LTR Retrotransposons In The Robusta Coffee Genome (Coffea canephora): Identification and Charaterization Of Elements From BAC-End and 454 Sequences

Coffee is one of the most important international trade commodities and is ranked as the second most valuable primary commodity exported by southern countries. Two species are mainly used in commercial production: Coffea arabica, known as Arabica and Coffea canephora, a perennial diploid species known as Robusta. Recently, 131,412 BAC-end (BES) and 106,459 454 sequences were generated from a C. canephora Double Haploid accession (DH200-94), which corresponds to almost 19 % of the estimated C. canephora genome size.

Here we present the identification and the characterization of LTR Retrotransposons in the C. canephora genome based on the analysis of BES and 454 sequences. To reconstruct the structure of LTR Retrotransposons, we used the Assisted Automated Assembler of Repeat Families algorithm (DeBarry et al., 2008) to assemble sequences into 37 different LTR-RTs contigs. The contig sizes range from 11,130 to 3,070 bp and nine of them were annotated as complete LTR-RTs elements. Based on a RT domain classification, we show that all LTR-RTs contigs belong to well defined LTR-RTs families. Among the 37 LTR-RTs contigs, 27 and 10 belong respectively to the Gypsy and Copia superfamilies. Twenty-three LTR-RTs contigs were found highly conserved in C. canephora EST sequences, and eight were found transcriptionally active in C. canephora leaves and/or fruits, suggesting that these LTR-RTs are potentially expressed.

One of the LTR-RTs contigs assembled here and called COPIA25 was characterized in details. COPIA25 belongs to the Copia Tork4 family of LTR-retrotransposons. It was found expressed by PCR amplification on C. canephora cDNA libraries. To investigate the origin of COPIA25 in coffee we retrieved 24 highly similar sequences from 18 model genomes and we analyzed their phylogenetic relationships. Surprisingly, elements from potato and banana clustered with COPIA25. A detailed analysis confirmed an outstanding nucleotide (75%) and amino acid conservations (82%) between COPIA25and the potato/banana elements. Considering the species divergence between coffee and banana (> 150 My) and coffee and potato (83-89 My), such remarkable conservation may suggest events of TE horizontal transfers.

Additional characterization of COPIA25 will produce new insight into the impact of this family into the Coffea genome evolution and diversity.