Comparative genomics of a bacterivorous green alga reveals evolutionary causalities and consequences of phago-mixotrophic mode of nutrition

John A. Burns, Amber Paasch, Apurva Narechania, Eunsoo Kim

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26 Scopus citations


Cymbomonas tetramitiformis - a marine prasinophyte - is one of only a few green algae that still retain an ancestral particulate-feeding mechanism while harvesting energy through photosynthesis. The genome of the alga is estimated to be 850 Mb-1.2 Gb in size - the bulk of which is filled with repetitive sequences - and is annotated with 37,366 protein-coding gene models. A number of unusual metabolic pathways (for the Chloroplastida) are predicted for C. tetramitiformis, including pathways for Lipid-A and peptidoglycan metabolism. Comparative analyses of the predicted peptides of C. tetramitiformis to sets of other eukaryotes revealed that nonphagocytes are depleted in a number of genes, a proportion of which have known function in feeding. In addition, our analysis suggests that obligatory phagotrophy is associated with the loss of genes that function in biosynthesis of small molecules (e.g., amino acids). Further, C. tetramitiformis and at least one other phago-mixotrophic alga are thus unique, compared with obligatory heterotrophs and nonphagocytes, in that both feeding and small molecule synthesis-related genes are retained in their genomes. These results suggest that early, ancestral host eukaryotes that gave rise to phototrophs had the capacity to assimilate building block molecules from inorganic substances (i.e., prototrophy). The loss of biosynthesis genes, thus, may at least partially explain the apparent lack of instances of permanent incorporation of photosynthetic endosymbionts in later-divergent, auxotrophic eukaryotic lineages, such as metazoans and ciliates.

Original languageEnglish
Pages (from-to)3047-3061
Number of pages15
JournalGenome Biology and Evolution
Issue number11
StatePublished - 1 Nov 2015

Bibliographical note

Funding Information:
The authors thank Aaron Heiss for valuable suggestions and comments on an earlier version of this article, Gabi Kastenmuller for her valuable suggestions concerning metabolic pathway analysis, and Jeremy Schmutz for helpful discussions on read filtering. The work was supported by the AMNH start-up grants awarded to E.K. and the National Science Foundation (award# IOS-1453639).

Publisher Copyright:
© The Author(s) 2015.


  • Chloroplastida
  • Cymbomonas
  • Green algae
  • Mixotrophy
  • Phagocytosis


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