The complete nucleotide sequence of the cassava (Manihot esculenta) chloroplast genome and the evolution of atpF in Malpighiales: RNA editing and multiple losses of a group II intron

  • Henry Daniell
  • Kenneth J. Wurdack
  • Anderson Kanagaraj
  • Seung-Bum Lee
  • Christopher Saski
  • Robert K. Jansen
Original Paper


The complete sequence of the chloroplast genome of cassava (Manihot esculenta, Euphorbiaceae) has been determined. The genome is 161,453 bp in length and includes a pair of inverted repeats (IR) of 26,954 bp. The genome includes 128 genes; 96 are single copy and 16 are duplicated in the IR. There are four rRNA genes and 30 distinct tRNAs, seven of which are duplicated in the IR. The infA gene is absent; expansion of IRb has duplicated 62 amino acids at the 3′ end of rps19 and a number of coding regions have large insertions or deletions, including insertions within the 23S rRNA gene. There are 17 intron-containing genes in cassava, 15 of which have a single intron while two (clpP, ycf3) have two introns. The usually conserved atpF group II intron is absent and this is the first report of its loss from land plant chloroplast genomes. The phylogenetic distribution of the atpF intron loss was determined by a PCR survey of 251 taxa representing 34 families of Malpighiales and 16 taxa from closely related rosids. The atpF intron is not only missing in cassava but also from closely related Euphorbiaceae and other Malpighiales, suggesting that there have been at least seven independent losses. In cassava and all other sequenced Malphigiales, atpF gene sequences showed a strong association between C-to-T substitutions at nucleotide position 92 and the loss of the intron, suggesting that recombination between an edited mRNA and the atpF gene may be a possible mechanism for the intron loss.


Bacterial Artificial Chromosome Cassava Chloroplast Genome Intron Loss Chloroplast Genome Sequence 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



Investigations reported in this article were supported in part by grants from the USDA (3611-21000-017-00D) and NIH (R01 GM 63879) to Henry Daniell. Research by Kenneth J. Wurdack and Robert K. Jansen was supported, in part, by NSF AToL grants EF 0431242 and DEB 0120709, respectively. The authors thank Kenneth Olsen, the Royal Botanic Gardens, Kew, and the herbaria cited for tissue or DNA samples.


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Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Henry Daniell
    • 1
  • Kenneth J. Wurdack
    • 2
  • Anderson Kanagaraj
    • 1
  • Seung-Bum Lee
    • 1
  • Christopher Saski
    • 3
  • Robert K. Jansen
    • 4
  1. 1.Department Molecular Biology and Microbiology, College of MedicineUniversity of Central Florida, 4000 Central Florida BlvdOrlandoUSA
  2. 2.Department of BotanySmithsonian InstitutionWashingtonUSA
  3. 3.Clemson University Genomics Institute, Biosystems Research ComplexClemson UniversityClemsonUSA
  4. 4.Section of Integrative Biology and Institute of Cellular and Molecular BiologyUniversity of TexasAustinUSA

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