Search

The large mitochondrial genomes of angiosperms are unusually dynamic because of recombination activities involving repeated sequences. These activities generate subgenomic forms and extensive genomic variation even within the same species. Such changes in genome structure are responsible for the rapid evolution of plant mitochondrial DNA and for the variants associated with cytoplasmic male sterility and abnormal growth phenotypes. Nuclear genes modulate these processes, and over the past decade, several of these genes have been identified. They are involved mainly in pathways of DNA repair by homologous recombination and mismatch repair, which appear to be essential for the faithful replication of the mitogenome. Mutations leading to the loss of any of these activities release error-prone repair pathways, resulting in increased ectopic recombination, genome instability, and heteroplasmy. We review the present state of knowledge of the genes and pathways underlying mitochondrial genome stability.

The genetic recombination process mediated by crossing over (CO) events is not random along chromosomes and its occurrence can drive molecular evolution and genome organization. In this study, a position-recoding algorithm was developed to convert cytological CO detected in tomato (Solanum lycopersicum) chromosomes into physical genome coordinates. The meiotic recombination profile displays a punctual distribution of the crossover frequency along the chromosomes, which may be used to conduct further analysis. The recombination profile is not uniform and follows the same distribution profile as the coding sequences. On analyzing the positions of resistance (R) genes we found that most nucleotide-binding domain-leucine-rich repeat (NB-LRR) loci accumulate in hot recombination regions of the distal subtelomeric regions, while few NB-LRR loci tend to reside in proximal cold recombination regions. As the local meiotic crossover frequency is known to make an important contribution to the molecular evolution rate of a genome region, this divergent drift of the resistance loci toward hot and cold recombination areas may reflect different evolution needs for the species with respect to plant-pathogen co-evolution. The generation of novel haplotypes, promoted by recombination reshuffling, is more favorable for R loci that require rapid diversification to overcome the emergence of new pathogen races. Instead, cold areas may be more advantageous for maintaining R genes that confer durable resistance over time. Knowledge of chromosome region recombination rates and R-gene distribution may be useful to steer future disease resistance breeding schemes and select favorable allele combinations.

In an attempt to track the chromosomal differentiation in the Dichroplus elongatus species group, we analyzed the karyotypes of four species with classical cytogenetic and mapping several multigene families through fluorescent in situ hybridization (FISH). We improved the taxon sampling of the D. elongatus species group adding new molecular data to infer the phylogeny of the genus and reconstruct the karyotype evolution. Our molecular analyses recovered a fully resolved tree with no evidence for the monophyly of Dichroplus. However, we recovered several stable clades within the genus, including the D. elongatus species group, under the different strategies of tree analyses (Maximum Parsimony and Maximum Likelihood). The chromosomal data revealed minor variation in the D. elongatus species group's karyotypes caused by chromosome rearrangements compared to the phylogenetically related D. maculipennis species group. The karyotypes of D. intermedius and D. exilis described herein showed the standard characteristics found in most Dichroplini, 2n = 23/24, X0♂ XX♀, Fundamental number (FN) = 23/24. However, we noticed two established pericentric inversions in D. intermedius karyotype, raising the FN to 27♂/28♀. A strong variation in the heterochromatic blocks distribution was evidenced at interespecific level. The multigene families' mapping revealed significant variation, mainly in rDNA clusters. These variations are probably caused by micro chromosomal changes, such as movement of transposable elements (TEs) and ectopic recombination. These observations suggest a high genomic dynamism for these repetitive DNA sequences in related species. The reconstruction of the chromosome character "variation in the FN" posits the FN = 23/24 as the ancestral state, and it is hypothesized that variations due to pericentric inversions has arisen independently three times in the evolutionary history of Dichroplus. One of these independent events occurred in the D. elongatus species group, where D. intermedius is the unique case with the highest FN described in the tribe Dichroplini., Centro de Estudios Parasitológicos y de Vectores, Facultad de Ciencias Naturales y Museo

International audience; In plants, the largest class of resistance (R) gene encodes nucleotide-binding leucine-rich repeat (NB-LRR) proteins. This multigene family is often organized in clusters of tightly linked genes. In the common bean (Phaseolus vulgaris L.) genome, most of the well-characterized large R gene clusters are not randomly distributed since they are often located at the ends of the linkage groups (LG), suggesting that this location is favorable for R gene proliferation. In addition, terminal knobs (heterochromatic blocks) are present at most chromosome (Chr) ends of P. vulgaris, and we have identified a satellite DNA referred to as khipu that is a component of most of them. Plasticity of subtelomeres has been described in various organisms such as yeast and human but is not well documented in plants. In common bean, the B4 cluster of R gene was shown to derive from the Co-2 R gene cluster through an ectopic recombination between non-homologous chromosomes in subtelomeric regions. These unusual features of common bean genome (subtelomeric localization of large NB-LRR sequences, the presence of terminal knobs, and plasticity of subtelomeres) have been investigated with the availability of the complete common bean genome sequence.

Epigenetics is known to be involved in recombination initiation, but the effects of specific epigenetic marks like DNA methylation on recombination are relatively unknown. Studies in Arabidopsis and the fungus Ascobolus immersus suggest that DNA methylation may suppress recombination rates and/or alter its distribution across the genome; however, these patterns appear complex, and more direct inquiries are needed. Unlike other organisms, Drosophila only have one known DNA methyltransferase, DNMT2, which is expressed in the ovaries and historically has been thought to be responsible for limited genomic DNA methylation. To test for a role of DNMT2 on the frequency and distribution of recombination, I compared recombination rates between Dnmt2 −/− and Dnmt2 +/− Drosophila melanogaster individuals in two euchromatic regions and one heterochromatic region across the genome. I failed to detect an altered pattern of recombination rate in the absence of DNMT2 in all regions surveyed, and conclude that other epigenetic effects are regulating recombination initiation in Drosophila.

Nucleotide diversity is greater in maize than in most organisms studied to date, so allelic pairs in a hybrid tend to be highly polymorphic. Most recombination events between such pairs of maize polymorphic alleles are crossovers. However, intragenic recombination events not associated with flanking marker exchange, corresponding to noncrossover gene conversions, predominate between alleles derived from the same progenitor. In these dimorphic heterozygotes, the two alleles differ only at the two mutant sites between which recombination is being measured. To investigate whether gene conversion at the bz locus is polarized, two large diallel crossing matrices involving mutant sites spread across the bz gene were performed and more than 2,500 intragenic recombinants were scored. In both diallels, around 90% of recombinants could be accounted for by gene conversion. Furthermore, conversion exhibited a striking polarity, with sites located within 150 bp of the start and stop codons converting more frequently than sites located in the middle of the gene. The implications of these findings are discussed with reference to recent data from genome-wide studies in other plants.

The ability to examine all chromatids from a single meiosis in yeast tetrads has been indispensable for defining the mechanisms of homologous recombination initiated by DNA double-strand breaks (DSBs). Using a broadly applicable strategy for the analysis of chromatids from a single meiosis at two recombination hotspots in mouse oocytes and spermatocytes, we demonstrate here the unidirectional transfer of information-gene conversion-in both crossovers and noncrossovers. Whereas gene conversion in crossovers is associated with reciprocal exchange, the unbroken chromatid is not altered in noncrossover gene conversion events, providing strong evidence that noncrossovers arise from a distinct pathway. Gene conversion frequently spares the binding site of the hotspot-specifying protein PRDM9, with the result that erosion of the hotspot is slowed. Thus, mouse tetrad analysis demonstrates how unique aspects of mammalian recombination mechanisms shape hotspot evolutionary dynamics.

