Biology subjects

van Treuren, R.

Publications and source records attributed to van Treuren, R..

3 recordsLinked to original sources

bioRxiv2023

Chromosome level assembly of wild spinach provides insights into the divergence of homo- and heteromorphic plant sex-chromosomes.

BackgroundCultivated spinach (Spinacia oleracea) is a highly nutritional crop species of great economical value that belongs to a genus of dioecious plant species with both homomorphic and heteromorphic sex chromosomes. The wild spinach species Spinacia turkestanica and Spinacia tetrandra are important genetic sources for improving cultivated spinach and excellent material for studying sex chromosome evolution in plants. However, until now there were no publicly available genome assemblies for these species. ResultsHere we sequenced and assembled the genomes of S. turkestanica and S. tetrandra and performed a tri-way comparative analysis with S. oleracea. We show that many abiotic- and biotic stress related gene clusters have expanded through tandem duplication in S. tetrandra after it diverged from the S. turkestanica - S. oleracea lineage. Focussing on the sex chromosomes we found that the previously identified inversion distinguishing the S. oleracea male- and female-SEX DETERMINING REGIONs (SDRs) is conserved in S. turkestanica. Although, the SDRs of these two species coincides with the PSEUDO AUTOSOMAL REGION of S. tetrandra the gene content is only partially conserved and the genetic factors determining sex in these species might differ. Finally, we show that recombination suppression between the S. tetrandra X- and Y-chromosomes resulted in a highly degenerated Y-chromosome and started before the species diverged from S. turkestanica and S. oleracea. ConclusionsWe expect that the novel wild spinach species genomes are of great value to the breeding community and evolutionary biologist especially focussing on the evolution of sex chromosomes in plants.

evolutionary biology↗

bioRxiv2023

Genome assembly and analysis of Lactuca virosa: implications for lettuce breeding

Lettuce (Lactuca sativa L.) is a leafy vegetable crop with ongoing breeding efforts related to quality, resilience, and innovative production systems. Genetic variation of important traits in close relatives is necessary to meet lettuce breeding goals. Lactuca virosa (2x=2n=18), a wild relative assigned to the tertiary lettuce gene pool, has a much larger genome (3.7 Gbp) than Lactuca sativa (2.5 Gbp). It has been used in interspecific crosses and is a donor to modern crisphead lettuce cultivars. Here, we present a de novo reference assembly of L. virosa with high continuity and complete gene space. This assembly facilitated comparisons to the genome of L. sativa and to that of the wild species L. saligna, a representative of the secondary lettuce gene pool. To assess the diversity in gene content, we classified the genes of the three Lactuca species as core, accessory and unique. In addition, we identified three interspecific chromosomal inversions compared to L. sativa, which each may cause recombination suppression and thus hamper future introgression breeding. Using three-way comparisons in both reference-based and reference-free manners, we show that the proliferation of long-terminal repeat elements has driven the genome expansion of L. virosa. Further, we performed a genome-wide comparison of immune genes, nucleotide-binding leucine-rich repeat, and receptor-like kinases among Lactuca spp. and indicate the evolutionary patterns and mechanisms behind their expansions. These genome analyses greatly facilitate the understanding of genetic variation in L. virosa, which is beneficial for the breeding of improved lettuce varieties.

plant biology↗

bioRxiv2022

The genome of Lactuca saligna, a wild relative of lettuce, provides insight into non-host resistance to the downy mildew Bremia lactucae

Lactuca saligna L. is a wild relative of cultivated lettuce (Lactuca sativa L.), with which it is partially interfertile. Hybrid progeny suffer from hybrid incompatibilities (HI), resulting in reduced fertility and distorted transmission ratios. Lactuca saligna displays broad spectrum resistance against lettuce downy mildew caused by Bremia lactucae Regel and is considered a non-host species. This phenomenon of resistance in L. saligna is called non-host resistance (NHR). One possible mechanism behind this NHR is through the plant-pathogen interaction triggered by pathogen-recognition receptors, including nucleotide-binding leucin-rich repeats (NLRs) and receptor-like kinases (RLKs). We report a chromosome-level genome assembly of L. saligna (accession CGN05327), leading to the identification of two large paracentric inversions (>50 Mb) between L. saligna and L. sativa. Genome-wide searches delineated the major resistance clusters as regions enriched in NLRs and RLKs. Three of the enriched regions co-locate with previously identified NHR intervals. RNA-seq analysis of Bremia infected lettuce identified several differentially expressed RLKs in NHR regions. Three tandem wall-associated kinase-encoding genes (WAKs) in the NHR8 interval display particularly high expression changes at an early stage of infection. We propose RLKs as strong candidate(s) for determinants for the NHR phenotype of L. saligna.

genomics↗