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Biology subjects

Di Stilio, V. S.

Publications and source records attributed to Di Stilio, V. S..

4 recordsLinked to original sources

LEAFY demonstrates ancestral reproductive functions in the gametophyte and not the sporophyte of the fern Ceratopteris richardii

Flowers are a key reproductive innovation of the angiosperms. They evolved as a modification of the ancestral plant life cycle whereby the haploid gamete-producing generation (gametophyte) became enclosed within the diploid, spore-producing generation (sporophyte). The transcription factor LEAFY (LFY) initiates angiosperm floral development, yet its lineage predates flowers and is found across all land plants. LFY function outside angiosperms is known from the moss Physcomitrium patens, where they control the first division of the sporophyte, and from the model fern Ceratopteris richardii, a vascular plant without seeds or flowers, where CrLFY1 and CrLFY2 maintain vegetative meristem activity. However, how LFYs reproductive role evolved remains unclear. Using over-expression, we uncover new roles for CrLFY1/2 in fern gametophyte reproduction, particularly in sperm cells and in the gametophytes multicellular notch meristem. No sporophytic reproductive function was detected, but over-expression supports a role in fern frond compounding and a conserved role in the zygotes first division. Our findings highlight an ancestral LFY function in fern haploid-stage reproduction, which may have been co-opted into the sporophyte during the origin of the flower. Summary StatementThe origin of LEAFYs floral function is unknown, with only vegetative roles known from seedless plants. We identify ancestral reproductive roles for the first time, unexpectedly in the fern gametophyte.

developmental biology↗

Enabling the Study of Gene Function in Gymnosperms: VIGS in Ephedra tweedieana

PremiseAs the sister clade to angiosperms, gymnosperms are key to enabling the reconstruction of ancestral gene regulatory networks for seed plants. However, tools to rapidly and efficiently investigate gene function in gymnosperms remain limited due to the challenges of long life cycles and large genome sizes. Species within the xerophytic genus Ephedra (Gnetales) have comparatively smaller genomes and shrubby growth habits with shorter life spans, making them better suited for greenhouse cultivation and laboratory experiments. Methods and ResultsHere, we implement Virus-Induced Gene Silencing (VIGS) to manipulate gene expression in Ephedra tweedieana. Agrobacterium-mediated vacuum infiltration of Tobacco Rattle Virus (TRV2 and TRV1) in seedlings resulted in highly efficient silencing of the E. tweedieana PHYTOENE DESATURASE ortholog EtwPDS. The expected photobleaching phenotype was observed as early as two weeks. It lasted at least three months, in stems, shoot tips, leaves, axillary meristems, and lateral branches of treated plants. ConclusionsThis first report of transient transformation and targeted gene silencing in a gymnosperm will further enable functional studies of the genetic mechanisms underpinning adaptations in this important and underrepresented lineage of seed plants.

plant biology↗

Facilitating candidate gene discovery in an emerging model plant lineage: Transcriptomic and genomic resources for Thalictrum (Ranunculaceae)

The plant genus Thalictrum is a representative of the order Ranunculales (a sister lineage to all other Eudicots) with diverse floral morphologies, encompassing four sexual systems and two pollination modes. Previous studies suggest multiple transitions from insect to wind pollination within this genus, in association with polyploidy and unisexual flowers, but the underlying genes remain unknown. We generated a draft reference genome for Thalictrum thalictroides, a representative of a clade with ancestral floral traits (diploidy, hermaphroditism, and insect pollination) and a model for functional studies. To facilitate candidate gene discovery in flowers with different sexual and pollination systems we also generated floral transcriptomes of T. thalictroides and of wind-pollinated, andromonoecious (staminate and hermaphroditic flowers on the same plant) T. hernandezii. The T. thalictroides draft genome assembly consisted of 44,860 contigs (N50=12,761 bp. and 243 Mbp. total length) and contained 84.5% conserved embryophyte single-copy genes. Floral transcriptomes from Illumina sequencing and de novo assembly contained representatives of most eukaryotic core genes (approximately 80%), with most of their genes falling into common orthologous groups (orthogroups). Simple Sequence Repeat (SSR) motifs were also identified, which together with the single-copy genes constitute a resource for population-level or phylogenetic studies. Finally, to validate the utility of these resources, putative candidate genes were identified for the different floral morphologies using stepwise dataset comparisons. In conclusion, we present genomic and transcriptomic resources for Thalictrum, including the first genome of T. thalictroides and potential candidate genes for flowers with distinct sexual and pollination systems.

genomics↗

Fluidigm2PURC: automated processing and haplotype inference for double-barcoded PCR amplicons

Premise of the studyTargeted enrichment strategies for phylogenomic inference are a time- and cost-efficient way to collect DNA sequence data for large numbers of individuals at multiple, independent loci. Automated and reproducible processing of these data is a crucial step for researchers conducting phylogenetic studies.\n\nMethods and ResultsWe present Fluidigm2PURC, an open source Python utility for processing paired-end Illumina data from double-barcoded PCR amplicons. In combination with the program PURC (Pipeline for Untangling Reticulate Complexes), our scripts process raw FASTQ files for analysis with PURC and use its output to infer haplotypes for diploids, polyploids, and samples with unknown ploidy. We demonstrate the use of the pipeline with an example data set from the genus Thalictrum L. (Ranunculaceae).\n\nConclusionsFluidigm2PURC is freely available for Unix-like operating systems on GitHub [https://github.com/pblischak/fluidigm2purc] and for all operating systems through Docker [https://hub.docker.com/r/pblischak/fluidigm2purc].

bioinformatics↗