Although homologous recombination can potentially provide viruses with vastly more evolutionary options than are available through mutation alone, there are considerable limits on the adaptive potential of this important evolutionary process. Primary among these is the disruption of favorable coevolved genetic interactions that can occur following the transfer of foreign genetic material into a genome. Although the fitness costs of such disruptions can be severe, in some cases they can be rapidly recouped by either compensatory mutations or secondary recombination events. Here, we used a maize streak virus (MSV) experimental model to explore both the extremes of recombination-induced genetic disruption and the capacity of secondary recombination to adaptively reverse almost lethal recombination events. Starting with two naturally occurring parental viruses, we synthesized two of the most extreme conceivable MSV chimeras, each effectively carrying 182 recombination breakpoints and containing thorough reciprocal mixtures of parental polymorphisms. Although both chimeras were severely defective and apparently noninfectious, neither had individual movement-, encapsidation-, or replication-associated genome regions that were on their own “lethally recombinant.” Surprisingly, mixed inoculations of the chimeras yielded symptomatic infections with viruses with secondary recombination events. These recombinants had only 2 to 6 breakpoints, had predominantly inherited the least defective of the chimeric parental genome fragments, and were obviously far more fit than their synthetic parents. It is clearly evident, therefore, that even when recombinationally disrupted virus genomes have extremely low fitness and there are no easily accessible routes to full recovery, small numbers of secondary recombination events can still yield tremendous fitness gains. IMPORTANCE Recombination between viruses can generate strains with enhanced pathological properties but also runs the risk of producing hybrid genomes with decreased fitness due to the disruption of favorable genetic interactions. Using two synthetic maize streak virus genome chimeras containing alternating genome segments derived from two natural viral strains, we examined both the fitness costs of extreme degrees of recombination (both chimeras had 182 recombination breakpoints) and the capacity of secondary recombination events to recoup these costs. After the severely defective chimeras were introduced together into a suitable host, viruses with between 1 and 3 secondary recombination events arose, which had greatly increased replication and infective capacities. This indicates that even in extreme cases where recombination-induced genetic disruptions are almost lethal, and 91 consecutive secondary recombination events would be required to reconstitute either one of the parental viruses, moderate degrees of fitness recovery can be achieved through relatively small numbers of secondary recombination events.

Inversions are an integral part of structural variation within species, and they play a leading role in genome reorganization across species. Work at both the cytological and genome sequence levels has revealed heterogeneity in the distribution of inversion breakpoints, with some regions being recurrently used. Breakpoint reuse at the molecular level has mostly been assessed for fixed inversions through genome sequence comparison, and therefore rather broadly. Here, we have identified and sequenced the breakpoints of two polymorphic inversions-E1 and E2 that share a breakpoint-in the extant Est and E1 + 2 chromosomal arrangements of Drosophila subobscura. The breakpoints are two medium-sized repeated motifs that mediated the inversions by two different mechanisms: E1 via staggered breaks and subsequent repair and E2 via repeat-mediated ectopic recombination. The fine delimitation of the shared breakpoint revealed its strict reuse at the molecular level regardless of which was the intermediate arrangement. The occurrence of other rearrangements in the most proximal and distal extended breakpoint regions reveals the broad reuse of these regions. This differential degree of fragility might be related to their sharing the presence outside the inverted region of snoRNA-encoding genes.

Many bacterial, viral and parasitic pathogens undergo antigenic variation to counter host immune defense mechanisms. In Plasmodium falciparum, the most lethal of human malaria parasites, switching of var gene expression results in alternating expression of the adhesion proteins of the Plasmodium falciparum-erythrocyte membrane protein 1 class on the infected erythrocyte surface. Recombination clearly generates var diversity, but the nature and control of the genetic exchanges involved remain unclear. By experimental and bioinformatic identification of recombination events and genome-wide recombination hotspots in var genes, we show that during the parasite’s sexual stages, ectopic recombination between isogenous var paralogs occurs near low folding free energy DNA 50-mers and that these sequences are heavily concentrated at the boundaries of regions encoding individual Plasmodium falciparum-erythrocyte membrane protein 1 structural domains. The recombinogenic potential of these 50-mers is not parasite-specific because these sequences also induce recombination when transferred to the yeast Saccharomyces cerevisiae. Genetic cross data suggest that DNA secondary structures (DSS) act as inducers of recombination during DNA replication in P. falciparum sexual stages, and that these DSS-regulated genetic exchanges generate functional and diverse P. falciparum adhesion antigens. DSS-induced recombination may represent a common mechanism for optimizing the evolvability of virulence gene families in pathogens.

Human chromosome 15q25 is involved in several disease-associated structural rearrangements, including microdeletions and chromosomal markers with inverted duplications. Using comparative fluorescence in situ hybridization, strand-sequencing, single-molecule, real-time sequencing and Bionano optical mapping analyses, we investigated the organization of the 15q25 region in human and nonhuman primates. We found that two independent inversions occurred in this region after the fission event that gave rise to phylogenetic chromosomes XIV and XV in humans and great apes. One of these inversions is still polymorphic in the human population today and may confer differential susceptibility to 15q25 microdeletions and inverted duplications. The inversion breakpoints map within segmental duplications containing core duplicons of the GOLGA gene family and correspond to the site of an ancestral centromere, which became inactivated about 25 million years ago. The inactivation of this centromere likely released segmental duplications from recombination repression typical of centromeric regions. We hypothesize that this increased the frequency of ectopic recombination creating a hotspot of hominid inversions where dispersed GOLGA core elements now predispose this region to recurrent genomic rearrangements associated with disease., Author summary Human chromosome 15 derived from a fission event that occurred in the ancestor of great apes. Following inactivation of the ancestral centromere at 15q25 a dispersal of segmental duplications took place, providing templates for ectopic recombination and predisposing the region to genomic instability. Different disease-associated microdeletions and chromosomal markers have been described with breakpoints mapping within these segmental duplications. To gain insight into the instability at 15q25, we sought to analyze this region in human and nonhuman primates using multiple genomics techniques and demonstrated the presence of two independent inversion events that occurred during great apes evolution. One of these inversions is still polymorphic in humans and may cause, in conjunction with a GOLGA core duplicon—a ~14 kbp chromosome 15 repeat, susceptibility to non-allelic homologous recombination leading to pathogenic recurrent rearrangements. Our results support the existence of a strong relationship between inversions and core duplicons and reinforce the hypothesis that GOLGA repeats play a fundamental role both in disease and evolution.

Meiotic recombination is a fundamental process ensuring proper disjunction of homologous chromosomes and allele shuffling in successive generations. In many species, this cellular mechanism occurs heterogeneously along chromosomes and mostly concentrates in tiny fragments called recombination hotspots. Specific DNA motifs have been shown to initiate recombination in these hotspots in mammals, fission yeast and drosophila. The aim of this study was to check whether recombination also occurs in a heterogeneous fashion in the highly recombinogenic honeybee genome and whether this heterogeneity can be connected with specific DNA motifs. We completed a previous picture drawn from a routine genetic map built with an average resolution of 93 kb. We focused on the two smallest honeybee chromosomes to increase the resolution and even zoomed at very high resolution (3.6 kb) on a fragment of 300 kb. Recombination rates measured in these fragments were placed in relation with occurrence of 30 previously described motifs through a Poisson regression model. A selection procedure suitable for correlated variables was applied to keep significant motifs. These fine and ultra-fine mappings show that recombination rate is significantly heterogeneous although poorly contrasted between high and low recombination rate, contrarily to most model species. We show that recombination rate is probably associated with the DNA methylation state. Moreover, three motifs (CGCA, GCCGC and CCAAT) are good candidates of signals promoting recombination. Their influence is however moderate, doubling at most the recombination rate. This discovery extends the way to recombination dissection in insects.

Meiotic recombination is known to influence GC-content evolution in large regions of mammalian genomes by favoring the fixation of G and C alleles and increasing the rate of A/T to G/C substitutions. This process is known as GC-biased gene conversion (gBGC). Until recently, genome-wide measures of fine-scale recombination activity were unavailable in mice. Additionally, comparative studies focusing on mouse were limited as the closest organism with its genome fully sequenced was rat. Here, we make use of the recent mapping of double strand breaks (DSBs), the first step of meiotic recombination, in the mouse genome and of the sequencing of mouse closely related subspecies to analyze the fine-scale evolutionary signature of meiotic recombination on GC-content evolution in recombination hotspots, short regions that undergo extreme rates of recombination. We measure substitution rates around DSB hotspots and observe that gBGC is affecting a very short region ( approximately 1 kbp) in length around these hotspots. Furthermore, we can infer that the locations of hotspots evolved rapidly during mouse evolution.

