Biology subjects

van Olst, M.

Publications and source records attributed to van Olst, M..

8 recordsLinked to original sources

bioRxiv2025

Extreme GC3 Codon Bias in a Novel Brown Seaweed Virus Results in Pseudoambigrammatic Characteristics

Although viruses are often studied in relation to disease, they can also offer valuable insights into RNA functionality. Due to their vast range of hosts and high mutation rates, viruses can quickly adapt to changing environments. It is therefore expected that viruses exploit all possible RNA functionalities to develop strategies for host infection and propagation. Our aim is to discover RNA viruses with survival strategies that reveal unknown RNA characteristics and functionalities. We have chosen seaweed as host organism because relatively little is known about RNA viruses in seaweed. Additionally, seaweeds are evolutionary distant from terrestrial plants and inhabit environments with entirely different conditions, increasing the likelihood of discovering new RNA viruses with unknown survival strategies. Here we report a new, unclassified negative-stranded single-strand RNA virus from seaweed Saccharina latissima that showed a unique genome characteristic. The novel virus, named SalaUV-NL1, contains a large segment of 7.065 nucleotides coding for a 2.296 amino acids protein and a small segment of 2.120 nucleotides coding for a 328 plus a potential 315+ amino acids protein. The large segment also appeared to have an additional large open reading frame (ORF) on the negative strand, suggesting it could be an ambigrammatic virus. However, the virus displayed an extreme GC3 codon bias (98%) in the (+)ORF, which differs from the typical avoidance of just the reverse-complement stop codons seen in ambigrammatic viruses. Consequently, the (-)ORF appears to occur accidental and is unlikely to encode a functional protein. Therefore, we have termed our virus to be pseudoambigrammatic. Several other viruses with the same pseudogrammatic high GC3 codon bias were identified in Genbank, most without a (-)ORF. The SalaUV-NL1 virus codon bias surpasses the high GC3 codon bias of the S. latissima host genes, however other species that host pseudoambigrammatic viruses do not display a high GC3 codon bias. Comparison of several variants of SalaUV-NL1 showed that the relative nucleotide change rate, particularly for silent changes from A/T to G/C, was extremely high (up to 81%). This novel virus demonstrates a new survival strategy of RNA viruses that is not yet understood.

genomics↗

bioRxiv2024

Discovery of new and variant Potyviruses in Asparagales plants from a Dutch urban botanic garden

Although viruses play an important role in human health and plant health, most viruses are still undetected. One of the reasons is that they may evolve in distinct natural habitats that are not yet extensively sampled for virus analysis. An example of such a habitat is urban botanic gardens. We analyzed 25 Asparagales plants with a mild to severe disease phenotype from a Dutch urban botanic garden for the presence of known an unknown virus types and virus variants by smallRNA-seq and RNA-seq. We found in all samples evidence for (past) Potyviridae presence, mostly Ornithogalum virus (OV) and Ornithogalum mosaic virus (OrMV), as well as a new Iris mild mosaic virus variant (IMMV) and a yet unknown species of Potyvirus. Also, presence of a new Betaflexivirus, a new Polerovirus and a new Phenuivirus were detected. Most analyzed plants harbored multiple viruses, 18 out of 25 plants showed evidence for three to seven viruses and 12 out of 13 viruses were present in four to 11 samples. In this study, we describe the characteristics of a newly discovered Potyvirus and identify several variants of known potyviruses. We place these findings in the context of known viruses. However, we were unable to link these potyviruses to any specific disease phenotype.

genomics↗

bioRxiv2024

A new Polerovirus species in plants from the Asparagaceae family defined by its RNA-silencing repressor protein P0

To contribute to the discovery of the global virome, we explored plants from an urban botanic garden in the Netherlands for new and variant plant viruses. Analyzing RNA from 25 plants from the Asparagaceae family with both RNA-seq, as well as smallRNA-seq revealed in six plants the presence of a variant Polerovirus from the Solemoviridae family that shows an overall RNA-sequence identity of 93% to the known Ornithogalum Virus 5 (OV-5). Amino acid sequence comparison of the complex set of proteins produced by the new virus revealed that all but Protein-0, showed high similarity (> 91%) with those of the OV-5 virus. The similarity between the new P0 protein and the OV-5 P0 protein, however, was for all variants less than 83%, well below the ICTV species protein-based demarcation criterium. Hence, we named the new virus Asparagaceae Polerovirus 1 (AspPolV-1).

genomics↗

bioRxiv2024

Discovery of a new Phenuivirus species in Lachenalia plants reveals possible co-evolution between 5' and 3' RNA sequence motifs

This study reports the discovery of a new Phenuivirus species, named Lachenalia Phenuivirus-1 (LacPhV-1), from Lachenalia plants in an urban botanic garden in Amsterdam. Using a combination of smallRNA-seq, RNA-seq, and advanced bioinformatics, we identified a segmented negative-strand RNA virus in the Phenuiviridae family. Our findings show significant divergence between this new virus and known Phenuiviruses, such as Tulip Streak Virus (TuSV) and Lactuca Big Vein associated Phlebovirus (LBVaPV), supporting its classification as a distinct species. Notably, the sequence differences found in the conserved 5 and 3 ends of these segments suggest potential co-evolution. Despite the observed genomic distances, there is significant conservation in the RdRp subdomain, underscoring evolutionary relationships among LacPhV-1, TuSV, and LBVaPV. Our findings expand the known global virome and highlight the importance of exploring plant viromes in diverse ecological settings to better understand virus evolution and diversity.

