Aylward, F. O. et al. (2021) ‘A Phylogenomic Framework for Charting the Diversity and Evolution of Giant Viruses’, PLOS Biology, 19:
e3001430.
Aylward, F. O., and Moniruzzaman, M. (2021) ‘ViralRecall—A Flexible
Command-Line Tool for the Detection of Giant Virus Signatures
in ‘Omic Data’, Viruses, 13: 150.
Bellas, C. et al. (2023) ‘Large-Scale Invasion of Unicellular Eukaryotic
Genomes by Integrating DNA Viruses’, Proceedings of the National
Academy of Sciences, 120: e2300465120.
Benson, G. (1999) ‘Tandem Repeats Finder: A Program to Analyze DNA
Sequences’, Nucleic Acids Research, 27: 573–80.
Bhattacharjee, A. S. et al. (2023) ‘Genomics Discovery of Giant Fungal
Viruses from Subsurface Oceanic Crustal Fluids’, ISME Communications, 3: 1–9.
Blanc-Mathieu, R. et al. (2021) ‘A Persistent Giant Algal Virus,
with a Unique Morphology, Encodes an Unprecedented Number
of Genes Involved in Energy Metabolism’, Journal of Virology, 95:
e02446–20.
Boltsis, I. et al. (2021) ‘Chromatin Conformation in Development
and Disease’, Frontiers in Cell and Developmental Biology, 9: 723859.
Buchfink, B., Xie, C., and Huson, D. H. (2015) ‘Fast and Sensitive Protein
Alignment Using DIAMOND’, Nature Methods, 12: 59–60.
Camacho, C. et al. (2009) ‘BLAST+: Architecture and Applications’,
BMC Bioinformatics, 10: 421.
Cantalapiedra, C. P. et al. (2021) ‘eggNOG-mapper V2: Functional
Annotation, Orthology Assignments, and Domain Prediction at
the Metagenomic Scale’, Molecular Biology and Evolution, 38: 5825–9.
́ T. (2009)
Capella-Gutiérrez, S., Silla-Martínez, J. M., and Gabaldon,
‘trimAl: A Tool for Automated Alignment Trimming in Large-Scale
Phylogenetic Analyses’, Bioinformatics, 25: 1972–3.
Cheng, S., Wong, G. K.-S., and Melkonian, M. (2021) ‘Giant DNA Viruses
Make Big Strides in Eukaryote Evolution’, Cell Host & Microbe, 29:
152–4.
Durand, N. C. et al. (2016) ‘Juicer Provides a One-Click System
for Analyzing Loop-Resolution Hi-C Experiments’, Cell Systems, 3:
95–8.
Eddy, S. R., and Pearson, W. R. (2011) ‘Accelerated Profile HMM
Searches’, PLOS Computational Biology, 7: e1002195.
Feschotte, C., and Gilbert, C. (2012) ‘Endogenous Viruses: Insights
into Viral Evolution and Impact on Host Biology’, Nature Reviews.
Genetics, 13: 283–96.
Flynn, J. M. et al. (2020) ‘RepeatModeler2 for Automated Genomic
Discovery of Transposable Element Families’, Proceedings of the
National Academy of Sciences, 117: 9451–7.
Gaïa, M. et al. (2023) ‘Mirusviruses Link Herpesviruses to Giant
Viruses’, Nature, 616: 783–9.
Gong, Z., Zhang, Y., and Han, G.-Z. (2020) ‘Molecular Fossils
Reveal Ancient Associations of dsDNA Viruses with Several Phyla
of Fungi’, Virus Evolution, 6: veaa008.
Gosling, P. et al. (2006) ‘Arbuscular Mycorrhizal Fungi and Organic
Farming’, Agriculture, Ecosystems & Environment, 113: 17–35.
Hannat, S. et al. (2021) ‘Diverse Trajectories Drive the Expression
of a Giant Virus in the Oomycete Plant Pathogen Phytophthora
parasitica’, Frontiers in Microbiology, 12: 662762.
Hingamp, P. et al. (2013) ‘Exploring Nucleo-Cytoplasmic Large DNA
Viruses in Tara Oceans Microbial Metagenomes’, The ISME Journal,
7: 1678–95.
Hoang, D. T. et al. (2018) ‘UFBoot2: Improving the Ultrafast Bootstrap
Approximation’, Molecular Biology and Evolution, 35: 518–22.
