Biology subjects

Carbonell-Bejerano, P.

Publications and source records attributed to Carbonell-Bejerano, P..

9 recordsLinked to original sources

bioRxiv2025

Minimizing detection bias of somatic mutations in a highly heterozygous oak genome

Somatic mutations are particularly relevant for long-lived organisms. Sources of somatic mutations include imperfect DNA repair, replication errors, and exogenous damage such as ultraviolet radiation. A previous study estimated a surprisingly low number of somatic mutations in a 234-year-old individual of the pedunculate oak (Quercus robur), known as the Napoleon Oak. It has been suggested that the true number of somatic mutations was underestimated due to gaps in the reference genome and too conservative filtering of potential mutations. We therefore generated new high-fidelity long-read data for the Napoleon Oak (n = 12) to produce both a pseudo-haploid genome assembly and a partially phased diploid assembly. The high heterozygosity allowed for complete reconstruction of phased and gapless centromeres for 22 of the 24 chromosomes. On the other hand, the high heterozygosity posed challenges for short-read alignments. Use of only the pseudo-haploid assembly as a reference led to potential misalignments, while use of only the diploid assembly reduced variant detection sensitivity. Since most somatic mutations are layer-specific, the observed frequency is expected relatively low, even where all cells in a single layer contain a specific mutation. To address this challenge, we employed a read assignment strategy, selecting the appropriate reference sequence (pseudo-haploid or diploid) based on alignment score and mapping quality. Ultimately, we identified 198 high-confidence somatic mutations, compared with 17 somatic mutations identified before with the same set of short reads. Our approach thus increased the total estimated annual mutation rate by a factor of five.

genomics↗

bioRxiv2024

In a nutshell: pistachio genome and kernel development

Pistachio is a sustainable nut crop with exceptional climate resilience and nutritional value. To advance pistachios as a future food source and a model system for hard-shelled fruits, we generated a chromosome-scale reference genome of the most widely grown pistachio cultivar (Pistacia vera Kerman) and a spatiotemporal developmental study of the hull, shell, and kernel. Our study defined four distinct stages of pistachio growth and maturation by integrating tissue-level physiological and molecular data from thousands of nuts across twenty-four time points over three growing seasons. Transcriptional and metabolic changes in the kernel elucidate molecular pathways governing nutritional quality, such as the accumulation of unsaturated fatty acids, which are vital for shelf-life and dietary value. This work yields new knowledge and resources that will inform other woody crops and facilitate further improvement of pistachio as a globally significant, sustainable, and nutritious crop.

plant biology↗

bioRxiv2023

Diploid genome assembly of the Malbec grapevine cultivar enables haplotype-aware analysis of transcriptomic differences underlying clonal phenotypic variation

1.To preserve their varietal attributes, established grapevine cultivars (Vitis vinifera L. ssp. vinifera) must be clonally propagated, due to their highly heterozygous genomes. Malbec is a France-originated cultivar appreciated for producing high-quality wines, and is the offspring of cultivars Prunelard and Magdeleine Noire des Charentes. Here, we have built a diploid genome assembly of Malbec, after trio binning of PacBio long reads into the two haploid complements inherited from either parent. After haplotype-aware deduplication and corrections, complete assemblies for the two haplophases were obtained with very low haplotype switch-error rate (<0.025). The haplophases alignment identified >25% of polymorphic regions. Gene annotation including RNA-seq transcriptome assembly and ab initio prediction evidence resulted in similar gene model numbers for both haplophases. The annotated diploid assembly was exploited in the transcriptomic comparison of four clonal accessions of Malbec that exhibited variation in berry composition traits. Analysis of the ripening pericarp transcriptome using either haplophases as reference yielded similar results, although some differences were observed. Particularly, among the differentially expressed genes identified only with the Magdeleine-inherited haplotype as reference, we observed an over-representation of hypothetically hemizygous genes. The higher berry anthocyanin content of clonal accession 595 was associated with increased abscisic acid responses, possibly leading to the observed overexpression of phenylpropanoid metabolism genes and deregulation of genes associated to abiotic stress response. Overall, the results highlight the importance of producing diploid assemblies to fully represent the genomic diversity of highly heterozygous woody crop cultivars and to unveil the molecular bases of clonal phenotypic variation.

