Amazing stuff!
"... Ancient events in plant evolution have left behind large, duplicated regions in their genomes.
... scientists found that deleting these large blocks of DNA can still lead to normal plants.
The findings demonstrate that large chromosomal deletions are a viable strategy in plant genetic engineering, which could now accelerate the development of streamlined, minimal plant genomes—a major goal in industries looking to create new plant-based biotechnologies. ...
The researchers used CRISPR-Cas9 to delete four large, duplicated blocks in Arabidopsis thaliana, a model plant commonly used in plant biology research. The deletions were then verified using whole-genome sequencing, which revealed minimal off-target effects. ..."
From the significance and abstract:
"Significance
Plant genomes are shaped by ancient polyploidy events, leaving behind extensive duplicated regions whose biological roles remain largely uncharacterized.
In this study, we demonstrate that targeted deletion of large, retained syntenic blocks in Arabidopsis thaliana results in viable plants, some with distinct phenotypes and widespread transcriptomic changes.
These findings challenge the assumption that such regions are essential and highlight the potential redundancy or modularity within plant genomes. Our approach of removing entire duplicated blocks offers a powerful strategy to functionally dissect conserved genomic regions, investigate gene linkage and dosage effects, and accelerate the development of streamlined, minimal plant genomes. This work establishes a scalable framework for genome engineering with broad implications for plant biology, synthetic genomics, and biotechnology.
Abstract
Plant genomes have undergone multiple rounds of whole-genome duplication (WGD) throughout their evolutionary history. As a result, many species, including Arabidopsis thaliana, retain duplicated genomic segments, or syntenic regions, which harbor large numbers of paralogous genes preserved from these ancient WGD events.
We deleted four large, duplicated blocks, ranging from ~115 kb to ~684 kb using Staphylococcus aureus Cas9 to explore the effects of knocking out these blocks in Arabidopsis.
Large deletions like these remain rare, especially in small and gene-dense plant genomes. Deletions were subsequently verified using whole-genome sequencing, which revealed minimal off-target effects.
The number of deleted genes ranged from 16 to 60, and transposable elements ranged from 4 to 112 among the four deleted blocks.
Two deletion lines showed distinct phenotypes resulting from the loss of many genes, while two others displayed no obvious defects, including for flowering time or hypocotyl elongation.
Moreover, RNA-sequencing revealed that expression compensation, where deletions of paralogous genes lead to the upregulation of intact paralogues, was not a general response to the deleted regions under the conditions tested.
Thus, it is possible to obtain viable plants when deleting large fragments that may be redundant or that contain nonessential genes.
These results demonstrate that large chromosomal deletions can be used as a tool for genome engineering approaches, such as genome minimization in plants and allele replacement using homology-directed repair and other precision editing methods. Targeted deletions of large chromosome fragments will be a valuable tool for research and biotechnology applications."
Fig. 4 Generation of deletion lines (deletions of retained duplicate regions or nonlethal genomic segments) and their applications.
No comments:
Post a Comment