Evolution of Cell Organelles Genomes

In eucaryotic cells there are two important organelles, mitochondria and plastids, which produce the energy and synthesize substances for cell metabolism respectively. These organelles are compartmentalized by two layers of membrane, have multiple copies of its genome, and are inherited in non-Mendelian fashion. It is now accepted that these organelles were originated from ancient endosymbionts of eukaryotic cell. Therefore, the genetic information from organelle genomes can provide an independent view of the phylogeny of their host organisms.

Both mitochondria and plastid have evolved via a process of genome reduction. The size of mitochondrial genome varies from 200 to 2500 kb while the plastid genomes are much less variable in size from 35 to 217 kb, but the majority of them are between 115-165 kb. So far, there are 49 genomes of plastids reported and only a few of 774 mitochondrial genomes sequenced belong to plant. It is clear, that the vast majority of plastid proteins are nucleus-encoded. The plastid genomes only have retained a small portion of sequences from their ancient endo-symbiotic ancestor and had transposed the majority of their genes to nucleus of host cells. There is no proof showing the transfer of nucleus-encoded gene to organelle genomes yet. Recently, there is evidence indicating that the chloroplast genes could be transferred to mitochondria. On the other hand, intergenomic mtDNA and cpDNA recombination seems to be a relatively low frequent phenomenon. Consequently, it could advantageous to use organelle genes for the analysis of phylogeny of plants. In our research line, we first focus on the study of the genome of chloroplast of common bean (Phaseolus vulgaris) and several of their varieties. The chloroplast of bean will be sequenced, analyzed, and compared. Further, some nuclear genes will also be sequenced to gain insight about the phylogeny of this important crop. Meanwhile, we will test the rearrangements within plastid genome and the gene transposition among the three compartments. The following questions will be in our research:

  1. What is the general structure of the chloroplast genome of Phaseolus vulgaris and the divergence pattern of its varieties?
  2. What is the phylogenetic relationship between the nucleus-encoded genes and chloroplast genes?
  3. Are there intra- or inter-molecule rearrangements within chloroplasts genomes?
  4. What is the amount of gene flow in between the genome compartments of beans?
  5. What is the effect of self-fertilization plant on the evolution of its plastid genome?


Xianwu Guo, design, performs experiments and data analysis.
Victor González, design experiments and data analysis.
Oscar Brito, Bachelor Thesis, DNA purification and template preparation.
Jose Luis Fernández, construction of DNA libraries.
Rosa I. Santamaría, DNA sequencing.
Patricia Bustos, assembly.
Guillermo Dávila, data analysis.

Evolutionary Genomics Program