Biology subjects

Cochetel, N.

Publications and source records attributed to Cochetel, N..

At least 19 recordsLinked to original sources

bioRxiv2026

Genetic Mapping Reveals a Major Locus for Boron Exclusion in Wild Vitis

Boron toxicity constrains grapevine (Vitis) production in irrigated arid and semi-arid regions, yet most available rootstocks are sensitive to excessive boron. Although underutilized Vitis species may harbor sources of adaptation, the genetic basis of natural variation in boron exclusion remains poorly understood, limiting the development of boron-tolerant rootstocks. We screened 267 wild Vitis accessions representing 16 species for their ability to limit leaf boron accumulation under excess boron conditions. Leaf boron concentration varied 190-fold among accessions and was highly heritable (entry-mean H^2 = 0.71). Its correlation with stomatal conductance was modest (r = 0.34), indicating that transpiration rate explained only a small proportion of the variation in leaf boron accumulation. Leaf boron was correlated with leaf chloride (r = 0.36), but their largely non-overlapping association profiles supported distinct genetic control. Genome-wide association analysis identified a suggestive association on chromosome 11. Independent quantitative trait locus mapping in a full-sib F1 population (n = 158) derived from Longii-9018 (V. acerifolia) x GRN3 (commercial rootstock) identified qBEx11.1 in the same syntenic region on chromosome 11, which explained 19.5% of the phenotypic variance. Positional candidate genes near the association peak included a pectinesterase and a MATE efflux transporter, suggesting roles for cell wall modification and membrane transport. Leaf spectral reflectance was associated with leaf boron concentration in both populations, particularly at visible and red-edge wavelengths, indicating potential for high-throughput phenotyping. Together, these findings identify qBEx11.1 as a priority locus for boron exclusion and support integrated genetic and spectral approaches for breeding boron-tolerant grapevine rootstocks.

plant biology↗

bioRxiv2026

Harnessing Vitis germplasm diversity to dissect and predict adventitious rooting traits in grapevine

Adventitious root formation (ARF) is a critical trait for the cost-effective propagation of grapevines in commercial nurseries. Poor rooting ability can limit the use and adoption of new rootstocks derived from underutilized Vitis species, constraining breeding efforts largely to the traditional trio: Vitis riparia, V. rupestris, and V. berlandieri. Despite its agronomic relevance, the genetic basis of ARF remains poorly characterized across the broader Vitis genus. In this study, we evaluated 308 accessions representing 18 Vitis species over three growing seasons, quantifying rooting performance at two developmental stages, callus-stage and post-transplant, alongside root biomass, cutting weight, and a derived transplant-response index. We observed extensive phenotypic variation both within and across species, and species rankings depended on the trait considered. V. riparia, V. rupestris and V. californica ranked among the top five species for all four rooting traits, whereas V. cinerea and V. candicans ranked among the lowest for root weight and post-transplant rooting. V. arizonica and V. acerifolia rooted well at the callus stage but were intermediate after transplanting, and V. berlandieri was among the weakest at the callus stage yet intermediate for post-transplant rooting. Repeatability was moderate to high for root weight (0.74) and callus-stage rooting (0.66), and lower for post-transplant rooting (0.47), reflecting both genetic control and season-to-season variation. Between-species differences accounted for 68% of the genetic variance in callus-stage rooting but only 10% in cutting weight. Rooting was associated with the climate of each accession's wild site of origin: after removing differences among species, accessions originating from sites with lower dry-season precipitation rooted better and produced more root biomass. Genome-wide association analysis using 3.4 million SNPs identified 54 significant SNPs resolving into 18 independent loci across four traits, with root weight contributing 12 of them. Candidate genes in linkage with these loci include a mitogen-activated protein kinase, a SCARECROW-LIKE GRAS transcription factor, PASTICCINO1, expansin A1, an AP2/ERF-RAV1 transcription factor, a tandem array of caffeoyl-CoA O-methyltransferases, and several sugar, peptide and nitrate transporters, implicating auxin-linked cell proliferation, cell wall and lignin remodeling, and solute transport. Genomic and phenomic prediction models yielded moderate accuracies across traits and seasons; up to r = 0.67 for post-transplant rooting within a season and r = 0.65 for previously unevaluated accessions. Moreover, the integration of spectral and genotypic data further improved predictive performance. Prediction accuracy was essentially flat between 5,000 and 50,000 markers. This study establishes a foundational framework for the genetic improvement of grapevine rootstocks, promoting broader use of resilient, high-performing, and clonally-propagable germplasm in viticulture.

