The draft genome sequence of cork oak

Ramos, António Marcos; Usié, Ana; Barbosa, Pedro; Barros, Pedro M.; Capote, Tiago; Chaves, Inês; Simões, Fernanda; Abreu, Isabel A.; Carrasquinho, Isabel; Faro, Carlos; Guimarães, Joana Bagoin; Mendonça, Diogo; Nóbrega, Filomena; Rodrigues, L.; Saibo, Nelson J. M.; Varela, Maria Carolina; Egas, Conceição; Matos, José; Miguel, Celia María Gonzalo; Oliveira, M. Margarida; Ricardo, Cândido Pinto; Gonçalves, Sónia

doi:10.1038/sdata.2018.69

Cited by 99 publications

(124 citation statements)

References 39 publications

(49 reference statements)

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“…But microevolution—comprising processes at the population level— leaves an imprint in the phylogeny; when such impressions persist, they can often be detected using topological methods that may be sensitive even to introgression along internal phylogenetic branches (Eaton et al ., 2015; Solís-Lemus & Ané, 2016; McVay et al ., 2017b). With multiple Fagaceae genomes now becoming available (Staton et al ., 2015; Plomion et al ., 2016, 2018; Sork et al ., 2016; Ramos et al ., 2018), we may soon be able to detangle the mosaic history of oaks and understand what story each gene tells. The current study makes clear that the phylogeny we unravel will neither be unitary nor told by a small subset of the genome, as the regions of the genome capturing the divergence history for one clade are not the regions capturing the divergence history of another.…”

Section: Resultsmentioning

confidence: 99%

Genomic landscape of the global oak phylogeny

Hipp

Manos

Hahn

et al. 2019

Preprint

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41• The tree of life is highly reticulate, with the history of population divergence buried amongst 42 phylogenies deriving from introgression and lineage sorting. In this study, we test the 43 hypothesis that there are regions of the oak (Quercus, Fagaceae) genome that are broadly 44 informative about phylogeny and investigate global patterns of oak diversity. 45• We utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 46 individuals representing ca. 250 oak species to infer a time-calibrated phylogeny of the world's 47• The support we find for the phylogeny contrasts with high genomic heterogeneity in 56 phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may 57 in fact depend on the gene flow that shapes the oak genome. 58 59

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Section: Resultsmentioning

confidence: 99%

Genomic landscape of the global oak phylogeny

Hipp

Manos

Hahn

et al. 2019

Preprint

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“…Complete sequences were retrieved from the cork oak genome version 1.0 (Ramos et al, 2018), except for QsATXR3 . Protein structure was analyzed using NCBI-CD 2 (Marchler-Bauer et al, 2016) and SMART searches 3 (Letunic and Bork, 2017).…”

Section: Methodsmentioning

confidence: 99%

Cork Oak Young and Traumatic Periderms Show PCD Typical Chromatin Patterns but Different Chromatin-Modifying Genes Expression

et al. 2018

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Plants are subjected to adverse conditions being outer protective tissues fundamental to their survival. Tree stems are enveloped by a periderm made of cork cells, resulting from the activity of the meristem phellogen. DNA methylation and histone modifications have important roles in the regulation of plant cell differentiation. However, studies on its involvement in cork differentiation are scarce despite periderm importance. Cork oak periderm development was used as a model to study the formation and differentiation of secondary protective tissues, and their behavior after traumatic wounding (traumatic periderm). Nuclei structural changes, dynamics of DNA methylation, and posttranslational histone modifications were assessed in young and traumatic periderms, after cork harvesting. Lenticular phellogen producing atypical non-suberized cells that disaggregate and form pores was also studied, due to high impact for cork industrial uses. Immunolocalization of active and repressive marks, transcription analysis of the corresponding genes, and correlations between gene expression and cork porosity were investigated. During young periderm development, a reduction in nuclei area along with high levels of DNA methylation occurred throughout epidermis disruption. As cork cells became more differentiated, whole nuclei progressive chromatin condensation with accumulation in the nuclear periphery and increasing DNA methylation was observed. Lenticular cells nuclei were highly fragmented with faint 5-mC labeling. Phellogen nuclei were less methylated than in cork cells, and in lenticular phellogen were even lower. No significant differences were detected in H3K4me3 and H3K18ac signals between cork cells layers, although an increase in H3K4me3 signals was found from the phellogen to cork cells. Distinct gene expression patterns in young and traumatic periderms suggest that cork differentiation might be under specific silencing regulatory pathways. Significant correlations were found between QsMET1, QsMET2, and QsSUVH4 gene expression and cork porosity. This work evidences that DNA methylation and histone modifications play a role in cork differentiation and epidermis induced tension-stress. It also provides the first insights into chromatin dynamics during cork and lenticular cells differentiation pointing to a distinct type of remodeling associated with cell death.

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“…robur, Plomion et al 2016Q. robur, Plomion et al , 2018; Q. suber, Ramos et al 2018;Fagus sylvatica, Mishra et al 2018), and these provide great prospects for future evolutionary genomics studies (Petit et al 2013;Parent et al 2015;Cannon et al 2018;Lesur et al 2018).…”

Section: Introductionmentioning

confidence: 99%

The loops of the N-SH2 binding cleft do not serve as allosteric switch in SHP2 activation

Anselmi¹,

Hub

2018

Preprint

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In the post-genomics era, non-model species like most Fagaceae still lack operational diversity resources for population genomics studies. We completed the analyses of Sanger sequences produced from over 800 gene fragments covering ~530 kb across the genic partition of European oaks in a range-wide sampling of 25 individuals (11 Quercus petraea, 13 Q. robur, one Q. ilex as an outgroup). Regions targeted represented broad functional categories potentially involved in species ecological preferences, and a random set of genes.Using a high-quality dedicated pipeline, we provide a detailed characterization of over 14500 polymorphisms, including ~12500 SNPs -218 being triallelic-, over 1500 insertion-deletions, and ~200 novel di-and tri-nucleotide SSR loci. This catalog also includes various summary statistics within and among species, gene ontology information, and standard formats to assist loci choice for genotyping projects. The distribution of nucleotide diversity and differentiation across genic regions are also described for the first time in those species (mean  close to ~0.0049 in Q. petraea and to ~0.0045 in Q. robur across random regions, and mean F ST ~0.13 across SNPs). Robust patterns were observed which emphasize a slightly but significantly higher diversity in Q. petraea, across a random gene set and in the abiotic stress functional category, and a heterogeneous landscape of both diversity and differentiation. These patterns are discussed in the context of both species documented introgression history despite strong reproductive barriers. The quality, representativity in terms of species genomic diversity, and usefulness of the resources provided are discussed for possible applications in medium scale landscape ecology projects, and as a reference resource for validation purposes in larger-scale re-sequencing projects. These are preferentially recommended in oaks in contrast to SNP array development, given the large nucleotide variation and low levels of linkage disequilibrium revealed.

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The draft genome sequence of cork oak

Cited by 99 publications

References 39 publications

Genomic landscape of the global oak phylogeny

Genomic landscape of the global oak phylogeny

Cork Oak Young and Traumatic Periderms Show PCD Typical Chromatin Patterns but Different Chromatin-Modifying Genes Expression

The loops of the N-SH2 binding cleft do not serve as allosteric switch in SHP2 activation

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