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Deborah Charlesworth - One of the best experts on this subject based on the ideXlab platform.
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improved reference genome uncovers novel sex linked regions in the Guppy poecilia reticulata
Genome Biology and Evolution, 2020Co-Authors: Bonnie A Fraser, Roberta Bergero, Deborah Charlesworth, James R Whiting, Josephine R Paris, Cameron J Weadick, Paul J Parsons, Felix Bemm, Margarete Hoffmann, Verena A KottlerAbstract:Theory predicts that the sexes can achieve greater fitness if loci with sexually antagonistic polymorphisms become linked to the sex determining loci, and this can favour the spread of reduced recombination around sex determining regions. Given that sex-linked regions are frequently repetitive and highly heterozygous, few complete Y chromosome assemblies are available to test these ideas. The Guppy system (Poecilia reticulata) has long been invoked as an example of sex chromosome formation resulting from sexual conflict. Early genetics studies revealed that male colour patterning genes are mostly but not entirely Y-linked, and that X-linkage may be most common in low predation populations. More recent population genomic studies of guppies have reached varying conclusions about the size and placement of the Y-linked region. However, this previous work used a reference genome assembled from short-read sequences from a female Guppy. Here, we present a new Guppy reference genome assembly from a male, using long-read PacBio single-molecule real-time sequencing (SMRT) and chromosome contact information. Our new assembly sequences across repeat- and GC-rich regions and thus closes gaps and corrects mis-assemblies found in the short-read female-derived Guppy genome. Using this improved reference genome, we then employed broad population sampling to detect sex differences across the genome. We identified two small regions that showed consistent male-specific signals. Moreover, our results help reconcile the contradictory conclusions put forth by past population genomic studies of the Guppy sex chromosome. Our results are consistent with a small Y-specific region and rare recombination in male guppies.
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using gc content to compare recombination patterns on the sex chromosomes and autosomes of the Guppy poecilia reticulata and its close outgroup species
Molecular Biology and Evolution, 2020Co-Authors: Deborah Charlesworth, Roberta Bergero, Jim Gardner, Yexin Zhang, Chay Graham, Lengxob YongAbstract:Genetic and physical mapping of the Guppy (P. reticulata) have shown that recombination patterns differ greatly between males and females. Crossover events occur evenly across the chromosomes in females, but in male meiosis they are restricted to the tip furthest from the centromere of each chromosome, creating very high recombination rates per megabase, as in pseudo-autosomal regions (PARs) of mammalian sex chromosomes. We used GC content to indirectly infer recombination patterns on Guppy chromosomes, based on evidence that recombination is associated with GC-biased gene conversion, so that genome regions with high recombination rates should be detectable by high GC content. We used intron sequences and 3rd positions of codons to make comparisons between sequences that are matched, as far as possible, and are all probably under weak selection. Almost all Guppy chromosomes, including the sex chromosome (LG12), have very high GC values near their assembly ends, suggesting high recombination rates due to strong crossover localisation in male meiosis. Our test does not suggest that the Guppy XY pair has stronger crossover localisation than the autosomes, or than the homologous chromosome in the close relative, the platyfish (Xiphophorus maculatus). We therefore conclude that the Guppy XY pair has not recently undergone an evolutionary change to a different recombination pattern, or reduced its crossover rate, but that the Guppy evolved Y-linkage due to acquiring a male-determining factor that also conferred the male crossover pattern. We also identify the centromere ends of Guppy chromosomes, which were not determined in the genome assembly.
