Variation in the Genetic Repertoire of Viruses Infecting Micromonas pusilla Reflects Horizontal Gene Transfer and Links to Their Environmental Distribution

Finke, Jan F.; Winget, Danielle M.; Chan, Amy M.; Suttle, Curtis A.

doi:10.3390/v9050116

Cited by 18 publications

(18 citation statements)

References 66 publications

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“…This hypothesis is supported by the unique genome structure of prasinophyte algae. It harbours large viral DNA in addition to their own genome [ 62 , 63 ], and HGT events are commonly observed between eukaryote genomes and viral DNAs [ 62 , 63 , 64 ]. In an alternative hypothesis, class II tRNA- IPT /AP- IPT could have originated by descent of the original eukaryotic tRNA- IPT from the LECA, following the tree of life to the green lineages, but was later lost in several plant lineages ( Fig 6D ).…”

Section: Discussionmentioning

confidence: 99%

Tangled history of a multigene family: The evolution of ISOPENTENYLTRANSFERASE genes

et al. 2018

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ISOPENTENYLTRANSFERASE (IPT) genes play important roles in the initial steps of cytokinin synthesis, exist in plant and pathogenic bacteria, and form a multigene family in plants. Protein domain searches revealed that bacteria and plant IPT proteins were to assigned to different protein domains families in the Pfam database, namely Pfam IPT (IPTPfam) and Pfam IPPT (IPPTPfam) families, both are closely related in the P-loop NTPase clan. To understand the origin and evolution of the genes, a species matrix was assembled across the tree of life and intensively in plant lineages. The IPTPfam domain was only found in few bacteria lineages, whereas IPPTPfam is common except in Archaea and Mycoplasma bacteria. The bacterial IPPTPfam domain miaA genes were shown as ancestral of eukaryotic IPPTPfam domain genes. Plant IPTs diversified into class I, class II tRNA-IPTs, and Adenosine-phosphate IPTs; the class I tRNA-IPTs appeared to represent direct successors of miaA genes were found in all plant genomes, whereas class II tRNA-IPTs originated from eukaryotic genes, and were found in prasinophyte algae and in euphyllophytes. Adenosine-phosphate IPTs were only found in angiosperms. Gene duplications resulted in gene redundancies with ubiquitous expression or diversification in expression. In conclusion, it is shown that IPT genes have a complex history prior to the protein family split, and might have experienced losses or HGTs, and gene duplications that are to be likely correlated with the rise in morphological complexity involved in fine tuning cytokinin production.

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Section: Discussionmentioning

confidence: 99%

Tangled history of a multigene family: The evolution of ISOPENTENYLTRANSFERASE genes

et al. 2018

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“…Indeed, a genomic comparison among Phycodnaviridae members PBCV-1 (Chloroviruses), EsV-1 (Phaeoviruses), and EhV-86 (Coccolithoviruses) yielded only 14 conserved homologs from a pool of ~1000 genes [ 102 ]. A more comprehensive look at these diverse genes can be found in genus-specific reviews of the Phycodnaviridae [ 17 , 47 , 51 , 103 , 104 , 105 ].…”

Section: Diversity Of Cultured Virus-host Systemsmentioning

confidence: 99%

Viruses of Eukaryotic Algae: Diversity, Methods for Detection, and Future Directions

Coy

Gann

Pound

et al. 2018

Viruses

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The scope for ecological studies of eukaryotic algal viruses has greatly improved with the development of molecular and bioinformatic approaches that do not require algal cultures. Here, we review the history and perceived future opportunities for research on eukaryotic algal viruses. We begin with a summary of the 65 eukaryotic algal viruses that are presently in culture collections, with emphasis on shared evolutionary traits (e.g., conserved core genes) of each known viral type. We then describe how core genes have been used to enable molecular detection of viruses in the environment, ranging from PCR-based amplification to community scale “-omics” approaches. Special attention is given to recent studies that have employed network-analyses of -omics data to predict virus-host relationships, from which a general bioinformatics pipeline is described for this type of approach. Finally, we conclude with acknowledgement of how the field of aquatic virology is adapting to these advances, and highlight the need to properly characterize new virus-host systems that may be isolated using preliminary molecular surveys. Researchers can approach this work using lessons learned from the Chlorella virus system, which is not only the best characterized algal-virus system, but is also responsible for much of the foundation in the field of aquatic virology.

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“…Counterintuitively, the recorded biological variables (viral abundance, bacterial abundance and chlorophyll concentration) were not significant predictors of diversity or community composition. While studies have found correlations between bacterial abundance and viral abundance or viral lysis (Mojica et al, 2016; Wigington et al, 2016; Finke et al, 2017) results from studies examining cyanophage diversity and viral or cellular abundances have been inconsistent. One study along a north-south transect in the Atlantic Ocean found that cyanomyovirus diversity was not correlated to any environmental variable, but was correlated to host diversity (Jameson et al, 2011).…”

Section: Discussionmentioning

confidence: 99%

“…In contrast to using marker genes, phylogenies based on the presence and absence of genes across genomes can be used to compare closely related viruses and are the best way to describe differences in their genetic repertoire (Yutin et al, 2014; Legendre et al, 2015; Finke et al, 2017). However, this approach requires full genome sequencing and annotation of isolates and thus cannot be used to study complex natural communities.…”

Section: Introductionmentioning

confidence: 99%

The Environment and Cyanophage Diversity: Insights From Environmental Sequencing of DNA Polymerase

Finke

Suttle

2019

Front. Microbiol.

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Globally distributed and abundant cyanophages in the family Myoviridae have dsDNA genomes with variable gene content, including host-derived auxiliary metabolic genes (AMGs) that potentially can facilitate viral replication. However, it is not well understood how this variation in gene content interacts with environmental variables to shape cyanomyovirus communities. This project correlated the genetic repertoire of cyanomyoviruses with their phyologeny, and investigated cyanomyovirus ecotype distribution as a function of environmental conditions across locations and seasons. Reference cyanomyovirus genomes were compared for their overlap in gene content to infer phyologenetic distances, and these distances were compared to distances calculated based on DNA polymerase (gp43) gene sequences. In turn, gp43 partial gene sequences amplified from natural cyanophage communities were used to describe cyanomyovirus community composition and to assess the relationship between environmental variables. The results showed the following: (1) DNA polymerase gene phylogeny generally correlated with the similarity in gene content among reference cyanomyoviruses, and thus can be used to describe environmental cyanomyovirus communities; (2) spatial and seasonal patterns in cyanomyovirus communities were related to environmental variables; (3) salinity and temperature, combined with nutrient concentration were predictors of cyanomyovirus richness, diversity and community composition. This study shows that environmental variables shape viral communities by drawing on a diverse seed bank of viral genotypes. From these results it is evident that that viral ecotypes with their corresponding genetic repertoires underlie selection pressures. However, the mechanisms involved in selecting for specific viral genotypes remain to be fully understood.

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Variation in the Genetic Repertoire of Viruses Infecting Micromonas pusilla Reflects Horizontal Gene Transfer and Links to Their Environmental Distribution

Cited by 18 publications

References 66 publications

Tangled history of a multigene family: The evolution of ISOPENTENYLTRANSFERASE genes

Tangled history of a multigene family: The evolution of ISOPENTENYLTRANSFERASE genes

Viruses of Eukaryotic Algae: Diversity, Methods for Detection, and Future Directions

The Environment and Cyanophage Diversity: Insights From Environmental Sequencing of DNA Polymerase

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