Long-Read-Based Genome Assembly Reveals Numerous Endogenous Viral Elements in the Green Algal Bacterivore Cymbomonas tetramitiformis

Yangtsho Gyaltshen, Andrey Rozenberg, Amber Paasch, John A. Burns, Sally Warring, Raegan T. Larson, Xyrus X. Maurer-Alcala, Joel Dacks, Apurva Narechania, Eunsoo Kim

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The marine tetraflagellate Cymbomonas tetramitiformis has drawn attention as an early diverging green alga that uses a phago-mixotrophic mode of nutrition (i.e., the ability to derive nourishment from both photosynthesis and bacterial prey). The Cymbomonas nuclear genome was sequenced previously, but due to the exclusive use of short-read (Illumina) data, the assembly suffered from missing a large proportion of the genome's repeat regions. For this study, we generated Oxford Nanopore long-read and additional short-read Illumina data and performed a hybrid assembly that significantly improved the total assembly size and contiguity. Numerous endogenous viral elements were identified in the repeat regions of the new assembly. These include the complete genome of a giant Algavirales virus along with many genomes of integrated Polinton-like viruses (PLVs) from two groups: Gezel-like PLVs and a novel group of prasinophyte-specific PLVs. The integrated ∼400kb genome of the giant Algavirales virus is the first account of the association of the uncultured viral family AG03 with green algae. The complete PLV genomes from C. tetramitiformis ranged between 15 and 25kb in length and showed a diverse gene content. In addition, heliorhodopsin gene-containing repeat elements of putative mirusvirus origin were identified. These results illustrate past (and possibly ongoing) multiple alga-virus interactions that accompanied the genome evolution of C. tetramitiformis.

Original languageEnglish
Article numberevad194
JournalGenome Biology and Evolution
Issue number11
StatePublished - 1 Nov 2023

Bibliographical note

Publisher Copyright:
© 2023 The Author(s). Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.


  • MCP
  • MinION
  • mixotroph
  • phagotroph
  • polinton
  • prasinophyte


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