Chromothripsis, or chromosome shattering, occurs after chromosomes missegregate, are pulverized and subsequently repaired erroneously, leading to highly complex structural rearrangements. In plants, chromothripsis has been observed as a result of mitotic malfunction connected with the incomplete loss of haploid inducer chromosomes during uniparental genome elimination. Uniparental genome elimination, a process that results in haploid induction, is a phenomenon that typically results in the loss of an entire parental chromosome set in early embryos, resulting in haploid plants. In Arabidopsis thaliana, genome elimination can be achieved via the manipulation of the centromere-specific histone H3 variant, CENH3. Genomic characterization of F1 progeny resulting from CENH3-mediated genome elimination crosses in Arabidopsis revealed haploids (~39%), diploids (~25%), and aneuploids (~37%). Within the aneuploid class, ~11% show evidence for chromothripsis. Here, we present a protocol to identify Arabidopsis aneuploids that have inherited chromothriptic chromosomes during genome elimination crosses and describe in detail how to perform in silico reconstructions for individuals with chromothripsis using the somatic mutation finder (SMuFin) tool.
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