genetics↗

bioRxiv2026

TPS Expression, Not Copy Number, Explains Aroma Diversity among Grapevine (Vitis vinifera L.) Cultivars

Terpenoids are major contributors to grapevine berry and wine aroma, with mono- and sesquiterpenoids exhibiting substantial variation among cultivars. However, the genetic basis of cultivar-specific terpenoid profiles remains only partially understood due to gene duplications that expanded the terpenoid synthase (TPS) gene family across different cultivars. Here, we compared haplotype-resolved genome assemblies for seven cultivars to analyze copy number variation and expression profiles of terpenoid biosynthesis genes and terpenoid accumulation throughout flower and berry development. These assemblies resolved duplicated TPS loci at the haplotype level, revealing extensive copy number variation across cultivars and between haplotypes within a cultivar, with up to 44 mono-TPS genes on a single haplotype. We identified eight specific monoterpenoids as key drivers of cultivar-specific profiles in ripe berries. Total TPS transcript abundance correlated strongly with total terpenoid accumulation over time. In contrast, TPS copy number was largely decoupled from both expression and terpenoid accumulation, indicating that expression regulation, rather than gene dosage, underlies aroma differences among cultivars. Transcript-metabolite network analysis revealed both expected correlations between specific TPS genes and putative products as well as novel associations. We functionally validated selected candidate TPS in Nicotiana benthamiana, characterizing -farnesene, {beta}-ocimene, and multi-product -terpineol synthases. The in vivo characterization demonstrated that minor sequence variations can alter catalytic activity and product profile. Together, these findings show that the extensive duplication of TPS genes in grapevine does not itself determine terpenoid output; instead, cultivar-specific aroma arises from how these genes are expressed and from sequence differences that shape enzyme activity.

plant biology↗

bioRxiv2026

Genomic compartmentalization of pervasive sex-biased gene expression in the vine mealybug Planococcus ficus

The vine mealybug, Planococcus ficus, is a globally invasive pest of grapevine and a vector of leafroll viruses. Like other mealybugs, it reproduces through paternal genome elimination, a sex-determination system that operates without sex chromosomes and is associated with extreme sexual dimorphism. To characterize genome organization and sex-biased expression in this species, we generated a long-read reference genome spanning 369 Mb with 23,489 annotated genes and macrosynteny conserved with the citrus mealybug, Planococcus citri. Resequencing of four California field individuals yielded a first whole-genome estimate of nucleotide diversity and 132 microsatellite markers for population monitoring. Among 2,129 candidate secreted proteins, a conserved core is shared with P. citri, but each species carries a distinct set of lineage-specific effectors. Comparing adult male and female transcriptomes, we found sex-biased expression to be pervasive and skewed toward females: 41% of tested genes differed between the sexes, with female-biased genes both more numerous and showing larger fold changes. These female-biased genes were not randomly distributed but concentrated in discrete blocks of coordinately expressed, tandemly duplicated gene families, a pattern not previously described in a mealybug. Male- and female-biased secreted proteins also differed in origin, with male-biased proteins drawn from a conserved repertoire shared with P. citri and female-biased proteins spanning a more lineage-specific pool. Together, these results reveal a female-skewed, spatially clustered architecture of sex-biased expression in a mealybug that lacks sex chromosomes, and provide genomic resources for managing an invasive vineyard pest.

genomics↗

bioRxiv2026

Cell-type-specific transcriptional plasticity in a multi-organ atlas reveals organ-independent companion cell regulatory programs in grapevine

