Puzzling observations from various eukaryotic genomes (part III)

We are continuing our discussion of eukaryotic genome evolution based on Dan Graur’s “Molecular and Genome Evolution”. In this post, we present a number of puzzling observations in various eukaryotic genomes. The title of each section also includes the page number of Graur’s book, where the observation is reported.

“Puzzling” here is defined in the context of traditional understanding of genome evolution, namely that the genomes evolve through random mutations, which become fixed in the population by natural selection and genetic drift.

Concerted Evolution (page 299)

In 1972, D. D. Brown et al. published on “a comparison of the ribosomal DNA’s of Xenopus laevis and Xenopus mulleri: the evolution of tandem genes”, where they reported an unexpected observation. In the genomes of Xenopus and all other eukaryotic organisms, the rRNA genes are present in hundreds of copies. In fact, there is a strong correlation between the number of rRNA genes and genome size (page 284). Brown et al. noticed that all those copies of rRNA genes within the genome of a Xenopus species had very similar mutations.

Here is the unexpected part. When rRNA genes from two different Xenopus species were compared, they were found to differ greatly from each other. It was as if all rRNA genes present in multiple locations of the genome evolve in a concerted fashion. Concerted evolution is not restricted to frogs or rRNA only. It has been observed in many other prokaryotic and eukaryotic organisms, and also for other gene families.

Unused Genes Cannot be Removed (Page 284)

Speaking of rRNA genes, here is another unexpected observation. Yeast genome, like all eukaryotic genomes, has many copies of rRNA genes and some are not even transcribed. Interestingly, the organism needed those extra untranscribed copies to maintain its genome. When they were lost or deleted, the genome became sensitive to DNA damage induced by mutagens.

Ultraconserved Sequences Do Nothing (page 126)

In the conventional understanding, a genomic region highly conserved between distant organisms is functional. A comparison of human, mouse and rat genomes showed the presence of “ultranconserved elements”, or identical sequences longer that 200nt. Are those regions extremely important so that they did not mutate at all? Strangely, Ahitub et al. (2007) did not see any phenotypic or developmenta abnormalit, when they deleted four such ultranconserved elements from the mouse genome.

The Genomes of “Living Fossils” May Not be Molecular Fossils (page 160)

Based on comparison of physical charactistics with the fossil records, some extant organisms are called “living fossils”. They did not change morphologically for a long period of time. Horseshoe crab, which looks identical to its 500 million year old fossil, is one example. However, Ngyuen et al. 1986 and Tokugana et al. 1993 did not see any slow rate of molecular evolution in its genes.

Programmed Genome Reduction/Rearrangement/Scrambling (page 7)

Horse parasite Parascaris univalens gets rid of 85% of its DNA during development !! Programmed genome reduction is not limited to any single lineage. Evidences have been seen in the genomes of nematodes, copepods, hagfish and lamprey.

Genome-wide rearrangesments are seen in unicellular eukaryotes such as foraminiferans and ciliates. These organisms have two different nuclei within a single cell, and those nuclei act similar to the nuclei in germline and somatic cells of multicellular organisms. Sometimes, the coding regions of genes are all screwed up, but programmed “unscrambling” process restores proper reading frames. Also noteworthy, somatic genomes may contain up to 25 million short chromosomes !!