Biology subjects

Brose, J.

Publications and source records attributed to Brose, J..

8 recordsLinked to original sources

bioRxiv2026

Time-dependent transcriptomic changes following protoplast isolation in plants

Protoplast isolation is widely used for plant functional genomics and single-cell analyses, but its impact on transcriptional and cell state dynamics remains incompletely understood. Here, we generated time-course RNA-seq data from leaf protoplasts of Arabidopsis, maize, and poplar, sampling at multiple time points following isolation, to systematically characterize global transcriptional dynamics across species. We identified two major drivers of transcriptional variation: a persistent protoplast isolation effect and a progressive time-dependent transcriptional program, which can be divided into early, middle, and late stages corresponding to an immediate stress response, metabolic and chromatin regulation dynamics, and sustained metabolic and proteostasis regulation, together with species-specific differences across stages. We observed a rapid loss of cell-type-specific transcriptional signatures within 6 hours in Arabidopsis and maize, whereas poplar showed a slower decline. Single-nucleus RNA-seq at 6 hours in maize confirmed attenuation of cell-type-specific transcriptional structure. Furthermore, leveraging this time-course dataset enables the identification of aberrant cell states in single-cell RNA-seq data, exemplified by clusters showing elevated activity of protoplast isolation-associated, middle-, and late-stage transcriptional programs characteristic of stress-like states. Together, our results provide a cross-species framework for dissecting protoplast-induced transcriptional and cell state dynamics and facilitate the systematic identification of stress-associated cell states in single-cell transcriptomic data.

plant biology↗

bioRxiv2026

A Comprehensive Epidermal Map from a Poplar Single-Cell Shoot Atlas Reveals New Trichome-Specific Genes

Poplar (Populus spp.) is a model system for tree biology. Specifically, P. tremula x P. alba INRA 717-1B4 (hereafter "poplar 717") has become an important platform for functional genomics and synthetic biology due to its rapid growth and ease of transgenesis. Here, we present a single-cell RNA-seq atlas of the poplar 717 shoot, including apical meristem, primary and secondary stems, and three stages of leaf development. Analysis of ca. 159,000 cells resolved 40 transcriptionally distinct clusters representing 7 major cell types, providing a high-resolution view of shoot development and tissue organization. We focused on the epidermis which constituted >15% of cells in the shoot atlas for in-depth characterization of epidermal heterogeneity. By integrating known marker genes with transcriptomic signatures consistent with established poplar leaf phytochemistry, we annotated epidermal cell subclusters corresponding to developmental stages, spatial location, and specialized cell types, including a distinct population of non-glandular trichomes. Coupling the single-cell RNA-seq atlas with bulk transcriptome data from glabrous mutants enabled the identification of novel trichome markers. Experimental validation of a representative trichome-specific promoter established a tool with potential to support cell type-targeted-metabolic engineering. We provide the poplar 717 atlas to the community through the BioPoplar Atlas Viewer (http://bio-poplar-atlas.com), providing a platform to explore the poplar transcriptome at single-cell resolution and a foundation for data-driven cell type-aware genetic engineering strategies in poplar.

plant biology↗

bioRxiv2025

Chromosome-scale genome assembly for Yellow Wood sorrel, Oxalis stricta

Yellow wood sorrel (Oxalis stricta L.), also known as sourgrass, juicy fruit, or sheep weed, is a member of the Oxalidaceae family. Yellow wood sorrel is commonly considered a weed and while native to North America, it is distributed across Europe, Asia, and Africa. To date, only two other genomes from the Oxalidaceae family have been published, star fruit (Averrhoa carambola L.) and Oxalis articulata Savingy. Here, we present a chromosome-scale assembly for O. stricta, revealing its allotetraploid nature and synteny within its two subgenomes as well as synteny with A. carambola and O. articulata. Using Oxford Nanopore Technologies long-read sequences coupled with chromatin capture sequencing, we generated a 436 Mb chromosome-scale assembly of O. stricta with a scaffold N50 length of 36.2 Mb that is anchored to 12 chromosomes across the two subgenomes. Assessment of the final genome assembly using the Long Terminal Repeat Assembly Index yielded a score of 13.12 and assessment of Benchmarking Universal Single Copy Orthologs revealed 99.3% complete orthologs; both metrics are suggestive of a high-quality reference genome. Total repetitive sequence content in the O. stricta genome was 39.7% with retroelements being the largest class of transposable elements. Annotation of protein-coding genes yielded 61,550 high confidence genes encoding 115,089 gene models. Synteny between the two O. stricta subgenomes was present in 91 syntenic blocks containing 40,705 genes, of which, 76.6% were present in 1:1 syntenic relationships between the two subgenomes. The availability of an annotated chromosome-scale high quality genome assembly for O. stricta will provide a launching point to understand the high fecundity of this weed and provide further foundation for comparative genomics within the Oxalidaceae.