Plants comprise both cell types shared across organs and those restricted to specific tissues. How the transcriptional programs defining cell identity are maintained or remodeled across organ contexts remains poorly understood, particularly in long-lived perennials, for which cell type-resolved transcriptomic data remain scarce. We generated a multi-organ single-nucleus transcriptomic atlas of the dwarf grapevine cultivar Pixie, comprising over 220,000 nuclei from nine organs, including roots, green stems, pre-anthesis flowers, dormant buds, young and old leaves, and berries at three developmental stages, each sampled in duplicates. We annotated 46 distinct cell types, reconstructed developmental trajectories within selected cell types, and inferred gene regulatory networks at cell type resolution. Broadly distributed cell types, including epidermis, xylem parenchyma, and phloem parenchyma, exhibited pronounced organ-dependent transcriptional divergence, with organ identity accounting for 65% of regulon activity variance across the atlas. In contrast, companion cells maintained organ-independent regulatory programs, representing the stable end of a continuum of transcriptional plasticity that spans shared cell types. We identified cell-type-specific transcription factor expression and inferred gene regulatory networks using motif-based regulon analysis, revealing candidate regulators of cell identity and tissue specialization. Together, this atlas provides a reference framework for cell type-resolved functional genomics in a perennial woody crop.

genomics↗

bioRxiv2026

Haplotype-specific expression of a terpene synthase underlies linalool variation in the grapevine cultivar Riesling

Grapevine cultivars vary widely in monoterpenoid content, yet the genetic and regulatory mechanisms underlying this variation remain poorly characterized beyond highly aromatic Muscat types. We profiled free volatiles and monoterpenoid glycosides in a Riesling x Cabernet Sauvignon F1 mapping population, revealing extensive variation and transgressive segregation consistent with multigenic control. QTL mapping identified 59 significant loci associated with 47 volatile compounds and monoterpene glycosides, including two major QTLs explaining 33.8% and 32.4% of phenotypic variance in (3S)-linalool accumulation. Integration of haplotype-resolved transcriptomics with metabolite data, enabled by a chromosome-scale diploid Riesling genome assembly, resolved a (3S)-linalool/nerolidol synthase cluster on chromosome 10 and identified VviTPS54 as the strongest candidate underlying linalool variation. VviTPS54 exhibited haplotype-specific expression strongly correlated with (3S)-linalool accumulation across genotypes, while no QTL was detected at the VviDXS1 locus and VviDXS1 expression was not correlated with terpene levels, indicating that regulatory variation within terpene synthase clusters, rather than methylerythritol phosphate (MEP) pathway flux, drives monoterpenoid composition in this population. These results establish regulatory variation of terpene synthases as a key mechanism underlying monoterpenoid diversity in grapevine and demonstrate that resolving such variation requires haplotype-phased genome assemblies coupled with haplotype-resolved transcriptomics to detect allele-specific expression differences at complex, heterozygous loci.

plant biology↗

bioRxiv2026

Genome-wide characterization of extant clonal diversity in Chilean Carmenere

Carmenere is a widely cultivated and internationally recognized grapevine cultivar in Chile, yet genetic variation among its clones remains poorly characterized. Early studies based on SSR and AFLP markers detected limited polymorphism, but these approaches interrogate only a small fraction of the genome, leaving the extent of clonal diversity unresolved. Here, we generated an improved chromosome-scale diploid genome assembly of Carmenere FPS clone 02 and characterized clonal genomic diversity by sequencing 36 biological replicates representing 12 clones maintained in Chile, including heritage selections rescued from old producer vineyards by Vina Santa Carolina as part of its Bloque Herencia conservation program, and commercial nursery-derived clones. Focusing on low-frequency variants and using replicate-aware consensus calling, we identified more than 9,000 private single nucleotide variants (SNVs) and small indels per clone, providing high-resolution markers for clonal identification. Although most variants were located in repetitive or intergenic regions, a subset affected coding sequences, with genes involved in plant-pathogen interactions, transport, and secondary metabolism most frequently impacted. While variant-affected genes associated with wine anthocyanin content, TA, pH, and alcohol percentage were identified, broader phenotypic characterization will be required to assess their biological significance. Overall, this study provides a genome-wide characterization of extant clonal diversity in Carmenere, with implications for clonal selection and genetic resource conservation.

genomics↗

bioRxiv2026

The dynamics of introgression across an adaptive radiation: examining hybrid speciation and parallel adaptation in North American Vitis

