The article highlights how multiplex genome editing overcomes gene redundancy in polyploid species, enabling simultaneous modification of multiple homoeologous genes and facilitating the study of subfunctionalization, neofunctionalization, and adaptive trait evolution.
Abstract
Evolutionary developmental biology (evo-devo) has transformed plant taxonomy by integrating comparative morphology, molecular genetics, and evolutionary theory to explain the origin and diversification of plant. Recent advances in gene editing, particularly CRISPR/Cas-based technologies, have further accelerated this transition from descriptive taxonomy to experimental validation of developmental and evolutionary hypotheses. This review examines the emerging role of CRISPR/Cas9, Cas12a, base editing, and prime editing in deciphering the genetic mechanisms underlying morphological evolution, functional homology, and species diversification in plants. The article highlights how multiplex genome editing overcomes gene redundancy in polyploid species, enabling simultaneous modification of multiple homoeologous genes and facilitating the study of subfunctionalization, neofunctionalization, and adaptive trait evolution. The integration of genome editing with single-cell transcriptomics, spatial genomics, and organelle genome research provides unprecedented resolution for reconstructing developmental pathways and ancestral traits while resolving long-standing taxonomic ambiguities. Furthermore, precision editing of regulatory elements and developmental genes offers direct experimental evidence linking genotype to phenotype, thereby strengthening phylogenetic inference and classification. Despite these advances, challenges such as off-target effects, genotype dependence, transformation inefficiency, limited reference genomes for non-model species, and regulatory concerns continue to constrain widespread application. Emerging strategies, including improved guide RNA design, transgene-free editing, and nanoparticle-mediated delivery are expected to overcome these limitations. Overall, the integration of gene editing and evo-devo provides a powerful framework for advancing plant evolution, taxonomy, and biodiversity research.
This review surveyed tropical plant species with published whole-genome assemblies and categorized them based on the primary aims of their genomic investigations, illustrating how integrative, multi-dimensional genomic datasets have provided robust insights into tropical plant evolution, adaptation, and trait biology.
The future of crop improvement using GEd technologies lies in the harmonisation or alignment of global policies and regulations to support the trade of agricultural produce and ensure that growers and consumers can benefit from GEd technology.
Michael G. K. Jones· Sugar Industry international· 0 citations
Epigenetic regulation has played a fundamental role in the evolution of plant reproduction. Across more than a billion years, ancestral genome-defense mechanisms in early eukaryotes were progressively expanded, diversified, and repurposed throughout the green lineage. Streptophyte algae assembled the first plant-specific methylation and small RNA systems, providing pre-adaptations for terrestrial reproduction. In bryophytes and early vascular plants, these systems became integrated into gametophyte development, sporogenesis, and meiotic genome protection. Seed plants experienced substantial diversification and expansion of chromatin regulators and small RNA machinery, enabling increasingly sophisticated control of cone, ovule, and embryo development. Angiosperms underwent the most dramatic rewiring of epigenetic pathways, including gene-family diversification, subfunctionalization, and the emergence of genomic imprinting, endosperm-specific demethylation, and lineage-specific reproductive small RNAs such as phasiRNAs. Convergent solutions, including imprinting, meiotic transposable element (TE) silencing, and TE-derived regulatory elements, arose independently across lineages. Rather than reflecting the emergence of entirely new molecular machinery, these innovations illustrate repeated functional co-option and regulatory rewiring of deeply conserved epigenetic modules. Ecological and life-history pressures further shaped epigenetic diversification, linking environmental stress, mating systems, and domestication to reproductive epigenetic plasticity. Recent evidence further demonstrates that epigenetic plasticity underlies the recurrent evolution of alternative reproductive strategies such as apomixis and contributes to reproductive responses to environmental stress. Advances in comparative epigenomics, single-cell technologies, and epigenome editing are now providing unprecedented opportunities to reconstruct the evolutionary history of reproductive epigenetic pathways and to harness them for crop improvement. Together, these findings reveal epigenetic regulation as a dynamic, modular, and deeply evolvable framework that has repeatedly enabled reproductive innovation throughout plant evolution.
Together, these advances establish SV-centered genomics as a critical framework for understanding plant genome evolution and accelerating precision crop improvement.
Ru-Yi Liu, Letong Huang, Jing-Ru Mu et al.· Plants· 0 citations
Current de-extinction efforts center on editing the genomes of extant species to express key traits that evolved in closely related extinct species. These complex projects require advances in genetic engineering pipelines coupled with animal model production as an approach to test hypotheses about genotype and phenotype associations. Here, we establish a multiplex genome engineering pipeline capable of introducing up to eleven genomic modifications across seven different genes simultaneously in viable founder mice. Our workflows achieved high editing efficiencies spanning three genome-editing modalities: Cas9 knockout, Cas9-mediated homology-dependent repair (HDR), and cytosine base editing and included editing of zygotes and embryonic stem cells. As a proof of concept, we produced six mouse models with modifications in genes involved in hair development and lipid metabolism, and the resulting mice displayed predicted hair phenotypes including curly, textured coats, and gold hair. This study advances methods of rapid establishment of complex genetic models, with a wide array of applications.
Rui Chen, M. Coquelin, Kanokwan Srirattana et al.· Cell Reports Methods· 0 citations
New methodologies were examined, including genome scanning, advanced assembly tools such as GetOrganelle, and multispecies merger phylogenetic reconstruction, highlighting the necessity of multi-genome integration, the application of pan-plastome methodologies, and the expanding possibilities of chloroplast synthetic biology and genome editing to improve agriculture.
Shaima Mahfood Ebrahim Abdulrahman, M. Karaismailoğlu· Bartın University Internatio...· 0 citations
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