Catastrophic chromosomal restructuring during genome elimination in plants
- University of California, Davis, United States
- Indian Institute of Science Education and Research, India
- Masaryk University, Czech Republic
- Howard Hughes Medical Institute, University of California, Davis, United States
Figures
Figure 1 with 1 supplement
Ploidy types resulting from centromere-mediated uniparental genome elimination.
The altered CENH3 ‘GFP-tailswap’ strain was hybridized to the recessive glabrous1-1 mutant. Mean percentages of haploid, diploid and aneuploid progeny obtained from crosses to three independent GFP-t…
Figure 1—figure supplement 1
Dosage plots and SNP analysis of diploids from GFP-tailswap haploid induction crosses.
(A) Dosage plots from all five Arabidopsis chromosomes in consecutive non-overlapping 100 kbp bins. (B) The corresponding SNP plot for the % haploid inducer genome (Col-0) present in each sample.
Figure 2 with 4 supplements
Characterization of the three distinct aneuploid types from GFP-tailswap haploid induction crosses.
(A–D) Dosage plots from all five Arabidopsis chromosomes in consecutive non-overlapping 100 kbp bins and the corresponding SNP plot for the % haploid inducer genome (Col-0) present in each sample. A …
Figure 2—figure supplement 1
Copy number and T-DNA positions of the GFP-tailswap transgene in three independently derived transgenic lines.
(A) The three lines used in this study and the insertion sites for each GFP-tailswap transgene are shown. Lines #11 and #17 carry four copies of the transgene and the transformation event resulted …
Figure 2—figure supplement 2
Dosage plots and SNP analysis of atypical aneuploids from GFP-tailswap haploid induction crosses.
(A–D). Dosage plots from all five Arabidopsis chromosomes in consecutive non-overlapping 100 kbp bins and the corresponding SNP plot for the % haploid inducer genome (Col-0) present in each sample. …
Figure 2—figure supplement 3
Diversity of primary trisomic aneuploids derived from a selfed triploid (Col-0 ecotype).
(A) Primary trisomics (2n = 10 + 1) for all five Arabidopsis chromosomes. (B–D) Higher order primary trisomics from our analysis. We observed (B) double primary trisomics (2n = 10 + 1 + 1), (C) …
Figure 2—figure supplement 4
Representative dosage plots from 96 individuals from a selfed GFP-tailswap haploid inducer.
Representative dosage plot of diploid individuals (94/96 = 98%) showing a euploid dosage from all five Arabidopsis chromosomes. We detected two selfed individuals with numerical whole chromosome …
Figure 3
Shattered chromosomes are confined to a single chromosome originating from the haploid inducer.
(A) Chromosome dosage plots based on non-overlapping 25 kbp bins across each chromosome for five aneuploid individuals with shattered chromosomes. The GFP-tailswap transgene insertion event that …
Figure 4 with 2 supplements
Stable inheritance and chromosome painting of a shattered aneuploid chromosome.
(A) Dosage analysis from 16 F2 individuals from a selfed FRAG00062 individual. Progeny individuals either inherited the shattered chromosome intact (n = 2) or appeared diploid (n = 14). (B) Cartoon …
Figure 4—figure supplement 1
Analysis of duplicated and triplicated blocks from FRAG00062.
(A) Cartoon of duplicated and triplicated blocks on the shattered aneuploid chromosome from FRAG00062. (B) Rearranged pattern from DNA fluorescence in situ hybridization (FISH) with the …
Figure 4—figure supplement 2
DNA FISH on the shattered aneuploid chromosome from FRAG00062.
(A) Cartoon of the regions used for chromosome painting experiments. (B–D) Meiotic spreads from male meiocytes with DNA painting probes shown in (A). Scale bars = 5 μm. The unpaired shattered …
Figure 5 with 2 supplements
Breakpoint junctions and enriched features surrounding breakpoints of duplicated and triplicated blocks.
(A) Plot of all chromosomes and corresponding dosage plots (blue line) from FRAG00062. Black curves depict novel junctions identified from genomic reconstruction of the shattered haploid inducer …
Figure 5—figure supplement 1
PCR confirmation of breakpoint junctions for FRAG00062.
