Biology subjects

Soltis, D.

Publications and source records attributed to Soltis, D..

3 recordsLinked to original sources

bioRxiv2024

Homoploid Hybridization Resolves the Origin of Octoploid Strawberries

The identity of the diploid progenitors of octoploid cultivated strawberry (Fragaria x ananassa) has been subject to much debate. Past work identified four subgenomes and consistent evidence for F. californica (previously named F. vesca subsp. bracteata) and F. iinumae as donors for subgenomes A and B, respectively, with conflicting results for the origins of subgenomes C and D. Here, reticulate phylogeny and admixture analysis support hybridization between F. viridis and F. vesca in the ancestry of subgenome A, and between F. nipponica and F. iinumae in the ancestry of subgenome B. Using an LTR-age-distribution-based approach, we estimate that the octoploid and its intermediate hexaploid and tetraploid ancestors emerged approximately 0.8, 2, and 3 million years ago, respectively. These results provide an explanation for previous reports of F. viridis and F. nipponica as donors of the C and D subgenomes and unify conflicting hypotheses about the evolutionary origin of octoploid Fragaria.

genetics↗

bioRxiv2024

Rapid radiation of a plant lineage sheds light on the assembly of dry valley biomes

Southwest China is characterized by high plateaus, large mountain systems, and deeply incised dry valleys formed by major rivers and their tributaries. Despite the considerable attention given to alpine plant radiations in this region, the timing and mode of the diversification of the numerous plant lineages in the dry valley habitat remains unknown. To address this knowledge gap, we investigate the macroevolution of Isodon (Lamiaceae), a lineage commonly distributed in the dry valleys in southwest China and wetter areas of Asia and Africa. We reconstructed a robust phylogeny encompassing nearly 90% of the approximately 140 extant Isodon species using transcriptome and genome-resequencing data. Our results suggest a rapid radiation of Isodon during the Pliocene that coincided with a habit shift from herbs to shrubs and a habitat shift from humid areas to dry valleys. The shrubby growth form likely acted as a preadaptation allowing for the movement of Isodon species into these valleys. Ecological analysis highlighted aridity and precipitation as key factors influencing the niche preferences of different growth forms and species richness of Isodon. Integrating our results with insights from tectonic movements in the Tibetan Plateau and adjacent regions, we infer that the interplay between topography and the evolution of the East Asian monsoon since the middle Miocene likely contributed to the formation of the dry valley biome in southwest China. This study enhances our understanding of evolutionary dynamics and ecological drivers shaping the distinctive flora of this region.

evolutionary biology↗

bioRxiv2024

Efficient Gene Editing and Overexpression of Gametophyte Transformation in a Model Fern

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-related nuclease (Cas) system allows precise and easy editing of genes in many plant species. However, this system has not yet been applied to any fern species due to the complex characteristics of fern genomes, genetics and physiology. Here, we established, for the first time, a protocol for gametophyte-based screening single-guide RNAs (sgRNAs) with high efficiency for CRISPR/Cas-mediated gene editing in a model fern species, Ceratopteris richardii. We utilized the C. richardii Actin promoter to drive sgRNA expression and enhanced CaMV 35S promoter to drive the expression of Streptococcus pyogenes Cas9 in this CRISPR-mediated editing system, which was employed to successfully edit a few genes (e.g., nucleotidase/phosphatase 1, CrSAL1; Cryptochrome 4, CRY4) and CrPDS, encoding a phytoene desaturase protein that resulted in an albino phenotype in C. richardii. Knockout of CrSAL1 resulted in significantly reduced stomatal conductance (gs), leaf transpiration rate (E), stomatal/pore length, and abscisic acid (ABA)-induced reactive oxygen species (ROS) accumulation in guard cells. Moreover, CrSAL1 overexpressing plants showed significantly increased net photosynthetic rate (A), gs, E and intrinsic water use efficiency (iWUE) as well as most of the stomatal traits and ROS production in guard cells compared to those in the wild-type (WT) plants. Taken together, the optimized CRISPR/Cas9 system provides a useful tool for functional genomics in a model fern species, allowing the exploration of fern gene functions for evolutionary biology, herbal medicine discovery and agricultural applications.

plant biology↗