Presentation Title

Characterization of Three DNA Transposable Elements Superfamilies in the Fairchild Genome

Start Date

November 2016

End Date

November 2016

Location

HUB 302-45

Type of Presentation

Poster

Abstract

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 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 identify active transposable elements in the novel reference genome in order to contribute to research on citrus diversity. The PIF/Harbinger, hAT, and TcMariner transposable element superfamilies are the current focus for annotation. Tree Analysis of Related Genes and Transposons (TARGeT) is used to identify Fairchild homologs of transposases 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 transposable element (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 duplication (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.

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Nov 12th, 1:00 PM Nov 12th, 2:00 PM

Characterization of Three DNA Transposable Elements Superfamilies in the Fairchild Genome

HUB 302-45

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 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 identify active transposable elements in the novel reference genome in order to contribute to research on citrus diversity. The PIF/Harbinger, hAT, and TcMariner transposable element superfamilies are the current focus for annotation. Tree Analysis of Related Genes and Transposons (TARGeT) is used to identify Fairchild homologs of transposases 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 transposable element (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 duplication (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.