Biology subjects

Schijlen, E.

Publications and source records attributed to Schijlen, E..

At least 19 recordsLinked to original sources

bioRxiv2026

Nod factor signaling controlled genes in Medicago truncatula nodules

O_LILegume nodule formation is induced by rhizobia secreted Nod factors (NFs). It has been shown that NF receptors also accumulate in the apex of Medicago truncatula nodules. However, the NF signaling induced transcriptional changes in there have never been studied. C_LIO_LIHere, we studied this by using NF signaling mutant TE7, a weak allele of IPD3, blocked in rhizobial release. Nodule apices were isolated with laser microdissection and used for transcriptional analysis. C_LIO_LIWe identified 1655 NF signaling controlled genes in nodule apex. By comparing this with the transcriptome data from VAMP721d&e RNAi nodule apices, we identified a subset of 445 genes whose expression depends on NF signaling and rhizobial release. Further, we compared the set of genes controlled by NF signaling in nodule apices with that controlled in root epidermis, and these showed only a small overlap. NIN is induced by NF signaling both in the root epidermis and in the nodule. By overexpression of NIN in TE7 and knock down of NIN in wildtype nodules we showed that NF signaling controlled rhizobial release depends on NIN. C_LIO_LINF signaling controls a distinct set of genes in nodules, the function of which depends at least in part on NIN. C_LI

Developmental Biology↗

bioRxiv2026

Reconstructing plant beneficial bacterial consortia by integrating dilution-to-extinction microbiome perturbation with genome-resolved synthetic ecology

Across the biosphere, microbiomes play essential roles in shaping the health of their host. One notable example of such a microbiome-associated phenotype is disease-suppressive soils, where susceptible plant hosts enrich and activate specific rhizosphere microbial consortia for protection against fungal root pathogens. However, identifying and reconstructing microbial consortia responsible for host protection remains challenging, given the inherent taxonomic and functional complexity of microbiomes. Here, we integrated metagenomic profiling of disease-suppressive microbiomes perturbed by dilution-to-extinction (DTE) with comprehensive culturing and synthetic ecology to identify the key bacterial taxa conferring suppressiveness to the fungal wheat pathogen Fusarium culmorum. Metagenomics of wheat rhizosphere samples along the DTE trajectory revealed bacterial taxa and functions associated with the disease-suppressive phenotype. Crosslinking these DTE metagenome data with a genome-sequenced collection of 336 rhizobacterial isolates from the suppressive soil allowed the reconstruction of synthetic communities (SynComs) of 11 de-replicated strains negatively associated with disease severity. Upon re-introduction in sterilized suppressive soils, this SynCom consistently reproduced the disease-suppressive phenotype. Paired time-series metagenomics and metatranscriptomics of the SynComs pinpointed candidate biosynthetic gene clusters, including a novel non-alpha poly-amino-acid (NAPAA) gene cluster from Arthrobacter, upregulated in presence of F. culmorum. Chemically synthesized NAPAA variants {varepsilon}-poly-L-lysine and {delta}-poly-L-ornithine significantly inhibited F. culmorum hyphal growth. Collectively, our work establishes a transformative strategy for reconstructing microbial consortia that recapitulates beneficial microbiome-associated phenotypes in plant and animal kingdoms.

microbiology↗

bioRxiv2025

Three novel genomes broaden the wild side of the Capsicum pangenome

This study presents three genome assemblies within the Capsicum genus, enabling comprehensive comparative analyses for the Annuum and Baccatum complexes within the genus. We produced highly continuous assemblies of the nuclear genomes and complete chloroplast assemblies. Subsequent genome annotation identified 34,580 genes in non-pungent C. annuum cv. ECW, and 32,704 and 33,994 genes in pungent C. chacoense and C. galapagoense, respectively. These assemblies, including the first complete genomes for C. chacoense and C. galapagoense, provide additional genomic resolution within the Capsicum genus. The novel genomes were analyzed within a pangenomic framework, integrating 16 Capsicum genomes across the Annuum, Baccatum, and Pubescens complexes. Homology grouping was used to identify core, accessory and unique genes and showed a wide spectrum of genetic diversity, particularly in homology groups exclusive to C. chacoense and C. galapagoense. Out of 79,267 homology groups identified, 13% were core groups, present in all accessions, corresponding to approximately 30% of core genes per genome. Comparative analyses revealed distinct species and genus specific genomic characteristics. Additionally, we used the graph pangenome to illustrate locus-level exploration by examining the Pun1 locus associated with capsaicinoid biosynthesis, identifying multiple Pun1-like genes including their genomic position and homology information. The integration of these new resources into a dynamic Capsicum pangenome framework provides a versatile platform for extracting genetic information relevant to both fundamental research and breeding applications.

