Exploration of Transposable Element Families in the Novel Citrus Genome Fairchild

Citrus alone accounts for $2 billion of California’s annual agricultural production value; its economic importance drives the large amount of citrus research performed at the University of California, Riverside. Transposable elements (TEs) are a major component of eukaryotic genomes and may contribute to citrus diversity. A multi-lab collaboration funded the PacBio sequencing of a UCR citrus variety of interest named Fairchild. The focus of this project is to annotate the entire collection of TEs in Fairchild and further characterize putatively active elements to form a basis for continued research on citrus diversity. The Tree Analysis of Related Genes and Transposons (TARGeT) software package is used to identify Fairchild homologs of transposases, the proteins responsible for element mobility, characterized in other angiosperms. The phylogenetic tree provided by TARGeT allows for selection of putative active homologs, identified by the shortest branches between two or more element nodes; this potentially indicates very recent TE replication events. To confirm a sequence as a TE, sequences flanking the transposases were examined for unique TE features such as terminal inverted repeats (TIRs) and target site of duplications (TSD). To date, several putative active elements of the hAT and PIF/Harbinger superfamilies in Fairchild have been selected as candidates for in vivo tests of activity in S. cerevisiae and A. thaliana.