Hu, G.-W. | bioRxiv Science

bioRxiv2024

Diverging repeatomes in holoparasitic Hydnoraceae uncover a playground of genome evolution

O_LIThe nuclear genomes of parasitic plants have undergone unique evolutionary trajectories to adapt to the heterotrophic lifestyle. These adaptations often involve large genomic alterations, potentially driven by repetitive DNAs. Despite the recognized role of repetitive DNAs for shaping plant genomes, their contribution to parasitic plant genome evolution remains largely unexplored. This study presents the first analysis of repetitive DNAs in eleven genomes of Hydnoraceae, a holoparasitic plant family. C_LIO_LIThe repetitive DNAs were identified and annotated de novo. Patterns of abundance and presence-absence were aligned with the phylogenetic relationships, geographical distribution, and host shifts, suggesting repetitive DNAs key role in shaping Hydnoraceae genomes. C_LIO_LIThe two Hydnoraceae genera, Hydnora and Prosopanche, exhibit distinct profiles. Eight Hydnora genomes are largely populated by long terminal repeat retrotransposons, while three Prosopanche genomes vary greatly in repetitive DNA composition, including P. bonacinae with massive amplifications of a single DNA transposon and P. panguanensis with over 15% 5S rDNA, compared to <0.1% in some Hydnoraceae. Both extremely low and very high abundance of 5S rDNA challenges our current understanding on chromosomal stabilization and rDNA transcription. C_LIO_LIThese genome dynamics, while inviting for further investigations, suggest rapidly evolving repeat profiles, potentially accelerated by the adaptation to the parasitic lifestyle. C_LI

evolutionary biology↗

bioRxiv2021

Integrating transcriptomes to investigate genes associated with adaptation to aquatic environments, and assess phylogenetic conflict and whole-genome duplications in Alismatales

Land plants first evolved from freshwater algae, and flowering plants returned to water as early as the Cretaceous and multiple times subsequently. Alismatales is the largest clade of aquatic angiosperms including all marine angiosperms, as well as terrestrial plants. We used Alismatales to explore plant adaptation to aquatic environments by analyzing a data set that included 95 samples (89 Alismatales species) covering four genomes and 91 transcriptomes (59 generated in this study). To provide a basis for investigating adaptation, we assessed phylogenetic conflict and whole-genome duplication (WGD) events in Alismatales. We recovered a relationship for the three main clades in Alismatales as (Tofieldiaceae, Araceae) + core Alismatids. We also found phylogenetic conflict among the backbone of the three main clades that could be explained by incomplete lineage sorting and introgression. Overall, we identified 18 putative WGD events across Alismatales. One of them occurred at the most recent common ancestor of core Alismatids, and three occurred at seagrass lineages. We also found that lineage and life-form were both important for different evolutionary patterns for the genes related to freshwater and marine adaptation. For example, several light or ethylene-related genes were lost in the seagrass Zosteraceae, but are present in other seagrasses and freshwater species. Stomata-related genes were lost in both submersed freshwater species and seagrasses. Nicotianamine synthase genes, which are important in iron intake, expanded in both submersed freshwater species and seagrasses. Our results advance the understanding of the adaptation to aquatic environments and whole-genome duplications using phylogenomics.

evolutionary biology↗