genomics↗

bioRxiv2025

High-resolution genome and genetic map of tetraploid Allium porrum expose pericentromeric recombination

We present the first reference genome of highly heterozygous autotetraploid Allium porrum (leek). Combining long-read sequencing with SNP-array screening of two experimental F1 populations, we generated a genetic map with 11,429 SNP markers across 8 linkage groups and a chromosome-scale assembly of Allium porrum (leek) totaling 15.2 Gbp in size. High quality of the reference genome is substantiated by 97.2% BUSCO completeness and a mapping rate of 96% for full-length transcripts. The linkage map exposes the recombination landscape of leek and confirms that crossovers are predominantly proximal located to the centromeres, contrasting with distal recombination landscapes observed in other Allium species. Comparative genomics revealing structural rearrangements between A. porrum and its relatives (A. fistulosum, A. sativum, A. cepa), suggests a closer genomic relationship to A. sativum. Our annotated high-quality reference genome delivers crucial insights into the leek genome structure, recombination landscape, and evolutionary relationships within the Allium genus, offering significant implications for breeding programs, facilitating marker-assisted selection and genetic improvement in leek.

plant 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↗

bioRxiv2022

Pollen sequencing reveals barriers and aberrant patterns of recombination in interspecific tomato hybrids

Tomato is the most consumed vegetable in the world. Increasing its natural resistance and resilience is key for ensuring food security within a changing climate. Plant breeders improve those traits by generating crosses of cultivated tomatoes with their wild relatives. Specific allele introgression relying on meiotic recombination, is hampered by structural divergence between parental genomes. However, previous studies of interspecific tomato hybridization focused in single cross or lacked resolution due to prohibitive sequencing costs of large segregating populations. Here, we used pooled-pollen sequencing to reveal unprecedented details of recombination patterns in five interspecific tomato hybrids. We detected hybrid-specific recombination coldspots that underscore the influence of structural divergence in shaping recombination landscape. Crossover regions and coldspots show strong association with specific TE superfamilies exhibiting differentially accessible chromatin between somatic and meiotic cells. We also found gene complexes associated with metabolic processes, stress resistance and domestication syndrome traits, revealing undesired consequences of recombination suppression to phenotypes. Finally, we demonstrate that by using resequencing data of wild and domesticated tomato populations, we can screen for alternative parental genomes to overcome recombination barriers. Overall, our results will allow breeders better informed decisions on generating disease-resistant and climate-resilient tomato.

genomics↗

bioRxiv2022

A TOMATO GENOME FROM THE ITALIAN RENAISSANCE PROVIDES INSIGHTS INTO COLUMBIAN AND PRE-COLUMBIAN EXCHANGE LINKS AND DOMESTICATION