DNA gel showing PCR assays performed using oligo pairs from a control region and from breakpoint junctions specific to FRAG00062 using DNA from a diploid sibling (top panel) or FRAG00062 (bottom …
Figure 5—figure supplement 2
Breakpoint junctions types from FRAG00062.
(A, B). Top: Junction sequence from direct sequencing of breakpoint junctions. Middle and bottom: Reference A. thaliana sequence. Sequences in common with the junction sequence are in blue and red. …
Figure 6
The process of genome elimination and connected models for chromosomal rearrangements.
Genome elimination ensues when a haploid inducer expressing a variant CENH3 protein mates with the wild type. In many cases, the chromosomes marked by the variant CENH3 missegregate in the embryo …
Figure 7
Dosage plots for lig4-2 haploids isolated from a haploid induction cross using diploid lig4-2 as the male donor.
Dosage plots of lig4-2 haploids based on 150 kbp non-overlapping bins across all five Arabidopsis chromosomes. Euploid chromosome dosage plots for lig4-2 haploids have the appearance of having a …
Tables
Table 1
Haploid induction frequency from genome elimination crosses using lig4-2 mutants
| Haploid Inducer ♀ | ♂ | Total | Aneuploid | Diploid | Haploid |
|---|---|---|---|---|---|
| GFP-tailswap | Ler gl1 | 606 | 33% | 28% | 39% |
| GFP-tailswap | lig4-2 | 148 | 8% | 9% | 83% * |
| lig4-2 GFP-tailswap | Ler gl1 | 173 | 29% | 31% | 40% |
| lig4-2 GFP-tailswap | lig4-2 | 159 | 14% | 5% | 81% * |
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Haploid inducer lines or haploid inducer line with the lig4-2 mutation were crossed to wild-type Ler gl1 or lig4-2 mutant pollen (*Student's t-test, p < 0.001).
Additional files
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Supplementary file 1
List of the aneuploid individuals from GFP-tailswap × Ler gl1-1 crosses used in this study. Unique identifiers (FRAG IDs) are listed for each individual, along with the GFP-tailswap parental lines as well as their corresponding aneuploid chromosome types. The final 16 columns indicate whether individuals exhibited the numerical, truncated or shattered aneuploid chromosome type, and which specific chromosomes displayed these features.
- https://doi.org/10.7554/eLife.06516.020
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Supplementary file 2
List of aneuploid individuals obtained from selfed Col-0 triploids. Unique identifiers (FRAG IDs) are listed for each individual and indicate which specific chromosomes displayed the numerical aneuploid chromosome type.
- https://doi.org/10.7554/eLife.06516.021
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Supplementary file 3
List of diploid and aneuploid individuals obtained from selfed GFP-tailswap. Unique identifiers (FRAG IDs) are listed for each individual and indicate which specific chromosomes displayed the numerical aneuploid chromosome type.
- https://doi.org/10.7554/eLife.06516.022
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Supplementary file 4
Breakpoint junctions from FRAG00062. The positions and types of repair for each breakpoint junction are indicated, along with their orientation as well as possible outcomes for a novel gene product.
- https://doi.org/10.7554/eLife.06516.023
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Supplementary file 5
Enrichment ratios of genomic features surrounding breakpoints from duplicated or triplicated blocks. The ratios of genomic features listed in column 1 are calculated using 1000 bp and 10,000 bp windows surrounding breakpoints from duplicated or triplicated blocks. Regions with enriched ratios has a value of > 1 while regions that are under-represented have values of < 1. Light orange boxes are indicated for p < 0.05 and light red boxes for p < 0.01.
- https://doi.org/10.7554/eLife.06516.024
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Supplementary file 6
Single nucleotide polymorphisms between Col-0 and Ler. A list of SNPs from Col-0 and Ler used in this study and their chromosomal positions.
- https://doi.org/10.7554/eLife.06516.025
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Supplementary file 7
BAC clones used for chromosome painting. Listing of the corresponding chromosome, BAC clone and associated GenBank accession used.
- https://doi.org/10.7554/eLife.06516.026
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Supplementary file 8
Oligonucleotides sequences for analysis of breakpoint junctions from FRAG00062.
- https://doi.org/10.7554/eLife.06516.027
