Biology subjects

Ritter, E. J.

Publications and source records attributed to Ritter, E. J..

4 recordsLinked to original sources

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↗

bioRxiv2024

Small, but mitey: Investigating the molecular genetic basis for mite domatia development and intraspecific variation in Vitis riparia using transcriptomics

* Here, we investigated the molecular genetic basis of mite domatia, structures on the underside of leaves that house mutualistic mites, and intraspecific variation in domatia size in Vitis riparia (riverbank grape). * Domatia and leaf traits were measured, and the transcriptomes of mite domatia from two genotypes of V. riparia with distinct domatia sizes were sequenced to investigate the molecular genetic pathways that regulate domatia development and intraspecific variation in domatia traits. * Key trichome regulators as well as auxin and jasmonic acid are involved in domatia development. Genes involved in cell wall biosynthesis, biotic interactions, and molecule transport/metabolism are upregulated in domatia, consistent with their role in domatia development and function. * This work is one of the first to date that provides insight into the molecular genetic bases of mite domatia. We identified key genetic pathways involved in domatia development and function, and uncovered unexpected pathways that provide an avenue for future investigation. We also found that intraspecific variation in domatia size in V. riparia seems to be driven by differences in overall leaf development between genotypes.

plant biology↗

bioRxiv2023

From buds to shoots: Insights into grapevine development from the Witch's Broom bud sport

Premise of StudyDevelopment is relatively understudied in woody vines, such as grapevine (Vitis vinifera). We used the Witchs Broom bud sport in grapevine to understand the developmental trajectories of the bud sports, as well as the potential genetic basis of the bud sport. MethodsWe phenotyped shoots, buds, and leaves of two independent cases of the Witchs Broom bud sport, in the Dakapo and Merlot varieties of grapevine, alongside wild-type counterparts of the same variety. We also performed Illumina and Oxford Nanopore sequencing on the two independent cases and two wild-type counterparts of the same variety. Key ResultsThe Dakapo and Merlot cases of Witchs Broom displayed severe developmental defects, with no fruit/clusters formed and dwarf vegetative features. However, the Dakapo and Merlot cases of Witchs Broom studied were also phenotypically different from one another, with distinct differences in bud and leaf development. We were able to identify unique genetic mutations in our two Witchs Broom cases that are strong candidates for the genetic basis of the bud sports. ConclusionsThe Witchs Broom bud sport in grapevine serves as a useful natural mutant in which to study grapevine development. The Witchs Broom bud sports in both varieties studied had dwarf phenotypes, but the two instances studied were also vastly different from one another. Future work on Witchs Broom bud sports in grapevine could provide more insight into development and the genetic pathways involved in grapevine.

plant biology↗

bioRxiv2020

Composite modeling of leaf shape across shoots discriminates Vitis species better than individual leaves

Premise of studyLeaf morphology is dynamic, continuously deforming during leaf expansion and among leaves within a shoot. We measured leaf morphology from over 200 vines over four years, and modeled changes in leaf shape along the shoot to determine if a composite "shape of shapes" can better capture variation and predict species identity compared to individual leaves. MethodsUsing homologous universal landmarks found in grapevine leaves, we modeled various morphological features as a polynomial function of leaf node. The resulting functions are used to reconstruct modeled leaf shapes across shoots, generating composite leaves that comprehensively capture the spectrum of possible leaf morphologies. ResultsWe found that composite leaves are better predictors of species identity than individual leaves from the same plant. We were able to use composite leaves to predict species identity of previously unassigned vines, which were verified with genotyping. DiscussionObservations of individual leaf shape fail to capture the true diversity between species. Composite leaf shape--an assemblage of modeled leaf snapshots across the shoot--is a better representation of the dynamic and essential shapes of leaves, as well as serving as a better predictor of species identity than individual leaves.

plant biology↗