AO_SCPLOWBSTRACTC_SCPLOWThe history of the tomatos interactions with humans spans both a pre-Columbian period of millennia of cultivation and domestication in South and Central America as well as the plants rise to becoming one of the worlds major cash crops following the arrival of Europeans in the Neotropics and the subsequent Columbian Exchange. In the process, the influence of successive regimes of artificial selection gave rise to an entangled species complex comprised of a wild ancestor and numerous cultivars exhibiting a great diversity of fruit phenotypes (often sorted in cherry and big types). Here, we provide a snapshot into these dynamics by presenting the ancient nuclear and plastid genomes of one of the oldest tomatoes still in existence: the almost half a millennium old En Tibi specimen from the Italian Renaissance. By placing the genome skimming data obtained from this specimen within the phylogenomic context of wild relatives and Neotropical tomato cultivars and land races, we are able to show that the most likely geographic origins of the specimens immediate ancestors, i.e. whence the exchange of this particular lineage originated, are around the Gulf of Mexico. We also show that this specimen was less inbred than present-day tomatoes, shedding light on the genomic signatures of historical domestication processes. Probing deeper into the ancestry that shaped extant genetic diversity within the complex, we reconstruct multiple ancestral populations with diffuse but distinct signatures in cherry and big tomatoes. The geographic structure of these ancestries within the nearest wild relative of tomatoes and the differential extent to which these ancestries are represented in domesticates points to early cultivation and human-assisted dispersal of tomatoes originating from the northern extreme of the natural range of the species. Our findings illustrate the inferences that can be drawn from ancient DNA extracted from herbarium specimens and historic plant collections. At the same time, we stress that our findings draw on multiple disciplines including ethnobotanical and historical research and on the (agri)cultural contributions of a variety of world cultures.

plant biology↗

bioRxiv2021

Genome and transcriptome architecture of allopolyploid okra (Abelmoschus esculentus)

We present the first annotated genome assembly of the allopolyploid okra (Abelmoschus esculentus). Analysis of telomeric repeats and gene rich regions suggested we obtained whole chromosome and chromosomal arm scaffolds. Besides long distal blocks we also detected short interstitial TTTAGGG telomeric repeats, possibly representing hallmarks of chromosomal speciation upon polyploidization of okra. Ribosomal RNA genes are organized in 5S clusters separated from the 18S-5.8S-28S units, clearly indicating an S-type rRNA gene arrangement. The assembly is consistent with cytogenetic and cytometry observations, identifying 65 chromosomes and 1.45Gb of expected genome size in a haploid sibling. Approximately 57% of the genome consists of repetitive sequence. BUSCO scores and A50 plot statistics indicated a nearly complete genome. Kmer distribution analysis suggests that approximately 75% has a diploid nature, and at least 15% of the genome is heterozygous. We did not observe aberrant meiotic configurations, suggesting there is no recombination among the sub-genomes. BUSCO configurations as well as k-mer clustering analysis pointed to the presence of at least 2 sub-genomes. These observations are indicative for an allopolyploid nature of the okra genome. Structural annotation, using gene models derived from mapped IsoSeq transcriptome data, generated over 130,000 putative genes. Mapped transcriptome data from public okra accessions of Asian origin confirmed the predicted genes, showing limited genetic diversity of 1SNP/2.1kb. The discovered genes appeared to be located predominantly at the distal ends of scaffolds, gradually decreasing in abundance toward more centrally positioned scaffold domains. In contrast, LTR retrotransposons were more abundant in centrally located scaffold domains, while less frequently represented in the distal ends. This gene and LTR-retrotransposon distribution is consistent with the observed heterochromatin organization of pericentromeric heterochromatin and distal euchromatin. The derived amino acid queries of putative genes were subsequently used for phenol biosynthesis pathway annotation in okra. Comparison against manually curated reference KEGG pathways from related Malvaceae species revealed the genetic basis for putative enzyme coding genes that likely enable metabolic reactions involved in the biosynthesis of dietary and therapeutic compounds in okra.

genomics↗

bioRxiv2021

Signal-based optical map alignment

In genomics, optical mapping technology provides long-range contiguity information to improve genome sequence assemblies and detect structural variation. Originally a laborious manual process, Bionano Genomics platforms now offer high-throughput, automated optical mapping based on chips packed with nanochannels through which unwound DNA is guided and the fluorescent DNA backbone and specific restriction sites are recorded. Although the raw image data obtained is of high quality, the processing and assembly software accompanying the platforms is closed source and does not seem to make full use of data, labeling approximately half of the measured signals as unusable. Here we introduce two new software tools, independent of Bionano Genomics software, to extract and process molecules from raw images (OptiScan) and to perform molecule-to-molecule and molecule-to-reference alignments using a novel signal-based approach (OptiMap). We demonstrate that the molecules detected by OptiScan can yield better assemblies, and that the approach taken by OptiMap results in higher use of molecules from the raw data. These tools lay the foundation for a suite of open-source methods to process and analyze high-throughput optical mapping data. The Python implementations of the OptiTools are publicly available through http://www.bif.wur.nl/.

