Transposable Elements as a Source of Variation in Citrus

We have used next generation sequencing to analyze the genomes of several varieties of clementine mandarins. The analysis included genome sequencing by Illumina with pair-en reads, mapping against the clementine reference genome sequence, variant calling (SNPs, small indels), copy number variation (CNV), search for large structural variations and comparative analysis between varieties.

We have identified a large deletion in Arrufatina chromosome 3 that might be related with the activity of a Mutator-like transposable element. This element contains a transposase and a zinc-finger domain that is typical of this family, and could be active in the Citrus genome. We have carried out the analysis of the Mut-like family of TEs in citrus clementina, and show their distribution in the genome as well as the phylogenetic relationships between them.

In a similar way, a large deletion at the end of chromosome 2 in Marisol could be also related with the presence of sequence coding for a non-LTR retrolelement reverse transcriptase-like protein that will be further characterized.