Biology subjects

van Beveren, F.

Publications and source records attributed to van Beveren, F..

8 recordsLinked to original sources

bioRxiv2026

Specialised root hair cells facilitate rhizobial infection

Legumes establish symbiotic partnerships with soil bacteria that convert atmospheric nitrogen into plant-available forms. Symbiotic bacteria enter through root hairs following recognition by cell surface receptors that help identify compatible symbionts. However, many root hairs express these receptors, and it has long remained unclear why only a small fraction become infected. Here, we use single-cell transcriptomics to show that legumes pre-specify a rare root hair population for infection before bacterial contact. These susceptible root hairs represent less than one percent of the total, express infection-associated genes prior to encountering symbionts and are conserved in distantly related legumes. Their abundance is regulated by the hormone ethylene and correlates with infection capacity. Our findings reveal that root hair cells do not respond uniformly to symbionts but are instead transcriptionally specialised in advance to control infection entry points. This pre-specification provides a mechanism to balance symbiotic benefits against pathogen infection risks and may exemplify a more general strategy used by multicellular hosts to spatially restrict microbial access.

plant biology↗

bioRxiv2025

Nissolia brasiliensis as a non-nodulating model legume

The nitrogen-fixing root nodule symbiosis (RNS) is specifically formed by four orders of angiosperms. The largest of these four orders include the legume family, the Fabaceae. Among legumes, historical model species have emerged, such as the RNS-forming Medicago truncatula and Lotus japonicus, or, more recently, Aeschynomene aevenia. By contrast, legume species that have lost RNS have been largely ignored. Here, we describe the first chromosome-level assembly for a non-RNS-forming legume, the tropical papilionoid Nissolia brasiliensis. We compared its genome to closely related legumes and identified genes associated with RNS. Finally, we developed a stable transformation protocol that can be deployed in the future to re-evolve RNS in legumes, a first step toward the goal of engineering RNS in non-legume crops.

plant biology↗

bioRxiv2024

Horizontal gene transfers and terpene metabolism drive plant-fungal interaction in Marchantia polymorpha

The liverwort Marchantia polymorpha has emerged as a model for studying plant immunity in bryophytes, providing unique insights into conserved defense mechanisms across land plants. By contrast, Marchantia-specific immune mechanisms have not been explored. In this study, we investigated the genetic basis of quantitative resistance in M. polymorpha against the fungal pathogen Colletotrichum nymphaeae, a naturally occurring compatible parasite. Through a combination of phenotypic, cytological and transcriptomic approaches, combined with genome-wide association studies (GWAS), we identified key defense-related genes and pathways. Transcriptomic analyses performed on two lines with contrasting suceptibilities to the pathogen revealed a strong overlap in immune responses between M. polymorpha and angiosperms, including the upregulation of PR proteins, transcription factors typically associated with biotic stresses, and enzymes involved in specialized metabolism. Leveraging the biological and genetic variability present in a collection of natural M. polymorpha accessions, highlight the role of horizontally transferred microbial-like terpene synthase (MTPSL) genes, which may contribute to the exceptional terpene diversity in liverworts and play a role in pathogen resistance. GWAS uncovered candidate loci associated with resistance traits, implicating both core immune components and specialized metabolic pathways. These results provide new insights into the specific molecular underpinnings of bryophyte immunity and underscore the evolutionary significance of horizontal gene transfer and specialized metabolites in shaping plant-pathogen interactions.

plant biology↗

bioRxiv2024

Ectomycorrhizal symbiosis evolved independently and by convergent gene duplication in rosid lineages

Many land plants rely on mutualistic symbiotic associations to thrive, starting with their common ancestor associating with arbuscular mycorrhizal (AM) fungi. Similar to AM symbiosis, multiple other intracellular symbiotic interactions have evolved in a variety of land plants. Ectomycorrhizal (ECM) symbiosis contrasts with these relationships as there is no intracellular accommodation of the symbiont inside the plant cell, but only intercellular colonization. This symbiotic relationship is common in a variety of seed plants, mostly trees and shrubs such as pines, willows and oaks. Although it is known which plant lineages are involved in ECM symbiosis, there has been little investigation into the evolutionary origin of ECM symbiosis in these lineages. Furthermore, the genetic innovations and transcriptomic response related to this symbiosis have been studied largely in a genus or species-specific context, which hinders the study of their evolutionary origins. In this study, we reconstruct the origin of ECM in the rosid clade, showing at least 16 independent origins, resulting in the 17 known extant ECM rosid lineages. Moreover, comparative genomics of these lineages highlight genes involved in cell wall remodeling which underwent duplications in a convergent manner across ectomycorrhizal lineages.

plant biology↗

bioRxiv2024

Nucleomorph phylogenomics suggests a deep and ancient origin of cryptophyte plastids within Rhodophyta

The evolutionary origin of red algae-derived complex plastids remains obscure. Cryptophyta, one of four eukaryotic lineages harboring these plastids, still contain nucleomorphs, which are highly reduced remnants of red algal nuclei. The genes present on nucleomorph genomes can be used for phylogenomic reconstruction in order to unravel the evolutionary origin of all red complex plastids and provide data independent from previously analyzed plastid-encoded proteins. Here, we leverage these genes in a first attempt at pinpointing the position of cryptophyte nucleomorphs within a comprehensive diversity of Rhodophyta, including new sequence representatives from seven deep-branching red algae. Our analysis, supported by a series of rigorous topology tests, places cryptophyte nucleomorphs as sister to the extremophilic, freshwater subphylum Cyanidiophytina. This conflicts with previously published analyses based on plastidial genes that placed red complex plastids closer to the mesophilic Rhodophytina. Regardless of exact placement, our results reject a nucleomorph origin within any known subgroup of Rhodophyta, instead suggesting an ancient origin of complex red plastids among the deepest branches of the red algal tree of life.