genomics↗

bioRxiv2025

An allelic resolution gene atlas for tetraploid potato provides insights into tuberization and stress resilience

Tubers are modified underground stems that enable asexual, clonal reproduction and serve as a mechanism for overwintering and avoidance of herbivory. Tubers are wide-spread across angiosperms with some species such as Solanum tuberosum L. (potato) serving as a vital crop for human consumption. Genes responsible for tuber initiation and disease resistance have been characterized in potato including StSP6A, a homolog of Flowering Time, that functions as tuberigen, the equivalent of florigen. To elucidate additional molecular and genetic mechanisms underlying potato biology including tuber initiation, tuber development, and stress responses, we generated a developmental and abiotic/biotic-stress gene expression atlas from 34 tissues and treatments of Atlantic, a tetraploid cultivar. Using the haplotype-phased tetraploid Atlantic genome assembly and expression abundances of 129,218 genes, we constructed gene coexpression modules that represent networks associated with distinct developmental stages as well as stress responses. Functional annotations were given to modules and used to identify genes involved in tuberization and stress resilience. Structural variation from a pan-genomic analysis across four cultivated potato genome assemblies as well as domestication and wild introgression data allowed for deeper insights into the modules to identify key genes involved in tuberization and stress responses. This study underscores the importance of transcriptional regulation in tuberization and provides a comprehensive framework for future research on potato development and improvement.

plant biology↗

bioRxiv2025

High resolution diel transcriptomes of autotetraploid potato reveal expression and sequence conservation among rhythmic genes

Photoperiodic changes in diel cycles of gene expression are pervasive in plants. Timing of circadian regulators together with light signals regulate multiple photoperiod dependent responses such as growth, flowering or tuber formation. However, for most genes the importance of cyclic mRNA levels is less clear. We analyzed the diel transcriptome of modern cultivated potato, a highly heterozygous autotetraploid. Clonal propagation and limited meiosis have led to the accumulation of deleterious alleles and therefore tetraploid potato is an ideal model system to investigate the conservation of cyclic expression and cyclic genes during the artificial selection process. We observed that cyclic alleles were more highly expressed than non-cyclic ones and were highly co-expressed not only under diel cycles but also across tissues, developmental stages and stress conditions. Moreover, the smaller ratio of non-synonymous to synonymous differences within cyclic as compared to non-cyclic allelic groups indicates that cyclic genes, in general, have more conserved core functions than those of non-cyclic ones. In accordance with this observation, fully rhythmic allelic groups were highly enriched in photosynthesis and ribosome biogenesis genes, which play core functions in plants. Furthermore, we investigated differences in cyclic expression patterns between photoperiods. We identified transcription factors potentially regulating the strong differences in phase between photoperiods observed in ribosome biogenesis and pathogen response genes. Finally, analyses of genes involved in tuber formation suggests that the regulation of CO gene transcription is not the only factor enabling tuberization under long days in modern cultivated potato. This study not only provides high quality diel transcriptomic datasets of cultivated potato but also important insight on the role of allelic diversity in rhythmic expression in plants.

plant biology↗

bioRxiv2024

CYP76BK1 orthologs catalyze furan and lactone ring formation in clerodane diterpenoids across the mint family

The Lamiaceae (mint family) is the largest known source of furanoclerodanes, a subset of clerodane diterpenoids with broad bioactivities including insect antifeedant properties. The Ajugoideae subfamily, in particular, accumulates significant numbers of structurally related furanoclerodanes. The biosynthetic capacity for formation of these diterpenoids is retained across most Lamiaceae subfamilies, including the early-diverging Callicarpoideae which forms a sister clade to the rest of Lamiaceae. VacCYP76BK1, a cytochrome P450 monooxygenase from Vitex agnus-castus, was previously found to catalyze the formation of the proposed precursor to furan and lactone-containing labdane diterpenoids. Through transcriptome-guided pathway exploration, we identified orthologs of VacCYP76BK1 in Ajuga reptans and Callicarpa americana. Functional characterization demonstrated that both could catalyze the oxidative cyclization of clerodane backbones to yield a furan ring. Subsequent investigation revealed a total of ten CYP76BK1 orthologs across six Lamiaceae subfamilies. Through analysis of available chromosome-scale genomes, we identified four CYP76BK1 members as syntelogs within a conserved syntenic block across divergent subfamilies. This suggests an evolutionary lineage that predates the speciation of the Lamiaceae. Functional characterization of the CYP76BK1 orthologs affirmed conservation of function, as all catalyzed furan ring formation. Additionally, some orthologs yielded two novel lactone ring moieties. The presence of the CYP76BK1 orthologs across Lamiaceae subfamilies closely overlaps with the distribution of reported furanoclerodanes. Together, the activities and distribution of the CYP76BK1 orthologs identified here support their central role in furanoclerodane biosynthesis within the Lamiaceae family. Our findings lay the groundwork for biotechnological applications to harness the economic potential of this promising class of compounds. Significance StatementThe discovery and functional characterization of CYP76BK1 orthologs across diverse Lamiaceae subfamilies revealed novel chemistry and their central role in furanoclerodane biosynthesis, providing insights into the metabolic landscape and dynamic evolution of this plant family over approximately 50 million years. These findings pave the way for targeted biosynthetic engineering efforts and the sustainable production of furanoclerodane compounds, offering promising prospects for agricultural and pharmaceutical applications.