Downloaded from https://academic.oup.com/ve/article/9/2/vead064/7334491 by Kyoto University user on 07 March 2024
orientation and with the same database hits. Then, we compared
the nucleotide sequences covering these ORFs to the amino acid
sequences of the reference sequences in RefSeq by using Dotter
v4.22 (Sonnhammer and Durbin 1995) to make dot-plots. On the
one hand, some of such neighboring ORFs were identified as candidates of genes with introns, when the ORFs are continuously
aligned with the reference sequences at the protein sequence
level. These regions were further examined with FGENESH v2.6
(Solovyev et al. 2006) to predict exons. When the program predicted two or more exons, the regions were assumed to contain
genes with introns. On the other hand, many other cases were
identified as pseudogenes. To maximize the gene annotation, we
also incorporated the original fungal gene annotations (Yildirir
et al. 2022) for some GEVE regions, that is, the regions with either
(1) genes with introns as identified above or (2) with no predicted
genes or pseudogenes by the above procedure. In the case of (1),
we overwrite the above gene annotations with the original fungal annotations. In the case of (2), we added the original fungal
annotations.
The ORFs were annotated using BLASTp in Diamond (Evalue < 10−5 ). Because previous studies may have annotated viral
insertions in fungal genomes as fungal genes, we used the NR
database excluding the sequences from the fungal class Glomeromycetes (NCBI: txid214506, which includes R. irregularis). In
annotating the sea slug viral regions, we used the NR database and
excluded all sequences of E. marginata (NCBI: txid1093978). The
best match for each ORF was used to determine the taxonomic
distribution of the ORFs (i.e. eukaryote, prokaryote, and virus). For
ORFs with the eukaryotic best hit (excluding E. marginata), we performed BLASTp to search against other predicted ORF in strain
4401 except for the 1.5-Mb viral region. Functional annotations
were retrieved using eggNOG-mapper v2.1.9 (Cantalapiedra et al.
2021).
To identify traces of genes, we extracted the genomic region
between two predicted ORFs and eliminated the regions shorter
than 100 bp before performing a BLASTx search using Diamond
(E-value < 10−5 ). The NR database and all predicted proteins on
viral regions identified by ViralRecall were used as the reference
and ‘–ultra-sensitive’ was selected as the parameter. We also used
Tandem Repeat Finder v4.09 (Benson 1999) to identify the tandem
repeats in the GEVE region, with ‘2 7 7 80 10 30 2000 -f -d -m’
selected as the parameter.
H. Zhao et al.
Maumus, F., and Blanc, G. (2016) ‘Study of Gene Trafficking between
Acanthamoeba and Giant Viruses Suggests an Undiscovered Family of Amoeba-Infecting Viruses’, Genome Biology and Evolution, 8:
3351–63.
Minh, B. Q. et al. (2020) ‘IQ-TREE 2: New Models and Efficient Methods
for Phylogenetic Inference in the Genomic Era’, Molecular Biology
and Evolution, 37: 1530–4.
Moniruzzaman, M. et al. (2020) ‘Widespread Endogenization of Giant
Viruses Shapes Genomes of Green Algae’, Nature, 588: 141–5.
Moniruzzaman, M., Erazo-Garcia, M. P., and Aylward, F. O. (2022)
‘Endogenous Giant Viruses Contribute to Intraspecies Genomic
Variability in the Model Green Alga Chlamydomonas reinhardtii’,
Virus Evolution, 8: veac102.
Ogata, H. et al. (2009) ‘Remarkable Sequence Similarity between
the Dinoflagellate-infecting Marine Girus and the Terrestrial
Pathogen African Swine Fever Virus’, Virology Journal, 6: 178.
Quinlan, A. R., and Hall, I. M. (2010) ‘BEDTools: A Flexible Suite
of Utilities for Comparing Genomic Features’, Bioinformatics, 26:
841–2.
Reteno, D. G. et al. (2015) ‘Faustovirus, an Asfarvirus-related New Lineage of Giant Viruses Infecting Amoebae’, Journal of Virology, 89:
6585–94.
Schulz, F. et al. (2020) ‘Giant Virus Diversity and Host Interactions
through Global Metagenomics’, Nature, 578: 432–6.
Schulz, F., Abergel, C., and Woyke, T. (2022) ‘Giant Virus Biology
and Diversity in the Era of Genome-Resolved Metagenomics’,
Nature Reviews. Microbiology, 20: 721–36.
Shukron, O. et al. (2019) ‘Statistics of Chromatin Organization during Cell Differentiation Revealed by Heterogeneous Cross-Linked
Polymers’, Nature Communications, 10: 2626.
Sievers, F., and Higgins, D. G. (2018) ‘Clustal Omega for Making Accurate Alignments of Many Protein Sequences’, Protein Science, 27:
135–45.
