Stable recombination hotspots in birds

Singhal, Sonal; Leffler, Ellen M.; Sannareddy, Keerthi; Turner, Isaac; Venn, Oliver; Hooper, Daniel M.; Strand, Alva I.; Li, Qiye; Raney, Brian J.; Balakrishnan, Christopher N.; Griffith, Simon C.; McVean, Gil; Przeworski, Molly

doi:10.1126/science.aad0843

Cited by 313 publications

(493 citation statements)

References 95 publications

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“…At the whole-genome level, similar results were found with 2/3 of COs overlapping genes, as this is the case for most COs in plants (reviewed in Mercier et al 2015). Our COs were found in the gene body and slightly more frequently in promoters and terminators, confirming the results observed in Arabidopsis (Choi et al 2013) as well as in avian (Singhal et al 2015;Smeds et al 2016) and in Saccharomyces species (Lam and Keeney 2015), where recombination pattern is highly conserved and localized to the promoter (TSS) and terminator (TTS) regions.…”

Section: Retrotransposons Associate With Reduced Recombination Ratesupporting

confidence: 79%

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High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism

et al. 2017

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During meiosis, crossovers (COs) create new allele associations by reciprocal exchange of DNA. In bread wheat (Triticum aestivum L.), COs are mostly limited to subtelomeric regions of chromosomes, resulting in a substantial loss of breeding efficiency in the proximal regions, though these regions carry 60-70% of the genes. Identifying sequence and/or chromosome features affecting recombination occurrence is thus relevant to improve and drive recombination. Using the recent release of a reference sequence of chromosome 3B and of the draft assemblies of the 20 other wheat chromosomes, we performed fine-scale mapping of COs and revealed that 82% of COs located in the distal ends of chromosome 3B representing 19% of the chromosome length. We used 774 SNPs to genotype 180 varieties representative of the Asian and European genetic pools and a segregating population of 1270 F 6 lines. We observed a common location for ancestral COs (predicted through linkage disequilibrium) and the COs derived from the segregating population. We delineated 73 small intervals (,26 kb) on chromosome 3B that contained 252 COs. We observed a significant association of COs with genic features (73 and 54% in recombinant and nonrecombinant intervals, respectively) and with those expressed during meiosis (67% in recombinant intervals and 48% in nonrecombinant intervals). Moreover, while the recombinant intervals contained similar amounts of retrotransposons and DNA transposons (42 and 53%), nonrecombinant intervals had a higher level of retrotransposons (63%) and lower levels of DNA transposons (28%). Consistent with this, we observed a higher frequency of a DNA motif specific to the TIR-Mariner DNA transposon in recombinant intervals. KEYWORDS recombination; meiosis; bread wheat; linkage disequilibrium; transposon; hotspot; sequence motif M EIOTIC recombination is a process that allows reshuffling of diversity by the reciprocal exchange of DNA called a crossover (CO). This phenomenon is conserved in most eukaryotes (for a review see Mercier et al. 2015) and follows the formation of a double-strand break (DSB) of DNA generated by the topoisomerase SPO11 complex. However, the number of DSBs is at least 10-to 50-fold greater than the number of COs which rarely exceeds three per bivalent chromosome per meiosis (Mercier et al. 2015). This paucity of COs per meiosis with regards to the number of DSBs suggests the existence of a tight control and regulation of recombination in plants that promote DSB repair in a manner that does not lead to COs. For example, the study of the two helicases AtFANCM and RECQ4 (AtRECQ4A and AtRECQ4B) (Crismani et al. 2012;Knoll et al. 2012;Girard et al. 2014;Séguéla-Arnaud et al. 2015) revealed three-and sixfold CO frequency increases in the Atfancm single mutant and the Atrecq4a/Atrecq4b double mutant, respectively, compared to the wild type. These increases result from additional COs from the class-II pathway which suggests that FANCM and RECQ4 prevent CO formation and direct recombination intermediates towar...

