DENG, C. H. | Search bioRxiv

bioRxiv2026

TEgenomeSimulator: A Flexible Framework for Simulating Genomes with Configurable Transposable Element Landscapes

Transposable elements (TEs) are major contributors to genome structure and evolution. However, our ability to study them is limited by the difficulty of annotating and curating them, especially in non-model organisms. This challenge is compounded by a lack of ground-truth datasets for benchmarking, which are nearly impossible to generate through manual curation alone. To overcome this critical limitation, we developed TEgenomeSimulator, a flexible framework for generating synthetic genomes with configurable TE landscapes. TEgenomeSimulator supports both randomly generated and biologically derived backbone sequences, enabling the modeling of TE insertions under diverse structural and evolutionary contexts. Benchmarking against existing simulators demonstrated that TEgenomeSimulator reproduces realistic TE composition, sequence divergence, and integrity distributions while offering greater flexibility in modeling chromosome-level structure. Its modular design offers a tuneable continuum between biological fidelity and experimental control, facilitating systematic benchmarking, algorithm development, and evolutionary modeling of TE dynamics in silico, filling a major gap in the field. The source code of TEgenomeSimulator and the scripts for this paper are available at https://github.com/Plant-Food-Research-Open/TEgenomeSimulator.

bioinformatics↗

bioRxiv2025

Systematic Analysis of the EXO70 Gene Family in Kiwifruit Species: Evolutionary Selection and Potential Functions in Plant Immunity

BackgroundKiwifruit (Actinidia spp.) is a commercially and nutritionally valuable fruit crop that faces increasing challenges from pathogens, particularly Pseudomonas syringae pv. actinidiae (Psa). The exocyst complex, especially the EXO70 subunit, has been demonstrated to play a crucial role in vesicle trafficking and plant immune responses in model species such as Arabidopsis thaliana. However, the function and evolution of EXO70 genes in fruit crops remain largely unexplored. ResultsWe conducted a comprehensive genome-wide analysis of the EXO70 gene family across five Actinidia species using Arabidopsis EXO70 sequences as queries. A total of 217 EXO70 genes (23 to 54 paralogues per species) were identified and classified into three subfamilies and nine clades (EXO70A-EXO70I), consistent with previous classifications in other plant taxa. Phylogenetic reconstruction and microsynteny analyzes revealed lineage- and genus-specific expansions of EXO70C members, as well as species-specific expansion events, particularly within the EXO70E and EXO70H clades. To investigate potential immune functions, yeast two-hybrid and in planta co-immunoprecipitation assays confirmed that kiwifruit EXO70B1 physically interacts with the immune hub protein kiwifruit RIN4_1. These interactions support conservation of the EXO70-RIN4 module in plant immunity. ConclusionsThis study provides the first comprehensive characterization of the EXO70 gene family across multiple kiwifruit species and uncovers candidate genes potentially involved in plant immunity through RIN4-mediated defense signaling. Notably, the expansion and diversification of the EXO70E and EXO70H clades suggest possible adaptive evolution within these clades and neofunctionalization. These findings provide valuable genomic resources and novel insights into the evolution of vesicle trafficking components in fruit crops, laying the groundwork for future efforts to enhance disease resistance in kiwifruit through breeding or biotechnological approaches.

plant biology↗