microbiology↗

bioRxiv2024

Conservation of symbiotic signalling across 450 million years of plant evolution

HighlightO_LIThe common symbiotic pathway is activated during arbuscular mycorrhizal symbiosis in Marchantia paleacea C_LIO_LIThe three core members of the common symbiotic pathway are essential for symbiosis in Marchantia paleacea C_LIO_LIThe molecular function of the CCaMK/CYCLOPS module is conserved across land plants C_LIO_LISymbiotic signalling has been conserved in plants for 450 million years C_LI The colonization of land by plants 450 million years ago revolutionized life on Earth1. The fossil record2 and genetic evidence in extant species3 suggest that this transition was facilitated by interactions with symbiotic arbuscular mycorrhizal (AM) fungi4. This ancestral symbiosis relied on the biosynthesis of chemicals by the host plant, both as signals5 and as nutrients3. In angiosperms, a signalling pathway involving the receptor-like kinase SYMRK/DMI26,7, the Calcium and Calmodulin-dependent protein kinase CCaMK/DMI38 and the transcription factor CYCLOPS/IPD39,10 has been described as the common symbiosis pathway (CSP), essential for the establishment of the AM symbiosis and the root-nodule symbiosis11. Phylogenetic and comparative phylogenomic analyses indicated an ancient origin of the CSP, present in all extant land plants forming intracellular symbioses12-15. Trans-complementation assays of the angiosperm mutants with orthologs from diverse species further indicated the conservation of the molecular function of the CSP across the embryophytes9,12,14-16. However, this correlative evidence did not allow testing the ancestral biological function of the CSP. In this study we demonstrate that SYMRK, CCaMK and CYCLOPS are essential for the colonization by AM fungi in bryophytes, indicating that plants have maintained a dedicated signalling pathway to support symbiotic interactions for 450 million years.

plant biology↗

bioRxiv2018

Homogenization of sub-genome secretome gene expression patterns in the allodiploid fungus Verticillium longisporum

Hybridization is an important evolutionary mechanism that can enable organisms to adapt to environmental challenges. It has previously been shown that the fungal allodiploid species Verticillium longisporum, causal agent of Verticillium stem striping in rape seed, has originated from at least three independent hybridization events between two haploid Verticillium species. To reveal the impact of genome duplication as a consequence of the hybridization, we studied the genome and transcriptome dynamics upon two independent V. longisporum hybridization events, represented by the hybrid lineages "A1/D1" and "A1/D3". We show that the V. longisporum genomes are characterized by extensive chromosomal rearrangements, including between parental chromosomal sets. V. longisporum hybrids display signs of evolutionary dynamics that are typically associated with the aftermath of allodiploidization, such as haploidization and a more relaxed gene evolution. Expression patterns of the two sub-genomes within the two hybrid lineages are more similar than those of the shared A1 parent between the two lineages, showing that expression patterns of the parental genomes homogenized within a lineage. However, as genes that display differential parental expression in planta do not typically display the same pattern in vitro, we conclude that sub-genome-specific responses occur in both lineages. Overall, our study uncovers the genomic and transcriptomic plasticity during evolution of the filamentous fungal hybrid V. longisporum and illustrate its adaptive potential. ImportanceVerticillium is a genus of plant-associated fungi that include a handful of plant pathogens that collectively affect a wide range of hosts. On several occasions, haploid Verticillium species hybridized into the stable allodiploid species Verticillium longisporum, which is, in contrast to haploid Verticillium species, a Brassicaceae specialist. Here, we studied the evolutionary genome and transcriptome dynamics of V. longisporum and the impact of the hybridization. V. longisporum genomes display a mosaic structure due do genomic rearrangements between the parental chromosome sets. Similar to other allopolyploid hybrids, V. longisporum displays an ongoing loss of heterozygosity and a more relaxed gene evolution. Also, differential parental gene expression is observed, with an enrichment for genes that encode secreted proteins. Intriguingly, the majority of these genes displays sub-genome-specific responses under differential growth conditions. In conclusion, hybridization has incited the genomic and transcriptomic plasticity that enables adaptation to environmental changes in a parental allele-specific fashion.

microbiology↗

bioRxiv2018

Nuclear and mitochondrial genomes of the hybrid fungal plant pathogen Verticillium longisporum display a mosaic structure

Allopolyploidization, genome duplication through interspecific hybridization, is an important evolutionary mechanism that can enable organisms to adapt to environmental changes or stresses. This increased adaptive potential of allopolyploids can be particularly relevant for plant pathogens in their quest for host immune response evasion. Allodiploidization likely caused the shift in host range of the fungal pathogen plant Verticillium longisporum, as V. longisporum mainly infects Brassicaceae plants in contrast to haploid Verticillium spp. In this study, we investigated the allodiploid genome structure of V. longisporum and its evolution in the hybridization aftermath. The nuclear genome of V. longisporum displays a mosaic structure, as numerous contigs consists of sections of both parental origins. V. longisporum encountered extensive genome rearrangements, whereas the contribution of gene conversion is negligible. Thus, the mosaic genome structure mainly resulted from genomic rearrangements between parental chromosome sets. Furthermore, a mosaic structure was also found in the mitochondrial genome, demonstrating its bi-parental inheritance. In conclusion, the nuclear and mitochondrial genomes of V. longisporum parents interacted dynamically in the hybridization aftermath. Conceivably, novel combinations of DNA sequence of different parental origin facilitated genome stability after hybridization and consecutive niche adaptation of V. longisporum.

genomics↗