Cenci Alberto auteur aut IRD Combes Marie-Christine auteur aut IRD Lashermes Philippe auteur aut IRD text journalArticle eng text/pdf born digital access Sequence comparison of orthologous regions enables estimation of the divergence between genomes, analysis of their evolution and detection of particular features of the genomes, such as sequence rearrangements and transposable elements. Despite the economic importance of Coffea species, little genomic information is currently available. Coffea is a relatively young genus that includes more than one hundred diploid species and a single tetraploid species. Three Coffea orthologous regions of 470-900 kb were analyzed and compared: both subgenomes of allotetraploid Coffea arabica (contributed by the diploid species Coffea eugenioides and Coffea canephora) and the genome of diploid C. canephora. Sequence divergence was calculated on global alignments or on coding and non-coding sequences separately. A search for transposable elements detected 43 retrotransposons and 198 transposons in the sequences analyzed. Comparative insertion analysis made it possible to locate 165 TE insertions in the phylogenetic tree of the three genomes/subgenomes. In the tetraploid C. arabica, a homoeologous non-reciprocal transposition (HNRT) was detected and characterized: a 50 kb region of the C. eugenioides derived subgenome replaced the C. canephora derived counterpart. Comparative sequence analysis on three Coffea genomes/subgenomes revealed almost perfect gene synteny, low sequence divergence and a high number of shared transposable elements. Compared to the results of similar analysis in other genera (Aegilops/Triticum and Oryza), Coffea genomes/subgenomes appeared to be dramatically less diverged, which is consistent with the relatively recent radiation of the Coffea genus. Based on nucleotide substitution frequency, the HNRT was dated at 10,000-50,000 years BP, which is also the most recent estimation of the origin of C. arabica. specialized Coffea Polyploidy Comparative genomics Sequence polymorphism Transposable element HNRT 076 020 78 1-2 135-145 2012 0167-4412 https://www.documentation.ird.fr/hor/fdi:010054234 10.1007/s11103-011-9852-3 0167-4412 [F B010054234] https://www.documentation.ird.fr/hor/fdi:010054234 https://www.documentation.ird.fr/intranet/publi/2011/12/010054234.pdf Accès réservé (Intranet de l'IRD) IRD - Base Horizon / Pleins textes 2012-01-10 2024-04-29 fdi:010054234 fre