A Gross Deletion Generated Independently by Spontaneous Mule Activation and Fast Neutron Irradiation Causes Fruit Precociousness in Clementine

Evidence linking gross structural variants and natural diversity in plants is very scarce. Based on short reads DNA sequencing, we show that the genomes of 2 Clemenules (Citrus clementine) derived cultivars, Arrufatina (a bud sport) and Nero (an irradiation induced mutant), share ca. a similar 2 MB hemizygous deletion in chromosome 3 that comprised about 244 primary transcripts. Both mutants show fruit precocity and are barely distinguishable except for the parthenocarpic habit of Nero. This genotype presented additional gross deletions and translocations.  An active 7 kb Mutator-like element found in Clemenules was present in Arrufatina in inverted orientation flanking the 5´ end of the deletion. This element was flanked by 9-bp target side duplications and displayed a putative ORF coding for a theoretical MULE transposase and 2 DNA binding domains. Within the 5´ end there were several motifs resembling those involved in recombination and translocation in human chromosomes. Comparative SNP analyses also identified a triplet repeat motif close to the center of the deletion coincident with a meiotic crossover. In conclusion, the data indicate that a similar gross deletion in chromosome 3 is associated with fruit precocity in both genotypes. In addition, the identification of the recombination elements may offer clues on the MULE transposition mechanism.