Cell Biology & Molecular Genetics

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Author: search.filters.author.Shahan, Rachel

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    Re-annotation of the woodland strawberry (Fragaria vesca) genome
    (Springer Nature, 2015-01-27) Darwis, Omar; Shahan, Rachel; Liu, Zhongchi; Slovin, Janet P; Alkharouf, Nadim W
    Fragaria vesca is a low-growing, small-fruited diploid strawberry species commonly called woodland strawberry. It is native to temperate regions of Eurasia and North America and while it produces edible fruits, it is most highly useful as an experimental perennial plant system that can serve as a model for the agriculturally important Rosaceae family. A draft of the F. vesca genome sequence was published in 2011 [Nat Genet 43:223,2011]. The first generation annotation (version 1.1) were developed using GeneMark-ES+[Nuc Acids Res 33:6494,2005]which is a self-training gene prediction tool that relies primarily on the combination of ab initio predictions with mapping high confidence ESTs in addition to mapping gene deserts from transposable elements. Based on over 25 different tissue transcriptomes, we have revised the F. vesca genome annotation, thereby providing several improvements over version 1.1. The new annotation, which was achieved using Maker, describes many more predicted protein coding genes compared to the GeneMark generated annotation that is currently hosted at the Genome Database for Rosaceae (http://www.rosaceae.org/). Our new annotation also results in an increase in the overall total coding length, and the number of coding regions found. The total number of gene predictions that do not overlap with the previous annotations is 2286, most of which were found to be homologous to other plant genes. We have experimentally verified one of the new gene model predictions to validate our results. Using the RNA-Seq transcriptome sequences from 25 diverse tissue types, the re-annotation pipeline improved existing annotations by increasing the annotation accuracy based on extensive transcriptome data. It uncovered new genes, added exons to current genes, and extended or merged exons. This complete genome re-annotation will significantly benefit functional genomic studies of the strawberry and other members of the Rosaceae.
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    A Network Approach to Identify Key Regulators of Fruit Development in Fragaria vesca, a Diploid Strawberry
    (2018) Shahan, Rachel; Liu, Zhongchi; Cell Biology & Molecular Genetics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Post-embryonic organogenesis is a feature unique to plants, an example of which is flower and fruit production. Previous work on strawberry fruit development has focused primarily on the latter stages, including ripening. Comparatively little is known about the molecular events underpinning fruit set, the pivotal stage at which fruit development proceeds or terminates. This thesis investigates early fruit development using Fragaria vesca, a diploid strawberry, as a model. In collaboration with a bioinformatician, I generated gene co-expression networks from 92 previously generated RNA-Seq libraries profiling multiple tissues and stages of strawberry flower and fruit development. I demonstrate the utility of co-expression networks in illuminating molecular processes underlying fruit development. Experimental validation of the networks includes demonstration of increased iron transport soon after fertilization and identification of FveUFO1 as an important regulator of floral meristem determinacy and floral organ identity. Using the co-expression networks, I discovered the surprising expression of FvFT1, a homolog of FLOWERING LOCUS T (FT), in the fleshy fruit immediately post-fertilization. In many plant species, the FT peptide is a non-cell autonomous signal that initiates flowering in response to inductive photoperiod. I found that FvFT1 expression is responsive to temperature, but not photoperiod, in strawberry fruit. Further, transcriptional activation is detectable in the vascular bundles connecting the fruit to the seeds, raising the possibility that FvFT1 may facilitate cross-tissue communication. Signal from an FvFT1-GFP translational fusion protein is visible in seed nuclei despite its localized transcription in the vasculature. However, analysis of FvFT1 RNAi plants failed to identify a fruit phenotype, possibly due to redundancy among three FvFT paralogs. Finally, to develop additional research tools for F. vesca, I isolated and tested fruit tissue-specific promoters based on genes identified with differential expression analyses. These analyses revealed genes strongly expressed in the receptacle fruit, thereby identifying potential regulators of early fruit development and attractive candidates for future study. Together, this work advances the systems-level infrastructure for studying molecular regulation of F. vesca fruit development, points to a novel role for FT distinct from its known function in floral initiation, and provides molecular tools useful to the F. vesca community.