Spo11 is considered responsible for initiation of meiotic recombination in higher organisms, but previous analysis using spo11 (RIP) mutants suggests that the his-3 region of Neurospora crassa experiences spo11-independent recombination. However, despite possessing several stop codons, it is conceivable that the mutants are not completely null. Also, since lack of spo11 interferes with chromosomal pairing and proper segregation at Meiosis I, spores can be partially diploid for a period after meiosis. Thus, it is possible that the recombination observed could be an abnormal event, occurring during the period of aneuploidy rather than during meiosis. To test the former hypothesis, we generated spo11 deletion homozygotes. Using crosses heteroallelic for his-3 mutations, we showed that His(+) progeny are generated in spo11 deletion homozygotes at a frequency at least as high as in wild type and, as in the spo11 (RIP) mutants, local crossing over is not reduced. To test the latter hypothesis, we utilised mutations in either end of a histone H1-GFP fusion gene, inserted between the recombination hotspot cog and his-3, in which GFP(+) spores arise as a result of recombination in a cross between the two GFP alleles. In a control cross homozygous for spo11 (+), the frequency at which GFP(+) spores arise is comparable to the frequency of His(+) spores and glowing nuclei first appear during prophase, prior to metaphase I, as expected for a product of meiotic recombination. Similarly in spo11 deletion homozygotes, GFP(+) spores arise at high frequency and glowing nuclei are first seen before metaphase, indicating that allelic recombination occurs during meiosis in the absence of spo11. We have therefore shown that spo11 is not essential for either his-3 allelic recombination or crossing over in the vicinity of his-3, and that spo11-independent allelic recombination is meiotic, indicating that there is a spo11-independent mechanism for initiation of recombination in Neurospora.

We analysed the size, relative age and chromosomal localization of nuclear sequences of plastid and mitochondrial origin (NUPTs-nuclear plastid DNA and NUMTs-nuclear mitochondrial DNA) in six completely sequenced plant species. We found that the largest insertions showed lower divergence from organelle DNA than shorter insertions in all species, indicating their recent origin. The largest NUPT and NUMT insertions were localized in the vicinity of the centromeres in the small genomes of Arabidopsis and rice. They were also present in other chromosomal regions in the large genomes of soybean and maize. Localization of NUPTs and NUMTs correlated positively with distribution of transposable elements (TEs) in Arabidopsis and sorghum, negatively in grapevine and soybean, and did not correlate in rice or maize. We propose a model where new plastid and mitochondrial DNA sequences are inserted close to centromeres and are later fragmented by TE insertions and reshuffled away from the centromere or removed by ectopic recombination. The mode and tempo of TE dynamism determines the turnover of NUPTs and NUMTs resulting in their species-specific chromosomal distributions.

Trans-lesion DNA polymerases (TLSPs) enable bypass of DNA lesions during replication and are also induced under stress conditions. Being only weakly dependent on their template during replication, TLSPs introduce mutations into DNA. The low processivity of these enzymes ensures that they fall off their template after a few bases are synthesized and are then replaced by the more accurate replicative polymerase. We find that the three TLSPs of budding yeast Saccharomyces cerevisiae Rev1, PolZeta (Rev3 and Rev7), and Rad30 are induced during meiosis at a time when DNA double-strand breaks (DSBs) are formed and homologous chromosomes recombine. Strains deleted for one or any combination of the three TLSPs undergo normal meiosis. However, in the triple-deletion mutant, there is a reduction in both allelic and ectopic recombination. We suggest that trans-lesion polymerases are involved in the processing of meiotic double-strand breaks that lead to mutations. In support of this notion, we report significant yeast two-hybrid (Y2H) associations in meiosis-arrested cells between the TLSPs and DSB proteins Rev1-Spo11, Rev1-Mei4, and Rev7-Rec114, as well as between Rev1 and Rad30. We suggest that the involvement of TLSPs in processing of meiotic DSBs could be responsible for the considerably higher frequency of mutations reported during meiosis compared with that found in mitotically dividing cells, and therefore may contribute to faster evolutionary divergence than previously assumed.

In terms of cytogenetics, entelegyne araneomorphs are the best studied clade of spiders. The typical karyotype of entelegyne males consists of acrocentric chromosomes, including 2 non-homologous X chromosomes. The present study is focused on the karyotype, nucleolus organising regions (NORs) and sex chromosome behaviour during meiosis of the entelegyne Wadicosa fidelis (Lycosidae). Preparations stained by Giemsa were used to study karyotype and meiosis. NORs were visualised by silver staining and fluorescence in situ hybridisation with 18S rDNA probe. The male karyotype consists of 28 acrocentric elements, including 2 X chromosomes. In contrast to the majority of other spiders, the male sex chromosomes pair during the major part of meiosis. Following an initial period of parallel pairing, the attachment of male sex chromosomes is restricted to centromeric areas and continues until metaphase II. Our study revealed an enormous number of NORs in the population from Galilee and indicates a considerable variability of NOR numbers in this population. The distal regions of 9 or 10 autosomal pairs contain NORs. The obtained data indicate the rapid spread of NORs in the karyotype of W. fidelis, which was presumably caused by ectopic recombinations and subsequent hybridisations of individuals with different NOR genotypes that produced heterozygotes.

International audience; Homologous recombination events occurring during meiotic prophase I ensure the proper segregation of homologous chromosomes at the first meiotic division. These events are initiated by programmed double-strand breaks produced by the Spo11 protein and repair of such breaks by homologous recombination requires a strand exchange activity provided by the Rad51 protein. We have recently reported that the absence of AtXrcc3, an Arabidopsis Rad51 paralogue, leads to extensive chromosome fragmentation during meiosis, first visible in diplotene of meiotic prophase I. The present study clearly shows that this fragmentation results from un- or mis-repaired AtSpo11-1 induced double-strand breaks and is thus due to a specific defect in the meiotic recombination process.

African trypanosomes cause human sleeping sickness and livestock trypanosomiasis in sub-Saharan Africa. We present the sequence and analysis of the 11 megabase-sized chromosomes of Trypanosoma brucei . The 26-megabase genome contains 9068 predicted genes, including ∼900 pseudogenes and ∼1700 T. brucei –specific genes. Large subtelomeric arrays contain an archive of 806 variant surface glycoprotein (VSG) genes used by the parasite to evade the mammalian immune system. Most VSG genes are pseudogenes, which may be used to generate expressed mosaic genes by ectopic recombination. Comparisons of the cytoskeleton and endocytic trafficking systems with those of humans and other eukaryotic organisms reveal major differences. A comparison of metabolic pathways encoded by the genomes of T. brucei, T. cruzi , and Leishmania major reveals the least overall metabolic capability in T. brucei and the greatest in L. major . Horizontal transfer of genes of bacterial origin has contributed to some of the metabolic differences in these parasites, and a number of novel potential drug targets have been identified.

Maintenance of the chromosomal copy number over generations and recombination between homologous chromosomes are hallmarks of meiotic cell division. This genetic exchange that take place during gamete formation leads to genetic diversity, the main driving force behind natural selection. Formation of chiasmata, the physical link between homologous chromosomes during meiosis, is a requisite for recombination. In addition, chiasmata also aid in proper segregation of homologous chromosomes and has a major impact on reproductive fitness. Given these facts it is intriguing that many insect species have forgone the need for genetic exchange between homologous chromosomes during meiosis. Geneticists for several decades knew that meiotic crossover and recombination is absent in Drosophila males and some female lepidopterans, a condition termed achiasmy. However, a good understanding of the mechanisms that cause achiasmy and the evolutionary benefits of achiasmy is currently lacking. In this article we will discuss possible genetic and molecular basis of achiasmy in male Drosophila.

