Pithovirus sibericum
Regular readers with very long memories may remember how I wrote about something big and potentially nasty emerging from Siberian permafrost back in 2014.
The 30,000-year-old monster in question was a form of giant virus then unknown to science, now named Pithoviruses sibericus. It came back to life when thawed. Since then, several other related pithoviruses have been discovered in soil and aquatic sources. Fortunately, all those discovered so far are parasitic only on one species of amoeba, Acanthamoeba castellanii and don't pose a threat to humans or multicellular life.
The question was, why are they so large, or more particularly, why do they have such a massive genome, including some genes normally found in complex cells. the Pithovirus species so far discovered have a genome of between 460 to 686 kb. Their genome, moreover, is similar to that of bacteria and archaea, in that it is DNA-based and forms a single circular 'chromosome'.
But it's not the fact that the first one was found in permafrost dating back 20,000 before 'Creation Week', difficult though that little inconvenience is for creationists; it is the account of how they acquired this massive genome that is the thing of nightmares for any creationists who understand the biology.
They acquired it by processes that give the lie to their basic dogma that new genetic information can't arise in a genome without 'God magic'.
A team of researchers have shown that they acquired new genetic information and such a massive genome by:
- Horizontal gene transfer (5% -7 %)
- Gene duplication (14% - 28%)
- Massive inversions of repeated sequences of DNA.
And this gives the lie to the ludicrous creationist dogma that no new information can arise by mutation because all mutations are deleterious. There is nothing deleterious in having a spare copy of a gene, nor in mutations in that spare copy, least of all if it gives a new function that increases fitness.
The researchers, from the Institut de Microbiologie de la Méditerranée, FR3479), IM2B, IOM, Aix–Marseille University, Centre National de la Recherche Scientifique, Marseille, France were led by Matthieu Legendre. Their findings are published, open access, in Molecular Biology and Evolution:
AbstractSo, the problem for creationism here is not so much that the giant virus was found in permafrost which is three times older than Earth, according to their mythology, nor that it is what they regard as an 'intelligently [sic] designed' parasite, designed to kill another 'intelligently [sic] designed organism - an amoeba - for no better reason than to produce new viruses to kill more amoebae.
Pithoviridae are amoeba-infecting giant viruses possessing the largest viral particles known so far. Since the discovery of Pithovirus sibericum, recovered from a 30,000-yr-old permafrost sample, other pithoviruses, and related cedratviruses, were isolated from various terrestrial and aquatic samples. Here, we report the isolation and genome sequencing of 2 Pithoviridae from soil samples, in addition to 3 other recent isolates. Using the 12 available genome sequences, we conducted a thorough comparative genomic study of the Pithoviridae family to decipher the organization and evolution of their genomes. Our study reveals a nonuniform genome organization in 2 main regions: 1 concentrating core genes and another gene duplications. We also found that Pithoviridae genomes are more conservative than other families of giant viruses, with a low and stable proportion (5% to 7%) of genes originating from horizontal transfers. Genome size variation within the family is mainly due to variations in gene duplication rates (from 14% to 28%) and massive invasion by inverted repeats. While these repeated elements are absent from cedratviruses, repeat-rich regions cover as much as a quarter of the pithoviruses genomes. These regions, identified using a dedicated pipeline, are hotspots of mutations, gene capture events, and genomic rearrangements that contribute to their evolution.
Introduction
Pithoviridae are amoeba-infecting giant viruses possessing the largest known viral particles. The prototype of the family, Pithovirus sibericum, was recovered almost 10 yr ago from a 30′000-yr-old permafrost sample (Legendre et al. 2014). Following this discovery, 6 additional isolates, all infecting Acanthamoeba castellanii, have been sequenced (Andreani et al. 2016; Levasseur et al. 2016.1; Bertelli et al. 2017; Rodrigues et al. 2018; Jeudy et al. 2020). Their dsDNA circular genomes range from 460 to 686 kb. The Pithoviridae are composed of 2 main clades: the pithoviruses and the cedratviruses. Both possess ovoid-shaped virions, capped by a cork-like structure at 1 extremity for the former and at both extremities for the latter.
[…]
In this study, we report the genome sequences of 2 new Pithoviridae viruses isolated from soil samples (Cedratvirus borely and Cedratvirus plubellavi), in addition to the recently isolated Cedratvirus lena (strain DY0), Cedratvirus duvanny (strain DY1), and Pithovirus mammoth (strain Yana14) (Alempic et al. 2023). The comparative analysis of these sequenced genomes, complemented with previously published Pithoviridae sequences (Legendre et al. 2014; Levasseur et al. 2016.1; Bertelli et al. 2017; Rodrigues et al. 2018; Jeudy et al. 2020), provides insight into the gene distribution and the evolution of the family. In addition, an in-depth study of pithoviruses genomes reveals that they are highly structured in regions composed of 2 main inverted repeats that have massively colonized their genomes and influenced their evolution.
Sofia Rigou, Alain Schmitt, Jean-Marie Alempic, Audrey Lartigue, Peter Vendloczki, Chantal Abergel, Jean-Michel Claverie, Matthieu Legendre
Pithoviruses Are Invaded by Repeats That Contribute to Their Evolution and Divergence from Cedratviruses
Molecular Biology and Evolution, Volume 40, Issue 11, November 2023, msad244, https://doi.org/10.1093/molbev/msad244
Copyright: © 2023 The authors.
Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)
The big problem for creationists here is in how new genetic information arose without the need for magic or supernatural intervention, but by perfectly well understood mechanisms, and mutations that were beneficial to the virus, not deleterious as creationist dogma say they all are.
This highlights the fact that their cult gurus, Behe, Dembski, and other dutiful propagandists for the Deception Institute, who feed them this demonstrably false information are trying to deceive them, for reasons which can only be guessed at but which are probably not far removed from the plan, outlined in the 'Wedge Strategy', to establish a fundamentalist, Taliban-style theocracy in the USA and elsewhere, to serve their own far-right political ambitions that no sane American would vote for if given an opportunity.
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