bioinformatics↗

bioRxiv2020

Braconidae revisited: Bracon brevicornis genome showcases the potential of linked-read sequencing in identifying a putative complementary sex determiner gene

Bracon brevicornis is an ectoparasitoid of a wide range of larval-stage Lepidopterans, including several pests of important crops, such as the corn borer, Ostrinia nubilalis. It is also one of the earliest documented cases of complementary sex determination in Hymenoptera. Here, we present the linked-read genome of B. brevicornis, complete with an ab initio-derived annotation and protein comparisons with fellow braconids, Fopius arisanus and Diachasma alloem. We demonstrate the potential of linked-read assemblies in exploring regions of heterozygosity and search for structural and homology-derived evidence of the complementary sex determiner gene (csd).

genomics↗

bioRxiv2019

An improved de novo assembly and annotation of the tomato reference genome using single-molecule sequencing, Hi-C proximity ligation and optical maps

The original Heinz 1706 reference genome was produced by a large team of scientists from across the globe from a variety of input sources that included 454 sequences in addition to full-length BACs, BAC and fosmid ends sequenced with Sanger technology. We present here the latest tomato reference genome (SL4.0) assembled de novo from PacBio long reads and scaffolded using Hi-C contact maps. The assembly was validated using Bionano optical maps and 10X linked-read sequences. This assembly is highly contiguous with fewer gaps compared to previous genome builds and almost all scaffolds have been anchored and oriented to the 12 tomato chromosomes. We have found more repeats compared to the previous versions and one of the largest repeat classes identified are the LTR retrotransposons. We also describe updates to the reference genome and annotation since the last publication. The corresponding ITAG4.0 annotation has 4,794 novel genes along with 29,281 genes preserved from ITAG2.4. Most of the updated genes have extensions in the 5 and 3 UTRs resulting in doubling of annotated UTRs per gene. The genome and annotation can be accessed using SGN through BLAST database, Pathway database (SolCyc), Apollo, JBrowse genome browser and FTP available at https://solgenomics.net.

genomics↗

bioRxiv2019

A blueprint of seed desiccation sensitivity in the genome of Castanospermum australe

O_LIMost angiosperms produce seeds that are desiccated on dispersal with the ability to retain viability in storage facilities for prolonged periods. However, some species produce desiccation sensitive seeds which rapidly lose viability in storage, precluding ex situ conservation. Current consensus is that desiccation sensitive seeds either lack or do not express mechanisms necessary for the acquisition of desiccation tolerance.\nC_LIO_LIWe sequenced the genome of Castanospermum australe, a legume species producing desiccation sensitive seeds, and characterized its seed developmental physiology and - transcriptomes.\nC_LIO_LIC. australe has a low rate of evolution, likely due to its perennial life-cycle and long generation times. The genome is syntenic with itself, with several orthologs of genes from desiccation tolerant legume seeds, from gamma whole-genome duplication events being retained. Changes in gene expression during development of C. australe seeds, as compared to desiccation tolerant Medicago truncatula seeds, suggest they remain metabolically active, prepared for immediate germination.\nC_LIO_LIOur data indicates that the phenotype of C. australe seeds arose through few changes in specific signalling pathways, precluding or bypassing activation of mechanisms necessary for acquisition of desiccation tolerance. Such changes have been perpetuated as the habitat in which dispersal occurs is favourable for prompt germination.\nC_LI

plant biology↗

bioRxiv2019

Pyrus Communis chromosome scale assembly

We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII Long read sequencing (PacBio), Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. A total of 496.9 million bases (Mb) corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 chromosomes of the pear genome. About 50% (247 Mb) of the genome consists of repetitive sequences. Comparison with previous assemblies of Pyrus communis and Pyrus x bretschneideri confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted.

bioinformatics↗

bioRxiv2019

Pseudo-chromosome length genome assembly of a double haploid ‘Bartlett’ pear (Pyrus communis L.)

