Although vanilla is one of the most valuable spices, there is a lack of understanding of the genomic variability of the main vanilla producing species, Vanilla planifolia, within its cultivated origin, Mexico. High genomic heterozygosity levels within the globally cultivated ‘Daphna’ genome have raised questions on the possibility of a hybrid origin and analogous genomic signatures of vanilla cultivated within its origin. This study investigated these questions by assessing whether the genomic structure of Mexican V. planifolia reflected domestication events. Whole genome re-sequencing was used to compare genome complexity between 15 cultivated accessions from different regions and gene pools. Results showed high levels of heterozygosity, ranging from 2.48% to 2.85%, in all but one accession, which exhibited a low level (0.403%). Chromosome-level comparative analyses revealed genomic variability among samples, but no signals of chromosome rearrangements. These findings support the hypotheses that cultivated vanilla resulted from hybridization and that multiple domestication events have shaped cultivated vanilla leading to the formation of landraces. High cultural diversity within this region further supports the occurrence of multiple domestication processes. These results may help to improve breeding and conservation efforts aiming to preserve the genetic diversity of this beloved spice threatened by climate change.

Although vanilla is one of the most popular flavours in the world, there is still uncertainty concerning the native distribution of the species that produces it, Vanilla planifolia. To circumscribe the native geographical extent of this economically important species more precisely, we propose a new landscape-based approach to incorporate information from open-source databases and validate occurrences. In this approach, we include metrics to account for habitat suitability and population sustainability in terms of the biotic (co-occurrence of pollinators and dispersers) and abiotic (habitat quality) factors limiting plant distributions. To further validate occurrences within the resulting distribution, we compare the presence of morphologically similar wild relatives, assess the heterogeneity of ecological niches and verify the correct identification of herbarium specimens. Results from this approach suggest that V. planifolia has a larger geographical distribution than previously recognized; we hypothesize that populations naturally dispersed from Mesoamerica and became established in South America (with a south-eastern limit in Brazil). The recognition of an improved estimate of the distribution of this species will increase the accuracy of predictive models, promote further species circumscription, improve the efficacy of conservation strategies, and help to ensure the sustainability of a valuable, sought-after spice.

Western North America has been experiencing persistent drought exacerbated by climate change for over two decades. This extreme climate event is a clear threat to native plant communities. Artemisia tridentata is a keystone shrub species in western North America and is threatened by climate change, urbanization, and wildfire. A drought Genotype × Environment (G × E) experiment was conducted to assess phenotypic plasticity and differential gene expression in A. tridentata. The G × E experiment was performed on diploid A. tridentata seedlings from two populations (one from Idaho, USA and one from Utah, USA), which experience differing levels of drought stress during the summer months. Photosynthetic data, leaf temperature, and gene expression levels were compared between treatments and populations. The Utah population maintained higher photosynthetic rates and photosynthetic efficiency than the Idaho population under drought stress. The Utah population also exhibited far greater transcriptional plasticity than the Idaho population and expressed genes of response pathways distinct from those of the Idaho population. Populations of A. tridentata differ greatly in their drought response pathways, likely due to differences in response pathways that have evolved under distinct climatic regimes. Epigenetic processes likely contribute to the observed differences between the populations.

A bstract: Phylogenomic discordance is pervasive and cannot always be resolved by increasing the amount of sequencing data alone. Biological processes such as polyploidy, hybridization, and incomplete lineage sorting are major contributors to discordance and must be accounted for to avoid misleading evolutionary interpretations. To better understand how these processes influence phylogenetic reconstruction, we conducted a comprehensive phylogenomic study in the complex genus Packera . With over 90 species and varieties, 40% of which exhibit polyploidy, aneuploidy, or other cytological complexities, Packera presents significant challenges for phylogenetic reconstruction. Given these complexities, we assessed different published paralog processing methods on the resulting evolutionary relationships and phylogenetic support of this group. We then applied three of these methods to evaluate their impact on tree topology and our understanding of Packera ’s evolutionary history by constructing a time-calibrated phylogeny, reconstructing historical biogeography, and testing for ancient reticulation. Phylogenetic outcomes varied based on the paralog processing method used, with no method performing the best over others. Our findings highlight the large impact of orthology inference and paralog processing on phylogenomic analyses, particularly in polyploid-rich groups such as Packera , and we offer guidance on methodological impacts along with practical recommendations. We note that gaining a robust understanding of Packera ’s evolutionary history requires more than computational approaches alone. While technological advancements have greatly expanded our ability to analyze genomic data, effective phylogenomic research still relies on strong taxon sampling and detailed species knowledge. Without careful attention to the biological context, such as reproductive boundaries, cytological variation, ecological interactions, and historical biogeographic processes, phylogenomic studies risk misinterpreting evolutionary history and processes. By accounting for these factors, we can begin to improve the accuracy of evolutionary reconstructions and gain deeper insights into the complex history of plant diversification.

The flowering plant order Asterales exhibits a striking disparity in species richness, with >30,000 species in Asteraceae compared to <50 in its sister family Calyceraceae. To investigate the genomic basis of this imbalance, we assembled three new chromosome-level genomes, including the first for Calyceraceae, and re-annotated five additional genomes. Comparative analyses revealed exceptionally high repeat content in both Asteraceae and Calyceraceae, pervasive chromosomal rearrangements, and evidence for shared and lineage-specific WGDs. In Asteraceae, tandem and dispersed duplications disproportionately drove expansions of gene families linked to secondary metabolism and stress response, while segmental duplicates bore signatures of adaptive selection for the regulation of biosynthetic and metabolic processes. Selective pressures on flowering time regulators suggest an evolved balance between regulatory flexibility and developmental constraint in floral diversification. These patterns reveal that, beyond ancient polyploidy, small-scale duplications and selective fine-tuning of regulatory networks underpinned the ecological versatility in Asteraceae, fueling its extraordinary diversification.