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using gc content to compare recombination patterns on the sex chromosomes and autosomes of the Guppy poecilia reticulata and its close outgroup species
bioRxiv, 2020Co-Authors: Deborah Charlesworth, Roberta Bergero, Jim Gardner, Yexin Zhang, Chay Graham, Lengxob YongAbstract:Summary/AbstractGenetic and physical mapping of the Guppy (P. reticulata) have shown that recombination patterns differ greatly between males and females. Crossover events occur evenly across the chromosomes in females, but in male meiosis they are restricted to the tip furthest from the centromere of each chromosome, creating very high recombination rates per megabase, similar to the high rates in mammalian sex chromosomes pseudo-autosomal regions (PARs). We here used the intronic GC content to indirectly infer the recombination patterns on Guppy chromosomes. This is based on evidence that recombination is associated with GC-biased gene conversion, so that genome regions with high recombination rates should be detectable by high GC content. Using intron sequences, which are likely to be under weak selection, we show that almost all Guppy chromosomes, including the sex chromosome (LG12) have very high GC values near their assembly ends, suggesting high recombination rates due to strong crossover localisation in male meiosis. Our test does not suggest that the Guppy XY pair has stronger crossover localisation than the autosomes, or than the homologous chromosome in a closely related fish, the platyfish (Xiphophorus maculatus). We therefore conclude that the Guppy XY pair has not recently undergone an evolutionary change to a different recombination pattern, or reduced its crossover rate, but that the Guppy evolved Y-linkage due to acquiring a male-determining factor that also conferred the male crossover pattern. The results also identify the centromere ends of Guppy chromosomes, which were not determined in the Guppy genome assembly.
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locating the sex determining region of linkage group 12 of Guppy poecilia reticulata
bioRxiv, 2020Co-Authors: Deborah Charlesworth, Roberta Bergero, Jim Gardner, Chay Graham, Lengxob YongAbstract:Abstract We describe new genetic mapping results from 6 full-sib families in the Guppy (Poecilia reticulata), two of which included recombinants between the X and Y chromosomes. These recombinants confirm that the Guppy sex-determining locus is in the region identified by all previous studies, including a recent report suggesting a candidate sex-determining gene in this fish, close to the pseudo-autosomal region (or PAR) at the chromosome terminus. Our results suggest the presence of some errors in the current assembly of the Guppy genome. In males, crossing over occurs at a very high rate in the PAR, and our genetic map of the region allows us to correct the marker order. We also identified two unplaced scaffolds carrying genes that map to the PAR. Genetic mapping cannot be used to order markers in the region where crossing over is infrequent. However, our recombinant male is informative about the order, under the reasonable assumption that crossovers are infrequent. Our mapping families and natural population samples also show that the recently proposed candidate for this species’ sex-determining gene is not completely sex-linked. We detect an association between individuals’ sex and an SNP in the sex-determining region, but not with a marker 0.9 Mb away from it, suggesting that variants in this region may be in linkage disequilibrium with the actual sex-determining factor, but that the factor itself has not yet been identified. So far, no consistently male-specific variant has been identified in the Guppy sex-determining region.
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Sexually dimorphic recombination can facilitate the establishment of sexually antagonistic polymorphisms in guppies
2018Co-Authors: Roberta Bergero, Jim Gardner, Beth Ann Bader, Lengxob Yong, Deborah CharlesworthAbstract:Recombination suppression between sex chromosomes is often stated to evolve in response to polymorphisms for mutations that affect fitness of males and females in opposite directions (sexually antagonistic, or SA, mutations), but direct empirical support is lacking. The sex chromosomes of the fish Poecilia reticulata (the Guppy) carry SA polymorphisms, making them excellent for testing this hypothesis for the evolution of sex linkage. We resequenced genomes of male and female guppies and, unexpectedly, found that variants on the sex chromosome indicate no extensive region with fully sex-linked genotypes, though many variants show strong evidence for partial sex linkage. We present genetic mapping results that help understand the evolution of the Guppy sex chromosome pair. We find very different distributions of crossing over in the two sexes, with recombination events in male meiosis detected only at the tips of the chromosomes. The Guppy may exemplify a route for sex chromosome evolution in which low recombination in males, likely evolved in a common ancestor, has facilitated the establishment of sexually antagonistic polymorphisms.
Christine Dreyer - One of the best experts on this subject based on the ideXlab platform.
