Until recently, precise genome editing has been limited to a few organisms. The ability of Cas9 to generate double stranded DNA breaks at specific genomic sites has greatly expanded molecular toolkits in many organisms and cell types. Before CRISPR‐Cas9 mediated genome editing,
This content will become publicly available on November 16, 2024
- NSF-PAR ID:
- 10486593
- Editor(s):
- Newton, Irene L.
- Publisher / Repository:
- American Society for Microbiology
- Date Published:
- Journal Name:
- Microbiology Resource Announcements
- Volume:
- 12
- Issue:
- 11
- ISSN:
- 2576-098X
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract P. patens was unique among plants in its ability to integrate DNA via homologous recombination. However, selection for homologous recombination events was required to obtain edited plants, limiting the types of editing that were possible. Now with CRISPR‐Cas9, molecular manipulations inP. patens have greatly expanded. This protocol describes a method to generate a variety of different genome edits. The protocol describes a streamlined method to generate the Cas9/sgRNA expression constructs, design homology templates, transform, and quickly genotype plants. © 2023 Wiley Periodicals LLC.Basic Protocol 1 : Constructing the Cas9/sgRNA transient expression vectorAlternate Protocol 1 : Shortcut to generating single and pooled Cas9/sgRNA expression vectorsBasic Protocol 2 : Designing the oligonucleotide‐based homology‐directed repair (HDR) templateAlternate Protocol 2 : Designing the plasmid‐based HDR templateBasic Protocol 3 : Inducing genome editing by transforming CRISPR vector intoP. patens protoplastsBasic Protocol 4 : Identifying edited plants. -
Premise Divergence in functional traits and adaptive responses to environmental change underlies the ecological advantage of polyploid plants in the wild. While established polyploids may benefit from combined outcomes of genome doubling, hybridization, and polyploidy‐enabled adaptive evolution, whether genome doubling alone can drive ecological divergence or whether the outcome is genetically variable remains less clear.
Methods Using synthetic, colchicine‐induced, autotetraploid (4
x ) plants derived from self‐pollinated diploid (2x ) seeds, and their colchicine‐treated but unconverted diploid (2x.nc ) full sibs from two diploid wild strawberry taxa (Fragaria vesca subsp.vesca andF. vesca subsp.bracteata ), we examined the effects of genome doubling on functional traits, heat stress tolerance, and fitness components across taxa and maternal families (i.e., genetic families) within taxa.Results Comparisons between 2
x and 2x .nc plants indicated a negligible effect of colchicine treatment on functional traits. Genome doubling increased stomatal length and decreased stomatal density, specific leaf area, and leaf vein density, recapitulating patterns observed in wild polyploidFragaria . Trichome density, heat stress tolerance, and relative growth rate were not significantly affected by genome doubling. Although clonal reproduction was reduced in response to genome doubling, this effect was strongly genetic‐family dependent.Conclusions The results suggest that genome doubling during incipient speciation alone can generate ecological divergence and variation among genetic lineages. This response potentially allows for rapid short‐term evolutionary adaptation and fuels genomic diversity and independent origins of polyploidy.
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Abstract Background Recent efforts to assemble and analyze the
Ambystoma mexicanum genome have dramatically improved the potential to develop molecular tools and pursue genome‐wide analyses of genetic variation.Results To better resolve the distribution and origins of genetic variation with
A mexicanum , we compared DNA sequence data for two laboratoryA mexicanum and oneA tigrinum to identify 702 million high confidence polymorphisms distributed across the 32 Gb genome. While the wild‐caughtA tigrinum was generally more polymorphic in a genome‐wide sense, several multi‐megabase regions were identified fromA mexicanum genomes that were actually more polymorphic thanA tigrinum . Analysis of polymorphism and repeat content reveals that these regions likely originated from the intentional hybridization ofA mexicanum andA tigrinum that was used to introduce thealbino mutation into laboratory stocks.Conclusions Our findings show that axolotl genomes are variable with respect to introgressed DNA from a highly polymorphic species. It seems likely that other divergent regions will be discovered with additional sequencing of
A mexicanum . This has practical implications for designing molecular probes and suggests a need to studyA mexicanum phenotypic variation and genome evolution across the tiger salamander clade. -
SUMMARY The Pacific crabapple (
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Summary From a single transgenic line harboring five
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