6 results on '"Bakker, L.V."'
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2. Genome architecture and genetic diversity of allopolyploid okra
- Author
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Nieuwenhuis, R., Hesselink, T., van den Broeck, H.C., Cordewener, J.H.G., Schijlen, E.G.W.M., Bakker, L.V., Diaz Trivino, S., Struss, Darush, de Hoop, Simon-Jan, de Jong, J.H.S.G.M., Peters, S.A., Nieuwenhuis, R., Hesselink, T., van den Broeck, H.C., Cordewener, J.H.G., Schijlen, E.G.W.M., Bakker, L.V., Diaz Trivino, S., Struss, Darush, de Hoop, Simon-Jan, de Jong, J.H.S.G.M., and Peters, S.A.
- Abstract
The allopolyploid okra (Abelmoschus esculentus) unveiled telomeric repeats flanking distal gene-rich regions and short interstitial TTTAGGG telomeric repeats, possibly representing hallmarks of chromosomal speciation. Ribosomal RNA (rRNA) genes organize into 5S clusters, distinct from the 18S–5.8S–28S units, indicating an S-type rRNA gene arrangement. The assembly, in line with cytogenetic and cytometry observations, identifies 65 chromosomes and a 1.45 Gb genome size estimate in a haploid sibling. The lack of aberrant meiotic configurations implies limited to no recombination among sub-genomes. k-mer distribution analysis reveals 75% has a diploid nature and 15% heterozygosity. The configurations of Benchmarking Universal Single-Copy Ortholog (BUSCO), k-mer, and repeat clustering point to the presence of at least two sub-genomes one with 30 and the other with 35 chromosomes, indicating the allopolyploid nature of the okra genome. Over 130 000 putative genes, derived from mapped IsoSeq data and transcriptome data from public okra accessions, exhibit a low genetic diversity of one single nucleotide polymorphisms per 2.1 kbp. The genes are predominantly located at the distal chromosome ends, declining toward central scaffold domains. Long terminal repeat retrotransposons prevail in central domains, consistent with the observed pericentromeric heterochromatin and distal euchromatin. Disparities in paralogous gene counts suggest potential sub-genome differentiation implying possible sub-genome dominance. Amino acid query sequences of putative genes facilitated phenol biosynthesis pathway annotation. Comparison with manually curated reference KEGG pathways from related Malvaceae species reveals the genetic basis for putative enzyme coding genes that likely enable metabolic reactions involved in the biosynthesis of dietary and therapeutic compounds in okra.
- Published
- 2024
3. The genome of Lactuca saligna, a wild relative of lettuce, provides insight into non-host resistance to the downy mildew Bremia lactucae : Lactuca saligna genome
- Author
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Xiong, W., Berke, Lidija, Michelmore, Richard, van Workum, F.J.M., Becker, F.F.M., Schijlen, E.G.W.M., Bakker, L.V., Peters, S.A., van Treuren, R., Jeuken, M.J.W., Bouwmeester, K., Schranz, M.E., Xiong, W., Berke, Lidija, Michelmore, Richard, van Workum, F.J.M., Becker, F.F.M., Schijlen, E.G.W.M., Bakker, L.V., Peters, S.A., van Treuren, R., Jeuken, M.J.W., Bouwmeester, K., and Schranz, M.E.
- Abstract
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.
- Published
- 2022
4. Meiotic recombination profiling of interspecific hybrid F1 tomato pollen by linked read sequencing
- Author
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Rommel Fuentes, Roven, Hesselink, T., Nieuwenhuis, Ronald, Bakker, L.V., Schijlen, E.G.W.M., van Dooijeweert, W., Diaz Trivino, S., de Haan, Jorn R., Sanchez Perez, G.F., Zhang, Xinyue, Fransz, Paul, de Jong, J.H.S.G.M., van Dijk, A.D.J., de Ridder, D., Peters, S.A., Rommel Fuentes, Roven, Hesselink, T., Nieuwenhuis, Ronald, Bakker, L.V., Schijlen, E.G.W.M., van Dooijeweert, W., Diaz Trivino, S., de Haan, Jorn R., Sanchez Perez, G.F., Zhang, Xinyue, Fransz, Paul, de Jong, J.H.S.G.M., van Dijk, A.D.J., de Ridder, D., and Peters, S.A.
