title: Micro-collinearity and genome evolution in the vicinity of an ethylene receptor gene of cultivated diploid and allotetraploid coffee species (Coffea).
abstract: Arabica coffee (Coffea arabica L.) is a self-compatible perennial allotetraploid species (2n=4x=44), whereas Robusta coffee (C. canephora L.) is a self-incompatible perennial diploid species (2n=2x=22). C. arabica (C(a) C(a) E(a) E(a) ) is derived from a spontaneous hybridization between two closely related diploid coffee species, C. canephora (CC) and C. eugenioides (EE). To investigate the patterns and degree of DNA sequence divergence between the Arabica and Robusta coffee genomes, we identified orthologous bacterial artificial chromosomes (BACs) from C. arabica and C. canephora, and compared their sequences to trace their evolutionary history. Although a high level of sequence similarity was found between BACs from C. arabica and C. canephora, numerous chromosomal rearrangements were detected, including inversions, deletions and insertions. DNA sequence identity between C. arabica and C. canephora orthologous BACs ranged from 93.4% (between E(a) and C(a) ) to 94.6% (between C(a) and C). Analysis of eight orthologous gene pairs resulted in estimated ages of divergence between 0.046 and 0.665 million years, indicating a recent origin of the allotetraploid species C. arabica. Analysis of transposable elements revealed differential insertion events that contributed to the size increase in the C(a) sub-genome compared to its diploid relative. In particular, we showed that insertion of a Ty1-copia LTR retrotransposon occurred specifically in C. arabica, probably shortly after allopolyploid formation. The two sub-genomes of C. arabica, C(a) and E(a) , showed sufficient sequence differences, and a whole-genome shotgun approach could be suitable for sequencing the allotetraploid genome of C. arabica.
authors: Hawaii Agriculture Research Center, Waipahu, HI 96797, USA.
authors: Qingyi
authors: Q
authors: Yu
authors: Romain
authors: R
authors: Guyot
authors: Alexandre
authors: A
authors: de Kochko
authors: Anne
authors: A
authors: Byers
authors: Rafael
authors: R
authors: Navajas-Pérez
authors: Brennick J
authors: BJ
authors: Langston
authors: Christine
authors: C
authors: Dubreuil-Tranchant
authors: Andrew H
authors: AH
authors: Paterson
authors: Valérie
authors: V
authors: Poncet
authors: Chifumi
authors: C
authors: Nagai
authors: Ray
authors: R
authors: Ming
mesh_terms: D022202:Chromosomes, Artificial, Bacterial / Q000235:genetics; D040503:Coffea / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics; D004171:Diploidy; D019143:Evolution, Molecular; D015723:Gene Library; D015321:Gene Rearrangement; D018745:Genome, Plant; D058977:Molecular Sequence Annotation; D016254:Mutagenesis, Insertional; D010940:Plant Proteins / Q000235:genetics*; D011123:Polyploidy; D011956:Receptors, Cell Surface / Q000235:genetics*; D018626:Retroelements; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D018744:DNA, Plant; D010940:Plant Proteins; D011956:Receptors, Cell Surface; D018626:Retroelements; C083750:ethylene receptors, plant