Widespread endogenization of giant viruses shapes genomes of green algae
1.
Feschotte, C. & Gilbert, C. Endogenous viruses: insights into viral evolution and impact on host biology. Nat. Rev. Genet. 13, 283–296 (2012).
CAS PubMed Article PubMed Central Google Scholar
2.
Holmes, E. C. The evolution of endogenous viral elements. Cell Host Microbe 10, 368–377 (2011).
CAS PubMed PubMed Central Article Google Scholar
3.
Fischer, M. G. Giant viruses come of age. Curr. Opin. Microbiol. 31, 50–57 (2016).
PubMed Article PubMed Central Google Scholar
4.
Wilhelm, S. W. et al. A student’s guide to giant viruses infecting small eukaryotes: from Acanthamoeba to zooxanthellae. Viruses 9, 46 (2017).
PubMed Central Article CAS Google Scholar
5.
Abergel, C., Legendre, M. & Claverie, J.-M. The rapidly expanding universe of giant viruses: Mimivirus, Pandoravirus, Pithovirus and Mollivirus. FEMS Microbiol. Rev. 39, 779–796 (2015).
CAS PubMed Article PubMed Central Google Scholar
6.
Weynberg, K. D., Allen, M. J. & Wilson, W. H. Marine prasinoviruses and their tiny plankton hosts: a review. Viruses 9, 43 (2017).
PubMed Central Article CAS Google Scholar
7.
Bhattacharya, D. & Medlin, A. L. Algal phylogeny and the origin of land plants. Plant Physiol. 116, 9–15 (1998).
CAS PubMed Central Article Google Scholar
8.
Jeanniard, A. et al. Towards defining the chloroviruses: a genomic journey through a genus of large DNA viruses. BMC Genomics 14, 158 (2013).
CAS PubMed PubMed Central Article Google Scholar
9.
Moniruzzaman, M., Martinez-Gutierrez, C. A., Weinheimer, A. R. & Aylward, F. O. Dynamic genome evolution and complex virocell metabolism of globally-distributed giant viruses. Nat. Commun. 11, 1710 (2020).
ADS CAS PubMed PubMed Central Article Google Scholar
10.
Filée, J. Genomic comparison of closely related giant viruses supports an accordion-like model of evolution. Front. Microbiol. 6, 593 (2015).
PubMed PubMed Central Google Scholar
11.
Van Etten, J. L. et al. Chloroviruses have a sweet tooth. Viruses 9, 88 (2017).
PubMed Central Article CAS Google Scholar
12.
Schvarcz, C. R. & Steward, G. F. A giant virus infecting green algae encodes key fermentation genes. Virology 518, 423–433 (2018).
CAS PubMed Article PubMed Central Google Scholar
13.
Sun, C., Feschotte, C., Wu, Z. & Mueller, R. L. DNA transposons have colonized the genome of the giant virus Pandoravirus salinus. BMC Biol. 13, 38 (2015).
PubMed PubMed Central Article CAS Google Scholar
14.
Marcet-Houben, M. & Gabaldón, T. Acquisition of prokaryotic genes by fungal genomes. Trends Genet. 26, 5–8 (2010).
CAS PubMed Article PubMed Central Google Scholar
15.
Rossoni, A. W. et al. The genomes of polyextremophilic cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions. eLife 8, e45017 (2019).
CAS PubMed PubMed Central Article Google Scholar
16.
Filée, J. Multiple occurrences of giant virus core genes acquired by eukaryotic genomes: the visible part of the iceberg? Virology 466–467, 53–59 (2014).
PubMed Article CAS PubMed Central Google Scholar
17.
Maumus, F. & Blanc, G. Study of gene trafficking between Acanthamoeba and giant viruses suggests an undiscovered family of amoeba-infecting viruses. Genome Biol. Evol. 8, 3351–3363 (2016).
CAS PubMed PubMed Central Article Google Scholar
18.
Gallot-Lavallée, L. & Blanc, G. A glimpse of nucleo-cytoplasmic large DNA virus biodiversity through the eukaryotic genomics window. Viruses 9, 17 (2017).
PubMed Central Article Google Scholar
19.
Maumus, F., Epert, A., Nogué, F. & Blanc, G. Plant genomes enclose footprints of past infections by giant virus relatives. Nat. Commun. 5, 4268 (2014).
ADS CAS PubMed PubMed Central Article Google Scholar
20.