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adenylate cyclase 5 is required for melanophore and male pattern development in the Guppy poecilia reticulata
Pigment Cell & Melanoma Research, 2015Co-Authors: Verena A Kottler, Detlef Weigel, Margarete Hoffmann, Axel Kunstner, Iris Koch, Matthias Flotenmeyer, Tobias Langenecker, Eshita Sharma, Christine DreyerAbstract:Summary Guppies (Poecilia reticulata) are colorful fish that have attracted the attention of pigmentation researchers for almost a century. Here, we report that the blond phenotype of the Guppy is caused by a spontaneous mutation in the Guppy ortholog of adenylate cyclase 5 (adcy5). Using double digest restriction site-associated DNA sequencing (ddRADseq) and quantitative trait locus (QTL) mapping, we linked the blond phenotype to a candidate region of 118 kb, in which we subsequently identified a 2-bp deletion in adcy5 that alters splicing and leads to a premature stop codon. We show that adcy5, which affects life span and melanoma growth in mouse, is required for melanophore development and formation of male orange pigmentation traits in the Guppy. We find that some components of the male orange pattern are particularly sensitive to loss of Adcy5 function. Our work thus reveals a function for Adcy5 in patterning of fish color ornaments.
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pigment pattern formation in the Guppy poecilia reticulata involves the kita and csf1ra receptor tyrosine kinases
Genetics, 2013Co-Authors: Verena A Kottler, Andrey Fadeev, Detlef Weigel, Christine DreyerAbstract:Males of the Guppy (Poecilia reticulata) vary tremendously in their ornamental patterns, which are thought to have evolved in response to a complex interplay between natural and sexual selection. Although the selection pressures acting on the color patterns of the Guppy have been extensively studied, little is known about the genes that control their ontogeny. Over 50 years ago, two autosomal color loci, blue and golden, were described, both of which play a decisive role in the formation of the Guppy color pattern. Orange pigmentation is absent in the skin of guppies with a lesion in blue, suggesting a defect in xanthophore development. In golden mutants, the development of the melanophore pattern during embryogenesis and after birth is affected. Here, we show that blue and golden correspond to Guppy orthologs of colony-stimulating factor 1 receptor a (csf1ra; previously called fms) and kita. Most excitingly, we found that both genes are required for the development of the black ornaments of Guppy males, which in the case of csf1ra might be mediated by xanthophore–melanophore interactions. Furthermore, we provide evidence that two temporally and genetically distinct melanophore populations contribute to the adult camouflage pattern expressed in both sexes: one early appearing and kita-dependent and the other late-developing and kita-independent. The identification of csf1ra and kita mutants provides the first molecular insights into pigment pattern formation in this important model species for ecological and evolutionary genetics.
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genetic linkage map of the Guppy poecilia reticulata and quantitative trait loci analysis of male size and colour variation
Proceedings of The Royal Society B: Biological Sciences, 2009Co-Authors: Namita Tripathi, Detlef Weigel, Margarete Hoffmann, Evamaria Willing, Christa Lanz, Christine DreyerAbstract:We report construction of a genetic linkage map of the Guppy genome using 790 single nucleotide polymorphism markers, integrated from six mapping crosses. The markers define 23 linkage groups (LGs), corresponding to the known haploid number of Guppy chromosomes. The map, which spans a genetic length of 899 cM, includes 276 markers linked to expressed genes (expressed sequence tag), which have been used to derive broad syntenic relationships of Guppy LGs with medaka chromosomes. This combined linkage map should facilitate the advancement of genetic studies for a wide variety of complex adaptive phenotypes relevant to natural and sexual selection in this species. We have used the linkage data to predict quantitative trait loci for a set of variable male traits including size and colour pattern. Contributing loci map to the sex LG for many of these traits.
