W187Transposable Elements in the Robusta Coffee Genome (Coffea canephora)
Time: 4:40 PM
Here we present the identification and classification of TEs in the 568 Mb genomic sequences of the C. canephora using a combination of ab initio, similarity and structure search approaches. We used mainly the REPET package V.2.1-RC (Flutre et al., 2011) to identify, classify and annotate TE. We found that 49% of the genomic sequences are composed of TEs similarly to other sequenced plant genomes such as banana, papaya, castor bean and soybean. Class I LTR retrotransposons represent the vast majority of identified elements, accounting to 42% of the genome assembly. Gypsy elements clearly outnumbering Copia elements since Ty3-Gypsy family covers 24.1% of the genome. Interestingly active non-autonomous LTR retrotransposons elements were detected and classified into a new subgroup of non–autonomous elements containing a capsid domain but lacking the polyprotein region. Finally in an attempt to study conservation of LTR retrotransposons between coffee and reference plant genomes, we identified an outstanding conservation of several Copia groups across very distantly related plant species, suggesting that conservation of such elements or horizontal transfer events might be more frequent than recognized actually.