Hybridization between species can contribute to parallel adaptive events and, in some cases, speciation. However, the prevalence of introgression is rarely measured across multiple species, meaning that it is rarely integrated with landscape-scale processes or connected to adaptive repeatability. Here, we analyzed whole-genome resequencing data from 639 accessions representing 48 Vitis species. Vitis is notable for the domesticated grapevine (V. vinifera), multiple economically important North American species, and as an example of a temperate adaptive radiation. Our dataset included population-level sampling for 19 species, from which we reconstructed individual- and species-level phylogenetic frameworks for the genus. The analyses uncovered widespread evidence of introgression, comprising [~]14% of the average Vitis genome. Introgression was associated with geographic distribution between species, and highly admixed individuals were more frequently found near ecological niche margins. Genetic analyses further indicated that previously recognized hybrid taxa, V. x doaniana and V. x champinii, likely represent hybrid swarms rather than distinct species. We also assessed patterns of adaptive repeatability across eight species with denser population sampling. For six of the eight species, most of the detected sweeps overlapped with sweeps in other species; on average, more recently diverged species shared more overlapping sweeps. Parallel sweep events were driven mostly by introgression, although a substantial fraction ([~]40%) was attributed to selection on ancestral standing variation. By integrating population genomic data across many species, this study highlights the central role of shared genetic variation across an adaptive radiation.

evolutionary biology↗

bioRxiv2025

Haplotype graph analysis of PdR1 uncovers resistance diversity to Pierce's Disease in Vitis arizonica and its hybrids

Previous genetic mapping studies indicate that multiple haplotypes of the Pierces disease (PD) Resistance 1 (PdR1) locus occur in Vitis arizonica and its hybrids. To characterize sequence diversity at this locus, we assembled chromosome-scale diploid genomes for four PD-resistant (PD-R) accessions: b43-17 (PdR1a/PdR1b), the backcross 07744-094 (PdR1c/PdR1-), b46-43 (PdR1e/PdR1f), and b42-26 (PdR1-/PdR1-), which displays quantitative PD resistance not associated with PdR1. Haplotype resolution of PdR1a, PdR1b, PdR1c, and PdR1e revealed substantial variation in intergenic repeat content and gene composition between PdR1 and their alternative haplotype at the PdR1 locus not associated with PD resistance phenotype (PdR1-), as well as among PdR1 haplotypes, demonstrating extensive sequence diversity at the PdR1 locus. Sequence graph analysis uncovered substantial structural divergence concentrated in approximately one quarter of the locus, together with smaller-scale variation across haplotypes. This analysis identified PdR1-specific graph nodes, showing that PdR1a and PdR1b share most of their PdR1-specific features, whereas PdR1c contains the highest number of private nodes, followed by PdR1e. Integration of sequence graph features with gene expression data further refined a set of defense-related candidate genes within PdR1c. Together, these results identify candidate genes for functional validation and indicate that multiple resistance determinants co-localized within the PdR1 locus may contribute to PD resistance, highlighting opportunities for targeted genetic improvement strategies.

genomics↗

bioRxiv2025

Dual single-nucleus gene expression atlas of grapevine and Erysiphe necator during early powdery mildew infection

We applied dual-organism single-nucleus transcriptomics to study the interaction between grapevine leaves and Erysiphe necator, the causal agent of powdery mildew, at one and five days post-infection, including controls and three biological replicates. We generated a grapevine leaf atlas encompassing over 100,000 nuclei, and a pathogen atlas of more than 3,000 nuclei. We successfully annotated all major grapevine cell types, including mesophyll, epidermis, phloem and xylem parenchyma, companion cells, and guard cells. We identified key E. necator structures, including appressoria, haustoria, and hyphae, and provided a list of novel cell type markers for both species. We reveal structure-specific gene expression programs in E. necator laying a foundation for future studies of fungal development and virulence mechanisms. In the host, we identified spatially distinct expression patterns of defense-related genes. As the infection progressed, we observed the activation of a coordinated immune response involving multiple cell types, mainly epidermal and mesophyll cells. High-dimensional weighted gene co-expression network analysis identified key hubs and networks associated with cell type-specific signaling and defense response. We describe a spatial separation of pattern- and effector-triggered immunity, supporting a model in which pattern-triggered immunity is activated at the site of pathogen contact and effector-triggered immunity is induced in surrounding tissue.

