Biology subjects

Whitt, L.

Publications and source records attributed to Whitt, L..

9 recordsLinked to original sources

bioRxiv2026

Identifying, phasing, and structurally annotating sex chromosomes for genome assemblies using CBS-tools

A complete reference genome for species with chromosomally-determined separate sexes should contain scaffolds for all sex chromosome homologs. However, sex chromosomes present distinct computational challenges compared to autosomes. Here we present a k-mer based analysis that utilizes whole-genome sequencing of a few sex-identified isolates: Cytogenetics-By-Sequencing (CBS) tools. Unlike other approaches that typically address one aspect of the sex chromosomes, CBS-tools strives to guide users from the discovery of the heterogametic sex through identifying the sex-determination region (SDR). The core of CBS-tools is automated quantification of sex-specific k-mers in order to predict the heterogametic sex. Using publicly-available datasets, CBS-tools correctly identified the known sex-system of the 31 species tested. Additionally, we used these k-mers to verify and correct phasing of sex chromosomes between haplotypes in species representing different sex-systems. Finally, we used these k-mers to delimit the SDR boundary using an interactive web platform. CBS-tools was developed with previously unexplored sex chromosome systems in mind, but is also suitable for well-examined sex chromosome pairs.

genomics↗

bioRxiv2026

Chromosome-level genome assemblies and annotations of Amaranthus spinosus, Amaranthus acanthochiton, Amaranthus arenicola, and Amaranthus floridanus

Amaranthus L. spans aggressive agricultural weeds, ornamentals, and ancient pseudocereals. Species within the genus vary in morphology, environmental tolerance, and sexual systems, making them well-suited for studying reproductive evolution and plant adaptation. To investigate sex chromosome architecture within the genus, we generated chromosome-level assemblies of a monoecious amaranth (Amaranthus spinosus) and three dioecious species (A. acanthochiton, A. arenicola, and A. floridanus) using PacBio high-fidelity (HiFi) long reads. We paired these data with Dovetail Genomics Omni-C sequencing to achieve haplotype resolution for A. spinosus and A. acanthochiton, and we used reference-guided scaffolding for the remaining two species. The assemblies are highly contiguous, with sizes ranging from 394.24 to 607.10 Mbp, contig N50 from 0.63 to 8.76 Mbp, and scaffold N50 from 22.44 to 37.97 Mbp. Evaluation of the assemblies and annotations revealed 96.3 to 97.6%, and 97.6 to 98.3% BUSCO completeness, respectively. Comparative genomic analysis revealed that the Chromosome 1 inversions and Robertsonian fusion previously reported in A. tuberculatus are conserved in A. acanthochiton and consistent with the architecture of A. arenicola and A. floridanus, suggesting that the evolution of dioecy in this clade predates subsequent speciation. In parallel, multiple homologs of Rf1 on Chromosome 3 of A. spinosus, a monoecious species that exhibits spatial separation of male and female flowers and is closely related to the dioecious A. palmeri, were identified. Together, this study provides foundational resources for advancing evolutionary, ecological, and agronomic research across the genus, including herbicide resistance evolution and weediness traits.

genomics↗

bioRxiv2026

Newly arisen indel governs a leaf shape polymorphism in the Ivy Leaf Morning Glory (Ipomoea hederacea)

Leaf shape varies widely across plant taxa and has repeatedly been shown to affect ecophysiology, interspecific interactions, and fitness. We used population genomics, genome wide association studies (GWAS), and comparative genomics to determine the genetic basis and evolutionary history of an uncharacterized Mendelian leaf shape polymorphism in Ipomoea hederacea. To do so, we assembled a reference genome and generated whole genome sequencing for 123 individuals from 55 populations. We identified a 117 kb indel that perfectly co-segregates with leaf shape by conducting a GWAS and assessing differences in coverage. Syntenic orthologs for genes on the indel were present in five other Ipomoea species with various leaf shapes, indicating the indel is a newly arisen deletion in I. hederacea despite similar leaf shape phenotypes in the other species. More broadly, these results illustrate how a range of leaf shape phenotypes can be produced by distinct genetic mechanisms even in closely related species. Although none of the genes on the indel itself are known leaf shape candidates, there are multiple leaf shape candidate genes in close proximity that are involved in the auxin biosynthesis pathway. Additionally, the genes within the indel have gene functions that could affect other potentially ecologically relevant traits that have previously been shown to be associated with leaf shape in I. hederacea. Therefore, the pleiotropic effects of the indel polymorphism can have important implications for understanding the ecological mechanisms influencing a well-documented leaf shape latitudinal cline in I. hederacea. Significance StatementIpomoea hederacea has been used to investigate the ecological and evolutionary effects of leaf shape because of a well-documented latitudinal leaf shape cline governed by an uncharacterized Mendelian polymorphism in this species. We identified a 117 kb indel that perfectly co-segregates with leaf shape in I. hederacea. The indel appears to be a distinct genetic mechanism than those governing similar leaf shapes in other closely related Ipomoea species. Additionally, possible pleiotropic effects of the indel on other traits has important implications for understanding the ecology and evolution of leaf shape variation in I. hederacea. Therefore, the results and the new genomic resources that we developed will facilitate future work understanding the genetic, developmental, and ecological mechanisms governing leaf shape variation.

plant biology↗

bioRxiv2025

A haplotype-resolved, chromosome-scale genome assembly and annotation for Carya glabra (pignut hickory; Juglandaceae)

