AUTHOR=Wang Yunsheng , Shahid Muhammad Qasim 

TITLE=Genome sequencing and resequencing identified three horizontal gene transfers and uncovered the genetic mechanism on the intraspecies adaptive evolution of Gastrodia elata Blume

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.1035157

DOI=10.3389/fpls.2022.1035157

ISSN=1664-462X

ABSTRACT=<p>Horizontal gene transfer is a rare and useful genetic mechanism in higher plants. <italic>Gastrodia elata</italic> Blume (<italic>GE</italic>) (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). <italic>GE</italic> is a “polytypic species” that currently comprised of five recognized forms according to the plant morphology. <italic>G. elata Blume forma elata</italic> (<italic>GEE</italic>) and <italic>G. elata Bl.f.glauca</italic> (<italic>GEG</italic>) are two common forms that naturally grow in different habitats with difference in altitude and latitude. <italic>G. elata Bl.f.viridis</italic> (<italic>GEV</italic>) often occurs sporadically in cultivated populations of <italic>GEE</italic> and <italic>GEG</italic>. However, the genetic relationships and genetic mechanism underpinned the divergent ecological adaptations of <italic>GEE</italic> and <italic>GEG</italic> have not been revealed. Here, we assembled a chromosome-level draft genome of <italic>GEE</italic> with 1.04 Gb. Among predicted 17,895 protein coding genes, we identified three HGTs. Meanwhile, we resequenced 10 <italic>GEE</italic> accessions, nine <italic>GEG</italic> accessions, and 10 <italic>GEV</italic> accessions, and identified two independent genetic lineages: <italic>GEG</italic>_pedigree (<italic>GEG</italic> individuals and <italic>GEV</italic> individuals collected from <italic>GEG</italic> populations) and <italic>GEE</italic>_pedigree (<italic>GEE</italic> individuals and <italic>GEV</italic> individuals collected from <italic>GEE</italic> populations), which strongly support the taxonomic status of <italic>GEE</italic> and <italic>GEG</italic> as subspecies, not as different forms. In highly differentiated genomic regions of <italic>GEE</italic>_pedigree and <italic>GEG</italic>_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 <italic>GEE</italic>_pedigree and <italic>GEG</italic>_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 <italic>GE</italic> and the new findings would deepen the understanding about ecological adaptation and evolution of <italic>GE</italic>.</p>