Genome mining reveals abiotic stress resistance genes in plant genomes acquired from microbes via HGT

Abstract

Colonization by beneficial microbes can enhance plant tolerance to abiotic stresses. However, there are still many unknown fields regarding the beneficial plant-microbe interactions. In this study, we have assessed the amount or impact of horizontal gene transfer (HGT)-derived genes in plants that have potentials to confer abiotic stress resistance. We have identified a total of 235 gene entries in fourteen high-quality plant genomes belonging to phyla Chlorophyta and Streptophyta that confer resistance against a wide range of abiotic pressures acquired from microbes through independent HGTs. These genes encode proteins contributed to toxic metal resistance (e.g., ChrA, CopA, CorA), osmotic and drought stress resistance (e.g., Na+/proline symporter, potassium/proton antiporter), acid resistance (e.g., PcxA, ArcA, YhdG), heat and cold stress resistance (e.g., DnaJ, Hsp20, CspA), oxidative stress resistance (e.g., GST, PoxA, glutaredoxin), DNA damage resistance (e.g., Rad25, Rad51, UvrD), and organic pollutant resistance (e.g., CytP450, laccase, CbbY). Phylogenetic analyses have supported the HGT inferences as the plant lineages are all clustering closely with distant microbial lineages. Deep-learning-based protein structure prediction and analyses, in combination with expression assessment based on codon adaption index (CAI) further corroborated the functionality and expressivity of the HGT genes in plant genomes. A case-study applying fold comparison and molecular dynamics (MD) of the HGT-driven CytP450 gave a more detailed illustration on the resemblance and evolutionary linkage between the plant recipient and microbial donor sequences. Together, the microbe-originated HGT genes identified in plant genomes and their participation in abiotic pressures resistance indicate a more profound impact of HGT on the adaptive evolution of plants.