title: Microcollinearity in an ethylene receptor coding gene region of the Coffea canephora genome is extensively conserved with Vitis vinifera and other distant dicotyledonous sequenced genomes.
abstract: BACKGROUND
  Coffea canephora, also called Robusta, belongs to the Rubiaceae, the fourth largest angiosperm family. This diploid species (2x = 2n = 22) has a fairly small genome size of approximately 690 Mb and despite its extreme economic importance, particularly for developing countries, knowledge on the genome composition, structure and evolution remain very limited. Here, we report the 160 kb of the first C. canephora Bacterial Artificial Chromosome (BAC) clone ever sequenced and its fine analysis.
  
  
  RESULTS
  This clone contains the CcEIN4 gene, encoding an ethylene receptor, and twenty other predicted genes showing a high gene density of one gene per 7.8 kb. Most of them display perfect matches with C. canephora expressed sequence tags or show transcriptional activities through PCR amplifications on cDNA libraries. Twenty-three transposable elements, mainly Class II transposon derivatives, were identified at this locus. Most of these Class II elements are Miniature Inverted-repeat Transposable Elements (MITE) known to be closely associated with plant genes. This BAC composition gives a pattern similar to those found in gene rich regions of Solanum lycopersicum and Medicago truncatula genomes indicating that the CcEIN4 regions may belong to a gene rich region in the C. canephora genome. Comparative sequence analysis indicated an extensive conservation between C. canephora and most of the reference dicotyledonous genomes studied in this work, such as tomato (S. lycopersicum), grapevine (V. vinifera), barrel medic M. truncatula, black cottonwood (Populus trichocarpa) and Arabidopsis thaliana. The higher degree of microcollinearity was found between C. canephora and V. vinifera, which belong respectively to the Asterids and Rosids, two clades that diverged more than 114 million years ago.
  
  
  CONCLUSIONS
  This study provides a first glimpse of C. canephora genome composition and evolution. Our data revealed a remarkable conservation of the microcollinearity between C. canephora and V. vinifera and a high conservation with other distant dicotyledonous reference genomes. Altogether, these results provide valuable information to identify candidate genes in C. canephora genome and serve as a foundation to establish strategies for whole genome sequencing. Future large-scale sequence comparison between C. canephora and reference sequenced genomes will help in understanding the evolutionary history of dicotyledonous plants.
authors.affiliation: UMR GDP, IRD BP 64501, Centre IRD de Montpellier, Montpellier Cedex 5, France. romain.guyot@mpl.ird.fr
authors.forename: Romain
authors.initials: R
authors.lastname: Guyot
authors.forename: Marion
authors.initials: M
authors.lastname: de la Mare
authors.forename: Véronique
authors.initials: V
authors.lastname: Viader
authors.forename: Perla
authors.initials: P
authors.lastname: Hamon
authors.forename: Olivier
authors.initials: O
authors.lastname: Coriton
authors.forename: José
authors.initials: J
authors.lastname: Bustamante-Porras
authors.forename: Valérie
authors.initials: V
authors.lastname: Poncet
authors.forename: Claudine
authors.initials: C
authors.lastname: Campa
authors.forename: Serge
authors.initials: S
authors.lastname: Hamon
authors.forename: Alexandre
authors.initials: A
authors.lastname: de Kochko
mesh_terms: D022202:Chromosomes, Artificial, Bacterial; D040503:Coffea / Q000235:genetics*; D017124:Conserved Sequence; D018744:DNA, Plant / Q000235:genetics; D019143:Evolution, Molecular; D015723:Gene Library; D017343:Genes, Plant; D018745:Genome, Plant; D008969:Molecular Sequence Data; D020161:Physical Chromosome Mapping; D010940:Plant Proteins / Q000235:genetics*; D011956:Receptors, Cell Surface / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D027843:Vitis / Q000235:genetics
chemical_list: D018744:DNA, Plant; D010940:Plant Proteins; D011956:Receptors, Cell Surface; C083750:ethylene receptors, plant