Biology subjects

Celton, J.-M.

Publications and source records attributed to Celton, J.-M..

4 recordsLinked to original sources

bioRxiv2026

LTR transposable elements contribution to the apple genome, methylome and transcriptome evolution in Malus domestica

The whole genome duplication (WGD) shared by apple (Malus domestica) and pear (Pyrus communis) dated 27 Mya was followed 21 Mya by a burst of transposable elements (TE), making these organisms a prime choice for studying the evolution of duplicated genes. In this study, we conducted a meta-analysis of 149 RNA-Seq datasets and focused on gene pairs for which one ohnolog was systematically under-expressed compared to its duplicate. To understand this systematic differential expression, we investigated the TE environment (TE type, TE divergence and insertion position) of these genes pairs and found that under-expressed genes in apple and pear were enriched in recent Class I LTR TE Copia and Gypsy insertions in their immediate genic environment. In apple, we identified a quantitative relationship between the number of LTR insertions in the genes' environments and the level of differential expression among pairs of ohnologs. Finally, we found that these under-expressed genes displayed either hypomethylated or hypermethylated profiles in their sequence in the CG and CHG contexts.

evolutionary biology↗

bioRxiv2019

Divergent DNA methylation signatures of juvenile seedlings grafts and adult apple trees

Plants are continuously exposed to environmental perturbations. Outcrossing annual plants can adapt rapidly to these changes via sexual mating and DNA mutations. However, perennial and clonally reproducing plants may have developed particular mechanisms allowing them to adapt to these changes and transmit this information to their offspring. It has been proposed that the mechanisms allowing this plasticity of response could come in the form of epigenetic marks that would evolve throughout a plants lifetime and modulate gene expression. To study these mechanisms, we used apple (Malus domestica) as a model perennial and clonally propagated plant. First, we investigated the DNA methylation patterns of mature trees compared to juvenile seedlings. While we did not observe a drastic genome-wide change in DNA methylation levels, we found clear changes in DNA methylation patterns localized in regions enriched in genes involved in photosynthesis. Transcriptomic analysis showed that genes involved in this pathway were overexpressed in seedlings. Secondly, we compared global DNA methylation of a newly grafted plant to its mother tree to assess if acquired epigenomic marks were transmitted via grafting. We identified clear changes, albeit showing weaker DNA methylation differences. Our results show that a majority of DNA methylation patterns from the tree are transmitted to newly grafted plants albeit with specific local differences. Both the epigenomic and transcriptomic data indicate that grafted plants are at an intermediate phase between an adult tree and seedling and inherit part of the epigenomic history of their mother tree.

plant biology↗

bioRxiv2019

Pyrus Communis chromosome scale assembly

We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII Long read sequencing (PacBio), Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. A total of 496.9 million bases (Mb) corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 chromosomes of the pear genome. About 50% (247 Mb) of the genome consists of repetitive sequences. Comparison with previous assemblies of Pyrus communis and Pyrus x bretschneideri confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted.

bioinformatics↗

bioRxiv2019

Pseudo-chromosome length genome assembly of a double haploid ‘Bartlett’ pear (Pyrus communis L.)

We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII Long read sequencing (PacBio), Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. A total of 496.9 million bases (Mb) corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 chromosomes of the pear genome. About 50% (247 Mb) of the genome consists of repetitive sequences. Comparison with previous assemblies of Pyrus communis. and Pyrus x bretschneideri confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted.

plant biology↗