plant biology↗

bioRxiv2025

Phased epigenomics and methylation inheritance in a historical Vitis vinifera hybrid

Epigenetic modifications, such as DNA methylation, regulate transcription and influence key biological traits. While many efforts were made to understand their stability in annual crops, their long-term persistence in clonally propagated plants remains poorly understood. Grapevine (Vitis vinifera) provides a unique model, with cultivars vegetatively propagated for centuries. Here, we assembled the phased genomes of Cabernet Sauvignon and its parental lineages, Cabernet Franc and Sauvignon Blanc, using HiFi long-reads and a gene map tenfold denser than existing maps. Using three clones per cultivar, we quantifyied methylation with very consistent short- and long-read sequencing and ensured both varietal representativeness and assessment of clonal variability. We leveraged the parent-progeny sequence graph to highlight allele-specific methylation and conserved transcriptomic patterns for genes and small RNA. Such a format was essential to integrate multi-omics data and revealed that despite less clonal conservation than genetic polymorphisms, methylation marks were remarkably inherited. By further demonstrating the linear-reference limitations, we determined the correct representation of genetic variants by the sequence graph is crucial for the accurate allelic quantification of the methylome. These findings reveal the remarkable stability of epigenetic marks in a model propagated by asexual reproduction. Using a phased sequence graph, we introduce a scalable framework that accounts for genomic variation, accurately quantifies allele-specific methylation, and supports multi-omics integration such as our evaluation of the transcriptional impact of epigenetic inheritance. This approach has broad implications for perennial crops, where epigenetic variation could influence traits relevant to breeding, adaptation, and long-term agricultural sustainability.

genomics↗

bioRxiv2025

Integration of diploid T2T parental genomes with progeny genomes and transcriptomes identifies resistance genes in the grape powdery mildew resistance loci Ren6 and Ren7 of Vitis piazeskii

The Chinese grape accession Vitis piasezkii DVIT2027 carries two loci associated with powdery mildew (PM) resistance loci, Ren6 and Ren7, which differ in timing and strength of response to Erysiphe necator. Both loci are consistent with recognition by intracellular immune receptors. To identify the underlying nucleotide-binding leucine-rich repeat (NLR) genes, we assembled chromosome-scale diploid genomes of DVIT2027 and the susceptible V. vinifera F2-35, parents of a segregating F1 population. We integrated these assemblies with deep resequencing data from eight F1 sib-lines carrying different Ren6/Ren7 combinations and generated trio-binned, parent-phased genomes for six progeny. This resolved both PM-resistant (PMR) and PM-susceptible (PMS) haplotypes at Ren6 and Ren7. Comparative analyses revealed extensive structural variation and complete haplotype specificity among NLRs, with several candidate genes lacking allelic counterparts in PMS haplotypes. Expression profiling across PMR sib-lines identified four and two CC-NBS-LRR genes potentially associated with Ren6 and Ren7, respectively. Sequence graph reconstruction of these loci across multiple V. piasezkii accessions revealed broad intraspecific diversity and DVIT2027-specific nodes, including within candidate NLR genes. These results provide a high-resolution view of Ren6 and Ren7 and support the identification of resistance gene candidates for functional validation and grapevine breeding.

plant biology↗

bioRxiv2025

The Genetic Basis of Microbiome Recruitment in Grapevine and its Association with Fermentative and Pathogenic Taxa

O_LIWhile grapevine is an exceptional perennial model for studying host-microbiome interactions, the host genomes role in microbiome assembly is often masked by environmental factors. This research provides a first insight into the genetic mechanisms shaping berry-associated microbial communities. C_LIO_LIUsing QTL mapping in a newly established population of 140 F1-progeny grapevine genotypes in a complete random block design, we were able to control abiotic effects and investigate how the host genome influences grape berry-associated bacterial and fungal communities. C_LIO_LIWe identify significant associations between various microorganisms and the grape genome, including pathogenic fungi such as Botrytis spp. and fermentative yeasts such as Saccharomyces cerevisiae. Many of these taxa map to the same genetic loci associated with plant immune responses, suggesting that specific genetic loci broadly influence microbial community assembly in fruits. C_LIO_LIOur findings demonstrate that grapevine genetics significantly shape the microbiome, even under varying environmental conditions; moreover, that broad, rather than known symbiont-specific mechanisms control microbial colonization of fruit, revealing an emergent "domino" effect with implications for plant-fungal-bacterial interactions. We provide a framework for understanding genotype-microbiome interactions in perennial plants, enabling future targeted experiments to establish causal relationships in microbiome recruitment and offer a potential avenue for breeding programs advancing sustainable viticulture. C_LI