Two retrotransposons from the superfamilies Copia and Gypsy named as Copia-LTR_SS and Gypsy-LTR_SS, respectively, were identified in the genomic bank of Sclerotinia sclerotiorum. These transposable elements (TEs) contained direct and preserved long terminal repeats (LTR). Domains related to codified regions for gag protein, integrase, reverse transcriptase and RNAse H were identified in Copia-LTR_SS, whereas in Gypsy-LTR_SS only domains for gag, reverse transcriptase and RNAse H were found. The abundance of identified LTR-Solo suggested possible genetic recombination events in the S. sclerotiorum genome. Furthermore, alignment of the sequences for LTR elements from each superfamily suggested the presence of a RIP (repeat-induced point mutation) silencing mechanism that may directly affect the evolution of this species.

Background The Pokey family of DNA transposons consists of two putatively autonomous groups, PokeyA and PokeyB, and two groups of Miniature Inverted-repeat Transposable Elements (MITEs), mPok1 and mPok2. This TE family is unusual as it inserts into a specific site in ribosomal (r)DNA, as well as other locations in Daphnia genomes. The goals of this study were to determine the distribution of the Pokey family in lineages of the Daphnia pulex species complex, and to test the hypothesis that unusally high PokeyA number in some isolates of Daphnia pulicaria is the result of recent transposition. To do this, we estimated the haploid number of Pokey, mPok, and rRNA genes in 45 isolates from five Daphnia lineages using quantitative PCR. We also cloned and sequenced partial copies of PokeyA from four isolates of D. pulicaria. Results Haploid PokeyA and PokeyB number is generally less than 20 and tends to be higher outside rDNA in four lineages. Conversely, the number of both groups is much higher outside rDNA (~120) in D. arenata, and PokeyB is also somewhat higher inside rDNA. mPok1 was only detected in D. arenata. mPok2 occurs both outside (~30) and inside rDNA (~6) in D. arenata, but was rare (≤2) outside rDNA in the other four lineages. There is no correlation between Pokey and rRNA gene number (mean = 240 across lineages) in any lineage. Variation among cloned partial PokeyA sequences is significantly higher in isolates with high number compared to isolates with an average number. Conclusions The high Pokey number outside rDNA in D. arenata and inside rDNA in some D. pulicaria isolates is consistent with a recent increase in transposition rate. The D. pulicaria increase may have been triggered by insertion of PokeyA into a region of transcriptionally active rDNA. The expansion in D. arenata (thought to be of hybrid origin) may be a consequence of release from epigenetic repression following hybridization. Previous work found D. obtusa to be very different from the D. pulex complex; mean PokeyA is higher in rDNA (~75), rDNA array size is nearly twice as large (415), and the two are positively correlated. The predominance of Pokey in only one location could be explained by purifying selection against ectopic recombination between elements inside and outside rDNA. Electronic supplementary material The online version of this article (doi:10.1186/s13100-016-0067-7) contains supplementary material, which is available to authorized users.

Meiosis distinguishes cells in the germ line from their somatic counterparts. Part of meiosis involves a bizarre series of events in which cells deliberately damage their DNA and then repair it. Of the many double-strand breaks that are generated, a minority are resolved as reciprocal exchanges between homologous chromosomes [1]. In a wide variety of species, recombination diversifies genomes and is required for the formation of viable gametes. Although the functional role of crossing over should impose strong selective constraints, the rate of recombination varies among individuals. Recombination rate shows resemblance among relatives [2], differs among inbred strains raised in a common environment [3], and responds to artificial selection [4], demonstrating a genetic component to individual rate differences that remains mostly unexplained. A handful of genes responsible for variation in recombination rate have been identified, including modifiers of the total number of crossovers [5–8] and loci that determine the genomic placement of recombination events [9]. As a fundamental part of gametogenesis, meiosis also plays a role in speciation, the means by which one species becomes two. A common observation is that otherwise viable hybrids between genetically differentiated lineages suffer from reduced fertility up to the point of complete sterility—an important reproductive barrier that keeps species distinct [10]. One stage during which problems appear is meiosis, when hybrid gametogenesis sometimes arrests. According to an influential model, hybrid sterility arises from disrupted interactions between different genes that evolved in separate populations [11,12]. The search for incompatibility genes that cause hybrid sterility has so far yielded a short list [13–15]. The fact that only a small number of genes are known to control variation in recombination rate or to contribute to hybrid sterility makes the discovery that one gene mediates both traits especially noteworthy. Prdm9 encodes a histone methyltransferase that modifies chromatin and is essential for meiosis in mice [16]. Decades of persistent effort from the group of Jiri Forejt demonstrated that incompatibility between Prdm9 and other loci causes sterility in F1 hybrid males formed by crossing two subspecies of house mice [17]. Subsequently, genetic mapping in crosses, population genetic analysis, bioinformatic prediction of DNA binding sites, and association studies jointly identified Prdm9 as a primary determinant of recombination hotspot location (short stretches of sequence within which most crossovers occur) in mice and humans [9,18–20]. The dual roles of Prdm9 reveal a tantalizing link between recombination and speciation at the genetic level and motivate the search for other genes that affect both processes. Now, progress from Jiri Forejt’s lab provides fresh evidence for a genetic connection between recombination and hybrid sterility. Balcova et al. (2016) [21] profile the genome-wide recombination rate by visualizing the immunolocalization pattern of the MLH1 mismatch repair protein that resolves double-strand breaks into crossovers (Fig 1). This powerful approach enables the total number of recombination events to be counted in individual spermatocytes. The authors first use the MLH1 technique to confirm that the genome of an inbred strain representing the house mouse subspecies Mus musculus musculus experiences an average of 4.7 more crossovers than the genome of an inbred strain descended primarily from M. m. domesticus (a 19% increase). Next, Balcova et al. (2016) measure recombination rates in a panel of inbred strains, each of which harbors single chromosomes from the M. m. musculus strain on the genomic background of the M. m. domesticus strain. By comparing rates in chromosome substitution strains with the appropriate parental strain, the authors identify three chromosomes that affect the genome-wide crossover number. The locus with the largest phenotypic effect is located on the X chromosome. Rate differences among substitution strains carrying pieces of the chromosome further localize the position of this modifier of the global recombination rate to a 4.7 Mb interval (nicknamed Meir1 by the authors). This locus lies within a broader part of the X chromosome previously shown to modulate recombination in crosses involving other subspecies of mice [22,23]. Fig 1 Image illustrating immunofluorescent cytology approach to measuring the genome-wide recombination rate (from Balcova et al., 2016). Several lines of evidence suggest that this region of the X chromosome genetically links recombination and speciation. First, the same interval is associated with multiple correlates of hybrid sterility. Small testes, low sperm count, and morphological abnormalities in sperm observed in F1 males from crosses between M. m. musculus mothers and M. m. domesticus fathers all map to this genomic location [24,25]. Second, hybrid male sterility due to one of the loci in this X-linked region (Hstx2) involves an incompatibility with Prdm9 [25]. Finally, the effects of this piece of the X chromosome on recombination and sterility show similar properties, including male specificity. The findings of Balcova et al. (2016), along with previous discoveries about Prdm9, raise the intriguing possibility that recombination and speciation are mechanistically coupled. Remarkably, both the fine-scale placement of crossovers (mediated by Prdm9) and the global recombination rate (controlled by Meir1) seem to be associated with hybrid sterility. The authors propose that the incompatibility between Prdm9 and Hstx2 could inhibit the repair of double-strand breaks, which could in turn lead to the disrupted synapsis of chromosomes and meiotic arrest observed in sterile F1 males [26,27]. Regardless of the mechanism, the larger implication is that evolutionary divergence in recombination genes can generate a frequently observed form of reproductive isolation. Once the causative gene(s) and mutation(s) corresponding to Meir1 and Hstx2 are identified in this system, important remaining questions can be answered. Do the joint effects on recombination and hybrid sterility reflect the pleiotropic activities of a single gene or multiple linked genes? What are the molecular, cellular, and developmental bases of these phenotypes? What is the evolutionary history of the causative mutations? Did natural selection drive phenotypic divergence, as seems to be the case for the rapidly evolving Prdm9 [28]? The results from Balcova et al. (2016) should also motivate similar studies in other organisms. The observations that recombination rate evolves and that hybrid sterility is a key reproductive barrier are phylogenetically widespread, leaving no obvious reason that the emerging connection between recombination and speciation should be restricted to mice.

