Biology subjects

Effgen, S.

Publications and source records attributed to Effgen, S..

3 recordsLinked to original sources

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

A gap-free tomato genome built from complementary PacBio and Nanopore long DNA sequences reveals extensive linkage drag during breeding

The assembly and scaffolding of plant crop genomes facilitates the characterization of genetically diverse cultivated and wild germplasm. The cultivated tomato has been improved through the introgression of genetic material from related wild species, including resistance to pandemic strains of Tobacco Mosaic virus (TMV) from Solanum peruvianum. Here we applied PacBio HiFi and ONT nanopore sequencing to develop independent, highly contiguous and complementary assemblies of an inbred TMV-resistant tomato variety. We merged the HiFi and ONT assemblies to generate a long-read-only assembly where all twelve chromosomes were represented as twelve contiguous sequences (N50=68.5 Mbp). The merged assembly was validated by chromosome conformation capture data and is highly consistent with previous tomato assemblies that made use of genetic maps and HiC for scaffolding. Our long-read-only assembly reveals that a complex series of structural variants linked to the TMV resistance gene likely contributed to linkage drag of a 64.1 Mbp region of the S. peruvianum genome during tomato breeding. We show that this minimal introgression region is present in six cultivated tomato hybrid varieties developed in three commercial breeding programs. Our results suggest that complementary long read technologies can facilitate the rapid generation of near complete genome sequences.

plant biology↗

bioRxiv2020

The evolutionary dynamics of genetic incompatibilities introduced by duplicated genes in Arabidopsis thaliana

Although gene duplications provide genetic backup and allow genomic changes under relaxed selection, they may potentially limit gene flow. When different copies of a duplicated gene are pseudo-functionalized in different genotypes, genetic incompatibilities can arise in their hybrid offspring. While such cases have been reported after manual crosses, it remains unclear whether they occur in nature and how they affect natural populations. Here we identified four duplicated-gene based incompatibilities including one previously not reported within an artificial Arabidopsis intercross population. Unexpectedly, however, for each of the genetic incompatibilities we also identified the incompatible alleles in natural populations based on the genomes of 1,135 Arabidopsis accessions published by the 1001 Genomes Project. Using the presence of incompatible allele combinations as phenotypes for GWAS, we mapped genomic regions which included additional gene copies which likely rescue the genetic incompatibility. Reconstructing the geographic origins and evolutionary trajectories of the individual alleles suggested that incompatible alleles frequently co-exist, even in geographically closed regions, and that their effects can be overcome by additional gene copies collectively shaping the evolutionary dynamics of duplicated genes during population history.

evolutionary biology↗