19/09/2020
Evolution is quick and non-random!
Gross Structural Inter-Chromosomal Rearrangements differentiate same species.
In the recent comparative genomics paper the authors, identified large chromosomal rearrangements of inversions, translocation, insertions and deletion types, between two C. elegans genomes of fragments from 10 Kbp to 200 Kbp and beyond. They identified also highest variability in subtelomeric regions and detected new genes in this regions not known before in C. elegans, which as they noted may act as genetic resources by providing redundant gene sets that can facilitate adaptation to new environments during evolution [1]. These findings were possible as the authors used for their studies long read PacBio sequencing to de-novo assemble the wild-type C. elegans genome and used comparative genomics studies to reveal differences against N2 C. elegans reference genome [1].
In our paper “The Genome Sequence of the North-European Cucumber (Cucumis sativus L.) Unravels Evolutionary Adaptation Mechanisms in Plants”, published in 2011 we have for the first time in a higher plant reported gross chromosomal “rearrangements of inversions and translocations type which differ two cucumber genotypes, growing in extremely diverse environmental conditions … of temperate Northern Europe and subtropical southeast Asia climate, respectively” [2].
As we wrote, at that time: “Reported in this work, extensive and numerous interchromosomal rearrangements between two cultivars of the same crop species is the novel evidence. It should also be noted, that beside such rearrangements, all of the genotypes are fertile. Though the observed genome rearrangements need further and deeper analysis, it could be concluded that those whole chromosomes shifts could represent adaptive changes, because are accepted and heritable. It could be also supposed that the view of evolutionary genomic adaptations emerging from the previous comparative genomics studies based on i.e. resequencing or hybridization data, is at least only partial and could lead to erroneous conclusions about the real mechanisms of organisms adaptive changes” [2].
Found in 2009 and reported in 2011 gross chromosomal rearrangements were the novel and not understood phenomenon at that time. Additionally because of the lack of methodology, wide use of mentioned resequencing or short-reads de-novo assembly methods, using genetic maps of different varieties for assemblies anchoring, but mostly because of assumption that the rearrangements are not possible between different genotypes of the same species have been making such discoveries impossible. “Regarding to the above comment, it seems that the discovery of global genomic changes (rearrangements) between two cucumber genomes, were possible only because of availability of two genomes sequences generated de-novo together with the use of diverse genome background genetic map” [2].
Even if almost 10 years ago we have shown that “through evolution, eukaryotic organisms have been equipped with a high degree of freedom with respect to … chromosomal rearrangements that allow for formation of new lines/varieties and species adapted to new ecological niches” [2] , it looks like it is possible only now to accept fast adaptive evolution within species which accepts gross structural chromosomal changes. Such a possibility totally changes the view on evolution which does not have to be slow and random but allow for adaptations through “quick” genome changes. The authors of the recent C. elegans paper also notice that: “…our findings suggest that a species can tolerate substantial structural changes in the genome without losing integrity as the same species and that new subtelomeres, and eventually new chromosomal contents, can evolve…” [1].
[1] Chuna Kim et al. Long-read sequencing reveals intra-species tolerance of substantial structural variations and new subtelomere formation in C. elegans. Genome Research 2019, https://doi.org/10.1101/gr.246082.118
[2] Rafał Wóycicki et al. The Genome Sequence of the North-European Cucumber (Cucumis sativus L.) Unravels Evolutionary Adaptation Mechanisms in Plants, PLoS ONE 2011, https://doi.org/10.1371/journal.pone.0022728
Cucumber (Cucumis sativus L.), a widely cultivated crop, has originated from Eastern Himalayas and secondary domestication regions includes highly divergent climate conditions e.g. temperate and subtropical. We wanted to uncover adaptive genome differences between the cucumber cultivars and what sor...