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opsin gene duplication and diversification in the Guppy a model for sexual selection
Proceedings of The Royal Society B: Biological Sciences, 2007Co-Authors: Margarete Hoffmann, Felix Breden, Detlef Weigel, Namita Tripathi, Stefan R Henz, Anna K Lindholm, Christine DreyerAbstract:Identification of genes that control variation in adaptive characters is a prerequisite for understanding the processes that drive sexual and natural selection. Male coloration and female colour perception play important roles in mate choice in the Guppy (Poecilia reticulata), a model organism for studies of natural and sexual selection. We examined a potential source for the known variation in colour perception, by analysing genomic and complementary DNA sequences of genes that code for visual pigment proteins. We find high sequence variability, both within and between populations, and expanded copy number for long-wave sensitive (LWS) opsin genes. Alleles with non-synonymous changes that suggest dissimilar spectral tuning properties occur in the same population and even in the same individual, and the high frequency of non-synonymous substitutions argues for diversifying selection acting on these proteins. Therefore, variability in tuning amino acids is partitioned within individuals and populations of the Guppy, in contrast to variability for LWS at higher taxonomic levels in cichlids, a second model system for differentiation owing to sexual selection. Since opsin variability parallels the extreme male colour polymorphism within Guppy populations, we suggest that mate choice has been a major factor driving the coevolution of opsins and male ornaments in this species.
Verena A Kottler - One of the best experts on this subject based on the ideXlab platform.
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improved reference genome uncovers novel sex linked regions in the Guppy poecilia reticulata
Genome Biology and Evolution, 2020Co-Authors: Bonnie A Fraser, Roberta Bergero, Deborah Charlesworth, James R Whiting, Josephine R Paris, Cameron J Weadick, Paul J Parsons, Felix Bemm, Margarete Hoffmann, Verena A KottlerAbstract:Theory predicts that the sexes can achieve greater fitness if loci with sexually antagonistic polymorphisms become linked to the sex determining loci, and this can favour the spread of reduced recombination around sex determining regions. Given that sex-linked regions are frequently repetitive and highly heterozygous, few complete Y chromosome assemblies are available to test these ideas. The Guppy system (Poecilia reticulata) has long been invoked as an example of sex chromosome formation resulting from sexual conflict. Early genetics studies revealed that male colour patterning genes are mostly but not entirely Y-linked, and that X-linkage may be most common in low predation populations. More recent population genomic studies of guppies have reached varying conclusions about the size and placement of the Y-linked region. However, this previous work used a reference genome assembled from short-read sequences from a female Guppy. Here, we present a new Guppy reference genome assembly from a male, using long-read PacBio single-molecule real-time sequencing (SMRT) and chromosome contact information. Our new assembly sequences across repeat- and GC-rich regions and thus closes gaps and corrects mis-assemblies found in the short-read female-derived Guppy genome. Using this improved reference genome, we then employed broad population sampling to detect sex differences across the genome. We identified two small regions that showed consistent male-specific signals. Moreover, our results help reconcile the contradictory conclusions put forth by past population genomic studies of the Guppy sex chromosome. Our results are consistent with a small Y-specific region and rare recombination in male guppies.
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adenylate cyclase 5 is required for melanophore and male pattern development in the Guppy poecilia reticulata
Pigment Cell & Melanoma Research, 2015Co-Authors: Verena A Kottler, Detlef Weigel, Margarete Hoffmann, Axel Kunstner, Iris Koch, Matthias Flotenmeyer, Tobias Langenecker, Eshita Sharma, Christine DreyerAbstract:Summary Guppies (Poecilia reticulata) are colorful fish that have attracted the attention of pigmentation researchers for almost a century. Here, we report that the blond phenotype of the Guppy is caused by a spontaneous mutation in the Guppy ortholog of adenylate cyclase 5 (adcy5). Using double digest restriction site-associated DNA sequencing (ddRADseq) and quantitative trait locus (QTL) mapping, we linked the blond phenotype to a candidate region of 118 kb, in which we subsequently identified a 2-bp deletion in adcy5 that alters splicing and leads to a premature stop codon. We show that adcy5, which affects life span and melanoma growth in mouse, is required for melanophore development and formation of male orange pigmentation traits in the Guppy. We find that some components of the male orange pattern are particularly sensitive to loss of Adcy5 function. Our work thus reveals a function for Adcy5 in patterning of fish color ornaments.