genomics↗

bioRxiv2024

A new Betaflexivirus species in Ferraria crispa plants

The global virome is still largely unknown. In this study we describe the discovery of a new Betaflexivirus species in Ferraria crispa plants. The plant samples were collected in an experiment of 25 Asparagales plants, obtained from an urban botanic garden in the Netherlands, and analyzed by smallRNA-seq as well as RNA-seq. The new Betaflexivirus only occurred in four Ferraria cripsa plants and was tentatively named Ferraria Betaflexivirus 1 (FerBfV-1). This Betaflexivirus showed an RNA genome structure characteristic for the genus Capillovirus, a single-stranded (+) RNA virus. The closest known Capilloviruses in GenBank showed a protein similarity less than 49%, which is well below the proposed demarcation value of species in this genus. Further comparison analysis of the Capillovirus genus revealed the possible presence of two groups.

genomics↗

bioRxiv2024

Discovery of novel RNA viruses in commercially relevant seaweeds Alaria esculenta and Saccharina latissima

Seaweeds are increasingly recognized as sustainable food sources; however, their large-scale cultivation faces challenges similar to land crops, including susceptibility to pathogens. Plant viruses pose a significant threat to global food security, yet little is known about the diversity of viruses in seaweeds. This study investigates virus-associated small interfering RNA (siRNA) responses in commercially relevant seaweed species to understand RNA virus diversity, particularly in edible varieties. Through small RNA sequencing of 16 samples from Saccharina latissima and Alaria esculenta, we identified three new RNA viruses Aev-NL1, Slv-NL2 and Slv-NL3, and one new DNA virus (phaeovirus). The partial genome of the new DNA virus was discovered in the A. esculenta samples and shared 67% DNA sequence identity with the major coat protein of the large double-stranded DNA phaeovirus Feldmannia irregularis virus a. In four out of five A. esculenta samples, a new bisegmented ormycovirus-like RNA virus (Aev-NL1) was identified. A similar new virus, Slv-NL1, was found in previously published S. latissima RNA-seq data, sharing 87% sequence identity with Aev-NL1. Lastly, two novel RNA viruses, Slv-NL2 and Slv-NL3, were discovered in all eight S. latissima samples sharing limited similarity at the genome level but high sequence identity at protein level of both ORFs (>94%). Further investigation of the novel viruses presence across our limited set of samples revealed no conclusive associations with diseased seaweed phenotypes. The discovery of four new viruses in only a limited set of samples highlights the presence of previously unrecognized viral diversity in seaweed, thereby underscoring the importance of understanding viral diversity in seaweed as its virome is currently understudied.

genomics↗

bioRxiv2022

Cellular Factors Involved in Transcriptome Dynamics in Early Zebrafish Embryogenesis

At gastrulation in the zebrafish embryogenesis, the embryonic genome is switched on to produce transcripts that are used for the maintenance and development of the embryo. In a previous study from late blastula to mid gastrula on the transcriptomes of 179 individual embryos, we capture the transcriptome dynamics via ten gene-expression types. Here we study the factors that regulate these transcriptome dynamics by in extensive silico analyses and two small-RNA sequencing experiments. We analyzed mechanisms that would make it possible for the embryo to achieve the tight regulation of gene expression that was observed, not only during development, but also when individual embryos were compared. We found that many of the gene-expression regulatory factors that are available to the embryo are operational in the different gene-expression types and act concurrently with not one mechanism prevailing in this developmental phase. We also saw that at least one of the regulatory mechanisms, the expression of members of the miRNA-430 family again is very tightly regulated, both during development as well as when miRNA expression from individual embryos is compared.

developmental biology↗

bioRxiv2019

An alternative spliceosome defined by distinct snRNAs in early zebrafish embryogenesis

Splicing removes intronic RNA sequences from pre-mRNA molecules and enables, by alternative splicing, the generation of multiple unique RNA molecules from a single gene. As such, splicing is an essential part of the whole translation system of a cell. The spliceosome is a ribonucleoprotein complex in which five small nuclear RNAs (snRNAs) are involved; U1, U2, U4, U5, and U6. For each of these snRNAs there are variant gene copies present in a genome. Furthermore, in many eukaryotic species there is an alternative, minor spliceosome that can splice a small number of specific introns. As we previously discovered an embryogenesis-specific ribosomal system in zebrafish early embryogenesis based on variant rRNA and snoRNA expression, we hypothesized that there may also be an embryogenesis-specific spliceosome. An inventory of zebrafish snRNA genes revealed clustered and dispersed loci for all but U2 major snRNAs. For each minor spliceosome snRNA, just one gene locus was found. Since complete snRNA molecules are hard to sequence, we employed a combined PCR-sequencing approach to measure the individual snRNA-variant presence. Analysis of egg and male-adult samples revealed embryogenesis-specific and somatic-specific variants for each major snRNA. These variants have substantial sequence differences, yet none in their mRNA binding sites. Given that many of the sequence differences are found in loop structures indicate possible alternative protein binding. Altogether, with this study we established that the spliceosome is also an element of the embryogenesis-specific translation system in zebrafish.

developmental biology↗