Guglielmini, J., Woo, A. C., Krupovic, M., Forterre, P. & Gaia, M. Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes. Proc. Natl Acad. Sci. USA 116, 19585–19592 (2019).
CAS PubMed Article PubMed Central Google Scholar
21.
Forterre, P. & Gaïa, M. Giant viruses and the origin of modern eukaryotes. Curr. Opin. Microbiol. 31, 44–49 (2016).
PubMed Article PubMed Central Google Scholar
22.
Piacente, F., Gaglianone, M., Laugieri, M. E. & Tonetti, M. G. The autonomous glycosylation of large DNA viruses. Int. J. Mol. Sci. 16, 29315–29328 (2015).
CAS PubMed PubMed Central Article Google Scholar
23.
Schulz, F. et al. Giant virus diversity and host interactions through global metagenomics. Nature 578, 432–436 (2020).
ADS CAS PubMed PubMed Central Article Google Scholar
24.
Abrahão, J. et al. Tailed giant Tupanvirus possesses the most complete translational apparatus of the known virosphere. Nat. Commun. 9, 749 (2018).
ADS PubMed PubMed Central Article CAS Google Scholar
25.
Wilson, W. H. et al. Complete genome sequence and lytic phase transcription profile of a Coccolithovirus. Science 309, 1090–1092 (2005).
ADS Article CAS Google Scholar
26.
Roux, S. et al. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature 537, 689–693 (2016).
Article CAS Google Scholar
27.
Koonin, E. V. & Krupovic, M. The depths of virus exaptation. Curr. Opin. Virol. 31, 1–8 (2018).
CAS PubMed Article PubMed Central Google Scholar
28.
Ochman, H., Lawrence, J. G. & Groisman, E. A. Lateral gene transfer and the nature of bacterial innovation. Nature 405, 299–304 (2000).
ADS CAS PubMed Article PubMed Central Google Scholar
29.
Groisman, E. A. & Ochman, H. Pathogenicity islands: bacterial evolution in quantum leaps. Cell 87, 791–794 (1996).
CAS PubMed Article PubMed Central Google Scholar
30.
Martin, W. F. Too much eukaryote LGT. BioEssays 39, 1700115 (2017).
Article Google Scholar
31.
Keeling, P. J. & Palmer, J. D. Horizontal gene transfer in eukaryotic evolution. Nat. Rev. Genet. 9, 605–618 (2008).
CAS PubMed Article PubMed Central Google Scholar
32.
Cock, J. M. et al. The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature 465, 617–621 (2010).
ADS CAS PubMed Article PubMed Central Google Scholar
33.
Delaroque, N., Maier, I., Knippers, R. & Müller, D. G. Persistent virus integration into the genome of its algal host, Ectocarpus siliculosus (Phaeophyceae). J. Gen. Virol. 80, 1367–1370 (1999).
CAS PubMed Article PubMed Central Google Scholar
34.
Delaroque, N. & Boland, W. The genome of the brown alga Ectocarpus siliculosus contains a series of viral DNA pieces, suggesting an ancient association with large dsDNA viruses. BMC Evol. Biol. 8, 110 (2008).
PubMed PubMed Central Article CAS Google Scholar
35.
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010).
PubMed PubMed Central Article CAS Google Scholar
36.
Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011).
ADS MathSciNet CAS PubMed PubMed Central Article Google Scholar
37.
El-Gebali, S. et al. The Pfam protein families database in 2019. Nucleic Acids Res. 47, D427–D432 (2019).
CAS PubMed PubMed Central Article Google Scholar
38.
Yutin, N., Wolf, Y. I., Raoult, D. & Koonin, E. V. Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution. Virol. J. 6, 223 (2009).
PubMed PubMed Central Article CAS Google Scholar
39.
Filée, J., Siguier, P. & Chandler, M. I am what I eat and I eat what I am: acquisition of bacterial genes by giant viruses. Trends Genet. 23, 10–15 (2007).
PubMed Article CAS PubMed Central Google Scholar
40.
Filée, J., Pouget, N. & Chandler, M. Phylogenetic evidence for extensive lateral acquisition of cellular genes by nucleocytoplasmic large DNA viruses. BMC Evol. Biol. 8, 320 (2008).
PubMed PubMed Central Article CAS Google Scholar
41.
Hoff, K. J. & Stanke, M. Predicting genes in single genomes with AUGUSTUS. Curr. Protoc. Bioinformatics 65, e57 (2019).
