Biology subjects

Susanto, T.

Publications and source records attributed to Susanto, T..

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↗

bioRxiv2021

Whole genome sequencing elucidates the species-wide diversity and evolution of fungicide resistance in the early blight pathogen Alternaria solani

Early blight of potato is caused by the fungal pathogen Alternaria solani and is an increasing problem worldwide. The primary strategy to control the disease is applying fungicides such as succinate dehydrogenase inhibitors (SDHI). SDHI-resistant strains, showing reduced sensitivity to treatments, appeared in Germany in 2013, five years after the introduction of SDHIs. Two primary mutations in the Sdh complex (SdhB-H278Y and SdhC-H134R) have been frequently found throughout Europe. How these resistances arose and spread, and whether they are linked to other genomic features, remains unknown. We performed whole-genome sequencing for A. solani isolates from potato fields across Europe (Germany, Sweden, Belgium, and Serbia) to better understand the pathogens genetic diversity in general and understand the development and spread of the genetic mutations that lead to SDHI resistance. We used ancestry analysis and phylogenetics to determine the genetic background of 48 isolates. The isolates can be grouped into 7 genotypes. These genotypes do not show a geographical pattern but appear spread throughout Europe. The Sdh mutations appear in different genetic backgrounds, suggesting they arose independently, and the observed admixtures might indicate a higher adaptive potential in the fungus than previously thought. Our research gives insights into the genetic diversity of A. solani on a genome level. The mixed occurrence of different genotypes and apparent admixture in the populations indicate higher genomic complexity than anticipated. The conclusion that SDHI tolerance arose multiple times independently has important implications for future fungicide resistance management strategies. These should not solely focus on preventing the spread of isolates between locations but also on limiting population size and the selective pressure posed by fungicides in a given field to avoid the rise of new mutations in other genetic backgrounds.

evolutionary biology↗