Nucleotide insertions/deletions are ubiquitous in eukaryotic genomes, and the resulting hemizygous (unpaired) DNA has significant, heritable effects on adjacent DNA. However, little is known about the genetic behavior of insertion DNA. Here, we describe a binary transgenic system to study the behavior of insertion DNA during meiosis. Transgenic Arabidopsis lines were generated to carry two different defective reporter genes on nonhomologous chromosomes, designated as "recipient" and "donor" lines. Double hemizygous plants (harboring unpaired DNA) were produced by crossing between the recipient and the donor, and double homozygous lines (harboring paired DNA) via self-pollination. The transfer of the donor's unmutated sequence to the recipient generated a functional β-glucuronidase gene, which could be visualized by histochemical staining and corroborated by polymerase chain reaction amplification and sequencing. More than 673 million seedlings were screened, and the results showed that meiotic ectopic recombination in the hemizygous lines occurred at a frequency >6.49-fold higher than that in the homozygous lines. Gene conversion might have been exclusively or predominantly responsible for the gene correction events. The direct measurement of ectopic recombination events provided evidence that an insertion, in the absence of an allelic counterpart, could scan the entire genome for homologous counterparts with which to pair. Furthermore, the unpaired (hemizygous) architectures could accelerate ectopic recombination between itself and interchromosomal counterparts. We suggest that the ectopic recombination accelerated by hemizygous architectures may be a general mechanism for interchromosomal recombination through ubiquitously dispersed repeat sequences in plants, ultimately contributing to genetic renovation and eukaryotic evolution.

Recombination is an engine of genetic diversity and therefore constitutes a key process in evolutionary biology and genetics. While the outcome of crossover recombination can readily be detected as shuffled alleles by following the inheritance of markers in pedigreed families, the more precise location of both crossover and non-crossover recombination events has been difficult to pinpoint. As a consequence, we lack a detailed portrait of the recombination landscape for most organisms and knowledge on how this landscape impacts on sequence evolution at a local scale. To localize recombination events with high resolution in an avian system, we performed whole-genome re-sequencing at high coverage of a complete three-generation collared flycatcher pedigree. We identified 325 crossovers at a median resolution of 1.4 kb, with 86% of the events localized to, Author Summary Homologous chromosomes exchange genetic material during cell division at meiosis by the process of crossover recombination. Although such crossover events are visually identifiable by cytogenetic techniques, it has remained a challenge to pinpoint the location of crossovers at the DNA sequence level. An emerging novel possibility to approach this challenge is to exploit the high resolution offered by re-sequencing of multiple individuals in species in which a genome assembly is available. Specifically, by sequencing members of a family, the inheritance of chromosomal segments can be followed and the location of crossover as well as non-crossover recombination determined. We performed such an endeavour in the collared flycatcher, a songbird species that has been in focus for extensive ecological and evolutionary research. We found that crossover events were concentrated to certain ‘hot-spot’ regions, and that the density of such events was highest in and close to genes. A higher rate of crossover recombination was found in males than in females and in males, but not in females, the rate of crossover increased towards ends of chromosomes. The location of non-crossovers was significantly associated with that of crossovers. We could further document an unbalanced transmission of genetic variants at non-crossover events via to the process of GC-biased gene conversion.

Human recombination rate varies greatly, but the forces shaping it remain incompletely understood. Here, we study the relationship between recombination rate and gene-regulatory domains defined by a gene and its linked control elements. We define these links using methylation quantitative trait loci (meQTLs), expression quantitative trait loci (eQTLs), chromatin conformation, and correlated activity across cell types. Each link type shows a “recombination valley” of significantly-reduced recombination rate compared to control regions, indicating preferential co-inheritance of genes and linked regulatory elements as a single unit. This recombination valley is most pronounced for gene-regulatory domains of early embryonic developmental genes, housekeeping genes, and constitutive regulatory elements, which are known to show increased evolutionary constraint across species. Recombination valleys show increased DNA methylation, reduced double-stranded break initiation, and increased repair efficiency, specifically in the lineage leading to the germ line, providing a potential molecular mechanism facilitating their maintenance by exclusion of recombination events.

In many mammals, including humans and mice, the zinc finger histone methyltransferase PRDM9 performs the first step in meiotic recombination by specifying the locations of hotspots, the sites of genetic recombination. PRDM9 binds to DNA at hotspots through its zinc finger domain and activates recombination by trimethylating histone H3K4 on adjacent nucleosomes through its PR/SET domain. Recently, the isolated PR/SET domain of PRDM9 was shown capable of also trimethylating H3K36 in vitro, raising the question of whether this reaction occurs in vivo during meiosis, and if so, what its function might be. Here, we show that full-length PRDM9 does trimethylate H3K36 in vivo in mouse spermatocytes. Levels of H3K4me3 and H3K36me3 are highly correlated at hotspots, but mutually exclusive elsewhere. In vitro, we find that although PRDM9 trimethylates H3K36 much more slowly than it does H3K4, PRDM9 is capable of placing both marks on the same histone molecules. In accord with these results, we also show that PRDM9 can trimethylate both K4 and K36 on the same nucleosomes in vivo, but the ratio of K4me3/K36me3 is much higher for the pair of nucleosomes adjacent to the PRDM9 binding site compared to the next pair further away. Importantly, H3K4me3/H3K36me3-double-positive nucleosomes occur only in regions of recombination: hotspots and the pseudoautosomal (PAR) region of the sex chromosomes. These double-positive nucleosomes are dramatically reduced when PRDM9 is absent, showing that this signature is PRDM9-dependent at hotspots; the residual double-positive nucleosomes most likely come from the PRDM9-independent PAR. These results, together with the fact that PRDM9 is the only known mammalian histone methyltransferase with both H3K4 and H3K36 trimethylation activity, suggest that trimethylation of H3K36 plays an important role in the recombination process. Given the known requirement of H3K36me3 for double strand break repair by homologous recombination in somatic cells, we suggest that it may play the same role in meiosis., Author Summary Genetic recombination is the meiotic process by which novel combinations of alleles are passed on to the next generation. This process accelerates evolution by creating genetic diversity, and is also essential for successful meiosis. In mammals, the enzyme PRDM9 initiates recombination and determines the subset of sites within the genome—called recombination hotspots—that recombine. PRDM9 does this by binding DNA at hotspots and placing epigenetic marks. Previously, PRDM9 was only known to place the H3K4me3 mark at hotspots in living cells. Here, we show that PRDM9 places the H3K36me3 mark at hotspots, and that H3K4me3 and H3K36me3 coincide only at regions of recombination in germ cells. We prove that this coincidence is driven almost entirely by PRDM9; there is dramatically less coincidence between H3K4me3 and H3K36me3 when PRDM9 is absent. These results reveal a new enzymatic function for PRDM9, and a new epigenetic signature at hotspots that may restrict recombination to these sites. Since aberrant recombination can cause aneuploidy resulting in fetal loss, and abnormal genome rearrangements that underlie many congenital syndromes and some cancers, a thorough understanding of this fundamental process has potentially far-reaching implications.

