Biology subjects

Schalamun, M.

Publications and source records attributed to Schalamun, M..

5 recordsLinked to original sources

bioRxiv2023

Plant recognition by Trichoderma harzianum elicits upregulation of a novel secondary metabolite cluster required for colonization

Trichoderma harzianum is a filamentous ascomycete frequently applied as biocontrol agent in agriculture. While mycoparasitism and antagonism of Trichoderma spp. against fungal pathogens are well known, early fungal responses to the presence of a plant await broader investigation. Analyzing early stages of plant-fungus communication we show that T. harzianum B97 chemotropically responds to a plant extract and that both plant and fungus alter secondary metabolite secretion upon recognition. We developed a strategy for omics-analysis simulating conditions of early plant recognition eliciting a chemotropic response in the fungus and found 102 genes to be differentially regulated, including nitrate and nitrite reductases. Additionally, the previously uncharacterized Plant Communication Associated (PCA) gene cluster was strongly induced upon recognition of the plant, comprises a palindromic DNA motif and was essential for plant colonization. The PCA-cluster is only present in the Harzianum clade of Trichoderma and closely related to a homologous cluster in Metarhizium spp. Horizontal gene transfer (HGT) was detected for PCA-cluster genes by plants, while the cluster in T. harzianum is likely under balancing or positive selection. Hence, the PCA-cluster mediates early fungus-plant chemical communication and may be responsible for the high potential of T. harzianum and closely related species for biocontrol applications. Plain language summaryInteractions of plants with fungi - beneficial or pathogenic - are crucial for the ecological function of both partners. Yet, the chemical "language" they use and how or when they use it is still insufficiently known. We describe discovery of a novel gene cluster, which is strongly induced upon plant recognition and essential for plant-fungal interkingdom interaction in the biocontrol-agent Trichoderma harzianum.

microbiology↗

bioRxiv2021

Integration of chemosensing and carbon catabolite repression impacts fungal enzyme regulation and plant associations

Fungal metabolism and enzyme production are regulated by nutrient availability and by interactions with the living environment. We investigated the mechanisms underpinning adaptation of the biotechnological fungus Trichoderma reesei to decaying plant biomass versus living plants. We found that concentration-gated response to glucose, the main molecule sensed from dead plant biomass, is mediated by a conserved signaling pathway downstream of G protein-coupled receptors (GPCRs), while the carbon catabolite repressor CRE1 is critical for glucose concentration gating. The GPCRs CSG1 and CSG2 are further required for root colonization and formation of appressorium like structures on plant surfaces. Acceleration of sexual development in the presence of plant roots and their interactions with fruiting bodies indicates preferential association with plants. Our results reveal a complex sensing network governing resource distribution, enzyme production and fungal development that explains previously observed phenomena in fermentations and opens new perspectives for industrial strain improvement and agriculture.

microbiology↗

bioRxiv2019

The draft nuclear genome assembly of Eucalyptus pauciflora: new approaches to comparing de novo assemblies

BackgroundSelecting the best genome assembly from a collection of draft assemblies for the same species remains a difficult task. Here, we combine new and existing approaches to help to address this, using the non-model plant Eucalyptus pauciflora (snow gum) as a test case. Eucalyptus pauciflora is a long-lived tree with high economic and ecological importance. Currently, little genomic information for Eucalyptus pauciflora is available.\n\nFindingsWe generated high coverage of long-(Nanopore, 174x) and short-(Illumina, 228x) read data from a single Eucalyptus pauciflora individual and compared assemblies from four assemblers with a variety of settings: Canu, Flye, Marvel, and MaSuRCA. A key component of our approach is to keep a randomly selected collection of ~10% of both long- and short-reads separate from the assemblies to use as a validation set with which to assess the assemblies. Using this validation set along with a range of existing tools, we compared the assemblies in eight ways: contig N50, BUSCO scores, LAI scores, assembly ploidy, base-level error rate, computing genome assembly likelihoods, structural variation and genome sequence similarity. Our result showed that MaSuRCA generated the best assembly, which is 594.87 Mb in size, with a contig N50 of 3.23 Mb, and an estimated error rate of ~0.006 errors per base.\n\nConclusionsWe report a draft genome of Eucalyptus pauciflora, which will be a valuable resource for further genomic studies of eucalypts. These approaches for assessing and comparing genomes should help in assessing and choosing among many potential genome assemblies for a single species.

genomics↗

bioRxiv2018

Assembly of chloroplast genomes with long- and short-read data: a comparison of approaches using Eucalyptus pauciflora as a test case

BackgroundChloroplasts are organelles that conduct photosynthesis in plant and algal cells. Chloroplast genomes code for around 130 genes, and the information they contain is widely used in agriculture and studies of evolution and ecology. Correctly assembling complete chloroplast genomes can be challenging because the chloroplast genome contains a pair of long inverted repeats (10-30 kb). The advent of long-read sequencing technologies should alleviate this problem by providing sufficient information to completely span the inverted repeat regions. Yet, long-reads tend to have higher error rates than short-reads, and relatively little is known about the best way to combine long- and short-reads to obtain the most accurate chloroplast genome assemblies. Using Eucalyptus pauciflora, the snow gum, as a test case, we evaluated the effect of multiple parameters, such as different coverage of long (Oxford nanopore) and short (Illumina) reads, different long-read lengths, different assembly pipelines, and different genome polishing steps, with a view to determining the most accurate and efficient approach to chloroplast genome assembly.\n\nResultsHybrid assemblies combining at least 20x coverage of both long-reads and short-reads generated a single contig spanning the entire chloroplast genome with few or no detectable errors. Short-read-only assemblies generated three contigs representing the long single copy, short single copy and inverted repeat regions of the chloroplast genome. These contigs contained few single-base errors but tended to exclude several bases at the beginning or end of each contig. Long-read-only assemblies tended to create multiple contigs with a much higher single-base error rate, even after polishing. The chloroplast genome of Eucalyptus pauciflora is 159,942 bp, contains 131 genes of known function, and confirms the phylogenetic position of Eucalyptus pauciflora as a close relative of Eucalyptus regnans.\n\nConclusionsOur results suggest that very accurate assemblies of chloroplast genomes can be achieved using a combination of at least 20x coverage of long- and short-reads respectively, provided that the long-reads contain at least ~5x coverage of reads longer than the inverted repeat region. We show that further increases in coverage give little or no improvement in accuracy, and that hybrid assemblies are more accurate than long-read-only or short-read-only assemblies.

genomics↗

bioRxiv2018

A comprehensive toolkit to enable MinION long-read sequencing in any laboratory

Long-read sequencing technologies are transforming our ability to assemble highly complex genomes. Realising their full potential relies crucially on extracting high quality, high molecular weight (HMW) DNA from the organisms of interest. This is especially the case for the portable MinION sequencer which potentiates all laboratories to undertake their own genome sequencing projects, due to its low entry cost and minimal spatial footprint. One challenge of the MinION is that each group has to independently establish effective protocols for using the instrument, which can be time consuming and costly. Here we present a workflow and protocols that enabled us to establish MinION sequencing in our own laboratories, based on optimising DNA extractions from a challenging plant tissue as a case study. Following the workflow illustrated we were able to reliably and repeatedly obtain > 8.5 Gb of long read sequencing data with a mean read length of 13 kb and an N50 of 26 kb. Our protocols are open-source and can be performed in any laboratory without special equipment. We also illustrate some more elaborate workflows which can increase mean and average read lengths if this is desired. We envision that our workflow for establishing MinION sequencing, including the illustration of potential pitfalls, will be useful to others who plan to establish long-read sequencing in their own laboratories.

genomics↗