Academic journal article Genetics

Fine-Scale Recombination Maps of Fungal Plant Pathogens Reveal Dynamic Recombination Landscapes and Intragenic Hotspots

Academic journal article Genetics

Fine-Scale Recombination Maps of Fungal Plant Pathogens Reveal Dynamic Recombination Landscapes and Intragenic Hotspots

Article excerpt

MEIOTIC recombination is a fundamental process that, in many eukaryotes, shapes genetic variation in populations and drives evolutionary changes. Studies based on experimental and empirical data have demonstrated that recombination in sexual organisms plays a crucial role in defining genome-wide neutral and nonneutral nucleotide variation patterns (Begun and Aquadro 1992; Spencer et al. 2006), rates of protein evolution (Betancourt et al. 2009), transposable element (TE) distribution (Rizzon etal. 2002), GC content (Meunier and Duret 2004), and codon-usage bias (Marais et al. 2003). Despite the ubiquitous occurrence of recombination, however, the mechanisms that determine the genome-wide and temporal distribution of crossover events are still poorly understood in most species.

Accurate genome-wide recombination maps are essential for studying the genomics and genetics of recombination. Recombination rates have been recorded in many species by direct observations of meiotic events using genetic crosses or pedigrees (for example Broman et al. 1998; Jeffreys et al. 1998; McMullen et al. 2009). Pedigree studies, however, rely on large numbers of individuals and produce only low-resolution rate estimates because of the relatively low number of meiotic events that can practically be observed (Stumpf and McVean 2003). Furthermore, many microbial eukaryotic species, including important pathogens, are difficult or even impossible to cross under laboratory conditions (Taylor et al. 2015). While experimental measures of recombination rate can be challenging in many species, advances in statistical analyses provide powerful tools to generate fine-scale recombination maps using population genomic data (e.g., Myers et al. 2005; Chan et al. 2012; Wang and Rannala 2014). These methods are based on genome-wide patterns of linkage disequilibrium (LD) among single nucleotide polymorphisms (SNPs) and have the potential to capture the history of recombination events in a population sample. Thus, recombination studies based on population genomic data have provided detailed insights into the genomics of recombination in a range of species (Winckler et al. 2005; Horton et al. 2012; Singhal et al. 2015; Hunter et al. 2016). In many organisms, but not all, the majority of recombination events tend to concentrate in short segments termed recombination hotspots (Petes 2001; Chan et al. 2012). In the human genome, >25,000 recombination hotspots have been identified, with a number of them showing a > 100-fold increase in recombination rates and exhibiting a strong impact on the overall recombination landscape and genome evolution in general (Myers et al. 2005; Winckler et al. 2005; Jeffreys and Neumann 2009).

Comparative analyses of recombination maps between closely related species have shed light on the dynamics of recombination landscapes in different taxa. A comparative analysis of recombination landscapes of chimpanzees and humans found a strong correlation of recombination rates at broad scales (whole-chromosome and megabase scale), whereas fine-scale recombination rates were considerably less conserved because of nonoverlapping recombination hotspots (Auton et al. 2012). The localization of recombination hotspots in primates and mice is in large part determined by PRDM9, a histone methyltransferase with an array of DNA-binding, Zn-finger domains (Myers et al. 2010). In some species-including species without PRDM9 such as yeast, plants, birds, and some mammals-recombination hotspots associate with particular functional features such as transcription start and stop sites as well as CpG islands (Horton etal. 2012; Choi etal. 2013; Lam and Keeney 2015; Singhal et al. 2015; Smeds et al. 2016). A model developed to explain the association of recombination hotspots and functional elements proposes that a depletion of nucleosome occupancy at these sites increases the accessibility of the recombination machinery (Kaplan et al. 2009; de Castro et al. …

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