Biology subjects

SOW, M. D.

Publications and source records attributed to SOW, M. D..

4 recordsLinked to original sources

bioRxiv2026

Chromosome-scale assembly of the Cupressus sempervirens genome unravels new insights into the evolutionary history of conifers

Conifers, which comprise nearly two-thirds of extant gymnosperm species, are ecologically and economically important but remain genomically understudied because of their exceptionally large, repeat-rich genomes. Here, we report a chromosome-level assembly of the haploid genome of Cupressus sempervirens generated using PacBio HiFi reads and scaffolded with optical and genetic maps. The 10 Gb assembly shows exceptional contiguity for a conifer genome (contig N50 = 29.8 Mb) and was organized into 11 pseudomolecules. Iso-Seq-supported annotation identified 42,980 protein-coding genes. Repetitive elements account for over 80% of the genome, with LTR retrotransposons alone representing 52.5%. Transposable elements (TE) are pervasive in both intergenic and genic regions and have a major impact on gene architecture: TE insertions within introns generate ultra-long introns, often exceeding 100 kb, and drive gene size expansion. Analyses of LTR retrotransposon dynamics indicate that genome enlargement in C. sempervirens was driven not by recent transpositional bursts, but by the long-term accumulation and incomplete removal of ancient LTR retrotransposons. Consistent with this pattern, paleogenomic reconstruction across representative gymnosperms found no evidence of whole-genome duplication in the Cupressus lineage. This reference genome provides a valuable resource for studying conifer genome evolution, gene structure, and traits of agronomic and ecological interest, including cypress pollinosis.

genomics↗

bioRxiv2026

Ancestral Genome Reconstruction.

AGR, for Ancestral Genome Reconstruction, is an automatic publicly available and open-source pipeline to infer paleogenomes from modern species genome comparisons exploiting the concept of inter-species chromosomal synteny relationships hierarchical clustering that can be used to unveil how ancestral genomes, genes, sequences and functions have been shaped during million years of present-day plant evolution.

genomics↗

bioRxiv2025

Drought-Induced Epigenetic Memory in the cambium of Poplar Trees persists and primes future stress responses

Understanding how perennial plants such as trees perceive, integrate and memorize repeated environmental stresses like water deficit is crucial in the context of climate change. We investigated short-term and trans-annual memory of water deficit in cambium derived tissues of poplars (Populus spp.) using two contrasting genotypes and four genetically modified epitypes with altered DNA methylation machinery. We found persistent changes in hormone profiles, gene expression and DNA methylation one week after stress relief, consistent with the definition of a multi-layered molecular short-term stress memory. These signatures revealed distinct adaptive strategies between genotypes and marked variability between epitypes, demonstrating that both genetic and epigenetic backgrounds drive stress memory. Trees exposed to water deficit in Year 1 displayed distinct physiological and molecular responses upon re-exposure in Year 2. The more sensitive genotype showed greater molecular plasticity, whereas the more tolerant genotype exhibited higher stability. A limited set of candidate genes was reactivated upon re-exposure together with persistent drought-induced CG methylation changes, supporting a role in long-term stress imprinting and potential priming. Our findings highlight the vascular cambium as a key persistent reservoir for short- to trans-annual stress memory in trees. They suggest that mitotically stable CG DNA methylation dynamics, shaped by genetic predisposition and acting through cis- and trans-regulatory routes, help fine-tune growth-survival strategies over longer time frames. This contrasts with the predominantly short-term stress memory described in annual species. These insights open perspectives for harnessing epigenetic variation in tree breeding and management under increasing drought frequency.

plant biology↗

bioRxiv2025

DNA methylation around transcription start sites not globally associated with transcription in natural and synthetic hexaploid wheat

Epigenetic mechanisms including DNA methylation are assumed to play crucial roles in the maintenance of genome integrity, regulation of gene expression and development, and their increasing exploitation in breeding applications is anticipated. However, the relationship between DNA methylation and gene expression remains ambiguous and difficult to generalize. Here we explored the hypothesized causality between the level of transcription and cytosine methylation at the 5 end of genes (around transcription start sites and start codons) in relation to whole-genome duplication in natural and synthetic allohexaploid wheat (Triticum/Aegilops complex). Using transcriptomes and a sequence capture protocol coupled with bisulfite sequencing, we observed sometimes significant, but overall very weak associations between gene expression and 5 end methylation on a genome-wide scale. In synthetic wheat allohexaploids, global methylation differences between subgenomes are not triggered by the polyploidization, as the subgenome patterns are rather faithfully inherited from parents. A small number of genes differentially methylated between the parents and synthetics was consistently recovered in reciprocal synthetics and subsequent generations. Differences in transcription between homeologs are not clearly associated with 5 end methylation in either natural or synthetic wheat. Overall, allopolyploidization triggers only minor methylation changes around transcription start sites and start codons of nascent wheat allopolyploids, and these are not statistically associated with differential expression. Although there is a measurable methylation difference between expressed and non-expressed genes, our results do not support the hypothesis that 5 end DNA methylation is engaged in the regulation of gene expression in natural and synthetic wheat. SIGNIFICANCE STATEMENTWhile agenome shock hypothesis predicts extensive transcriptomic and epigenetic reorganization after polyploidization, DNA methylation patterns around transcription start sites are generally undisturbed in nascent wheat allohexaploids. Although this stability might indicate importance for gene regulation, a clear relationship between DNA methylation and transcription was not observed either on a genome-wide scale, or among triads of homeologous genes.

genomics↗