Abstract
Viruses in the family Phycodnaviridae infect autotrophic protists in aquatic environments. Application of a PCR assay targeting the DNA polymerase of viruses in this family has revealed that phycodnaviruses are quite diverse and appear to be widespread, but a limited number of environments have been examined so far. In this study, we examined the sequence diversity among viral DNA pol genes amplified by PCR from subtropical coastal waters of O‘ahu, Hawai‘i. A total of 18 novel prasinovirus-like sequences were detected along with two other divergent sequences that differ at the genus-level relative to other sequences in the family. Of the 20 new sequence types reported here, three were serendipitously found to contain protein introns, or inteins. Sequence analysis of the inteins suggested that all three have self-splicing domains and are apparently capable of removing themselves from the translated polymerase protein. Two of the three also appear to be ‘active’, meaning they encode all the motifs necessary for a complete dodecapeptide homing endonuclease, and are therefore capable of horizontal transfer. A subsequent PCR survey of our samples with intein-specific primers suggested that intein-containing phycodnaviruses are common in this environment. A search for similar sequences in metagenomic data sets from other oceans indicated that viral inteins are also widespread, but how these genetic parasites might be influencing the ecology and evolution of phycodnaviruses remains unclear.
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Acknowledgements
We thank Sara Yeo for her help with sample collection in Kāne‘ohe Bay, Olivia Nigro for advice and assistance, Matthias Fischer for enlightening conversations on intein biology, and Amarendran Subramanian for assistance with DIALIGN-TX. We thank Barbara Bruno, Education Director of the Center for Microbial Oceanography: Research and Education (C-MORE) and Sharon Ziegler-Chong of the Pacific Internship Programs for Exploring Science for supporting BFA through the University of Hawai‘i Hawaiian Internship Program. This work was supported by grants from the National Science Foundation (EF 04-2599) and The University of Hawai‘i Sea Grant College Program (R/EL-37). This is contribution no. 91 to the C-MORE publication series.
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Culley, A., Asuncion, B. & Steward, G. Detection of inteins among diverse DNA polymerase genes of uncultivated members of the Phycodnaviridae. ISME J 3, 409–418 (2009). https://doi.org/10.1038/ismej.2008.120
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DOI: https://doi.org/10.1038/ismej.2008.120
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