PubMed PubMed Central Google Scholar
42.
Stanke, M. & Morgenstern, B. AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints. Nucleic Acids Res. 33, W465–W467 (2005).
CAS PubMed PubMed Central Article Google Scholar
43.
Gu, Z., Gu, L., Eils, R., Schlesner, M. & Brors, B. circlize implements and enhances circular visualization in R. Bioinformatics 30, 2811–2812 (2014).
CAS PubMed PubMed Central Article Google Scholar
44.
O’Leary, N. A. et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 44, D733–D745 (2016).
PubMed Article CAS PubMed Central Google Scholar
45.
Kiełbasa, S. M., Wan, R., Sato, K., Horton, P. & Frith, M. C. Adaptive seeds tame genomic sequence comparison. Genome Res. 21, 487–493 (2011).
PubMed PubMed Central Article CAS Google Scholar
46.
Federhen, S. The NCBI Taxonomy database. Nucleic Acids Res. 40, D136–D143 (2012).
CAS PubMed Article PubMed Central Google Scholar
47.
Huerta-Cepas, J., Serra, F. & Bork, P. ETE 3: reconstruction, analysis, and visualization of phylogenomic data. Mol. Biol. Evol. 33, 1635–1638 (2016).
CAS PubMed PubMed Central Article Google Scholar
48.
Pagès, H., Aboyoun, P., Gentleman, R. & DebRoy, S. Biostrings: efficient manipulation of biological strings. R package version 2.56.0 https://bioconductor.org/packages/Biostrings (2020).
49.
Bao, Z. & Eddy, S. R. Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res. 12, 1269–1276 (2002).
CAS PubMed PubMed Central Article Google Scholar
50.
Delcher, A. L., Phillippy, A., Carlton, J. & Salzberg, S. L. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res. 30, 2478–2483 (2002).
PubMed PubMed Central Article Google Scholar
51.
Tatusov, R. L., Galperin, M. Y., Natale, D. A. & Koonin, E. V. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28, 33–36 (2000).
CAS PubMed PubMed Central Article Google Scholar
52.
Haft, D. H. et al. TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Res. 29, 41–43 (2001).
CAS PubMed PubMed Central Article Google Scholar
53.
Huerta-Cepas, J. et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 47, D309–D314 (2019).
CAS PubMed Article PubMed Central Google Scholar
54.
Moniruzzaman, M. et al. Virus–host relationships of marine single-celled eukaryotes resolved from metatranscriptomics. Nat. Commun. 8, 16054 (2017).
ADS CAS PubMed PubMed Central Article Google Scholar
55.
Guindon, S. et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307–321 (2010).
CAS PubMed Article PubMed Central Google Scholar
56.
Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011).
PubMed PubMed Central Google Scholar
57.
Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).
PubMed PubMed Central Article CAS Google Scholar
58.
Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 47, W256–W259 (2019).
CAS PubMed PubMed Central Article Google Scholar
59.
Lechner, M. et al. Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinformatics 12, 124 (2011).
PubMed PubMed Central Article Google Scholar
60.
Csardi G, N. T. The igraph software package for complex network research. InterJournal Complex Systems 1695, 1–9 (2006).
61.
Burns, J. A., Paasch, A., Narechania, A. & Kim, E. Comparative genomics of a bacterivorous green algae reveals evolutionary causalities and consequences of phago-mixotrophic mode of nutrition. Genome Biol. Ecol. 7, 3047–3061 (2015).
CAS Article Google Scholar
62.
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
CAS PubMed PubMed Central Article Google Scholar
63.
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
CAS PubMed PubMed Central Article Google Scholar
64.
Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659 (2006).
CAS PubMed Article PubMed Central Google Scholar
65.
Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007).
CAS PubMed Article PubMed Central Google Scholar
66.
Martinez-Gutierrez, C. A. & Aylward, F. O. Strong purifying selection is associated with genome streamlining in epipelagic Marinimicrobia. Genome Biol. Evol. 11, 2887–2894 (2019).
CAS PubMed PubMed Central Article Google Scholar
67.
Huerta-Cepas, J. et al. eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 44, D286–D293 (2016).
CAS PubMed Article PubMed Central Google Scholar
68.
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).
CAS PubMed PubMed Central Article Google Scholar
69.
Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A. & Jermiin, L. S. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods 14, 587–589 (2017).
CAS PubMed PubMed Central Article Google Scholar More
