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Oxytricha trifallax: A Russian doll set of confounding genetic complexity

Oxytricha trifallax.jpg
oxytricha trifallax

The eukaryote smashes and rearranges its genome.

Our results show that a great diversity of scrambled gene maps are present in the germline genome of O. trifallax. The presence of such highly nested architectures was a surprise and suggests that layers upon layers of MDS and gene translocations constantly alter the genome, while the detection of highly scrambled patterns reveals architectures that transcend simple twists and turns of the DNA. We present new metrics of topological genome complexity, that go beyond the linear nature of eukaryotic chromosomes and consider their deeply structured and layered history. While several models of genome rearrangement have been reported, the unprecedented levels of rearrangements in this system necessitate additional descriptive and mathematical tools, some of which have applications in biology (Assis et al. 2008) while others generate new mathematical concepts as in (Burns et al. 2013). From this initial description,several open questions arise: Do nested architectures affect other genomic properties? Is there any relationship between either gene expression, or the rearrangement pathway, and chromosome nesting? A preliminary analysis of RNAseq data (Swart et al. 2013), suggests weak or no correlation between the IDI and the temporal order of gene expression during development. We anticipate that future studies of DNA rearrangements and transcriptional dynamics will provide insights into these questions.

Furthermore, how do these patterns arise in evolution? Do nested and highly scrambled patterns accumulate gradually or in a catastrophic event, like chromothripsis (Maher and Wilson 2012)? Are the combinations of patterns serendipitous, or is there an biological process that drives the introduction of higher levels of scrambling? Future studies of related organisms should address population variation, and measure the level of variation, in chromosome structures at different scales of evolutionary divergence. In particular, surveys of the orthologous loci for the notable cases studied here in earlier diverged spirotrichous ciliates (as in Chang et al. (2005) and Hogan et al. (2001)) have the potential to reveal much about the evolutionary steps that gave rise to such complex, intertwined genome architectures.More.

Paper. (open access): Jasper Braun, Lukas Nabergall, Rafik Neme, Laura F. Landweber, Masahico Saito, and Nataša Jonoska, Russian doll genes and complex chromosome rearrangements in Oxytricha trifallax, G3 Genes/Genomes/Genetics, March 15, 2018 as doi:10.1534/g3.118.200176

This is not the genome of the splintered lectern. How would such bewildering but functional complexity arise within the life of this universe if it depended on Darwinian methods? No one can admit, of course, that it does not happen that way and easily keep their job. So there is likely to be far more progress in cataloguing it than in accounting for it.

See also: Dramatic recent finding: There is a new DNA structure in our cells, beyond the double helix


Attempt to explain the assembly of the bacterial flagellum, “a complex process involving more than 70 genes”



"No one can admit, of course, that it does not happen that way and easily keep their job." True indeed. Truth Will Set You Free
From the abstract:
. Such genome architectures are remarkably tolerant of encrypted MIC loci, because RNA-guided processes during MAC development reorganize the gene fragments in the correct order to resemble the parental MAC sequence.
Where MAC is the macro nucleus and MIC is the micro nucleus. What do they mean by encryption? Only intelligent agents use encryption or are they using the word in a different way? I've read the article but am not sure I understand it. Any insights would be appreciated. Latemarch

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