The shift to reductionist biology at the dawn of the genome era yielded a 'parts list' of plant genes and a nascent understanding of complex biological processes. Today, with the genomics era in full swing, advances in high-definition genomics enabled precise temporal and spatial analyses of biological systems down to the single-cell level. These insights, coupled with artificial intelligence-driven in silico design, are propelling the development of the first synthetic plants. By integrating reductionist and systems approaches, researchers are not only reimagining plants as sources of food, fiber, and fuel but also as 'environmental thermostats' capable of mitigating the impacts of a changing climate.
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http://dx.doi.org/10.1111/nph.20382 | DOI Listing |
New Phytol
January 2025
Plant Molecular and Cellular Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037-100210, USA.
The shift to reductionist biology at the dawn of the genome era yielded a 'parts list' of plant genes and a nascent understanding of complex biological processes. Today, with the genomics era in full swing, advances in high-definition genomics enabled precise temporal and spatial analyses of biological systems down to the single-cell level. These insights, coupled with artificial intelligence-driven in silico design, are propelling the development of the first synthetic plants.
View Article and Find Full Text PDFNew Phytol
January 2025
School of Environment and Science, Griffith University, 170 Kessels Road, Nathan, Qld, 4111, Australia.
Genomics has revolutionised the study of invasive species, allowing evolutionary biologists to dissect mechanisms of invasion in unprecedented detail. Botanical research has played an important role in these advances, driving much of what we currently know about key determinants of invasion success (e.g.
View Article and Find Full Text PDFNat Commun
January 2025
Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, USA.
Single-cell RNA sequencing (scRNA-seq) is widely used in plant biology and is a powerful tool for studying cell identity and differentiation. However, the scarcity of known cell-type marker genes and the divergence of marker expression patterns limit the accuracy of cell-type identification and our capacity to investigate cell-type conservation in many species. To tackle this challenge, we devise a novel computational strategy called Orthologous Marker Gene Groups (OMGs), which can identify cell types in both model and non-model plant species and allows for rapid comparison of cell types across many published single-cell maps.
View Article and Find Full Text PDFTrends Microbiol
December 2024
Department of Plant Pathology and Microbiology, Institute of Environmental Science, The Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel. Electronic address:
Bacteria colonize every niche on Earth and play key roles in many environmental and host-associated processes. The sequencing revolution revealed the remarkable bacterial genetic and proteomic diversity and the genomic content of cultured and uncultured bacteria. However, deciphering functions of novel proteins remains a high barrier, often preventing the deep understanding of microbial life and its interaction with the surrounding environment.
View Article and Find Full Text PDFJ Mol Evol
December 2024
Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 3Er Circuito de Ciudad Universitaria, Coyoacán, 04510, Mexico City, Mexico.
The massive increase in the amount of plastid genome data have allowed researchers to address a variety of evolutionary questions within a wide range of plant groups. While plastome structure is generally conserved, some angiosperm lineages exhibit structural changes. Such is the case of the megadiverse order Asterales, where rearrangements in plastome structure have been documented.
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