Genome sequencing and resequencing identified three horizontal gene transfers and uncovered the genetic mechanism on the intraspecies adaptive evolution of Blume.

Horizontal gene transfer is a rare and useful genetic mechanism in higher plants. Blume () (Orchidaceae), well known as traditional medicinal material in East Asia, adopts a heterotrophic lifestyle, thus being considered to be more prone to horizontal gene transfer (HGT). is a "polytypic species" that currently comprised of five recognized forms according to the plant morphology. () and () are two common forms that naturally grow in different habitats with difference in altitude and latitude. () often occurs sporadically in cultivated populations of and . However, the genetic relationships and genetic mechanism underpinned the divergent ecological adaptations of and have not been revealed. Here, we assembled a chromosome-level draft genome of with 1.04 Gb. Among predicted 17,895 protein coding genes, we identified three HGTs. Meanwhile, we resequenced 10 accessions, nine accessions, and 10 accessions, and identified two independent genetic lineages: _pedigree ( individuals and individuals collected from populations) and _pedigree ( individuals and individuals collected from populations), which strongly support the taxonomic status of and as subspecies, not as different forms. In highly differentiated genomic regions of _pedigree and _pedigree, three chalcone synthase-encoding genes and one Phox/Bem1p (PB1) domain of encoding Auxin (AUX)/Indoleacetic acid (IAA) were identified in selection sweeping genome regions, which suggested that differentiation between _pedigree and _pedigree was promoted by the selection of genes related to photoresponse and growth and development. Overall, this new genome would be helpful for breeding and utilization of and the new findings would deepen the understanding about ecological adaptation and evolution of .