The Saccharomyces cerevisae RAD3 gene is the homolog of human XPD, an essential gene encoding a DNA helicase of the TFIIH complex involved in both nucleotide excision repair (NER) and transcription. Some mutant alleles of RAD3 (rad3-101 and rad3-102) have partial defects in DNA repair and a strong hyper-recombination (hyper-Rec) phenotype. Previous studies showed that the hyper-Rec phenotype associated with rad3-101 and rad3-102 can be explained as a consequence of persistent single-stranded DNA gaps that are converted to recombinogenic double-strand breaks (DSBs) by replication. The systems previously used to characterize the hyper-Rec phenotype of rad3 strains do not detect the reciprocal products of mitotic recombination. We have further characterized these events using a system in which the reciprocal products of mitotic recombination are recovered. Both rad3-101 and rad3-102 elevate the frequency of reciprocal crossovers about 100-fold. Mapping of these events shows that three-quarters of these crossovers reflect DSBs formed at the same positions in both sister chromatids (double sister-chromatid breaks, DSCBs). The remainder reflects DSBs formed in single chromatids (single chromatid breaks, SCBs). The ratio of DSCBs to SCBs is similar to that observed for spontaneous recombination events in wild-type cells. We mapped 216 unselected genomic alterations throughout the genome including crossovers, gene conversions, deletions, and duplications. We found a significant association between the location of these recombination events and regions with elevated gamma-H2AX. In addition, there was a hotspot for deletions and duplications at the IMA2 and HXT11 genes near the left end of chromosome XV. A comparison of these data with our previous analysis of spontaneous mitotic recombination events suggests that a sub-set of spontaneous events in wild-type cells may be initiated by incomplete NER reactions, and that DSCBs, which cannot be repaired by sister-chromatid recombination, are a major source of mitotic recombination between homologous chromosomes., The research was supported by: NIH grants GM24110 and GM52319 to TDP; ACS grant CA059365 and NIH grant GM100618 to SLA; and Spanish Ministry of Economy and Competitiveness Grants BFU2010-16372 and BFU2013-42918-P to AA.

Recombination, both crossover and gene conversion, plays fundamental roles in evolution by generating novel allele combinations, as well as by increasing the genetic diversity and facilitating natural selection. In many fungal species, recombination is also critical for sex (mating-type) determination and sexual development, and the evolution of the mating-type locus (MAT) is likely strongly influenced by recombination (or lack thereof). On the other hand, in some fungal species, the presence of a mating-type locus on a chromosome can affect its recombinational landscape. Additionally, while in some cases the MAT locus is associated with repressed crossing-over within, there are also examples where recombination hot spots are present within or in the proximity of the MAT locus. Given the diverse mating systems and mating-type determination mechanisms in different species, fungi as well as other microbial eukaryotes provide rich resources to study the effects of recombination on mechanisms of sex determination and sexual development, as well as the evolution of sex determination systems and sex chromosomes in general.

We herein study genetic recombination in three cattle populations from France, New Zealand, and the Netherlands. We identify 2,395,177 crossover (CO) events in 94,516 male gametes, and 579,996 CO events in 25,332 female gametes. The average number of COs was found to be larger in males (23.3) than in females (21.4). The heritability of global recombination rate (GRR) was estimated at 0.13 in males and 0.08 in females, with a genetic correlation of 0.66 indicating that shared variants are influencing GRR in both sexes. A genome-wide association study identified seven quantitative trait loci (QTL) for GRR. Fine-mapping following sequence-based imputation in 14,401 animals pinpointed likely causative coding (5) and noncoding (1) variants in genes known to be involved in meiotic recombination (HFM1, MSH4, RNF212, MLH3, MSH5) for 5/7 QTL, and noncoding variants (3) in RNF212B for 1/7 QTL. This suggests that this RNF212 paralog might also be involved in recombination. Most of the identified mutations had significant effects in both sexes, with three of them each accounting for ∼10% of the genetic variance in males.

In higher eukaryotes, meiotic cell divisions produce sperm and eggs. Haploid DNA content in germ cells is achieved by one round of DNA replication, followed by two successive rounds of cell division. To successfully segregate chromosomes to daughter cells in the first meiotic cell division, homologous chromosomes (homologs) must find each other and stably pair. In most organisms studied to date, including mammals, homolog recognition and pairing is achieved by DNA recombination interactions that are initiated by developmentally programmed DNA double-stranded breaks (DSBs).5 Evolutionary geneticists have long appreciated the role of meiotic recombination in reshuffling genetic material from one generation to the next (see e.g. ref. 6). Gene mapping efforts are possible thanks only to this feature of meiosis. What has received less attention in this field is the fact that meiotic recombination also has an essential function in chromosome pairing7–9 and in establishing a physical connection (crossover) between homologs,10, 11 which in turn is critical for chromosome segregation. To initiate recombination, mouse spermatocytes typically make 200–250 DSBs per nucleus.12, 13 As meiosis progresses, most of these DSBs are repaired without the exchange of flanking chromosome arms (non-crossover) while a subset matures into crossovers involving a reciprocal exchange between homologs14 (see also Cole et al., this volume). Recombination failure leads to inviable gametes.7, 9 Once a DSB is made, the proper partner — the unbroken template for homologous recombination — must be located and engaged in a stable pairing interaction. Not all chromosomes, however, are on a level playing field with regard to pairing. Autosomal chromosomes are homologous along their entire length (~60–200 Mb, depending on the chromosome) and are hence able to pair from end to end. The X and Y chromosomes, on the other hand, are non-homologous save for a short segment called the pseudoautosomal region (PAR).3 X-Y chromosome homology search and pairing therefore can only be mediated by DSBs in the PAR, conceivably making X-Y segregation particularly difficult. Indeed, X-Y aneuploidy is a common paternally inherited chromosome disorder.2 In most cells, however, X-Y chromosome segregation is completed successfully, raising the question how the challenging task of recombination between heteromorphic sex chromosomes is achieved. We applied sophisticated cytological methods to investigate DSB formation and pairing of the PARs in mice, and review here our recent findings on mechanisms that secure faithful X-Y recombination.4

Meiotic crossover (CO) recombination involves a reciprocal exchange between homologous chromosomes. COs are often associated with gene conversion at the exchange site where genetic information is unidirectionally transferred from one chromosome to the other. COs and independent assortment of homologous chromosomes contribute significantly to the promotion of genomic diversity. What has not been appreciated is the contribution of another product of meiotic recombination, noncrossovers (NCOs), which result in gene conversion without exchange of flanking markers. Here, we review our comprehensive analysis of recombination at a highly polymorphic mouse hotspot. We found that NCOs make up ∼90% of recombination events. Preferential recombination initiation on one chromosome allowed us to estimate the contribution of CO and NCO gene conversion to transmission distortion, a deviation from Mendelian inheritance in the population. While NCO gene conversion tracts are shorter, and thus have a more punctate effect, their higher frequency translates into an approximately two-fold greater contribution than COs to gene conversion-based allelic shuffling and transmission distortion. We discuss the potential impact of mammalian NCO characteristics on evolution and genomic diversity.

Humans suffer from high rates of fetal aneuploidy, often arising from the absence of meiotic crossover recombination between homologous chromosomes1. Meiotic recombination is initiated by double-strand breaks (DSBs) generated by the SPO11 transesterase2. In yeast and worms, at least one buffering mechanism, crossover homeostasis, maintains crossover numbers despite variation in DSB numbers3–8. We show here that mammals display progressive homeostatic control of recombination. In wild-type mouse spermatocytes, focus numbers for early recombination proteins (RAD51, DMC1) were highly variable from cell to cell, whereas foci of the crossover marker MLH1 showed little variability. Furthermore, mice with greater or fewer copies of the Spo11 gene — with correspondingly greater or fewer numbers of early recombination foci — displayed relatively invariant crossover numbers. Homeostatic control is enforced during at least two stages, after the formation of early recombination intermediates and later while these intermediates mature toward crossovers. Thus, variability within the mammalian meiotic program is robustly managed by homeostatic mechanisms to control crossover formation, probably to suppress aneuploidy. Meiotic recombination exemplifies how order can be progressively implemented in a self-organizing system despite natural cell-to-cell disparities in the underlying biochemical processes.

We use the ancestral influence graph (AIG) for a two-locus, two-allele selection model in the limit of a large population size to obtain an analytic approximation for the probability of ultimate fixation of a single mutant allele A. We assume that this new mutant is introduced at a given locus into a finite population in which a previous mutant allele B is already segregating with a wild type at another linked locus. We deduce that the fixation probability increases as the recombination rate increases if allele A is either in positive epistatic interaction with B and allele B is beneficial or in no epistatic interaction with B and then allele A itself is beneficial. This holds at least as long as the recombination fraction and the selection intensity are small enough and the population size is large enough. In particular this confirms the Hill–Robertson effect, which predicts that recombination renders more likely the ultimate fixation of beneficial mutants at different loci in a population in the presence of random genetic drift even in the absence of epistasis. More importantly, we show that this is true from weak negative epistasis to positive epistasis, at least under weak selection. In the case of deleterious mutants, the fixation probability decreases as the recombination rate increases. This supports Muller’s ratchet mechanism to explain the accumulation of deleterious mutants in a population lacking recombination.

