Lateral gene transfer generates accessory genes that accumulate at different rates within a grass lineage

Lateral gene transfer (LGT) is the movement of DNA between organism
without sexual reproduction. The acquired genes represent genetic
novelties that have independently evolved in the donor’s genome.
Phylogenetic methods have shown that LGT is widespread across the entire
grass family, although we know little about the underlying dynamics. We
identify laterally acquired genes in five de novo reference genomes from
the same grass genus (four Alloteropsis semialata and one Alloteropsis
angusta). Using additional resequencing data for a further 40 Alloteropsis
individuals, we place the acquisition of each gene onto a phylogeny using
stochastic character mapping, and then infer rates of gains and losses. We
detect 168 laterally acquired genes in the five reference genomes [32-100
per genome]. Exponential decay models indicate that the rate of LGT
acquisitions [6-28 per Ma] and subsequent losses [11-24% per Ma] varied
significantly among lineages. Laterally acquired genes were lost at a
higher rate than vertically inherited loci [0.02-0.8% per Ma]. This high
turnover creates intraspecific gene content variation, with a
preponderance of them occurring as accessory genes in the Alloteropsis
pangenome. This rapid turnover generates standing variation that can
ultimately fuel local adaptation.