Biology subjects

Fuentes, R. R.

Publications and source records attributed to Fuentes, R. R..

3 recordsLinked to original sources

bioRxiv2026

MeiCOfi: Meiotic CrossOver Finder in haploid, diploid, polyploid and hyper-recombinant genomes

During the meiotic cell division, homologous chromosomes pair and recombine, leading to large reciprocal exchanges of genetic information. In most species, meiotic crossovers (COs) are crucial for normal chromosome segregation and they generate genetic diversity, which can be acted upon by natural selection in wild populations or by breeders to combine desirable traits in a genome. Identifying the position and frequency of COs is therefore essential in both classical genetics studies and breeding programmes. However, a computational tool capable of accurately detecting COs across diverse contexts, including varying marker densities, genome size and structure, recombination rate, and ploidy, remains lacking. We developed MeiCOfi (Meiotic CrossOver Finder) to detect meiotic crossover events at high-resolution from low-coverage genome sequencing data. We evaluated it using data from Arabidopsis thaliana, rice, barley and both intra- and inter-specific tomato hybrids, encompassing a wide range of genome complexities and marker densities. It reliably detects crossovers in hyper-recombinant A. thaliana with up to 62 CO per backcross offspring and in haploid gametes from barley with sequencing coverage as low as 0.1x. It can identify crossovers in polyploid genomes, including simulated recombinant tetraploids and also real data from tetraploid tomato hybrid offspring. Our results demonstrate that MeiCOfi can robustly identify crossovers in diverse genomic contexts.

bioinformatics↗

bioRxiv2025

Chromosome-scale Solanum pennellii and Solanum cheesmaniae genome assemblies reveal structural variants, repeat content and recombination barriers of the tomato clade

Crop wild relatives are important resources for improving cultivated crops, yet the precise introgression of wild genetic material into cultivated crops is often difficult and cannot be fully defined without high-quality genome assemblies. Here we used PacBio HiFi, ONT ultra-long and Hi-C sequencing approaches to generate chromosome-scale de novo genome assemblies of two wild species related to the domesticated tomato (Solanum lycopersicum) -- the broadly stress-resistant Solanum pennellii (accession LA0716) and the salt-resistant Solanum cheesmaniae (accession LA1039). K-mer and BUSCO analysis of both assemblies demonstrated above 99% completeness and the improved S. pennellii genome adds 146 Mbp to the 12 chromosomes compared with the original reference. We aligned the new assemblies with seven gold-standard assemblies from the Lycopersicon clade, using Solanum tuberosum as an outgroup, and identified shared and species-specific structural variants. The repeat content of all nine assemblies was characterized, providing evidence for independent explosions of Tekay (gypsy superfamily) retrotransposons in S. pennellii and S. peruvianum. Whole genome sequencing of 709 recombinant plants derived from male and female backcrosses of three different hybrids (S.pennellii, S. cheesemaniae and Solanum lycopersicum cv. Micro-Tom crossed with Solanum lycopersicum cv. Moneyberg-TMV) revealed higher crossover rate in female meiosis. Recombination landscape analysis identified conserved female-enhanced recombination regions, and coldspots that were completely devoid of meiotic crossovers including megabase-scale inversions and insertion-deletion polymorphisms between S. lycopersicum and S. pennellii. In summary, we harnessed our high-quality S. pennellii and S. cheesmaniae genome assemblies to reveal how repeat content diverged in nature and during breeding, and uncovered how reproductive gender interacts with structural variants to dictate the recombination landscape in tomato hybrids.

plant biology↗

bioRxiv2022

Pollen sequencing reveals barriers and aberrant patterns of recombination in interspecific tomato hybrids

Tomato is the most consumed vegetable in the world. Increasing its natural resistance and resilience is key for ensuring food security within a changing climate. Plant breeders improve those traits by generating crosses of cultivated tomatoes with their wild relatives. Specific allele introgression relying on meiotic recombination, is hampered by structural divergence between parental genomes. However, previous studies of interspecific tomato hybridization focused in single cross or lacked resolution due to prohibitive sequencing costs of large segregating populations. Here, we used pooled-pollen sequencing to reveal unprecedented details of recombination patterns in five interspecific tomato hybrids. We detected hybrid-specific recombination coldspots that underscore the influence of structural divergence in shaping recombination landscape. Crossover regions and coldspots show strong association with specific TE superfamilies exhibiting differentially accessible chromatin between somatic and meiotic cells. We also found gene complexes associated with metabolic processes, stress resistance and domestication syndrome traits, revealing undesired consequences of recombination suppression to phenotypes. Finally, we demonstrate that by using resequencing data of wild and domesticated tomato populations, we can screen for alternative parental genomes to overcome recombination barriers. Overall, our results will allow breeders better informed decisions on generating disease-resistant and climate-resilient tomato.

genomics↗