Carya glabra (2n = 4x = 64), also known as pignut hickory, is a widely distributed species in the walnut family (Juglandaceae). Native to the central and eastern United States and southeastern Canada, C. glabra plays an important ecological role as a common upland forest species; it is closely related to several economically valuable nut trees, including C. illinoinensis (pecan). A deeper understanding of the genetics of C. glabra is essential for studying its evolutionary history and biology, with potential implications for agricultural improvement of pecan. Here, we present the first nuclear genome assembly and annotation of C. glabra. The assembly is chromosome-level and phased, representing the first assembled polyploid genome in the genus Carya. A total of 64 pseudochromosomes were assembled and phased into four haplotypes. The haplotype A assembly spans 600.4 Mb, comprises 55.0% repetitive sequences, and contains 30,947 protein-coding genes, with a BUSCO completeness score of 97.7%. Functional annotation assigned 94.3% of haplotype A genes to gene families, and 79.7% and 86.3% of genes were annotated with Gene Ontology terms and protein domains, respectively; 635 putative plant disease resistance genes were found in haplotype A. The other three haplotypes exhibited similarly high-quality annotation metrics. Our genomic analyses also suggest that C. glabra is an autotetraploid. Comparative genomic analyses revealed high collinearity among the four haplotypes of C. glabra and the published genomes of three other Carya species, although structural variation among the genomes of these species was identified. In addition, we provide an improved chloroplast genome assembly and the first mitochondrial genome for C. glabra. Importantly, most members of the research team are undergraduate students; the sequenced individual is located in McCarty Woods, a Conservation Area on the University of Florida campus. This work highlights the value of genome assembly efforts as powerful tools for teaching genomics and supporting conservation initiatives. This first high-quality reference genome for C. glabra provides a valuable resource for studying Carya, a genus of significant ecological and economic importance. Article summaryCarya glabra (pignut hickory) is a common upland forest species in North America. This species is a member of the walnut family (Juglandaceae), which includes many economically important nut trees. Here, we present the first nuclear genome assembly and annotation of C. glabra. The assembly is chromosome-level and phased. The haplotype A assembly contains 30,947 protein-coding genes, with a BUSCO completeness score of 97.7%. Our genomic analyses suggest that C. glabra is an autopolyploid. We also provide chloroplast and mitochondrial genome assemblies. This nuclear genome provides a valuable resource for studying Carya, a genus of significant ecological and economic importance.

genomics↗

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↗

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

A comparative approach for selecting orthologous candidate genes underlying signal in genome-wide association studies across multiple species

Advances in quantitative genetics have enabled researchers to identify genomic regions associated with changes in phenotype. However, genomic regions can contain hundreds to thousands of genes, and progressing from genomic regions to causative genes is still challenging. In genome-wide association studies (GWAS) measuring elemental accumulation (ionomic) traits, only 5% of loci overlap genes known to control the ionome - indicating that many causal genes are still unknown. To identify candidates for the remaining 95% loci, we developed a method that uses GWAS studies across multiple species to identify conserved causative genes. By Filtering the Results of Multi-species, Analogous, GWAS Experiments (FiREMAGE) we were able to take the GWAS of 19 ionomic traits in Arabidopsis, soybean, rice, maize, and sorghum, and identify alleles affecting trait variation at conserved genes. Permutation testing demonstrated that GWAS loci affecting the same trait contained homologs more often than expected by chance. Most of the top 10% most significant conserved candidate sets encoded alleles in all five species, highlighting the conservation of ionomic genetic regulators in flowering plants. The candidates include proteins with known biochemical functions that regulate the ionome, validating the approach. In addition to genes with known functions, this approach also identified many conserved genes underlying GWAS loci affecting the same trait in multiple species that have no previously identified function in regulating the ionome, providing a path to discover the as yet unknown mechanisms of element accumulation in plants. This method enables the identification of conserved genes of previously unknown function via GWAS. Author summaryQuantitative genetics identifies a genomic region of interest but not the causal gene. We developed an approach to narrow these gene lists using genetic loci affecting elemental (i.e., calcium, iron, zinc) accumulation. Comparative genomics and GWAS demonstrates that alleles at evolutionarily conserved genes alter the same phenotype in multiple species. This produced a list of conserved candidate genes including previously known elemental regulators and genes whose elemental accumulation mechanism has yet to be determined. Combining datasets across species boosted the signal at these loci. This approach accelerates the discovery of new functional roles of genes.

genetics↗

bioRxiv2018

A curated list of genes that control elemental accumulation in plants.

Understanding the mechanisms underlying plants adaptation to their environment will require knowledge of the genes and alleles underlying elemental composition. Modern genetics is capable of quickly, and cheaply indicating which regions of DNA are associated with particular phenotypes in question, but most genes remain poorly annotated, hindering the identification of candidate genes. To help identify candidate genes underlying elemental accumulations, we have created the known ionome gene (KIG) list: a curated collection of genes experimentally shown to change uptake, accumulation, and distribution of elements. We have also created an automated computational pipeline to generate lists of KIG orthologs in other plant species using the PhytoMine database. The current version of KIG consists of 176 known genes covering 5 species, 23 elements and their 1588 orthologs in 10 species. Analysis of the known genes demonstrated that most were identified in the model plant Arabidopsis thaliana, and that transporter coding genes and genes altering the accumulation of iron and zinc are overrepresented in the current list.

plant biology↗