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pigment pattern formation in the Guppy poecilia reticulata involves the kita and csf1ra receptor tyrosine kinases
Genetics, 2013Co-Authors: Verena A Kottler, Andrey Fadeev, Detlef Weigel, Christine DreyerAbstract:Males of the Guppy (Poecilia reticulata) vary tremendously in their ornamental patterns, which are thought to have evolved in response to a complex interplay between natural and sexual selection. Although the selection pressures acting on the color patterns of the Guppy have been extensively studied, little is known about the genes that control their ontogeny. Over 50 years ago, two autosomal color loci, blue and golden, were described, both of which play a decisive role in the formation of the Guppy color pattern. Orange pigmentation is absent in the skin of guppies with a lesion in blue, suggesting a defect in xanthophore development. In golden mutants, the development of the melanophore pattern during embryogenesis and after birth is affected. Here, we show that blue and golden correspond to Guppy orthologs of colony-stimulating factor 1 receptor a (csf1ra; previously called fms) and kita. Most excitingly, we found that both genes are required for the development of the black ornaments of Guppy males, which in the case of csf1ra might be mediated by xanthophore–melanophore interactions. Furthermore, we provide evidence that two temporally and genetically distinct melanophore populations contribute to the adult camouflage pattern expressed in both sexes: one early appearing and kita-dependent and the other late-developing and kita-independent. The identification of csf1ra and kita mutants provides the first molecular insights into pigment pattern formation in this important model species for ecological and evolutionary genetics.
Lengxob Yong - One of the best experts on this subject based on the ideXlab platform.
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using gc content to compare recombination patterns on the sex chromosomes and autosomes of the Guppy poecilia reticulata and its close outgroup species
Molecular Biology and Evolution, 2020Co-Authors: Deborah Charlesworth, Roberta Bergero, Jim Gardner, Yexin Zhang, Chay Graham, Lengxob YongAbstract:Genetic and physical mapping of the Guppy (P. reticulata) have shown that recombination patterns differ greatly between males and females. Crossover events occur evenly across the chromosomes in females, but in male meiosis they are restricted to the tip furthest from the centromere of each chromosome, creating very high recombination rates per megabase, as in pseudo-autosomal regions (PARs) of mammalian sex chromosomes. We used GC content to indirectly infer recombination patterns on Guppy chromosomes, based on evidence that recombination is associated with GC-biased gene conversion, so that genome regions with high recombination rates should be detectable by high GC content. We used intron sequences and 3rd positions of codons to make comparisons between sequences that are matched, as far as possible, and are all probably under weak selection. Almost all Guppy chromosomes, including the sex chromosome (LG12), have very high GC values near their assembly ends, suggesting high recombination rates due to strong crossover localisation in male meiosis. Our test does not suggest that the Guppy XY pair has stronger crossover localisation than the autosomes, or than the homologous chromosome in the close relative, the platyfish (Xiphophorus maculatus). We therefore conclude that the Guppy XY pair has not recently undergone an evolutionary change to a different recombination pattern, or reduced its crossover rate, but that the Guppy evolved Y-linkage due to acquiring a male-determining factor that also conferred the male crossover pattern. We also identify the centromere ends of Guppy chromosomes, which were not determined in the genome assembly.
