HGTScanner : Detecting horizontal gene transfer at the fine scale using whole organelle genomes

Horizontal gene transfer (HGT) has profoundly shaped eukaryotic organellar genomes like plant mitochondria. Yet no generalized tools are currently available to efficiently characterize HGT across these genomes due to both high structural complexity and low sequence divergence compared to prokaryotic HGTs. Accurate identification of HGT, including the genomic location and donor lineage, is critical for understanding its impact on genetic novelty and genome evolution as well as species interactions that generate HGTs. Here, we introduce HGTScanner, a Python tool to characterize HGT across whole organellar genomes. HGTScanner automatically establishes homology, produces alignments and phylogenies, and tests hypotheses of HGT based on BLAST, phylogeny and synteny. It contains a built‐in database of green plant (Viridiplantae) organellar sequences to facilitate the characterization of promiscuous mitochondrial HGTs and mitochondrial plastid DNAs (MTPTs) in plants but may also be adapted to other organisms like fungi which share many similar genomic features. Using benchmark data from the early diverging angiosperm Amborella and parasitic plant Orobanchaceae, we demonstrate that HGTScanner can effectively locate and identify the donor lineages of MTPT and HGT. In Amborella, we recovered the well‐documented fusion of moss and green algae mitochondria, and discovered prevalent HGTs from the New Caledonian parasitic plant Hachettea (Mystropetalaceae). In the parasitic Orobanchaceae, non‐native MTPTs are strongly linked with their sympatrically distributed host plants. HGTScanner is an efficient and flexible tool that can drive discoveries of HGT without a priori knowledge regarding the donor identity. The sympatric distribution of donor‐recipient pairs in HGT events suggests that HGTs can serve as valuable genetic markers for organismal interactions across time and terrain.