Disrupted meiotic behaviour of inversion carriers may be responsible for suboptimal sperm parameters in these carriers. This study investigated meiotic recombination, synapsis, transcriptional silencing and chromosome segregation effects in a pericentric inv(1) carrier. Recombination (MLH1), synapsis (SYCP1, SYCP3) and transcriptional inactivation (γH2AX, BRCA1) were examined by fluorescence immunostaining. Chromosome specific rates of recombination were determined by fluorescence in-situ hybridization. Furthermore, testicular sperm was examined for aneuploidy and segregation of the inv(1). Our findings showed that global recombination rates were similar to controls. Recombination on the inv(1) and the sex chromosomes were reduced. The inv(1) associated with the XY body in 43.4% of cells, in which XY recombination was disproportionately absent, and 94.3% of cells displayed asynapsed regions which displayed meiotic silencing regardless of their association with the XY body. Furthermore, a low frequency of chromosomal imbalance was observed in spermatozoa (3.4%). Our results suggest that certain inversion carriers may display unimpaired global recombination and impaired recombination on the involved and the sex chromosomes during meiosis. Asynapsis or inversion-loop formation in the inverted region may be responsible for impaired spermatogenesis and may prevent sperm-chromosome imbalance. In infertile men who are carriers of chromosome abnormalities, adequate sperm production can be impaired. Meiosis, a cell division process in which spermatozoa are produced, can be impaired by the interaction of the abnormal chromosome with its homologous pair or with other chromosomes. In meiosis, a process called ‘recombination' occurs, where homologous chromosomes pair up and exchange genetic material. Recombination is important in ensuring equal distribution of chromosomes during meiosis. When these processes are disrupted, sperm production can be impaired. In this study, we investigated meiosis in an infertile man carrying an inversion on chromosome 1, a particular type of chromosome abnormality. We used fluorescence microscopy techniques to examine recombination, the fidelity of chromosome pairing (synapsis) and chromosome distribution in the meiotic cells obtained from testicular tissue. Spermatozoa was also studied for proper chromosome distribution. Meiotic cells and spermatozoa from five fertile men that did not have any chromosome abnormalities were used as a reference group. Our results showed that recombination involving the affected chromosome, and between the sex-determining chromosomes were reduced compared with the reference. The abnormal chromosome associated with the sex chromosomes in 43.4% of the meiotic cells, in which recombination was noticeably absent between the sex chromosomes. Despite these findings, the frequency of chromosomally abnormal spermatozoa was not greater than the reference. Our findings suggest that certain chromosome inversions may have impaired recombination on the involved and the sex chromosomes. However, this impairment may be a protective factor against the production of chromosomally abnormal spermatozoa.

Meiotic recombination lies at the heart of sexual reproduction. It is essential for producing viable gametes with a normal haploid genomic content and its dysfunctions can be at the source of aneuploidies, such as the Down syndrome, or many genetic disorders. Meiotic recombination also generates genetic diversity that is transmitted to progeny by shuffling maternal and paternal alleles along chromosomes. Recombination takes place at non-random chromosomal sites called 'hotspots'. Recent evidence has shown that their location is influenced by properties of chromatin. In addition, many studies in somatic cells have highlighted the need for changes in chromatin dynamics to allow the process of recombination. In this review, we discuss how changes in the chromatin landscape may influence the recombination map, and reciprocally, how recombination events may lead to epigenetic modifications at sites of recombination, which could be transmitted to progeny.

The eukaryotic recombinases RAD51 and DMC1 are essential for DNA strand-exchange between homologous chromosomes during meiosis. RAD51 is also expressed during mitosis, and mediates homologous recombination (HR) between sister chromatids. It has been suggested that DMC1 might be involved in the switch from intersister chromatid recombination in somatic cells to interhomolog meiotic recombination. At meiosis, the Arabidopsis Atrad51 null mutant fails to synapse and has extensive chromosome fragmentation. The Atdmc1 null mutant is also asynaptic, but in this case chromosome fragmentation is absent. Thus in plants, AtDMC1 appears to be indispensable for interhomolog homologous recombination, whereas AtRAD51 seems to be more involved in intersister recombination. In this work, we have studied a new AtRAD51 knock-down mutant, Atrad51-2, which expresses only a small quantity of RAD51 protein. Atrad51-2 mutant plants are sterile and hypersensitive to DNA double-strand break induction, but their vegetative development is apparently normal. The meiotic phenotype of the mutant consists of partial synapsis, an elevated frequency of univalents, a low incidence of chromosome fragmentation and multivalent chromosome associations. Surprisingly, non-homologous chromosomes are involved in 51% of bivalents. The depletion of AtDMC1 in the Atrad51-2 background results in the loss of bivalents and in an increase of chromosome fragmentation. Our results suggest that a critical level of AtRAD51 is required to ensure the fidelity of HR during interchromosomal exchanges. Assuming the existence of asymmetrical DNA strand invasion during the initial steps of recombination, we have developed a working model in which the initial step of strand invasion is mediated by AtDMC1, with AtRAD51 required to check the fidelity of this process.

At the population level, recombination mediates the efficiency with which selection can eliminate deleterious mutations. At the individual level, deleterious alleles may influence recombination, which would change the rate at which linkage disequilibrium is eroded and thereby alter the efficiency with which deleterious alleles are purged. Here, we test whether the presence of a deleterious allele on one autosome affects recombination on another autosome. We find that deleterious alleles not only alter the rate but also the pattern of recombination. However, there is little support that different deleterious alleles affect recombination in a consistent manner. Because we have detailed information on individual females across their lifetimes, we are able to examine how recombination patterns change with age and find that these patterns are also affected by the presence of deleterious alleles. The differences among genotypes or among age classes are large enough to add substantial noise to genetic mapping experiments that do not consider these sources of variation.

Chiasmata resulting from interhomolog recombination are critical for proper chromosome segregation at meiotic metaphase I, thus preventing aneuploidy and consequent deleterious effects. Recombination in meiosis is driven by programmed induction of double strand breaks (DSBs), and the repair of these breaks occurs primarily by recombination between homologous chromosomes, not sister chromatids. Almost nothing is known about the basis for recombination partner choice in mammals. We addressed this problem using a genetic approach. Since meiotic recombination is coupled with synaptonemal complex (SC) morphogenesis, we explored the role of axial elements – precursors to the lateral element in the mature SC - in recombination partner choice, DSB repair pathways, and checkpoint control. Female mice lacking the SC axial element protein SYCP3 produce viable, but often aneuploid, oocytes. We describe genetic studies indicating that while DSB-containing Sycp3−/− oocytes can be eliminated efficiently, those that survive have completed repair before the execution of an intact DNA damage checkpoint. We find that the requirement for DMC1 and TRIP13, proteins normally essential for recombination repair of meiotic DSBs, is substantially bypassed in Sycp3 and Sycp2 mutants. This bypass requires RAD54, a functionally conserved protein that promotes intersister recombination in yeast meiosis and mammalian mitotic cells. Immunocytological and genetic studies indicated that the bypass in Sycp3−/− Dmc1−/− oocytes was linked to increased DSB repair. These experiments lead us to hypothesize that axial elements mediate the activities of recombination proteins to favor interhomolog, rather than intersister recombinational repair of genetically programmed DSBs in mice. The elimination of this activity in SYCP3- or SYCP2-deficient oocytes may underlie the aneuploidy in derivative mouse embryos and spontaneous abortions in women.

