by changes in mRNA poly(A) length, transcript abundance and ribosome protein composition. An integration of multiomics data suggests that the epitranscriptome modulates responses to nutritional, developmental and environmental changes through buffering, filtering, and focusing the final products of gene expression.

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Maritime Pine Genomics in Focus

Cited by 4 publications

References 330 publications

Epigenetic memory of temperature sensed during somatic embryo maturation in 2-year-old maritime pine trees

Epigenetic memory of temperature sensed during somatic embryo maturation in 2-year-old maritime pine trees

A new gene encoding a cytosolic glutamine synthetase in pine is linked to developing tissues

Epitranscriptome changes triggered by ammonium nutrition regulate the proteome response of maritime pine roots

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