genomics↗

bioRxiv2022

Report of mutation biases mirroring selection in Arabidopsis thaliana unlikely to be entirely due to variant calling errors

It has recently been proposed that the uneven distribution of epigenomic features might facilitate reduced mutation rate in constrained regions of the Arabidopsis thaliana genome, even though previous work had shown that it would be difficult for reduced mutation rates to evolve on a gene-by-gene basis. A solution to Lynchs equations for the barrier imposed by genetic drift on the evolution of targeted hypomutation can, however, come from epigenomic features that are enriched in certain portions of the genome, for example, coding regions of essential genes, and which simultaneously affect mutation rate. Such theoretical considerations draw on what is known about DNA repair guided by epigenomic features. A recent publication challenged these conclusions, because several mutation data sets that support a lower mutation rate in constrained regions suffered from variant calling errors. Here we show that neither homopolymer errors nor elevated mutation rates at transposable elements are likely to entirely explain reported mutation rate biases. Observed mutation biases are also supported by a meta-analysis of several independent germline mutation data sets, with complementary experimental data providing a mechanistic basis for reduced mutation rate in genes and specifically in essential genes. Finally, models derived from the drift-barrier hypothesis demonstrate that mechanisms linking DNA repair to chromatin marks and other epigenomic features can evolve in response to second-order selection on emergent mutation biases.

evolutionary biology↗

bioRxiv2022

Relationship between biased mutagenesis and H3K4me1-targeted DNA repair in plants

Mutation is the ultimate source of genetic variation. Mutation rate variability has been observed within plant genomes, but the underlying mechanisms have been unclear. We previously found that mutations occur less often in functionally constrained regions of the genome in Arabidopsis thaliana and that this mutation rate reduction is predicted by H3K4me1, a histone modification found in the gene bodies of actively expressed and evolutionarily conserved genes in plants. We reanalyzed de novo germline single base substitutions in fast neutron irradiated mutation accumulation lines in Kitaake rice (Oryza sativa) and found the same reduction in mutations associated with H3K4me1, gene bodies, and constrained genes as in A. thaliana, suggesting conserved mechanisms for mutation reduction in plants. Here, we characterize a model of targeted DNA repair to explain these observations; PDS5C and MSH6 DNA repair-related proteins target H3K4me1 through their Tudor domains, resulting in nearby DNA experiencing elevated repair. Experimental data and in-silico modeling support the high affinity of the Tudor domain for H3K4me1 in both proteins, and that this affinity is conserved between plant species. ChIP-seq data from PDS5C confirms its localization to conserved and low mutation rate genome regions. Somatic and germline mutations observed by deep sequencing of wild-type and MSH6 knockout lines confirm that MSH6 preferentially repairs gene bodies and H3K4me1-enriched regions. These findings inspire further research to characterize the origins of mechanisms of targeted DNA repair in eukaryotes and their consequences on tuning the evolutionary trajectories of genomes.

genomics↗

bioRxiv2022

Pushing the limits of HiFi assemblies reveals centromere diversity between two Arabidopsis thaliana genomes

Although long-read sequencing can often enable chromosome-level reconstruction of genomes, it is still unclear how one can routinely obtain gapless assemblies. In the model plant Arabidopsis thaliana, other than the reference accession Col-0, all other accessions de novo assembled with long-reads until now have used PacBio continuous long reads (CLR). Although these assemblies sometimes achieved chromosome-arm level contigs, they inevitably broke near the centromeres, excluding megabases of DNA from analysis in pan-genome projects. Since PacBio high-fidelity (HiFi) reads circumvent the high error rate of CLR technologies, albeit at the expense of read length, we compared a CLR assembly of accession Ey15-2 to HiFi assemblies of the same sample performed by five different assemblers starting from subsampled data sets, allowing us to evaluate the impact of coverage and read length. We found that centromeres and rDNA clusters are responsible for 71% of contig breaks in the CLR scaffolds, while relatively short stretches of GA/TC repeats are at the core of >85% of the unfilled gaps in our best HiFi assemblies. Since the HiFi technology consistently enabled us to reconstruct gapless centromeres and 5S rDNA clusters, we demonstrate the value of the approach by comparing these previously inaccessible regions of the genome between two A. thaliana accessions.

