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ARS Home » Midwest Area » Ames, Iowa » Corn Insects and Crop Genetics Research » Research » Publications at this Location » Publication #346917
Title: A mechanism for genome size reduction following genomic rearrangements

Author
item REN, LONGHUI - Iowa State University
item HUANG, WEI - Iowa State University
item CANNON, ETHALINDA - Iowa State University
item BERTIOLI, DAVID - University Of Georgia
item Cannon, Steven

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/18/2018
Publication Date: 10/9/2018
Citation: Ren, L., Huang, W., Cannon, E., Bertioli, D.J., Cannon, S.B. 2018. A mechanism for genome size reduction following genomic rearrangements. Frontiers in Genetics. https://doi.org/10.3389/fgene.2018.00454.
DOI: https://doi.org/10.3389/fgene.2018.00454

Interpretive Summary: Evolution of species occurs through the evolution of genomes, which hold the genetic information that determines all biological characteristics of an individual. Although genome sequences have been determined for many species, many details of the mechanisms of genome evolution remain unknown. The research in this paper investigated how the genomes of wild relatives of peanut have evolved over the two million years since they separated into distinct species. An important result is that when a chromosome breaks (a relatively common event in a million-year time span), the broken pieces shrink in a predictable way. This offsets the tendency for chromosomes (and genomes) to gradually grow in size, as "transposon" sequences duplicate and copy themselves throughout the genome. These results have practical implications for plant breeders: in chromosomes recombine in particular ways, and at different rates and recombination densities. In a chromosome that has recently broken, genes and genetic markers will tend to be farther apart from one another than in chromosomes that have been intact for long evolutionary time periods. This knowledge will help researchers and breeders design experiments with greater efficiency and effectiveness.

Technical Abstract: The factors behind genome size evolution have been of great interest, considering that eukaryotic genomes vary in size by more than three orders of magnitude. Using a model of two wild peanut relatives, Arachis duranensis and Arachis ipaensis, in which one genome experienced large rearrangements, we find that the main determinant in genome size reduction is a set of inversions that occurred in A. duranensis, and subsequent net sequence removal in the inverted regions. We observe a general pattern in which sequence is lost more rapidly at newly distal (telomeric) regions than it is gained at newly proximal (pericentromeric) regions – resulting in net sequence loss in the inverted regions. The major driver of this process is recombination, determined by the chromosomal location. Any type of genomic rearrangement that exposes proximal regions to higher recombination rates can cause genome size reduction by this mechanism. In comparisons between A. duranensis and A. ipaensis, we find that the inversions all occurred in A. duranensis. Sequence loss in those regions was primarily due to removal of transposable elements. Illegitimate recombination is likely the major mechanism responsible for the sequence removal, rather than unequal intrastrand recombination. We also measure the relative rate of genome size reduction in these two Arachis diploids. We also test our model in other plant species and find that it applies in all cases examined, suggesting our model is widely applicable.