Biology subjects

Timilsena, P. R.

Publications and source records attributed to Timilsena, P. R..

3 recordsLinked to original sources

bioRxiv2024

Local Gene Duplications Drive Extensive NLR Copy Number Variation Across Multiple Genotypes of Theobroma cacao

Nucleotide-binding leucine rich repeat receptors (NLR) are an essential component of plant immunity. NLR evolution is complex and dynamic, with rapid expansions, contractions, and polymorphism. Hundreds of high-quality plant genomes generated over the last two decades provide substantial insight into the evolutionary dynamics of NLR genes. Despite steadily decreasing sequencing costs, the difficulty of sequencing, assembling, and annotating high-quality genomes has resulted in comparatively little genome-wide information on intraspecies NLR diversity. In this study, we investigated the evolution of NLR genes across 11 high-quality genomes of the chocolate tree, Theobroma cacao L. We found 3-fold variation in NLR copy number across genotypes, a pattern driven primarily by expansion of NLR clusters via tandem and proximal duplication. Our results indicate local duplications can radically reshape gene families over short evolutionary time scales, creating extensive intraspecific variation and a source of NLR diversity that could be utilized to enrich our understanding of both plant-pathogen interactions and resistance breeding.

evolutionary biology↗

bioRxiv2023

Cross-species single-cell annotation with orthologous marker gene groups

Single-cell RNA sequencing (scRNA-seq) technology has been widely used in characterizing various cell types from in plant growth and development1-6. Applications of this technology in Arabidopsis have benefited from the extensive knowledge of cell-type identity markers7,8. Contrastingly, accurate labeling of cell types in other plant species remains a challenge due to the scarcity of known marker genes9. Various approaches have been explored to address this issue; however, studies have found many closest orthologs of cell-type identity marker genes in Arabidopsis do not exhibit the same cell-type identity across diverse plant species10,11. To address this challenge, we have developed a novel computational strategy called Orthologous Marker Gene Groups (OMGs). We demonstrated that using OMGs as a unit to determine cell type identity enables assignment of cell types by comparing 15 distantly related species. Our analysis revealed 14 dominant clusters with substantial conservation in shared cell-type markers across monocots and dicots.

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↗