We report an improved assembly and scaffolding of the European pear (Pyrus communis L.) genome (referred to as BartlettDHv2.0), obtained using a combination of Pacific Biosciences RSII Long read sequencing (PacBio), Bionano optical mapping, chromatin interaction capture (Hi-C), and genetic mapping. A total of 496.9 million bases (Mb) corresponding to 97% of the estimated genome size were assembled into 494 scaffolds. Hi-C data and a high-density genetic map allowed us to anchor and orient 87% of the sequence on the 17 chromosomes of the pear genome. About 50% (247 Mb) of the genome consists of repetitive sequences. Comparison with previous assemblies of Pyrus communis. and Pyrus x bretschneideri confirmed the presence of 37,445 protein-coding genes, which is 13% fewer than previously predicted.

plant biology↗

bioRxiv2019

A high-resolution, chromosome-assigned Komodo dragon genome reveals adaptations in the cardiovascular, muscular, and chemosensory systems of monitor lizards

Monitor lizards are unique among ectothermic reptiles in that they have a high aerobic capacity and distinctive cardiovascular physiology which resembles that of endothermic mammals. We have sequenced the genome of the Komodo dragon (Varanus komodoensis), the largest extant monitor lizard, and present a high resolution de novo chromosome-assigned genome assembly for V. komodoensis, generated with a hybrid approach of long-range sequencing and single molecule physical mapping. Comparing the genome of V. komodoensis with those of related species showed evidence of positive selection in pathways related to muscle energy metabolism, cardiovascular homeostasis, and thrombosis. We also found species-specific expansions of a chemoreceptor gene family related to pheromone and kairomone sensing in V. komodoensis and several other lizard lineages. Together, these evolutionary signatures of adaptation reveal genetic underpinnings of the unique Komodo sensory, cardiovascular, and muscular systems, and suggest that selective pressure altered thrombosis genes to help Komodo dragons evade the anticoagulant effects of their own saliva. As the only sequenced monitor lizard genome, the Komodo dragon genome is an important resource for understanding the biology of this lineage and of reptiles worldwide.

genomics↗

bioRxiv2018

A high-quality sequence of Rosa chinensis to elucidate genome structure and ornamental traits

Rose is the worlds most important ornamental plant with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Rose has a complex genome with high heterozygosity and various ploidy levels. Our objectives were (i) to develop the first high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short read sequencing, and anchoring to a high-density genetic map and (ii) to study the genome structure and the genetic basis of major ornamental traits.\n\nWe produced a haploid rose line from R. chinensis Old Blush and generated the first rose genome sequence at the pseudo-molecule scale (512 Mbp with N50 of 3.4 Mb and L75 of 97). The sequence was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features including the pericentromeric regions through annotation of TE families and positioned centromeric repeats using FISH. Genetic diversity was analysed by resequencing eight Rosa species. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and number of flower petals. A rose APETALA2 homologue is proposed to be the major regulator of petals number in rose. This reference sequence is an important resource for studying polyploidisation, meiosis and developmental processes as we demonstrated for flower and prickle development. This reference sequence will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.

genomics↗

bioRxiv2017

Correcting palindromes in long reads after whole-genome amplification

Next-generation sequencing requires sufficient DNA to be available. If limited, whole-genome amplification is applied to generate additional amounts of DNA. Such amplification often results in many chimeric DNA fragments, in particular artificial palindromic sequences, which limit the usefulness of long reads from technologies such as PacBio and Oxford Nanopore. Here, we present Pacasus, a tool for correcting such errors in long reads. We demonstrate on two real-world datasets that it markedly improves subsequent read mapping and de novo assembly, yielding results similar to these that would be obtained with non-amplified DNA. With Pacasus long-read technologies become readily available for sequencing targets with very small amounts of DNA, such as single cells or even single chromosomes.

genomics↗