Solovyev, V. et al. (2006) ‘Automatic Annotation of Eukaryotic Genes,
Pseudogenes and Promoters’, Genome Biology, 7: S10.
Sonnhammer, E. L., and Durbin, R. (1995) ‘A Dot-Matrix Program with
Dynamic Threshold Control Suited for Genomic DNA and Protein
Sequence Analysis’, Gene, 167: GC1–10.
Yildirir, G. et al. (2022) ‘Long Reads and Hi-C Sequencing Illuminate
the Two-Compartment Genome of the Model Arbuscular Mycorrhizal Symbiont Rhizophagus irregularis’, New Phytologist, 233:
1097–107.
Yoshikawa, G. et al. (2019) ‘Medusavirus, a Novel Large DNA Virus Discovered from Hot Spring Water’, Journal of Virology, 93: e02130–18.
Yu, X. et al. (2010) ‘A Geminivirus-Related DNA Mycovirus that Confers Hypovirulence to a Plant Pathogenic Fungus’, Proceedings of
the National Academy of Sciences, 107: 8387–92.
Downloaded from https://academic.oup.com/ve/article/9/2/vead064/7334491 by Kyoto University user on 07 March 2024
Huff, J. T., Zilberman, D., and Roy, S. W. (2016) ‘Mechanism for DNA
Transposons to Generate Introns on Genomic Scales’, Nature, 538:
533–6.
Hyatt, D. et al. (2010) ‘Prodigal: Prokaryotic Gene Recognition
and Translation Initiation Site Identification’, BMC Bioinformatics,
11: 119.
Kalyaanamoorthy, S. et al. (2017) ‘ModelFinder: Fast Model Selection
for Accurate Phylogenetic Estimates’, Nature Methods, 14: 587–9.
Karki, S., Moniruzzaman, M., and Aylward, F. O. (2021) ‘Comparative Genomics and Environmental Distribution of Large dsDNA
Viruses in the Family Asfarviridae’, Frontiers in Microbiology, 12:
657471.
Kazlauskas, D. et al. (2020) ‘Diversity and Evolution of B-family DNA
Polymerases’, Nucleic Acids Research, 48: 10142–56.
Kondo, H., Botella, L., and Suzuki, N. (2022) ‘Mycovirus Diversity
and Evolution Revealed/Inferred from Recent Studies’, Annual
Review of Phytopathology, 60: 307–36.
Krupovic, M., Makarova, K. S., and Koonin, E. V. (2022) ‘Cellular
Homologs of the Double Jelly-Roll Major Capsid Proteins Clarify the Origins of an Ancient Virus Kingdom’, Proceedings of the
National Academy of Sciences, 119: e2120620119.
Krupovic, M., Yutin, N., and Koonin, E. (2020) ‘Evolution of a Major
Virion Protein of the Giant Pandoraviruses from an Inactivated
Bacterial Glycoside Hydrolase’, Virus Evolution, 6: veaa059.
Letunic, I., and Bork, P. (2019) ‘Interactive Tree of Life (Itol) V4:
Recent Updates and New Developments’, Nucleic Acids Research,
47: W256–59.
Li, H. et al. 1000 Genome Project Data Processing Subgroup (2009)
‘The Sequence Alignment/Map Format and SAMtools’, Bioinformatics, 25: 2078–9.
Li, M. et al. (2018) ‘Horizontal Gene Transfer from Bacteria and Plants
to the Arbuscular Mycorrhizal Fungus Rhizophagus irregularis’,
Frontiers in Plant Science, 9: 701.
Li, P. et al. (2020) ‘A Tripartite ssDNA Mycovirus from a Plant
Pathogenic Fungus Is Infectious as Cloned DNA and Purified
Virions’, Science Advances, 6: eaay9634.
Li, H., and Birol, I. (2018) ‘Minimap2: Pairwise Alignment
for Nucleotide Sequences’, Bioinformatics, 34: 3094–100.
Maeda, T. et al. (2021) ‘Chloroplast Acquisition without the Gene
Transfer in Kleptoplastic Sea Slugs, Plakobranchus ocellatus’, Elife,
10: e60176.
Matsuyama, T. et al. (2020) ‘A Novel Asfarvirus-like Virus Identified as
a Potential Cause of Mass Mortality of Abalone’, Scientific Reports,
10: 4620.
Maumus, F. et al. (2014) ‘Plant Genomes Enclose Footprints of past
Infections by Giant Virus Relatives’, Nature Communications, 5:
4268.
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