Yu Q.Y., Guyot Romain, Kochko Alexandre de, Byers A., Navajas-Perez R., Langston B.J., Dubreuil Tranchant Christine, Paterson A.H., Poncet Valérie, Nagai C., Ming R. (2011). Micro-collinearity and genome evolution in the vicinity of an ethylene receptor gene of cultivated diploid and allotetraploid coffee species (Coffea). Plant Journal, 67 (2), p. 305-317. ISSN 0960-7412.
Titre du document
Micro-collinearity and genome evolution in the vicinity of an ethylene receptor gene of cultivated diploid and allotetraploid coffee species (Coffea)
Année de publication
2011
Auteurs
Yu Q.Y., Guyot Romain, Kochko Alexandre de, Byers A., Navajas-Perez R., Langston B.J., Dubreuil Tranchant Christine, Paterson A.H., Poncet Valérie, Nagai C., Ming R.
Source
Plant Journal, 2011,
67 (2), p. 305-317 ISSN 0960-7412
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 ((CCEEa)-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.
Plan de classement
Sciences du monde végétal [076]
Localisation
Fonds IRD [F B010053685]
Identifiant IRD
fdi:010053685