genomics↗

bioRxiv2021

Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates

Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field-based model species for genetics and epigenetics. The availability of a high quality reference genome is vital for understanding pennycress physiology and for clarifying its evolutionary history within the Brassicaceae. Here, we present a chromosome-level genome assembly of var. MN106-Ref with improved gene annotation, and use it to investigate gene structure differences between two accessions (MN108 and Spring32-10) that are highly amenable to genetic transformation. We describe small RNAs, pseudogenes, and transposable elements, and highlight tissue specific expression and methylation patterns. Resequencing of forty wild accessions provides insights into genome-wide genetic variation as well as QTL regions for flowering time and a seedling color phenotype. Altogether, these data will serve as a tool for pennycress improvement in general and for translational research across the Brassicaceae.

plant biology↗

bioRxiv2020

Clonal propagation history shapes the intra-cultivar genetic diversity in Malbec grapevines

Grapevine (Vitis vinifera L.) cultivars are clonally propagated to preserve their varietal attributes. However, novel genetic variation still accumulates due to somatic mutations. Aiming to study the potential impact of clonal propagation history on grapevines intra-cultivar genetic diversity, we have focused on Malbec. This cultivar is appreciated for red wines elaboration, it was originated in Southwestern France and introduced into Argentina during the 1850s. Here, we generated whole-genome resequencing data for four Malbec clones with different historical backgrounds. A stringent variant calling procedure was established to identify reliable clonal polymorphisms, additionally corroborated by Sanger sequencing. This analysis retrieved 941 single nucleotide variants (SNVs), occurring among the analyzed clones. Based on a set of validated SNVs, a genotyping experiment was custom-designed to survey Malbec genetic diversity. We successfully genotyped 214 samples and identified 14 different clonal genotypes, that clustered into two genetically divergent groups. Group-Ar was driven by clones with a long history of clonal propagation in Argentina, while Group-Fr was driven by clones that have longer remained in Europe. Findings show the ability of such approaches for clonal genotypes identification in grapevines. In particular, we provide evidence on how human actions may have shaped Malbec extant genetic diversity pattern.

genomics↗

bioRxiv2020

Mutation bias shapes gene evolution in Arabidopsis thaliana

Classical evolutionary theory maintains that mutation rate variation between genes should be random with respect to fitness 1-4 and evolutionary optimization of genic mutation rates remains controversial 3,5. However, it has now become known that cytogenetic (DNA sequence + epigenomic) features influence local mutation probabilities 6, which is predicted by more recent theory to be a prerequisite for beneficial mutation rates between different classes of genes to readily evolve 7. To test this possibility, we used de novo mutations in Arabidopsis thaliana to create a high resolution predictive model of mutation rates as a function of cytogenetic features across the genome. As expected, mutation rates are significantly predicted by features such as GC content, histone modifications, and chromatin accessibility. Deeper analyses of predicted mutation rates reveal effects of introns and untranslated exon regions in distancing coding sequences from mutational hotspots at the start and end of transcribed regions in A. thaliana. Finally, predicted coding region mutation rates are significantly lower in genes where mutations are more likely to be deleterious, supported by numerous estimates of evolutionary and functional constraint. These findings contradict neutral expectations that mutation probabilities are independent of fitness consequences. Instead they are consistent with the evolution of lower mutation rates in functionally constrained loci due to cytogenetic features, with important implications for evolutionary biology8.

evolutionary biology↗