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using gc content to compare recombination patterns on the sex chromosomes and autosomes of the Guppy poecilia reticulata and its close outgroup species
bioRxiv, 2020Co-Authors: Deborah Charlesworth, Roberta Bergero, Jim Gardner, Yexin Zhang, Chay Graham, Lengxob YongAbstract:Summary/AbstractGenetic and physical mapping of the Guppy (P. reticulata) have shown that recombination patterns differ greatly between males and females. Crossover events occur evenly across the chromosomes in females, but in male meiosis they are restricted to the tip furthest from the centromere of each chromosome, creating very high recombination rates per megabase, similar to the high rates in mammalian sex chromosomes pseudo-autosomal regions (PARs). We here used the intronic GC content to indirectly infer the recombination patterns on Guppy chromosomes. This is based on evidence that recombination is associated with GC-biased gene conversion, so that genome regions with high recombination rates should be detectable by high GC content. Using intron sequences, which are likely to be under weak selection, we show that almost all Guppy chromosomes, including the sex chromosome (LG12) have very high GC values near their assembly ends, suggesting high recombination rates due to strong crossover localisation in male meiosis. Our test does not suggest that the Guppy XY pair has stronger crossover localisation than the autosomes, or than the homologous chromosome in a closely related fish, the platyfish (Xiphophorus maculatus). We therefore conclude that the Guppy XY pair has not recently undergone an evolutionary change to a different recombination pattern, or reduced its crossover rate, but that the Guppy evolved Y-linkage due to acquiring a male-determining factor that also conferred the male crossover pattern. The results also identify the centromere ends of Guppy chromosomes, which were not determined in the Guppy genome assembly.
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locating the sex determining region of linkage group 12 of Guppy poecilia reticulata
bioRxiv, 2020Co-Authors: Deborah Charlesworth, Roberta Bergero, Jim Gardner, Chay Graham, Lengxob YongAbstract:Abstract We describe new genetic mapping results from 6 full-sib families in the Guppy (Poecilia reticulata), two of which included recombinants between the X and Y chromosomes. These recombinants confirm that the Guppy sex-determining locus is in the region identified by all previous studies, including a recent report suggesting a candidate sex-determining gene in this fish, close to the pseudo-autosomal region (or PAR) at the chromosome terminus. Our results suggest the presence of some errors in the current assembly of the Guppy genome. In males, crossing over occurs at a very high rate in the PAR, and our genetic map of the region allows us to correct the marker order. We also identified two unplaced scaffolds carrying genes that map to the PAR. Genetic mapping cannot be used to order markers in the region where crossing over is infrequent. However, our recombinant male is informative about the order, under the reasonable assumption that crossovers are infrequent. Our mapping families and natural population samples also show that the recently proposed candidate for this species’ sex-determining gene is not completely sex-linked. We detect an association between individuals’ sex and an SNP in the sex-determining region, but not with a marker 0.9 Mb away from it, suggesting that variants in this region may be in linkage disequilibrium with the actual sex-determining factor, but that the factor itself has not yet been identified. So far, no consistently male-specific variant has been identified in the Guppy sex-determining region.
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Sexually dimorphic recombination can facilitate the establishment of sexually antagonistic polymorphisms in guppies
2018Co-Authors: Roberta Bergero, Jim Gardner, Beth Ann Bader, Lengxob Yong, Deborah CharlesworthAbstract:Recombination suppression between sex chromosomes is often stated to evolve in response to polymorphisms for mutations that affect fitness of males and females in opposite directions (sexually antagonistic, or SA, mutations), but direct empirical support is lacking. The sex chromosomes of the fish Poecilia reticulata (the Guppy) carry SA polymorphisms, making them excellent for testing this hypothesis for the evolution of sex linkage. We resequenced genomes of male and female guppies and, unexpectedly, found that variants on the sex chromosome indicate no extensive region with fully sex-linked genotypes, though many variants show strong evidence for partial sex linkage. We present genetic mapping results that help understand the evolution of the Guppy sex chromosome pair. We find very different distributions of crossing over in the two sexes, with recombination events in male meiosis detected only at the tips of the chromosomes. The Guppy may exemplify a route for sex chromosome evolution in which low recombination in males, likely evolved in a common ancestor, has facilitated the establishment of sexually antagonistic polymorphisms.
