Biology subjects

dePamphilis, C.

Publications and source records attributed to dePamphilis, C..

3 recordsLinked to original sources

bioRxiv2024

The evolution of pectate lyase-like genes across land plants, and their roles in haustorium formation in parasitic plants

Parasitic plants in Orobanchaceae are noxious agricultural pests that severely impact crops worldwide. These plants acquire water and nutrients from their hosts through a specialized organ called the haustorium. A key step in haustorium development involves cell wall modification. In this study, we identified and analyzed the evolutionary relationships of pectate lyase-like (PLL) genes across parasitic plants and other non-parasitic land plant lineages. To support detailed examination of gene models and paralogous gene family members, we used published parasitic plant genomes, as well as a recently generated draft genome assembly and annotation of Triphysaria versicolor. One particular PLL gene, denoted as PLL1 in parasitic Orobanchaceae, emerged as an important candidate gene for parasitism. Our previous comparative transcriptomic analyses showed that PLL1 underwent neofunctionalization via an expression shift from floral tissues in non-parasitic relatives to haustoria in parasitic species. It belongs to the largest sub-clade of the PLL gene family, is highly upregulated in haustoria, and shows signatures of relaxed purifying selection and 15 individual sites with signatures of adaptive evolution. To explore its function in haustorium development, we manipulated PLL1 expression in T. versicolor, a model parasitic species from Orobanchaceae, using direct transformation with the parasite and host-induced-gene-silencing (HIGS). For HIGS, we generated transgenic Medicago hosts expressing hairpin RNAs targeting the PLL1 gene in T. versicolor. An average 60% reduction of PLL1 transcript level was observed in both direct transformation and HIGS treatments, leading to an increased frequency of poorly adhered parasites with fewer xylem connections and a smaller proportion of mature haustoria. These findings demonstrate that PLL1 plays a crucial role in haustorium development and suggest it as a promising target for managing parasitic weeds. Notably, the success of HIGS even before the establishment of a functional haustorium highlights the possibility of early intervention against parasitism.

plant biology↗

bioRxiv2022

PlantTribes2: tools for comparative gene family analysis in plant genomics

Plant genome-scale resources are being generated at an increasing rate as sequencing technologies continue to improve and raw data costs continue to fall; however, the cost of downstream analyses remains large. This has resulted in a considerable range of genome assembly and annotation qualities across plant genomes due to their varying sizes, complexity, and the technology used for the assembly and annotation. To effectively work across genomes, researchers increasingly rely on comparative genomic approaches that integrate across plant community resources and data types. Such efforts have aided the genome annotation process and yielded novel insights into the evolutionary history of genomes and gene families, including complex non-model organisms. The essential tools to achieve these insights rely on gene family analysis at a genome-scale, but they are not well integrated for rapid analysis of new data, and the learning curve can be steep. Here we present PlantTribes2, a scalable, easily accessible, highly customizable, and broadly applicable gene family analysis framework with multiple entry points including user provided data. It uses objective classifications of annotated protein sequences from existing, high-quality plant genomes for comparative and evolutionary studies. PlantTribes2 can improve transcript models and then sort them, either genome-scale annotations or individual gene coding sequences, into pre-computed orthologous gene family clusters with rich functional annotation information. Then, for gene families of interest, PlantTribes2 performs downstream analyses and customizable visualizations including, (1) multiple sequence alignment, (2) gene family phylogeny, (3) estimation of synonymous and non-synonymous substitution rates among homologous sequences, and (4) inference of large-scale duplication events. We give examples of PlantTribes2 applications in functional genomic studies of economically important plant families, namely transcriptomics in the weedy Orobanchaceae and a core orthogroup analysis (CROG) in Rosaceae. PlantTribes2 is freely available for use within the main public Galaxy instance and can be downloaded from GitHub or Bioconda. Importantly, PlantTribes2 can be readily adapted for use with genomic and transcriptomic data from any kind of organism.

bioinformatics↗

bioRxiv2021

Towards a catalog of pome tree architecture genes: the draft 'd'Anjou' genome (Pyrus communis L.)

The rapid development of sequencing technologies has led to a deeper understanding of horticultural plant genomes. However, experimental evidence connecting genes to important agronomic traits is still lacking in most non-model organisms. For instance, the genetic mechanisms underlying plant architecture are poorly understood in pome fruit trees, creating a major hurdle in developing new cultivars with desirable architecture, such as dwarfing rootstocks in European pear (Pyrus communis). Further, the quality and content of genomes vary widely. Therefore, it can be challenging to curate a list of genes with high-confidence gene models across reference genomes. This is often an important first step towards identifying key genetic factors for important traits. Here we present a draft genome of P. communis dAnjou and an improved assembly of the latest P. communis Bartlett genome. To study gene families involved in tree architecture in European pear and other rosaceous species, we developed a workflow using a collection of bioinformatic tools towards curation of gene families of interest across genomes. This lays the groundwork for future functional studies in pear tree architecture. Importantly, our workflow can be easily adopted for other plant genomes and gene families of interest.

plant biology↗