Micro-collinearity and genome evolution in the vicinity of an ethylene receptor gene of cultivated diploid and allotetraploid coffee species (Coffea)

Qingyi Yu, Romain Guyot, Alexandre De Kochko, Anne Byers, Rafael Navajas-Pérez, Brennick J. Langston, Christine Dubreuil-Tranchant, Andrew H. Paterson, Valérie Poncet, Chifumi Nagai, Ray Ming

Research output: Contribution to journalArticlepeer-review

Abstract

Summary 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 aC aE aE 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. The Plant Journal

Original languageEnglish (US)
Pages (from-to)305-317
Number of pages13
JournalPlant Journal
Volume67
Issue number2
DOIs
StatePublished - Jul 1 2011

Keywords

  • Coffea
  • allotetraploid
  • comparative genomics
  • evolution
  • genetic divergence
  • transposable elements

ASJC Scopus subject areas

  • Genetics
  • Plant Science
  • Cell Biology

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