A large region of suppressed recombination surrounds the sex-determining locus of the self-fertile fungus Neurospora tetrasperma. This region encompasses nearly one-fifth of the N. tetrasperma genome and suppression of recombination is necessary for self-fertility. The similarity of the N. tetrasperma mating chromosome to plant and animal sex chromosomes and its recent origin (

Long interspersed nuclear element 1 (L1) retrotransposons are the only autonomously mobile human transposable elements. L1 retrotransposition has shaped our genome via insertional mutagenesis, sequence transduction, pseudogene formation, and ectopic recombination. However, L1 germline retrotransposition dynamics are poorly understood because de novo insertions occur very rarely: the frequency of disease-causing retrotransposon insertions suggests that one insertion event occurs in roughly 18–180 gametes. The method described here recovers full-length L1 insertions by using hybridization enrichment to capture L1 sequences from multiplex PCR-amplified DNA. Enrichment is achieved by hybridizing L1-specific biotinylated oligonucleotides to complementary molecules, followed by capture on streptavidin-coated paramagnetic beads. We show that multiplex, long-range PCR can amplify single molecules containing full-length L1 insertions for recovery by hybridization enrichment. We screened 600 µg of sperm DNA from one donor, but no bone fide de novo L1 insertions were found, suggesting a L1 retrotransposition frequency of

Meiosis is a highly conservative process, which plays important role in the life cycles of all sexually reproductive organisms, while the pairing, synapsis, and recombination are the key events in this process and have become the hotspots in meiosis studies. At present, we cannot observe the process of cross and recombination of chromosomes directly in plant meiosis, and generally conclude the process by analysis the genetic population. In the present study, we analyzed 32 DH lines using graphical genotypes, and found 4 chromosomes out of 32 DH lines had regional heterozygosis, which was further confirmed using STS markers. We suggested that it may cause by repair incompletion or mis-repair of chromsome. These results provid some directly evidence for explaining the mechanism of plant meiosis.

In mythology, the Trickster is an archetype who typically behaves selfishly and delights in playing tricks and breaking ordinary rules. In many myths and folktales, however, the Trickster also brings new knowledge and, ultimately, has positive effects on the community. Transposable elements (TEs) might have played such a role in the story of genome evolution. TEs can cause nonroutine genetic events like insertional mutations and ectopic recombination that provide a fundamental source of genetic variation, but they can also be a potential threat to genome integrity. Thus, the activity of TEs is usually controlled by an array of sophisticated mechanisms for genome defense. Recent findings indicate that TEs are important components of eukaryotic genomes, often to a much larger extent than ever anticipated. In this review, I focus on the contributions of TEs to various aspects of genome evolution. In addition, why TEs are specific targets for the genome defense mechanisms is discussed.

Gene conversion (conversion), the unidirectional transfer of DNA sequence information, occurs as a byproduct of recombinational repair of broken or damaged DNA molecules. Whereas excision repair processes replace damaged DNA by copying the complementary sequence from the undamaged strand of duplex DNA, recombinational mechanisms copy similar sequence, usually in another molecule, to replace the damaged sequence. In mitotic cells the other molecule is usually a sister chromatid, and the repair does not lead to genetic change. Less often a homologous chromosome or homologous sequence in an ectopic position is used. Conversion results from repair in two ways. First, if there was a double-strand gap at the site of a break, homologous sequence will be used as the template for synthesis to fill the gap, thus transferring sequence information in both strands. Second, recombinational repair uses complementary base pairing, and the heteroduplex molecule so formed is a source of conversion, both as heteroduplex and when donor (undamaged template) information is retained after correction of mismatched bases in heteroduplex. There are mechanisms that favour the use of sister molecules that must fail before ectopic homology can be used. Meiotic recombination events lead to the formation of crossovers required in meiosis for orderly segregation of pairs of homologous chromosomes. These events result from recombinational repair of programmed double-strand breaks, but in contrast with mitotic recombination, meiotic recombinational events occur predominantly between homologous chromosomes, so that transfer of sequence differences by conversion is very frequent. Transient recombination events that do not form crossovers form both between homologous chromosomes and between regions of ectopic homology, and leave their mark in the occurrence of frequent non-crossover conversion, including ectopic conversion.

During meiosis, the formation of viable haploid gametes from diploid precursors requires that each homologous chromosome pair be properly segregated to produce an exact haploid set of chromosomes. Genetic recombination, which provides a physical connection between homologous chromosomes, is essential in most species for proper homologue segregation. Nevertheless, recombination is repressed specifically in and around the centromeres of chromosomes, apparently because rare centromeric (or pericentromeric) recombination events, when they do occur, can disrupt proper segregation and lead to genetic disabilities, including birth defects. The basis by which centromeric meiotic recombination is repressed has been largely unknown. We report here that, in fission yeast, RNAi functions and Clr4-Rik1 (histone H3 lysine 9 methyltransferase) are required for repression of centromeric recombination. Surprisingly, one mutant derepressed for recombination in the heterochromatic mating-type region during meiosis and several mutants derepressed for centromeric gene expression during mitotic growth are not derepressed for centromeric recombination during meiosis. These results reveal a complex relation between types of repression by heterochromatin. Our results also reveal a previously undemonstrated role for RNAi and heterochromatin in the repression of meiotic centromeric recombination and, potentially, in the prevention of birth defects by maintenance of proper chromosome segregation during meiosis.

We examined chromosomal distribution of major ribosomal DNAs (rDNAs), clustered in the nucleolar organizer regions (NORs), in 18 species of moths and butterflies using fluorescence in situ hybridization (FISH) with a codling moth (Cydia pomonella) 18S rDNA probe. Most species showed one or two rDNA clusters in their haploid karyotype but exceptions with four to eleven clusters also occurred. Our results in a compilation with previous data revealed dynamic evolution of rDNA distribution in Lepidoptera except Noctuoidea, which showed a highly uniform rDNA pattern. In karyotypes with one NOR, interstitial location of rDNA prevailed, whereas two-NOR karyotypes showed mostly terminally located rDNA clusters. A possible origin of the single interstitial NOR by fusion between two NOR-chromosomes with terminal rDNA clusters lacks support in available data. In some species, spreading of rDNA to new, mostly terminal chromosome regions was found. The multiplication of rDNA clusters without alteration of chromosome numbers rules out chromosome fissions as a major mechanism of rDNA expansion. Based on rDNA dynamics in Lepidoptera and considering the role of ordered nuclear architecture in karyotype evolution, we propose ectopic recombination, i.e. homologous recombination between repetitive sequences of non-homologous chromosomes, as a primary motive force in rDNA repatterning.

In the grasshopper Abracris flavolineata it was documented huge intrapopulation variation for 18S rDNA in individuals collected in six populations, but causes for this pattern was not understand yet. In this work we aimed to elucidate the molecular structure, evolutionary patterns of the rDNA 18S distribution and its causes in the genome of A. flavolineata. It was used a combination of classical cytogenetic techniques, mapping of18S rDNA through Fluorescence in situ hybridization (FISH) and genomics analyses from entire sequenced genome by Illumina hiseq 2000. It was analyzed 48 individuals collected in six distantly sampling places from Brazil and Argentina. FISH analyses confirmed the variability of 18S rDNA for all six populations that presented between 6-11 chomosomes labeled. Signals were observed in chromosomes 1, 3, 6 and 9 in all individuals and also it was noticed variation of cluster sizes. It was not found a fixed pattern at intra- or interpopulation levels in population from the same geographic region or between distant ones. Silver nitrate staning revealed Nocleolar Organizer Regions (NORs) in chromosome 9 of all individuals, indicating that the expression of the rDNA cluster in this chromosome could be under selection to be expressed, and also could represent ancestral placement of this sequence. It is a pattern also shared with congeneric species. In some individuals chromosome 10 presented NORs, however for some of them FISH signals in this bivalent was not observed, indicating cryptic loci in accordance with ‘dispersion-amplification-deletion’ model, suggested also for rDNA dispersion for other grasshoppers. Finally the reconstruction of entire 45S rDNA presented different coverages in the conserved genes (18S, 5.8S e 25S) and in the internal transcripts (ITS 1 e ITS 2) reveling that huge part of the copies are pseudogenes. The transposons Nimb and R2 are present in 45S rDNA, although apparently they are not able to transpose sequences. All data together suggests that the high amount of rDNA in A. flavolineata genome is caused by occurrence of pseudogene sequences that were moved random between chromosomes caused most parsimonialy by ectopic recombination, extra-chromosomal DNA or even by transposons not localized in the 45S cluster