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Section: Retrotransposons Associate With Reduced Recombination Ratesupporting

confidence: 79%

“…In avian (Singhal et al 2015;Smeds et al 2016) and in Saccharomyces species (Lam and Keeney 2015), recombination patterns are highly conserved during evolution. This led us to assay using another approach to reveal historical recombination using LD and coalescent theory (r-map) (Li and Stephens 2003;Crawford et al 2004) in wheat.…”

Section: Discussionmentioning

confidence: 99%

High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism

et al. 2017

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“…increased by a factor of 1.79, 1.81 and 1.93, respectively. Within birds, such a highly nonuniform distribution of recombination events has been observed only in zebra finches and long-tailed finches so far (Singhal et al, 2015), yet it should be noted that even more extreme examples of a skewed distribution of recombination can be found in other organisms (for example, corn (Zea mays); Gore et al, 2009). In the following, we will discuss the effect of this nonuniform distribution of crossovers on precision and bias of Pedigree and Marker F.…”

Section: Mendelian Noise In Gwibdmentioning

confidence: 99%

Meiotic recombination shapes precision of pedigree- and marker-based estimates of inbreeding

2016

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The proportion of an individual's genome that is identical by descent (GWIBD) can be estimated from pedigrees (inbreeding coefficient 'Pedigree F') or molecular markers ('Marker F'), but both estimators come with error. Assuming unrelated pedigree founders, Pedigree F is the expected proportion of GWIBD given a specific inbreeding constellation. Meiotic recombination introduces variation around that expectation (Mendelian noise) and related pedigree founders systematically bias Pedigree F downward. Marker F is an estimate of the actual proportion of GWIBD but it suffers from the sampling error of markers plus the error that occurs when a marker is homozygous without reflecting common ancestry (identical by state). We here show via simulation of a zebra finch and a human linkage map that three aspects of meiotic recombination (independent assortment of chromosomes, number of crossovers and their distribution along chromosomes) contribute to variation in GWIBD and thus the precision of Pedigree and Marker F. In zebra finches, where the genome contains large blocks that are rarely broken up by recombination, the Mendelian noise was large (nearly twofold larger s.d. values compared with humans) and Pedigree F thus less precise than in humans, where crossovers are distributed more uniformly along chromosomes. Effects of meiotic recombination on Marker F were reversed, such that the same number of molecular markers yielded more precise estimates of GWIBD in zebra finches than in humans. As a consequence, in species inheriting large blocks that rarely recombine, even small numbers of microsatellite markers will often be more informative about inbreeding and fitness than large pedigrees.

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“…There are at least two types of hotspots ( figure 3). The first type, probably ancestral, is found in fungi, plants, birds and some mammals; these hotspots are temporally stable (up to millions of years) and concentrated near promoter regions and transcription start sites [178,[182][183][184][185]. The second type is likely derived and is found in other mammals, including mice and humans, where the positioning of hotspots is determined by the zinc-finger protein PRDM9.…”

Section: (D) the Localization Of Crossovers And Recombination Hotspotsmentioning

confidence: 99%

Evolutionary mysteries in meiosis

Lenormand

Engelstädter

Johnston

et al. 2016

Phil. Trans. R. Soc. B

120

133

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One contribution of 15 to a theme issue 'Weird sex: the underappreciated diversity of sexual reproduction'. Meiosis is a key event of sexual life cycles in eukaryotes. Its mechanistic details have been uncovered in several model organisms, and most of its essential features have received various and often contradictory evolutionary interpretations. In this perspective, we present an overview of these often 'weird' features. We discuss the origin of meiosis (origin of ploidy reduction and recombination, two-step meiosis), its secondary modifications (in polyploids or asexuals, inverted meiosis), its importance in punctuating life cycles (meiotic arrests, epigenetic resetting, meiotic asymmetry, meiotic fairness) and features associated with recombination (disjunction constraints, heterochiasmy, crossover interference and hotspots). We present the various evolutionary scenarios and selective pressures that have been proposed to account for these features, and we highlight that their evolutionary significance often remains largely mysterious. Resolving these mysteries will likely provide decisive steps towards understanding why sex and recombination are found in the majority of eukaryotes.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.

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Stable recombination hotspots in birds

Cited by 313 publications

References 95 publications

High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism

High-Resolution Mapping of Crossover Events in the Hexaploid Wheat Genome Suggests a Universal Recombination Mechanism

Meiotic recombination shapes precision of pedigree- and marker-based estimates of inbreeding

Evolutionary mysteries in meiosis

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