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TitleMicro-collinearity and genome evolution in the vicinity of an ethylene receptor gene of cultivated diploid and allotetraploid coffee species (Coffea)
AuthorsQingyi Yu1, Romain Guyot, Alexandre de Kochko3, Anne Byers, Rafael Navajas-Perez, Brennick J. Langston,
Christine Dubreuil-Tranchant, Andrew H. Paterson, Valerie Poncet, Chifumi Nagai1 and Ray Ming
PublicationThe Plant Journal (2011) 67, 305-317
AbstractArabica 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
(CaCaEaEa) 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 Ea and Ca) to 94.6% (between Ca 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 Ca 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, Ca and Ea, showed sufficient sequence
differences, and a whole-genome shotgun approach could be suitable for sequencing the allotetraploid
genome of C. arabica.

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