- Abstract
Genome wide screening of pooled pollen samples from a single interspecific F1 hybrid obtained from a cross between tomato, Solanum lycopersicum and its wild relative, Solanum pimpinellifolium using linked read sequencing of the haploid nuclei, allowed profiling of the crossover (CO) and gene conversion (GC) landscape. We observed a striking overlap between cold regions of CO in the male gametes and our previously established F6 recombinant inbred lines (RILs) population. COs were overrepresented in non‐coding regions in the gene promoter and 5′UTR regions of genes. Poly‐A/T and AT rich motifs were found enriched in 1 kb promoter regions flanking the CO sites. Non‐crossover associated allelic and ectopic GCs were detected in most chromosomes, confirming that besides CO, GC represents also a source for genetic diversity and genome plasticity in tomato. Furthermore, we identified processed break junctions pointing at the involvement of both homology directed and non‐homology directed repair pathways, suggesting a recombination machinery in tomato that is more complex than currently anticipated.
- Published
- 2020
5. Large-scale genetic perturbations reveal regulatory networks and an abundance of gene-specific repressors
- Author
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Kemmeren, P.P.C.W., Sameith, K., van de Pasch, L.A.L., Benschop, J.J., Lenstra, T.L., Margaritis, A., O'Duibhir, E., Apweiler, E., van Wageningen, S., Ko, C.W., van Heesch, S.A.A.C., Kashani, M.M., Ampatziadis-Michailidis, G., Brok, M.O., Brabers, N.A.C.H., Miles, A.J., Bouwmeester, D., van Hooff, S.R., van Bakel, H.H.M.J., Sluiters, E.C., Bakker, L.V., Snel, B., Lijnzaad, P., van Leenen, D., Groot Koerkamp, M.J.A., Holstege, F.C.P., Theoretical Biology and Bioinformatics, Sub Theoretical Biology & Bioinformatics, Theoretical Biology and Bioinformatics, and Sub Theoretical Biology & Bioinformatics
- Subjects
Genetics ,Regulation of gene expression ,biology ,Biochemistry, Genetics and Molecular Biology(all) ,Saccharomyces cerevisiae ,Gene regulatory network ,Computational biology ,biology.organism_classification ,Interactome ,General Biochemistry, Genetics and Molecular Biology ,Chromatin ,Gene Knockout Techniques ,Genetic Techniques ,Transcription (biology) ,Gene Expression Regulation, Fungal ,Gene Regulatory Networks ,Transcriptome ,Transcription factor ,Gene ,Gene Deletion - Abstract
SummaryTo understand regulatory systems, it would be useful to uniformly determine how different components contribute to the expression of all other genes. We therefore monitored mRNA expression genome-wide, for individual deletions of one-quarter of yeast genes, focusing on (putative) regulators. The resulting genetic perturbation signatures reflect many different properties. These include the architecture of protein complexes and pathways, identification of expression changes compatible with viability, and the varying responsiveness to genetic perturbation. The data are assembled into a genetic perturbation network that shows different connectivities for different classes of regulators. Four feed-forward loop (FFL) types are overrepresented, including incoherent type 2 FFLs that likely represent feedback. Systematic transcription factor classification shows a surprisingly high abundance of gene-specific repressors, suggesting that yeast chromatin is not as generally restrictive to transcription as is often assumed. The data set is useful for studying individual genes and for discovering properties of an entire regulatory system.
- Published
- 2014
6. Large-scale genetic perturbations reveal regulatory networks and an abundance of gene-specific repressors
- Author
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Theoretical Biology and Bioinformatics, Sub Theoretical Biology & Bioinformatics, Kemmeren, P.P.C.W., Sameith, K., van de Pasch, L.A.L., Benschop, J.J., Lenstra, T.L., Margaritis, A., O'Duibhir, E., Apweiler, E., van Wageningen, S., Ko, C.W., van Heesch, S.A.A.C., Kashani, M.M., Ampatziadis-Michailidis, G., Brok, M.O., Brabers, N.A.C.H., Miles, A.J., Bouwmeester, D., van Hooff, S.R., van Bakel, H.H.M.J., Sluiters, E.C., Bakker, L.V., Snel, B., Lijnzaad, P., van Leenen, D., Groot Koerkamp, M.J.A., Holstege, F.C.P., Theoretical Biology and Bioinformatics, Sub Theoretical Biology & Bioinformatics, Kemmeren, P.P.C.W., Sameith, K., van de Pasch, L.A.L., Benschop, J.J., Lenstra, T.L., Margaritis, A., O'Duibhir, E., Apweiler, E., van Wageningen, S., Ko, C.W., van Heesch, S.A.A.C., Kashani, M.M., Ampatziadis-Michailidis, G., Brok, M.O., Brabers, N.A.C.H., Miles, A.J., Bouwmeester, D., van Hooff, S.R., van Bakel, H.H.M.J., Sluiters, E.C., Bakker, L.V., Snel, B., Lijnzaad, P., van Leenen, D., Groot Koerkamp, M.J.A., and Holstege, F.C.P.
- Published
- 2014
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