other microorganisms, such as viruses, van Regenmortel28
also described a lack of higher taxonomic classification
than the family.
In conclusion, it seems that baraminic analysis can be
performed on microorganisms such as NCLDVs, however,
as of yet, only a few species have been analyzed. Though
this analysis serves as a starting point, much more careful
thought is needed to proceed in taxonomic analysis of
microorganisms from a biblical perspective.
Materials and methods
NCLDV protein sequences were retrieved from the COG
website: ftp://ftp.ncbi.nih.gov/pub/wolf/COGs/NCVOG. All
20,086 protein sequences from 49 species were BLASTed
(BLASTP) against each other, with an e-score < 1e- 4. A
Jaccard Coefficient Value J was calculated between each
possible pair of 1,176 species, where 0 ≤ J ≤ 1, and where
J = |A∩B|/(|A|+|B|+|A∩B|) for species A and B. The
Jaccard Coefficient Values (JCVs) were put into a matrix
and visualized by the heatmap function in R, version 3. 1. 3.
Lighter colours mean higher JCVs. The JCV is a measure
of how similar the gene content of two genomes. A JCV
of 1 means that the two organisms have the exact same
genes. The lower the JCV, the less related two viruses are
to each other. Protein sequences for Epizootic hematopoietic
necrosis virus, Pandoravirus inopinatum, Mollivirus
sibericum, Diadromus pulchellus ascovirus 6a, Ambystoma
tigrinum virus, Tiger frog virus, Tunis virus, Cannes 8
virus, and Insectomime virus were downloaded from NCBI.
Figure 2 was generated by using CLC Genomics, version 8.
The JCV values for all NCLDV species pairs can be found
in Supplementary data file 1.
I would hereby like to thank Robin M. Wyle for critically
reading the manuscript.
1. Claverie, J.M. and Ogata, H., Ten good reasons not to exclude giruses from
the evolutionary picture, Nat. Rev. Microbiol.
7( 8):615, 2009.
2. O’Micks, J., Creation perspective of nucleocytoplasmic large DNA viruses,
30( 3): 110 – 117, 2017.
3. Yutin, N., Wolf, Y.I., Raoult, D. and Koonin, E.V., Eukaryotic large nucleocytoplasmic DNA viruses: clusters of orthologous genes and reconstruction
of viral genome evolution, Virol. J. 6:223, 2009.
4. Rost, B., Twilight zone of protein sequence alignments, Protein Eng
5. Koonin, E.V., Krupovic, M. and Yutin, N., Evolution of double-stranded DNA
viruses of eukaryotes: from bacteriophages to transposons to giant viruses,
Ann. N. Y. Acad. Sci. 1341: 10–24, 2015.
6. Santini, S., Jeudy, S., Bartoli, J. et al., Genome of Phaeocystis globosa virus
PgV-16T highlights the common ancestry of the largest known DNA viruses
infecting eukaryotes, Proc. Natl. Acad. Sci. USA
110( 26):10800–10805, 2013.
7. Dunigan, D. D., Fitzgerald, L.A. and Van Etten, J.L., Phycodnaviruses: a peek
at genetic diversity, Virus Res.
117( 1):11932, 2006.
8. Derelle, E., Ferraz, C., Escande, M. L., Eychenié, S. and Cooke, R., Life-cycle
and genome of OtV5, a large DNA virus of the pelagic marine unicellular
green alga Ostreococcus tauri, PLoS One
3( 5):e2250, 2008.
9. Bellec, L., Grimsley, N., Moreau, H. and Desdevises, Y., Phylogenetic analysis
of new Prasinoviruses (Phycodnaviridae) that infect the green unicellular algae
Ostreococcus, Bathycoccus and Micromonas, Environ. Microbiol. Rep.
10. Arslan, D., Legendre, M., Seltzer, V., Abergel, C. and Claverie, J.M., Distant
Mimivirus relative with a larger genome highlights the fundamental features
of Megaviridae, Proc. Natl. Acad. Sci. USA
108( 42):17486–17491, 2011.
11. Legendre, M., Arslan, D., Abergel, C. and Claverie, J.M., Genomics of
Megavirus and the elusive fourth domain of life, Commun. Integr. Biol.
12. Boughalmi, M., Pagnier, I., Aherfi, S. et al., First isolation of a Marseillevirus
in the Diptera Syrphidae Eristalis tenax, Intervirology
56( 6):386–394, 2013a.
