Feschotte, C. & Gilbert, C. Endogenous viruses: insights into viral evolution and impact on host biology. Nat. Rev. Genet. 13, 283–296 (2012).
Holmes, E. C. The evolution of endogenous viral elements. Cell Host Microbe 10, 368–377 (2011).
Fischer, M. G. Giant viruses come of age. Curr. Opin. Microbiol. 31, 50–57 (2016).
Wilhelm, S. W. et al. A student’s guide to giant viruses infecting small eukaryotes: from Acanthamoeba to zooxanthellae. Viruses 9, 46 (2017).
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).
Weynberg, K. D., Allen, M. J. & Wilson, W. H. Marine prasinoviruses and their tiny plankton hosts: a review. Viruses 9, 43 (2017).
Bhattacharya, D. & Medlin, A. L. Algal phylogeny and the origin of land plants. Plant Physiol. 116, 9–15 (1998).
Jeanniard, A. et al. Towards defining the chloroviruses: a genomic journey through a genus of large DNA viruses. BMC Genomics 14, 158 (2013).
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).
Filée, J. Genomic comparison of closely related giant viruses supports an accordion-like model of evolution. Front. Microbiol. 6, 593 (2015).
Van Etten, J. L. et al. Chloroviruses have a sweet tooth. Viruses 9, 88 (2017).
Schvarcz, C. R. & Steward, G. F. A giant virus infecting green algae encodes key fermentation genes. Virology 518, 423–433 (2018).
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).
Marcet-Houben, M. & Gabaldón, T. Acquisition of prokaryotic genes by fungal genomes. Trends Genet. 26, 5–8 (2010).
Rossoni, A. W. et al. The genomes of polyextremophilic cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions. eLife 8, e45017 (2019).
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).
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).
Gallot-Lavallée, L. & Blanc, G. A glimpse of nucleo-cytoplasmic large DNA virus biodiversity through the eukaryotic genomics window. Viruses 9, 17 (2017).
Maumus, F., Epert, A., Nogué, F. & Blanc, G. Plant genomes enclose footprints of past infections by giant virus relatives. Nat. Commun. 5, 4268 (2014).
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).
Forterre, P. & Gaïa, M. Giant viruses and the origin of modern eukaryotes. Curr. Opin. Microbiol. 31, 44–49 (2016).
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).
Schulz, F. et al. Giant virus diversity and host interactions through global metagenomics. Nature 578, 432–436 (2020).
Abrahão, J. et al. Tailed giant Tupanvirus possesses the most complete translational apparatus of the known virosphere. Nat. Commun. 9, 749 (2018).
Wilson, W. H. et al. Complete genome sequence and lytic phase transcription profile of a Coccolithovirus. Science 309, 1090–1092 (2005).
Roux, S. et al. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature 537, 689–693 (2016).
Koonin, E. V. & Krupovic, M. The depths of virus exaptation. Curr. Opin. Virol. 31, 1–8 (2018).
Ochman, H., Lawrence, J. G. & Groisman, E. A. Lateral gene transfer and the nature of bacterial innovation. Nature 405, 299–304 (2000).
Groisman, E. A. & Ochman, H. Pathogenicity islands: bacterial evolution in quantum leaps. Cell 87, 791–794 (1996).
Martin, W. F. Too much eukaryote LGT. BioEssays 39, 1700115 (2017).
Keeling, P. J. & Palmer, J. D. Horizontal gene transfer in eukaryotic evolution. Nat. Rev. Genet. 9, 605–618 (2008).
Cock, J. M. et al. The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature 465, 617–621 (2010).
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).
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).
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010).
Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011).
El-Gebali, S. et al. The Pfam protein families database in 2019. Nucleic Acids Res. 47, D427–D432 (2019).
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).
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).
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).
Hoff, K. J. & Stanke, M. Predicting genes in single genomes with AUGUSTUS. Curr. Protoc. Bioinformatics 65, e57 (2019).
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).
Gu, Z., Gu, L., Eils, R., Schlesner, M. & Brors, B. circlize implements and enhances circular visualization in R. Bioinformatics 30, 2811–2812 (2014).
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).
Kiełbasa, S. M., Wan, R., Sato, K., Horton, P. & Frith, M. C. Adaptive seeds tame genomic sequence comparison. Genome Res. 21, 487–493 (2011).
Federhen, S. The NCBI Taxonomy database. Nucleic Acids Res. 40, D136–D143 (2012).
Huerta-Cepas, J., Serra, F. & Bork, P. ETE 3: reconstruction, analysis, and visualization of phylogenomic data. Mol. Biol. Evol. 33, 1635–1638 (2016).
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).
Bao, Z. & Eddy, S. R. Automated de novo identification of repeat sequence families in sequenced genomes. Genome Res. 12, 1269–1276 (2002).
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).
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).
Haft, D. H. et al. TIGRFAMs: a protein family resource for the functional identification of proteins. Nucleic Acids Res. 29, 41–43 (2001).
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).
Moniruzzaman, M. et al. Virus–host relationships of marine single-celled eukaryotes resolved from metatranscriptomics. Nat. Commun. 8, 16054 (2017).
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).
Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011).
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).
Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res. 47, W256–W259 (2019).
Lechner, M. et al. Proteinortho: detection of (co-)orthologs in large-scale analysis. BMC Bioinformatics 12, 124 (2011).
Csardi G, N. T. The igraph software package for complex network research. InterJournal Complex Systems 1695, 1–9 (2006).
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).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
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).
Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007).
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).
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).
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).
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).
Source: Ecology - nature.com