Biology subjects

Allsing, N.

Publications and source records attributed to Allsing, N..

7 recordsLinked to original sources

bioRxiv2025

Pangenome of U.S. ex-PVP and Wild Sorghum Reveals Structural Variants and Selective Sweeps Shaping Adaptation and Trait Improvement

Sorghum is a cereal crop grown for food, feed, and biofuel, yet the genomic diversity of elite commercial lines remains underexplored. Here, we assembled a sorghum pangenome from long-read sequences of 46 U.S. ex-Plant Variety Protection Act (ex-PVP) cultivars and a haplotype-resolved assembly of one wild accession. The pangenome revealed largely conserved genomic architecture across elite lines but identified presence-absence variations (PAVs) in 28% of gene families, including genes involved in stress responses and starch metabolism, such as STARCH BRANCHING ENZYME I (SBE1). Selective sweep analyses detected strong signals at key flowering-time loci (Ma1/SbPRR37, Ma2, Ma6) and circadian/light regulators (PHOT1, DET1, XAP5), with PHYA showing copy number variations (CNVs). Analysis of 24 wild accessions, beyond the core pangenome panel, detected CNVs in MULTIDRUG AND TOXIC COMPOUND EXTRUSION (MATE) transporters, potentially reflecting selection or breeding for enhanced herbicide detoxification. These results highlight breeding-shaped regions and position the pangenome as a resource for sorghum improvement.

genomics↗

bioRxiv2025

Transcriptomic stress responses in Vaccinium spp. F1 hybrids: Implications for temperature-resilient cranberry breeding using a crop wild relative

O_LICranberry (Vaccinium macrocarpon) is an important North American fruit crop with vulnerability to temperature extremes and a relatively recent domestication history. Hybridization with a cold-adapted crop wild relative (CWR), V. oxycoccos, offers a strategy for improving temperature stress tolerance. C_LIO_LIWe conducted RNA sequencing (RNA-seq) on V. macrocarpon and F1 hybrids between V. macrocarpon and V. oxycoccos subjected to acute heat and cold stress, capturing early transcriptional responses up to 30 minutes (heat) and 95 minutes (cold) after treatment onset. We then evaluated differences in responses across genotypes and stress conditions. C_LIO_LIDifferential expression analysis and functional profiling revealed cold-induced differences in pathways related to photosynthesis, ribosomes, defense, and hormone signaling. No subgenome-specific functional specialization was observed. Two F1 hybrids exhibited suggestive cold resilience, with expression changes elevated at 60 minutes but declining by 95 minutes. Hybrids also displayed substantial regulatory variation under stress and transgressive downregulation of photosynthesis genes under ambient conditions. C_LIO_LIThese findings suggest that V. oxycoccos introgression could be utilized in breeding cold-tolerant cranberry cultivars. Variation observed between F1 hybrids reflects the diversity introduced through CWR germplasm and provides opportunities for selection. Conservation of V. oxycoccos and other CWRs remains critical for future crop improvement. C_LI Plain Language SummaryCranberries face increasing threats from temperature extremes. We explored crossbreeding cultivated cranberry (Vaccinium macrocarpon) and a cold-adapted wild relative (V. oxycoccos) to improve resilience to temperature stress. Hybrids showed different gene expression patterns from their parents, especially under cold stress. Our findings support the value of wild relatives in crop improvement and emphasize the importance of protecting wild plant diversity.

plant biology↗

bioRxiv2025

Domoic acid biosynthesis and genome expansion in Nitzschia navis-varingica

Production of the neurotoxin domoic acid (DA) by benthic diatom Nitzschia navis-varingica poses considerable health and economic concerns. In this study, we employed whole genome sequencing and transcriptomic analyses of regionally distinct N. navis-varingica strains to unravel the genomic underpinnings of DA biosynthesis. Our analyses revealed sizable genomes--characterized by an abundance of repetitive elements and noncoding DNA--that exceed the size of any other pennate diatoms. Central to our findings is the discovery of an expanded domoic acid biosynthesis (dab) gene cluster, spanning over 60 kb and marked by a unique organization that includes core genes interspersed with additional genetic elements. Phylogenetic and syntenic comparisons indicate that transposition events may have driven the expansion and reorganization of this cluster. Biochemical assays validated that the kainoid synthase encoded by dabC catalyzes the formation of isodomoic acid B, thereby establishing a distinct chemotype in contrast to the DA profiles of planktonic diatoms. These results highlight the evolutionary trajectory of DA biosynthesis in diatoms and potential advantages conferred by genome expansion and enzyme diversification in dynamic marine environments. IMPORTANCEDomoic acid (DA) is a potent neurotoxin produced by marine micro- and macroalgae problematic to fisheries and toxic to humans and animals. Our study elucidates the molecular mechanisms underlying DA production in the widespread Western Pacific benthic diatom, Nitzschia navis-varingica. Genomic and biochemical insights add information to our understanding of the evolution of toxin production across diverse phyla and also fill a gap in the knowledge of secondary metabolism in marine diatoms. These findings provide a genetic framework for identifying toxin production and its impacts in the benthos of vulnerable, coastal ecosystems.