microbiology↗

bioRxiv2025

The Genetic Basis of Chloride Exclusion in Grapevines

Mediterranean regions are among the most important areas for global grape production, characterized by dry climates and frequent challenges associated with soil salinity. In these environments, chloride toxicity is a major factor limiting vine growth and fruit quality. Despite the critical role of chloride exclusion in salinity tolerance, the genetic mechanisms underlying this trait remain poorly understood. In this study, we leveraged one of the largest Vitis germplasm collections, comprising 335 accessions from 18 wild and cultivated Vitis species, to characterize natural variation in chloride exclusion. This diverse panel, which includes accessions from the southwestern United States and Mexico, captures a broad range of evolutionary adaptations to abiotic stress, providing an unprecedented opportunity to investigate the genetic basis of salinity tolerance. Using genome-wide association (GWA) and quantitative trait loci (QTL) mapping, we identified a major QTL on chromosome 8 containing candidate genes encoding cation/H exchangers (CHX), which are involved in ion transport and homeostasis. To validate these findings, we analyzed a mapping population derived from V. acerifolia longii 9018 and the commercial rootstock GRN3, confirming the chromosome 8 locus as a major determinant of chloride exclusion. Structural variant analysis revealed key non-synonymous substitutions within CHX genes, suggesting potential functional roles in salinity tolerance. Additionally, we discovered a novel QTL on chromosome 19 enriched with G-type lectin S-receptor-like serine/threonine-protein kinases, known regulators of stress signaling. By integrating extensive phenotypic and genomic data across a diverse Vitis collection, this study provides novel insights into the genetic architecture of chloride exclusion and identifies valuable candidate genes for breeding salt-tolerant rootstocks.

genetics↗

bioRxiv2025

Smoke exposure triggers rapid transcriptional changes and reveals glycosyltransferases linked to smoke taint in ripening grape berries

With the increasing frequency of wildfires, vineyards are more often exposed to smoke, resulting in a higher risk of smoke taint in wine. This taint imparts undesirable "smoky" and "ashy" aromas and causes significant economic losses. Smoke-derived volatile phenols (VPs) in grape berries, metabolized into stable, non-volatile glycoconjugates via glycosyltransferases (GTs), underlie smoke taint formation. Here, we present the dwarf grapevine cultivar Pixie as a model system for smoke taint research. We generated a phased, telomere-to-telomere diploid genome using HiFi long-read sequencing, along with an expression atlas spanning 30 replicated samples across various tissues and developmental stages. We also constructed a second telomere-to-telomere assembly for Pinot Noir to assess GT expression during berry ripening in the field. Controlled smoke-exposure experiments profiled GT expression and enabled transcriptome-wide analyses at multiple time points. We measured VPs in both smoke-exposed and control samples, revealing 12 GT1 genes significantly upregulated by smoke, named Vitis vinifera smoke-inducible UGTs (VviSIUGTs). Their expression peaked one day post-exposure and declined by day three, mirroring glycoside accumulation dynamics. Gene co-expression network analyses highlighted stress-responsive modules enriched in these VviSIUGTs, while transcription factor binding site analyses pinpointed stress-related regulatory elements in their promoters. These findings provide new insights into the molecular basis of smoke taint and identify potential targets for breeding and biotechnological interventions aimed at developing grapevine cultivars with reduced susceptibility to smoke damage.

plant biology↗

bioRxiv2024

Evolutionary history of the grape sex-determining region in angiosperms and emergence of dioecy in Vitaceae

