Utilising nuclear encoded plastid DNA to identify donors of grass-to-grass lateral gene transfer

Abstract

Determining the correct donor species/lineages of grass-to-grass lateral gene transfer (LGT) is vital for deducing specific donor features that could help inform the mechanism of transfer. This requires a dataset spanning a broad range of species to achieve the phylogenetic resolution necessary for precise donor inference. As grass-to-grass LGT often involves the transfer of multi-gene DNA fragments, they can contain additional sequences that allow for accurate orthologous comparisons, such as nuclear DNA of plastid origin (NUPTs). Here we systematically scan for NUPTs in the genomes of four Alloteropsis semialata accessions, whose LGTs have previously been characterised. Using the abundant Panicoideae chloroplast sequences, we reconstruct NUPT phylogenies and infer two lateral acquisitions: one from Paniceae/Digitaria and another from Andropogoneae/Eremochloa adjacent to a previously identified LGT. We then assembled and included an additional 12 Eremochloa chloroplast genomes in the analysis and showed the likely donor was Eremochloa attenuata. Subsequent short-read mapping from E. attenuata to the nuclear region flanking this NUPT showed consistent coverage across the region, including the previously identified LGT, supporting co-transfer. Overall this study highlights the potential for NUPTs to better identify the donors of grass-to-grass LGT.