genomics↗

bioRxiv2025

Triploidy is prominent in the duckweed Lemna minor complex

Duckweeds (Lemnaceae Martinov) are aquatic monocotyledonous flowering plants comprising five genera and 35 recognized species, known for being the smallest and fastest-growing flowering plants on Earth. Many species are morphologically indistinguishable due to their highly reduced structures, yet molecular evidence suggests that visually similar clones may represent distinct species or hybrids. For example, clonal accessions of the globally distributed Lemna minor in the Landolt Duckweed Collection exhibit genome size variations of several hundred megabases (Mb), raising questions about their taxonomic classification and evolutionary origins. We analyzed 58 presumed L. minor clones to resolve these relationships using a comprehensive suite of methods, including whole-genome sequencing (WGS), flow-cytometric genome size measurements, molecular markers, chromosome counting, and genomic in situ hybridization (GISH). Our findings reveal extensive genome plasticity within the "Lemna minor complex," identifying diploid and triploid L. minor clones, as well as di-haploid and triploid interspecific hybrids called L. x japonica (L. minor x L. turionifera), L. x mediterranea (L. minor x L. gibba), and a novel African-clade distinct from known L. minor lineages. Triploidy was prevalent, occurring in 29% of the clones, and was associated with enhanced growth under optimal conditions but reduced performance under high light and temperature. These findings highlight the widespread role of triploidy, cryptic species, and hybridization in the L. minor complex, emphasizing the importance of multiple approaches for accurately classifying duckweed species and understanding their evolutionary trajectories.

plant biology↗

bioRxiv2024

The evolution of heteromorphic sex chromosomes in plants

Sex chromosomes in cannabis and hop were identified a century ago because of their obvious visible differences in size (heteromorphy). However, we know little about the genes they contain that control the development of the inflorescences. Here we assembled genomes, with phased sex chromosomes, for hop and cannabis. The XY chromosomes share an origin prior to the divergence between the genera >36 MYA. Due to the inheritance patterns of the XYs, the male-specific region of the Y is highly-degenerated, with substantial gene loss, while the X shows faster rates of molecular evolution. Consistent with the theory that these species lack an active-Y system, no clear sex-determining genes reside on the Y. Instead, an X-linked homolog of aminocyclopropane-1-carboxylate synthase (ACS), that is involved in the ethylene biosynthesis pathway, determines the fate of the female inflorescence. Beyond sex determination, the sex chromosomes contribute to the sexual dimorphism in ecology and physiology and have played a role in the domestication and breeding of these species.

evolutionary biology↗

bioRxiv2024

Soil depth determines the microbial communities in Sorghum bicolor fields

Sorghum bicolor, an important global crop, adapted to thrive in hotter and drier conditions than maize or rice, has deep roots that interact with a unique and stratified soil microbiome that plays a crucial role in plant health, growth, and carbon storage. Microbiome studies on agricultural soils, particularly fields growing S. bicolor, have been mostly limited to surface soils (<30 cm). Here we investigated the abiotic factors of soil properties, field location, depth, and the biotic factors of sorghum type across 38 genotypes on the soil microbiome. Utilizing 16S rRNA gene amplicon sequencing, our analysis reveals significant changes in microbial composition and decreasing diversity at increasing soil depths within S. bicolor regardless of genotype or fields. Notably, specific microbial families, such as Thermogemmatisporaceae and an unclassified family within the ABS-6 order, were enriched in deeper soil layers beyond 30 cm. Additionally, microbial richness and diversity declined with depth, reaching a minimum at the 60 - 90 cm layer, with layers beyond 90 cm increasing in alpha diversity. These findings highlight the importance of soil depth in agricultural soil microbiome studies.

microbiology↗

bioRxiv2024

Domesticated cannabinoid synthases amid a wild mosaic cannabis pangenome

Cannabis sativa is a globally significant seed-oil, fiber, and drug-producing plant species. However, a century of prohibition has severely restricted legal breeding and germplasm resource development, leaving potential hemp-based nutritional and fiber applications unrealized. Existing cultivars are highly heterozygous and lack competitiveness in the overall fiber and grain markets, relegating hemp to less than 200,000 hectares globally1. The relaxation of drug laws in recent decades has generated widespread interest in expanding and reincorporating cannabis into agricultural systems, but progress has been impeded by the limited understanding of genomics and breeding potential. No studies to date have examined the genomic diversity and evolution of cannabis populations using haplotype-resolved, chromosome-scale assemblies from publicly available germplasm. Here we present a cannabis pangenome, constructed with 181 new and 12 previously released genomes from a total of 156 biological samples from both male (XY) and female (XX) plants, including 42 trio phased and 36 haplotype-resolved, chromosome-scale assemblies. We discovered widespread regions of the cannabis pangenome that are surprisingly diverse for a single species, with high levels of genetic and structural variation, and propose a novel population structure and hybridization history. Conversely, the cannabinoid synthase genes contain very low levels of diversity, despite being embedded within a variable region containing multiple pseudogenized paralogs and distinct transposable element arrangements. Additionally, we identified variants of acyl-lipid thioesterase (ALT) genes2 that are associated with fatty acid chain length variation and the production of the rare cannabinoids, tetrahydrocannabinol varin (THCV) and cannabidiol varin (CBDV). We conclude the Cannabis sativa gene pool has only been partially characterized, and that the existence of wild relatives in Asia remains likely, while its potential as a crop species remains largely unrealized.

plant biology↗