Dioecy, defined by the presence of either female or male flowers on separate individual plants, is rare in angiosperms. However, it has independently evolved multiple times from hermaphroditic ancestors. In Vitis spp., flower sex is determined by a [~]200-kbp region with five genes involved in flower development and sexual identity. This study traces the evolutionary history of the Vitis sex-determining region (SDR) to assess whether it evolved in a conserved flowering-related locus. We analyzed the conservation of the Vitis SDR across 42 plant genomes and found collinearity in all 39 angiosperms, but not in non-flowering plants. The number of collinear genes and their rank-normalized gene conservation score were higher in the Vitis SDR compared to the rest of the genome, indicating its importance for flowering. We further explored SDR conservation within the Vitaceae family by long-read sequencing and haplotype phasing of eight species, including the outgroup Leea coccinea. Similarly, the Vitis SDR was highly conserved across the Vitaceae genomes, although variations in region size, primarily attributed to differences in repetitive elements, were observed. Interestingly, no recombination suppression was found in the dioecious Tetrastigma, suggesting a different sex determination mechanism. In Muscadinia rotundifolia, linkage disequilibrium analysis, haplotype comparison, and gene expression profiling showed that muscadine grapes have similar SDR boundaries and candidate sex-determining genes as Vitis. These results suggest that dioecy emerged in a common ancestor of the two grape genera at a locus associated with flower morphology and fertility, highly conserved in flowering plants.

evolutionary biology↗

bioRxiv2024

The assembly and annotation of two teinturier grapevine varieties, Dakapo and Rubired

BackgroundTeinturier grapevine varieties were first described in the 16th century and have persisted due to their deep pigmentation. Unlike most other grapevine varieties, teinturier varieties produce berries with pigmented flesh due to anthocyanin production within the flesh. As a result, teinturier varieties are of interest not only for their ability to enhance the pigmentation of wine blends but also for their health benefits. Here, we assembled and annotated the Dakapo and Rubired genomes, two teinturier varieties. FindingsFor Dakapo, we used a combination of Nanopore sequencing, Illumina sequencing, and scaffolding to the existing grapevine genome assembly to generate a final assembly of 508.5 Mbp with an N50 scaffold length of 25.6 Mbp and a BUSCO score of 98.0%. A combination approach of de novo annotation and lifting over annotations from the existing grapevine reference genome resulted in the annotation of 36,940 genes in the Dakapo assembly. For Rubired, PacBio HiFi reads were assembled, scaffolded, and phased to generate a diploid assembly with two haplotypes 474.7-476.0 Mbp long. The diploid genome has an N50 scaffold length of 24.9 Mbp and a BUSCO score of 98.7%, and both haplotype-specific genomes are of similar quality. De novo annotation of the diploid Rubired genome yielded annotations for 56,681 genes. ConclusionsThe Dakapo and Rubired genome assemblies and annotations will provide genetic resources for future investigations into berry flesh pigmentation and other traits of interest in grapevine.

genomics↗

bioRxiv2023

Comparative pangenomic insights into the distinct evolution of virulence factors among grapevine trunk pathogens

The permanent organs of grapevines (V. vinifera L.), like other woody perennials, are colonized by various unrelated pathogenic ascomycete fungi secreting cell wall-degrading enzymes and phytotoxic secondary metabolites that contribute to host damage and disease symptoms. Trunk pathogens differ in the symptoms they induce and the extent and speed of damage. Isolates of the same species often display a wide virulence range, even within the same vineyard. This study focuses on Eutypa lata, Neofusicoccum parvum, and Phaeoacremonium minimum, causal agents of Eutypa dieback, Botryosphaeria dieback, and Esca, respectively. We sequenced fifty isolates from viticulture regions worldwide and built nucleotide-level, reference-free pangenomes for each species. Through examining genomic diversity and pangenome structure, we analyzed intraspecific conservation and variability of putative virulence factors, focusing on functions under positive selection, and recent gene-family dynamics of contraction and expansion. Our findings reveal contrasting distributions of putative virulence factors in the core, dispensable, and private genomes of each pangenome. For example, CAZymes were prevalent in the core genomes of each pangenome, whereas biosynthetic gene clusters were prevalent in the dispensable genomes of E. lata and P. minimum. The dispensable fractions were also enriched in Gypsy transposable elements and virulence factors under positive selection (polyketide synthases genes in E. lata and P. minimum glycosyltransferases in N. parvum). Our findings underscore the complexity of the genomic architecture in each species and provide insights into their adaptive strategies, enhancing our understanding of the underlying mechanisms of virulence.

genomics↗