The Rate and Tract Length of Gene Conversion between Duplicated Genes

Mansai, Sayaka P; Kado, Tomoyuki; Innan, Hideki

doi:10.3390/genes2020313

Cited by 42 publications

(60 citation statements)

References 100 publications

(81 reference statements)

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“…The Cf resistance genes, for example, also reside in clusters that showed clear evidence of sequence exchange between paralogs, which is thought to generate novel resistance specificities [13,14]. However, nucleotide identity between the protease genes is <62% (Table S1), which is below the >80% identity required for homogenization [15,16], and alignments of tomato and potato Rcr3 and Pip1 did not display any larger stretch of shared polymorphisms ( Figure S1F), indicating that Rcr3 and Pip1 evolved independently at least since the speciation of tomato and potato, 7.3 million years ago [5].…”

Section: Resultsmentioning

confidence: 99%

Functional Divergence of Two Secreted Immune Proteases of Tomato

et al. 2015

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Rcr3 and Pip1 are paralogous secreted papain-like proteases of tomato. Both proteases are inhibited by Avr2 from the fungal pathogen Cladosporium fulvum, but only Rcr3 acts as a co-receptor for Avr2 recognition by the tomato Cf-2 immune receptor. Here, we show that Pip1-depleted tomato plants are hyper-susceptible to fungal, bacterial, and oomycete plant pathogens, demonstrating that Pip1 is an important broad-range immune protease. By contrast, in the absence of Cf-2, Rcr3 depletion does not affect fungal and bacterial infection levels but causes increased susceptibility only to the oomycete pathogen Phytophthora infestans. Rcr3 and Pip1 reside on a genetic locus that evolved over 36 million years ago. These proteins differ in surface-exposed residues outside the substrate-binding groove, and Pip1 is 5- to 10-fold more abundant than Rcr3. We propose a model in which Rcr3 and Pip1 diverged functionally upon gene duplication, possibly driven by an arms race with pathogen-derived inhibitors or by coevolution with the Cf-2 immune receptor detecting inhibitors of Rcr3, but not of Pip1.

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Section: Resultsmentioning

confidence: 99%

Functional Divergence of Two Secreted Immune Proteases of Tomato

et al. 2015

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“…Following Wiuf and Hein (2000), the tract length for every IGC event, l , is extracted from a geometric distribution with parameter q = λ/L:

P_{q} (l) = q {(1 - q)}^{l - 1} .

Instead of randomly choosing the direction in which the IGC tract extends (either 3′ or 5′), we determine the IGC tract extending l/2 sites to the left and l/2 to the right of the initiation point or junction. Mansai et al (2011) proposed a similar model in which there is an independent exponential elongation of the gene conversion tract in both directions from the initiation point. We deviate from previous models (Wiuf and Hein 2000; Thornton 2007; Mansai et al 2011) in limiting IGC tracts to the duplicate regions by the simple procedure of truncating any tract that extends beyond the duplicate blocks.…”

Section: Methodsmentioning

confidence: 99%

Interplay of Interlocus Gene Conversion and Crossover in Segmental Duplications Under a Neutral Scenario

Hartasánchez

Vallès-Codina

Brasó-Vives

et al. 2014

G3 Genes|Genomes|Genetics

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Interlocus gene conversion is a major evolutionary force that drives the concerted evolution of duplicated genomic regions. Theoretical models successfully have addressed the effects of interlocus gene conversion and the importance of crossover in the evolutionary fate of gene families and duplications but have not considered complex recombination scenarios, such as the presence of hotspots. To study the interplay between interlocus gene conversion and crossover, we have developed a forward-time simulator that allows the exploration of a wide range of interlocus gene conversion rates under different crossover models. Using it, we have analyzed patterns of nucleotide variation and linkage disequilibrium within and between duplicate regions, focusing on a neutral scenario with constant population size and validating our results with the existing theoretical models. We show that the interaction of gene conversion and crossover is nontrivial and that the location of crossover junctions is a fundamental determinant of levels of variation and linkage disequilibrium in duplicated regions. We also show that if crossover activity between duplications is strong enough, recurrent interlocus gene conversion events can break linkage disequilibrium within duplicates. Given the complex nature of interlocus gene conversion and crossover, we provide a framework to explore their interplay to help increase knowledge on molecular evolution within segmental duplications under more complex scenarios, such as demographic changes or natural selection.

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“…The higher estimate is somewhat in excess of the most extreme prior indirect estimate. For estimates of the mean tract length and proportion of the genome that are part of such tracts (19), see SI Appendix, Table S9. In terms of the total span of DNA recombined, the impact of COs is greater than gene conversion, even using our upper estimate, as the span of each CO event is so long.…”

Section: Inclusion Of Very Short and Long Tracts Modestly Increases Genementioning

confidence: 99%

Great majority of recombination events in Arabidopsis are gene conversion events

Yang

Yuan

Wang

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

105

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The evolutionary importance of meiosis may not solely be associated with allelic shuffling caused by crossing-over but also have to do with its more immediate effects such as gene conversion. Although estimates of the crossing-over rate are often well resolved, the gene conversion rate is much less clear. In Arabidopsis, for example, nextgeneration sequencing approaches suggest that the two rates are about the same, which contrasts with indirect measures, these suggesting an excess of gene conversion. Here, we provide analysis of this problem by sequencing 40 F 2 Arabidopsis plants and their parents. Small gene conversion tracts, with biased gene conversion content, represent over 90% (probably nearer 99%) of all recombination events. The rate of alteration of protein sequence caused by gene conversion is over 600 times that caused by mutation. Finally, our analysis reveals recombination hot spots and unexpectedly high recombination rates near centromeres. This may be responsible for the previously unexplained pattern of high genetic diversity near Arabidopsis centromeres.W hen considering the population genetic impact of recombination, classical theories predominantly concentrate on the impact of allelic shuffling, mediated by crossing-over, and the effect this has on linkage disequilibrium and, in turn, the effect the fate of one allele has on its genomic neighbors (1). However, when programmed double-strand breaks (DSBs) are introduced into chromosomes to initiate meiotic recombination, both crossover (CO) and noncrossover (non-CO) recombination events can occur.

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The Rate and Tract Length of Gene Conversion between Duplicated Genes

Cited by 42 publications

References 100 publications

Functional Divergence of Two Secreted Immune Proteases of Tomato

Functional Divergence of Two Secreted Immune Proteases of Tomato

Interplay of Interlocus Gene Conversion and Crossover in Segmental Duplications Under a Neutral Scenario

Great majority of recombination events in Arabidopsis are gene conversion events

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