Roberta Bergero - One of the best experts on this subject based on the ideXlab platform.
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improved reference genome uncovers novel sex linked regions in the Guppy poecilia reticulata
Genome Biology and Evolution, 2020Co-Authors: Bonnie A Fraser, Roberta Bergero, Deborah Charlesworth, James R Whiting, Josephine R Paris, Cameron J Weadick, Paul J Parsons, Felix Bemm, Margarete Hoffmann, Verena A KottlerAbstract:Theory predicts that the sexes can achieve greater fitness if loci with sexually antagonistic polymorphisms become linked to the sex determining loci, and this can favour the spread of reduced recombination around sex determining regions. Given that sex-linked regions are frequently repetitive and highly heterozygous, few complete Y chromosome assemblies are available to test these ideas. The Guppy system (Poecilia reticulata) has long been invoked as an example of sex chromosome formation resulting from sexual conflict. Early genetics studies revealed that male colour patterning genes are mostly but not entirely Y-linked, and that X-linkage may be most common in low predation populations. More recent population genomic studies of guppies have reached varying conclusions about the size and placement of the Y-linked region. However, this previous work used a reference genome assembled from short-read sequences from a female Guppy. Here, we present a new Guppy reference genome assembly from a male, using long-read PacBio single-molecule real-time sequencing (SMRT) and chromosome contact information. Our new assembly sequences across repeat- and GC-rich regions and thus closes gaps and corrects mis-assemblies found in the short-read female-derived Guppy genome. Using this improved reference genome, we then employed broad population sampling to detect sex differences across the genome. We identified two small regions that showed consistent male-specific signals. Moreover, our results help reconcile the contradictory conclusions put forth by past population genomic studies of the Guppy sex chromosome. Our results are consistent with a small Y-specific region and rare recombination in male guppies.
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using gc content to compare recombination patterns on the sex chromosomes and autosomes of the Guppy poecilia reticulata and its close outgroup species
Molecular Biology and Evolution, 2020Co-Authors: Deborah Charlesworth, Roberta Bergero, Jim Gardner, Yexin Zhang, Chay Graham, Lengxob YongAbstract:Genetic and physical mapping of the Guppy (P. reticulata) have shown that recombination patterns differ greatly between males and females. Crossover events occur evenly across the chromosomes in females, but in male meiosis they are restricted to the tip furthest from the centromere of each chromosome, creating very high recombination rates per megabase, as in pseudo-autosomal regions (PARs) of mammalian sex chromosomes. We used GC content to indirectly infer recombination patterns on Guppy chromosomes, based on evidence that recombination is associated with GC-biased gene conversion, so that genome regions with high recombination rates should be detectable by high GC content. We used intron sequences and 3rd positions of codons to make comparisons between sequences that are matched, as far as possible, and are all probably under weak selection. Almost all Guppy chromosomes, including the sex chromosome (LG12), have very high GC values near their assembly ends, suggesting high recombination rates due to strong crossover localisation in male meiosis. Our test does not suggest that the Guppy XY pair has stronger crossover localisation than the autosomes, or than the homologous chromosome in the close relative, the platyfish (Xiphophorus maculatus). We therefore conclude that the Guppy XY pair has not recently undergone an evolutionary change to a different recombination pattern, or reduced its crossover rate, but that the Guppy evolved Y-linkage due to acquiring a male-determining factor that also conferred the male crossover pattern. We also identify the centromere ends of Guppy chromosomes, which were not determined in the genome assembly.
