Biology subjects

Gottschalk, C.

Publications and source records attributed to Gottschalk, C..

7 recordsLinked to original sources

bioRxiv2025

Ragnarok: a flexible and RApid GeNe Annotation (ROcKs) pipeline deployed through Nextflow

MotivationHigh-quality genome assemblies and pangenomes are increasingly accessible and achievable due to advances in third-generation sequencing and assembly algorithms, but genome annotation remains a critical bottleneck. Existing gene annotation pipelines often require complex installations, multiple steps, long runtimes, and produce variable results, which impede quality and the downstream usage of the annotations. ResultsWe developed RAGNAROK (RApid GeNe Annotation ROcKs), a modular annotation pipeline built on Nextflow and Apptainer that integrates ab initio prediction, transcriptome and protein evidence, repeat annotation, functional assignment, and quality assessment into a single reproducible workflow. Moreover, RAGNAROK utilizes GPU acceleration and parallelization to produce high-quality gene annotations. We benchmarked against BRAKER3 across five diverse, reference-quality plant genomes and demonstrated that RAGNAROK achieved higher sensitivity, precision, and F1 scores at the exon, transcript, and gene levels. Furthermore, we demonstrated RAGNAROKs improvement in re-annotating a suite of five Rosaceae genomes that were previously annotated using MAKER. Overall, RAGNAROK produced more ideal mono:multi-exonic gene ratios, improved BUSCO completeness scores, and reduced missing gene content compared to other pipelines. Additionally, RAGNAROK consistently outperformed BRAKER3 in runtime, scaling efficiently from small to gigabase-scale genomes. RAGNAROK provides a flexible, rapid, scalable, and accurate solution for de novo and re-annotation of plant genomes. Its modular design and workflow scalability lay the foundation for future extensions to animal, fungal, and other eukaryotic genomes. Availability and ImplementationRAGNAROK is available as a GitHub repository at https://github.com/ryandkuster/ragnarok.

bioinformatics↗

bioRxiv2025

Development of Rosaceae Crop-Specific Nanopore Models for Community Use Through the Genome Database for Rosaceae

Oxford Nanopore Technologies (ONT) sequencing platforms have enabled scientists to generate sequence reads of 20 kilobase or more, which has facilitated the assembly of complete genomes. Nanopore sequencing involves recording the change in electrical signals as the DNA molecule transverses the pore. Converting this signal information into bases - a process called basecalling - is challenging and require the implementation of machine learning. The models developed for ONT basecallers have continually improved. However, the mean quality of the reads generated fall below a Phred score of 20 (99% accuracy), the target quality for high-quality genome assembly, when used on challenging plant samples. These low-quality base calls limit the ability to conduct de novo genome assembly, accurate phasing of haplotypes, and long-read genotyping. To overcome these shortcomings, we fine-tuned ONTs high accuracy basecalling model using Bonito, an AI-based deep learning basecaller, to develop crop-specific models for five important species in the Rosaceae family. These species include highly valuable tree crops such as apple, peach, pear, plum, and sweet cherry. Through the development of an automated training pipeline, we were able to achieve [~]14% higher mean and median basecall quality, and a [~]20% increase in total reads with Phred scores >15. These results were achieved without significantly affecting the read length N50s and total reads called. As a result, these new crop-specific models will enable members of the Rosaceae genomics community to produce higher quality ONT sequencing data. Furthermore, we are releasing our automated pipeline to facilitate others to train their own organism or crop-specific models.

genomics↗

bioRxiv2025

Improved genome assembly of double haploid Prunus persica siblings Lovell 2D and Lovell 5D and the peach NLRome

Prunus persica (peach) has long served as a model fruit tree for studying phenological events. It has a relatively small genome and exhibits tremendous plasticity in climate tolerances due to the high variation of chill requirements, bloom times, and fruit ripening times. The peach variety Lovell 2D was used to generate one of the first high-quality genome assemblies for a tree species, using Sanger sequencing of genetic-map ordered BAC clones. A key to the high quality of this early assembly was the use of a doubled haploid variety, which eliminates the challenges posed by mixed haplotypes. Here, we re-sequenced and assembled the Lovell 2D genome along with a doubled haploid sibling Lovell 5D using 3rd generation technologies. The resulting genomes were significantly more contiguous than the current Lovell 2D reference genome (ver2.0 updated in 2017) and are closer to the estimated total genome size for peach (265Mb). In addition, new gene, transposable element (TE), and Nucleotide-binding domain and Leucine-rich repeat receptor (NLR) annotations were performed to enhance the integrity and utility of the genome. These updated peach doubled-haploid reference assemblies will provide the research community with an improved reference genome for genomics-guided studies and breeding efforts.

genomics↗

bioRxiv2024

Genome-Wide Associations within Diverse Wild Apple Germplasm for Postharvest Blue Mold Resistance to Penicillium expansum

