Andrew C. Willoughby

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.

The ability of organisms to replace and regenerate anatomical structures following their loss or damage has piqued the curiosity of biologists for centuries. In addition to Development's ‘Model systems for regeneration’ collection, which introduced some of the most well-studied model organisms in the field, we published a Perspective in 2024 highlighting some of the lesser-known species with extraordinary regenerative abilities from plants to vertebrates ( Accorsi et al., 2024). Here, we revisit this topic again, hearing the perspectives of five experts, each of whom studies an amazing species with remarkable regenerative potential.

Andrew C Willoughby; Illuminating the future: Enhanced glowing plants achieved by rewiring metabolism, The Plant Cell, , koae286, https://doi.org/10.1093/p

Andrew C Willoughby; Air plant genomes shed light on photosynthesis innovation, The Plant Cell, , koae213, https://doi.org/10.1093/plcell/koae213

The domestication of strawberries (Fragaria x ananassa) stands as an example of remarkable agricultural advancement, with the original hybrids arising less than 300 years ago ( Liston et al. 2014). Contrary to what one might expect from a speedy and recent domestication process starting from small founder populations, cultivated strawberries exhibit substantial genetic diversity, attributable to subsequent hybridization events ( Hardigan et al. 2021).

The discovery of Cas9 nuclease has revolutionized the field of gene editing, allowing for precise and programmable modifications to DNA. Many gene-editing techniques stemming from CRISPR-Cas9 (CRISPR) rely on the creation of double-stranded breaks (DSBs) in DNA. However, DSBs pose a threat to the replication process and therefore need to be repaired. The repair of CRISPR-induced DSBs can have varying effects on the genome, with nonhomologous end joining causing small insertions or deletions at the site of the break and homologous recombination potentially leading to crossovers between homologous chromosomes or gene conversion. Targeted crossovers and gene conversion are highly sought-after outcomes in plant breeding for segregating undesirable alleles. These events can enable targeted gene replacement or the elimination of undesirable transgenes, making this process invaluable to the improvement of crops ( He et al. 2022). Aviva Samach, Fabrizio Mafessoni, Or Gross, and colleagues (Samach et al. 2023) present an assay that detects loss of heterozygosity (LOH) and can be used to study the genomic consequences of DSBs. They induce and can visually identify targeted crossover induction (see Fig.) and also the occurrence of chromothripsis, a process not well studied in plants but characterized by large and severe chromosome rearrangements. This visual assay adds new uses to a growing group of unconventional tools that reduce the need for microscopes or other equipment for particular experiments and screens ( Liu et al. 2019, Chen et al. 2023, Sun et al. 2023). These may lower financial and infrastructure barriers to plant biology research, expanding the abilities of universities, field sites, and classrooms.

When people enjoy salty snacks at a bar, their thirst can be quenched with an extra drink. The plant in the window, however, is unable to place an order. To cope with osmotic stress induced by drought conditions, plants rapidly increase their intracellular calcium and produce abscisic acid, a plant hormone involved in many stress responses. These signaling processes cause plants to close their stomata to prevent water loss and shape their root architecture to find more water—strategies needed for short- and long-term osmotic stress ( Zhu 2016; Robbins and Dinneny 2018).