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using gc content to compare recombination patterns on the sex chromosomes and autosomes of the Guppy poecilia reticulata and its close outgroup species
bioRxiv, 2020Co-Authors: Deborah Charlesworth, Roberta Bergero, Jim Gardner, Yexin Zhang, Chay Graham, Lengxob YongAbstract:Summary/AbstractGenetic and physical mapping of the Guppy (P. reticulata) have shown that recombination patterns differ greatly between males and females. Crossover events occur evenly across the chromosomes in females, but in male meiosis they are restricted to the tip furthest from the centromere of each chromosome, creating very high recombination rates per megabase, similar to the high rates in mammalian sex chromosomes pseudo-autosomal regions (PARs). We here used the intronic GC content to indirectly infer the recombination patterns on Guppy chromosomes. This is based on evidence that recombination is associated with GC-biased gene conversion, so that genome regions with high recombination rates should be detectable by high GC content. Using intron sequences, which are likely to be under weak selection, we show that almost all Guppy chromosomes, including the sex chromosome (LG12) have very high GC values near their assembly ends, suggesting high recombination rates due to strong crossover localisation in male meiosis. Our test does not suggest that the Guppy XY pair has stronger crossover localisation than the autosomes, or than the homologous chromosome in a closely related fish, the platyfish (Xiphophorus maculatus). We therefore conclude that the Guppy XY pair has not recently undergone an evolutionary change to a different recombination pattern, or reduced its crossover rate, but that the Guppy evolved Y-linkage due to acquiring a male-determining factor that also conferred the male crossover pattern. The results also identify the centromere ends of Guppy chromosomes, which were not determined in the Guppy genome assembly.
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locating the sex determining region of linkage group 12 of Guppy poecilia reticulata
bioRxiv, 2020Co-Authors: Deborah Charlesworth, Roberta Bergero, Jim Gardner, Chay Graham, Lengxob YongAbstract:Abstract We describe new genetic mapping results from 6 full-sib families in the Guppy (Poecilia reticulata), two of which included recombinants between the X and Y chromosomes. These recombinants confirm that the Guppy sex-determining locus is in the region identified by all previous studies, including a recent report suggesting a candidate sex-determining gene in this fish, close to the pseudo-autosomal region (or PAR) at the chromosome terminus. Our results suggest the presence of some errors in the current assembly of the Guppy genome. In males, crossing over occurs at a very high rate in the PAR, and our genetic map of the region allows us to correct the marker order. We also identified two unplaced scaffolds carrying genes that map to the PAR. Genetic mapping cannot be used to order markers in the region where crossing over is infrequent. However, our recombinant male is informative about the order, under the reasonable assumption that crossovers are infrequent. Our mapping families and natural population samples also show that the recently proposed candidate for this species’ sex-determining gene is not completely sex-linked. We detect an association between individuals’ sex and an SNP in the sex-determining region, but not with a marker 0.9 Mb away from it, suggesting that variants in this region may be in linkage disequilibrium with the actual sex-determining factor, but that the factor itself has not yet been identified. So far, no consistently male-specific variant has been identified in the Guppy sex-determining region.
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Sexually dimorphic recombination can facilitate the establishment of sexually antagonistic polymorphisms in guppies
2018Co-Authors: Roberta Bergero, Jim Gardner, Beth Ann Bader, Lengxob Yong, Deborah CharlesworthAbstract:Recombination suppression between sex chromosomes is often stated to evolve in response to polymorphisms for mutations that affect fitness of males and females in opposite directions (sexually antagonistic, or SA, mutations), but direct empirical support is lacking. The sex chromosomes of the fish Poecilia reticulata (the Guppy) carry SA polymorphisms, making them excellent for testing this hypothesis for the evolution of sex linkage. We resequenced genomes of male and female guppies and, unexpectedly, found that variants on the sex chromosome indicate no extensive region with fully sex-linked genotypes, though many variants show strong evidence for partial sex linkage. We present genetic mapping results that help understand the evolution of the Guppy sex chromosome pair. We find very different distributions of crossing over in the two sexes, with recombination events in male meiosis detected only at the tips of the chromosomes. The Guppy may exemplify a route for sex chromosome evolution in which low recombination in males, likely evolved in a common ancestor, has facilitated the establishment of sexually antagonistic polymorphisms.