plant biology↗

bioRxiv2024

K-mer Genome-wide Association Study for Anthracnose and BCMV Resistance in the Andean Diversity Panel

Limited genomic resources and closely linked marker-trait associations for common beans (Phaseolus vulgaris L.) have limited breeders from fully utilizing molecular genetics technologies to maximize genetic gain. The emergence of virulent races of anthracnose (caused by Colletotrichum lindemuthianum) and Bean Common Mosaic Virus (BCMV) highlight the need for improved methods to identify and incorporate pan-genomic variation in breeding for disease resistance. We sequenced the P. vulgaris Andean Diversity Panel (ADP) and performed a genome-wide association study (GWAS) to identify associations for resistance to BCMV and eight races of anthracnose. Historical single nucleotide polymorphism (SNP)-chip and phenotypic data enabled a three-way comparison between SNP-chip, reference-based whole genome shotgun sequence (WGS)-SNP, and reference-free k-mer GWAS. Across all traits, there was excellent concordance between SNP-chip, WGS-SNP, and k-mer GWAS results--albeit at a much higher marker resolution for the WGS data sets. Significant k-mer haplotype variation revealed selection of the linked I-gene and Co-u traits in North American breeding lines and cultivars. Due to k-mer mapping criteria and the absence of target loci in the reference genome due to structural variation, only 9.1 to 47.3% of the significantly associated k-mers were mapped to the reference genome. To determine the genetic context of cis-associated k-mers, we generated whole genome assemblies of four ADP accessions and identified an expanded local repertoire of disease resistance genes associated with resistance to anthracnose and BCMV. With access to variant data in the context of a pan-genome, high resolution mapping of agronomic traits for common bean is now feasible. CORE IDEASO_LIK-mer-based GWAS offers new advantages for mapping pan-genomic variation C_LIO_LIComparison of reference-based SNP to reference-free k-mer GWAS C_LIO_LINovel discovery of cis-associated k-mers for dry bean disease resistance C_LI PLAIN LANGUAGE SUMMARYImproving disease resistance in crop species such as bean is critical. We surveyed the genomes of a diverse set of bean lines and identified sequences associated with resistance to a fungal and viral pathogen. Access to the genomes of this diversity panel of beans will permit additional discoveries on the role of structural variation in phenotypes, including disease resistance.

plant biology↗

bioRxiv2024

Chromosome-scale Salvia hispanica L. (Chia) genome assembly reveals rampant Salvia interspecies introgression

Salvia hispanica L. (Chia), a member of the Lamiaceae, is an economically important crop in Mesoamerica, with health benefits associated with its seed fatty acid composition. Chia varieties are distinguished based on seed color including mixed white and black (Chia pinta) and black (Chia negra). To facilitate research on Chia and expand on comparative analyses within the Lamiaceae, we generated a chromosome-scale assembly of a Chia pinta accession and performed comparative genome analyses with a previously published Chia negra genome assembly. The Chia pinta and negra genome sequences were highly similar as shown by a limited number of single nucleotide polymorphisms and extensive shared orthologous gene membership. There is an enrichment of terpene synthases in the Chia pinta genome relative to the Chia negra genome. We sequenced and analyzed the genomes of 20 Chia accessions with differing seed color and geographic origin revealing population structure within S. hispanica and interspecific introgressions of Salvia species. As the genus Salvia is polyphyletic, its evolutionary history remains unclear. Using large-scale synteny analysis within the Lamiaceae and orthologous group membership, we resolved the phylogeny of Salvia species. This study and its collective resources further our understanding of genomic diversity in this food crop and the extent of inter-species hybridizations in Salvia. PLAIN LANGUAGE SUMMARYChia pinta is an economically important crop due to the high fatty acid present in the seeds. There are multiple types of Chia based on the seeds color including mixed which and black (Chia pinta), black (Chia negra), and white (Chia blanca). We generated a genome assembly of Chia pinta and compared it to existing genome assemblies. While the assemblies are highly similar there are key differences in terpene synthase composition between Chia pinta and Chia negra. We also sequenced 20 other Chia accessions with different seed color and geographic origin to determine a population structure within Chia. We generated genomic resources to further our understanding of this food crop. ABBREVIATIONSBGC Biosynthetic gene cluster BUSCO Benchmarking Universal Single Copy Orthologs GO Gene ontology SNP Single nucleotide polymorphism TIR Terminal inverted repeat TPS Terpene synthase WGS Whole genome shotgun

genomics↗