Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity

V. Seplyarskiy, M. Logacheva, A. Penin, M. Baranová, E. Leushkin, N. Demidenko, A. Klepikova, F. Kondrashov, A. Kondrashov, T. James, Molecular Biology and Evolution 31 (2014) 3016–3025.

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Author
Seplyarskiy, Vladimir B; Logacheva, Maria D; Penin, Aleksey A; Baranová, Maria A; Leushkin, Evgeny V; Demidenko, Natalia V; Klepikova, Anna V; Kondrashov, FyodorIST Austria ; Kondrashov, Alexey S; James, Timothy Y
Abstract
Recombination between double-stranded DNA molecules is a key genetic process which occurs in a wide variety of organisms. Usually, crossing-over (CO) occurs during meiosis between genotypes with 98.0-99.9% sequence identity, because within-population nucleotide diversity only rarely exceeds 2%. However, some species are hypervariable and it is unclear how CO can occur between genotypes with less than 90% sequence identity. Here, we study CO in Schizophyllum commune, a hypervariable cosmopolitan basidiomycete mushroom, a frequently encountered decayer of woody substrates. We crossed two haploid individuals, from the United States and from Russia, and obtained genome sequences for their 17 offspring. The average genetic distance between the parents was 14%, making it possible to study CO at very high resolution. We found reduced levels of linkage disequilibrium between loci flanking the CO sites indicating that they are mostly confined to hotspots of recombination. Furthermore, CO events preferentially occurred in regions under stronger negative selection, in particular within exons that showed reduced levels of nucleotide diversity. Apparently, in hypervariable species CO must avoid regions of higher divergence between the recombining genomes due to limitations imposed by the mismatch repair system, with regions under strong negative selection providing the opportunity for recombination. These patterns are opposite to those observed in a number of less variable species indicating that population genomics of hypervariable species may reveal novel biological phenomena.
Publishing Year
Date Published
2014-11-01
Journal Title
Molecular Biology and Evolution
Acknowledgement
The authors are grateful to Georgii Bazykin for valuable discussion and to the DNA sequencing facility at Engelhardt Institute of Molecular Biology for Sanger sequencing. This study was supported by the Russian government grant No 11.G34.31.0008 and by Plan Nacional (BFU2012-31329), Howard Hughes Medical Institute International Early Career Scientist Award and EMBO Young Investigator Program, and core funds provided by the University of Michigan.
Volume
31
Issue
11
Page
3016 - 3025
IST-REx-ID
845

Cite this

Seplyarskiy V, Logacheva M, Penin A, et al. Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. Molecular Biology and Evolution. 2014;31(11):3016-3025. doi:10.1093/molbev/msu242
Seplyarskiy, V., Logacheva, M., Penin, A., Baranová, M., Leushkin, E., Demidenko, N., … James, T. (2014). Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. Molecular Biology and Evolution, 31(11), 3016–3025. https://doi.org/10.1093/molbev/msu242
Seplyarskiy, Vladimir, Maria Logacheva, Aleksey Penin, Maria Baranová, Evgeny Leushkin, Natalia Demidenko, Anna Klepikova, Fyodor Kondrashov, Alexey Kondrashov, and Timothy James. “Crossing-over in a Hypervariable Species Preferentially Occurs in Regions of High Local Similarity.” Molecular Biology and Evolution 31, no. 11 (2014): 3016–25. https://doi.org/10.1093/molbev/msu242.
V. Seplyarskiy et al., “Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity,” Molecular Biology and Evolution, vol. 31, no. 11, pp. 3016–3025, 2014.
Seplyarskiy V, Logacheva M, Penin A, Baranová M, Leushkin E, Demidenko N, Klepikova A, Kondrashov F, Kondrashov A, James T. 2014. Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. Molecular Biology and Evolution. 31(11), 3016–3025.
Seplyarskiy, Vladimir, et al. “Crossing-over in a Hypervariable Species Preferentially Occurs in Regions of High Local Similarity.” Molecular Biology and Evolution, vol. 31, no. 11, Oxford University Press, 2014, pp. 3016–25, doi:10.1093/molbev/msu242.

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