Post-harvest disease caused by the blue mold fungus, Penicillium expansum, accounts for a substantial proportion of economic losses in United States apple industry. Multiple modes of entry in the apple supply chain, plus emerging fungicide resistance, limit the current and long-term viability of using chemical controls alone. Previous phenotypic screens of Malus accessions in the USDA-ARS apple germplasm have identified varying levels of blue mold disease resistance in some wild apple accessions and hybrids. These wild apple species contain reservoirs of genetic resistance that can be integrated into apple breeding programs to complement the previously identified qM-Pe3.1 marker from M. sieversii. We sought to identify these novel loci by combining historical phenotypes of the USDA-ARS wild apple germplasm with low-pass genomic sequencing to perform association mapping. Multi-locus mixed models identified five single nucleotide polymorphisms (SNPs) significantly associated with reduction of post-harvest rot under high concentration of P. expansum inoculum, and one SNP associated under low inoculum concentration. Within a 25,000 base pair window of these SNPs, we found candidate genes encoding proteins with known pathogen immune response and defense roles, such as a Cobra-like 7, flavin monooxygenase, LRR receptors, PR5-like receptor kinase, and a putative resistance protein RGA3. We present these loci as targets for identifying accessions with beneficial alleles that can be targeted for fine mapping and use in Malus breeding programs to achieve M. domestica lines with natural post-harvest rot resistance.

genetics↗

bioRxiv2023

Genome of the North American wild apple species Malus angustifolia

Apple (Malus x domestica Borkh.) production faces many challenges stemming from abiotic and biotic stresses. Abiotic stressors, such as extreme temperatures, droughts, and spring frosts, can lead to diminished yields and tree loss, while biotic stresses like fire blight and pest infestations further reduce tree health and fruit quality. To lessen the threat of these challenges, plant breeders aim to introduce resistance and resilience genes into cultivated varieties. However, high-relatedness among cultivated varieties and breeding lines, coupled with the long juvenility and generation times in apples, hinder the breeding process. The introduction of resistance traits from wild relatives is also constrained by these factors, as well as the lack of genomic resources that could assist in accelerating the introgression process. Herein, we report the assembly and annotation of Malus angustifolia, the Southern Crabapple, one of Eastern North Americas native species. Using a combination of Pacific Biosciences High Fidelity reads, Next-generation short read sequencing, as well as chromatin conformation capture sequencing, we achieve an extremely contiguous haplotype-resolved assembly. We perform comparative haplotypic analyses to identify SNPs and large structural variants, shedding light on the genomic landscape of M. angustifolia. Finally, we explore the phylogenetic and syntenic relationships between Eurasian Malus progenitors and the recently sequenced North American species, contributing valuable insights to the broader understanding of apple evolution and potential breeding strategies.

genomics↗

bioRxiv2023

A haplotype resolved chromosome-scale assembly of North American wild apple Malus fusca and comparative genomics of the fire blight Mfu10 locus.

The Pacific crabapple (Malus fusca) is a wild relative of the commercial apple (Malus x domestica). With a range extending from Alaska to Northern California, M. fusca is extremely hardy and disease resistant. The species represents an untapped genetic resource for development of new apple cultivars with enhanced stress resistance. However, gene discovery and utilization of M. fusca has been hampered by the lack of genomic resources. Here, we present a high-quality, haplotype-resolved, chromosome-scale genome assembly and annotation for M. fusca. The genome was assembled using high-fidelity long-reads and scaffolded using genetic maps and high-throughput chromatin conformation capture sequencing, resulting in one of the most contiguous apple genomes to date. We annotated the genome using public transcriptomic data from the same species taken from diverse plant structures and developmental stages. Using this assembly, we explored haplotypic structural variation within the genome of M. fusca, identifying thousands of large variants. We further showed high sequence co-linearity with other domesticated and wild Malus species. Finally, we resolve a known quantitative trait locus associated with resistance to fire blight (Erwinia amylovora). Insights gained from the assembly of a reference-quality genome of this hardy wild apple relative will be invaluable as a tool to facilitate DNA-informed introgression breeding.

genomics↗

bioRxiv2018

Identification of cereulide producing Bacillus cereus by MALDI-TOF MS

The Bacillus (B.) cereus group is genetically highly homogenous and consists of nine recognized species which are present worldwide. B. cereus sensu stricto play an important role in food-borne diseases by producing different toxins. Yet, only a small percentage of B. cereus strains are able to produce the heat stable depsipeptide cereulide, the causative agent of emetic food poisonings. To minimize the entry of emetic B. cereus into the food chain, food business operators are dependent on efficient and reliable methods enabling the differentiation between emetic and non-emetic strains. Currently, only time-consuming cell bioassays, molecular methods and tandem mass spectrometry are available for this purpose. Thus, the aim of the present study was to establish a fast and reliable method for the differentiation between emetic and non-emetic strains by MALDI-TOF MS. Selected isolates/strains of the B. cereus group (total n=110, i.e. emetic n=45, non-emetic n=65) were cultured on sheep blood agar for 48h.\n\nSubsequently, the cultures were directly analyzed by MALDI-TOF MS without prior extraction steps (direct smear method). The samples were measured in linear positive ionization mode in the mass range of m/z 800 - 1,800 Da. Using ClinProTools 3.0 statistical software and flex analyst, a differentiation between emetic and non-emetic isolates was possible with a rate of correct identification of 99.1 % by means of the evaluation of two specific biomarkers (m/z 1171 and 1187 Da).\n\nImportanceBacillus (B.) cereus plays an important role in food-borne diseases due to the production of different toxins, e.g. the heat stable depsipeptide cereulide. Only a small number of B. cereus strains are able to produce this toxin, the causative agent of emetic food poisonings. To minimize the entry of emetic B. cereus into the food chain, food business operators require efficient and reliable methods enabling the differentiation between emetic and non-emetic strains. The aim of the present study was to develop a fast and reliable method for the differentiation between emetic and non-emetic strains by MALDI-TOF MS. A differentiation between emetic and non-emetic isolates was possible with a rate of correct identification of 99.1 % by means of the evaluation of two specific biomarkers (m/z 1171 and 1187 Da).

microbiology↗