13. Boughalmi, M., Pagnier, I., Aherfi, S. et al., First isolation of a giant virus from
wild Hirudo medicinalis leech: Mimiviridae isolation in Hirudo medicinalis,
5( 12):2920–2930, 2013b.
14. Yoosuf, N., Pagnier, I., Fournous, G., Robert, C., Raoult, D. et al., Draft
genome sequences of Terra1 and Terra2 viruses, new members of the family
Mimiviridae isolated from soil, Virology 452–453: 125–32, 2014.
15. Lef kowitz, E. J., Wang, C. and Upton, C., Poxviruses: past, present and future,
117( 1): 105–118, 2006.
16. Aherfi, S., Boughalmi, M., Pagnier, I., et al. Complete genome sequence of
Tunisvirus, a new member of the proposed family Marseilleviridae. Arch
Virol 159( 9):2349–2358, 2014a.
17. Colson, P., Fancello, L., Gimenez, G., Armougom, F. and Desnues,
C., Evidence of the megavirome in humans, J. Clin. Virol.
57( 3):191–200, 2013.
18. Aherfi, S., La Scola, B., Pagnier, I., Raoult, D. and Colson, P., The expanding
family Marseilleviridae, Virology 466–467: 27–37, 2014b.
19. Doutre, G., Arfib, B., Rochette, P. et al., Complete Genome Sequence of a
New Member of the Marseilleviridae Recovered from the Brackish Submarine
Spring in the Cassis Port-Miou Calanque, France, Genome Announc.
e01148-15, 2015, doi: 10.1128/genomeA.01148-15.
20. Aherfi, S., Pagnier, I., Fournous, G. et al., Complete genome sequence of
Cannes 8 virus, a new member of the proposed family ‘Marseilleviridae’,
47( 3):550–555, 2013.
21. Wei, Y.L., Hu, J., Li, S.J. et al., Genome sequence and organization analysis
of Heliothis virescens ascovirus 3f isolated from a Helicoverpa zea larva,
J. Invertebr. Pathol. 122: 40–3, 2014.
22. Stasiak, K., Demattei, M.V., Federici, B. A. and Bigot, Y., Phylogenetic position
of the Diadromus pulchellus ascovirus DNA polymerase among viruses with
large double-stranded DNA genomes, J. Gen. Virol.
81( 12):3059–3072, 2000.
23. Abergel, C., Legendre, M. and Claverie, J.M., The rapidly expanding universe
of giant viruses: Mimivirus, Pandoravirus, Pithovirus and Mollivirus, FEMS
39( 6):779–796, 2015.
24. Park, Y., Kim, G.D. and Choi, T.J., Molecular cloning and characterization
of the DNA adenine methyltransferase gene in Feldmannia sp. Virus, Virus
34( 2):177–183, 2007.
25. Holopainen, R., Ohlemeyer, S., Schütze, H., Bergmann, S.M. and Tapiovaara,
H., Ranavirus phylogeny and differentiation based on major capsid protein,
DNA polymerase and neurofilament triplet H1-like protein genes, Dis. Aquat.
85( 2): 81–91, 2009.
26. Eaton, H.E., Metcalf, J., Penny, E. et al., Comparative genomic analysis of
the family Iridoviridae: re-annotating and defining the core set of iridovirus
genes, Virol. J. 4: 11, 2007.
27. Dixon, L.K., Chapman, D.A., Netherton, C.L. and Upton, C., African swine
fever virus replication and genomics, Virus Res. 173( 1): 3–14, 2013.
28. Van Regenmortel, M.H.V., Introduction to the species concept in virus
taxonomy; in: Van Regenmortel, M.H.V., Fauquet, C.M., Bishop, D.H.L.,
Carstens, E.B., Estes, M.K., Lemon, S.M., Maniloff, J., Mayo, M.A.,
McGeoch, D.J., Pringle, C.R. and Wickner, R.B. (Eds.), Virus Taxonomy,
Seventh Report of the International Committee on Taxonomy of Viruses,
Academic Press, San Diego, CA, pp. 3–16, 2000.
Jean O'Micks has a Ph.D. in biology. He has been an
active creationist for 15 years and takes a great interest
in molecular biology. He has published a number of
articles in Journal of Creation.