https://wp.unil.ch/genomeeee/2012/05/31/rapid-evolution-of-enormous-multichromosomal-genomes-in-flowering-plant-mitochondria-with-exceptionally-high-mutation-rates/ Blog of a tutorial of Ecole doctorale de biologie UNIL Mon, 08 Nov 2021 16:12:41 +0000 hourly 1 https://wordpress.org/?v=5.8.1 https://wp.unil.ch/genomeeee/2012/05/31/rapid-evolution-of-enormous-multichromosomal-genomes-in-flowering-plant-mitochondria-with-exceptionally-high-mutation-rates/#comment-6 Mon, 11 Jun 2012 08:13:47 +0000 http://wp.unil.ch/genomeeee/2012/05/31/rapid-evolution-of-enormous-multichromosomal-genomes-in-flowering-plant-mitochondria-with-exceptionally-high-mutation-rates/#comment-6 Indeed, assembly of such template containing thousand of mitochondrial genomes may be challenging. Repeat regions are particularly difficult to assemble, and there is a risk to collapse repeat regions. However, such “errors” would decrease the assembly size. The presence of multiples copies of mitochondrial genomes can theoretically detect by an extremely high coverage compared to the nuclear genome. But, because the nuclear genome is not yet available, it was not possible to perform such comparison. Evidences of mitochondrial genome expansion provided by the authors in Silene conica and Silene noctiflora are quite convincing, as compared to other members within the genus. I agree that many of the mitochondrial chromosomes lacks intact genes, which may indicates that genes undergoes duplication followed by degeneration – as you suggested -. Nevertheless, the genome expansion is not correlated with the gene content. As shown in table 1, the gene repertoire in fast evolving species, do not exhibit significant degeneration. Here, the vast majority of the genome is composed by noncoding regions without significant contribution of a particular type of repeat. ]]> https://wp.unil.ch/genomeeee/2012/05/31/rapid-evolution-of-enormous-multichromosomal-genomes-in-flowering-plant-mitochondria-with-exceptionally-high-mutation-rates/#comment-5 Wed, 06 Jun 2012 21:50:09 +0000 http://wp.unil.ch/genomeeee/2012/05/31/rapid-evolution-of-enormous-multichromosomal-genomes-in-flowering-plant-mitochondria-with-exceptionally-high-mutation-rates/#comment-5 Mitochondrial genomes are odd though: there are ~20 copies per mitochondrion, and 1000-2000 mitochondria per cell.One can envisage a situation where some mitochondria have a mutation inactivating gene A, while others have a mutation inactivating gene B: now you have to maintain both of these populations within the cell. Depending on the dynamics of mutation rate, mitochondrial genome replication, recombination and gene conversion, these (initially identical) copies could subsequently diverge from each other.Rinse and repeat – with a high mutation rate – and you end up with a large population of mitochondrial chromosomes, each retaining only a small number of functional genes, with the remainder of each circle degenerated into random rubbish.Is that really “genome expansion” in the same way you’d talk about changes in nuclear genome size? I guess it’s related, in that one mechanism for nuclear genome expansion is by duplication of a genome segment followed by degeneration or neofunctionalisation of the duplicated genes – but in the mitochondrial case, the “duplication” is inherent in the fact that you started with thousands of copies per cell!There may be an interesting analogy to be drawn with the proliferation of repeats on Y chromosomes as they degenerate. ]]>