Papers by Roberta Bergero
Alignment of gene cs4991 in fasta format
SSRN Electronic Journal, 2019
Turnovers of sex chromosomes — where an ancestral sex-determining region is replaced by a new one... more Turnovers of sex chromosomes — where an ancestral sex-determining region is replaced by a new one, or moves to a new genomic location, often on a different chromosome — have rarely been studied within a phylogenetic context that allows the ancestral states to be inferred. Here we compare three closely related species of the fish genus Poecilia, P. reticulata (the guppy), P. picta and P. parae, which reveals that the guppy Y chromosome evolved from an ancestral X chromosome, the first documented case of an X chromosome evolving to become a new Y chromosome. We show that the sex determining locus in all three species is carried on the same chromosome, chromosome 12 in P. reticulata. However, whereas the guppy Y chromosome retains essentially all genes found on the X chromosome, P. picta’s Y chromosome has lost most of them, and is highly degenerated. The few X-linked genes that have retained detectable Y copies in P. picta are almost all homologues of guppy pseudo-autosomal genes. Microsatellite genotyping shows that P. parae also has a degenerated Y chromosome. The guppy Y chromosome must therefore have evolved from an ancestral X chromosome after the split from P. picta and P. parae. Another close relative, the platyfish, must also descend from the same ancestor with a highly degenerated Y chromosome, and its sex chromosome pair is an autosome in both the guppy and P. picta. This evidence for repeated and independent changes supports a role for genetic degeneration in sex chromosome turnovers.
Proceedings of the National Academy of Sciences, 2019
Giornale botanico italiano, 1994
Mycologia, 1997
... Roberta Bergero Giorgio Buffa Anna Maria Luppi-Mosca Dipartimento di Biologia vegetale dell&a... more ... Roberta Bergero Giorgio Buffa Anna Maria Luppi-Mosca Dipartimento di Biologia vegetale dell'Universitd di Torino, Vile Mattioli 25, 10125 Torino, Italy ... Bisset and Parkinson, 1980; Maggi et al., 1990; Ram-belli et al., 1983; Tiwari and Rai, 1977; Wicklow, 1973, 1978; Wicklow ...
Molecular Biology and Evolution, 2009
Molecular Biology and Evolution, 2010
Patterns of codon usage bias (CUB) convey useful information about the selection on synonymous co... more Patterns of codon usage bias (CUB) convey useful information about the selection on synonymous codons induced by gene expression and contribute to an understanding of substitution patterns observed at synonymous sites. They can also be informative about the distinctive evolutionary properties of sex chromosomes such as genetic degeneration of the Y chromosome, dosage compensation, and hemizygosity of the X chromosome in males, which can affect the selection on codon usage. Here, we study CUB in Silene latifolia, a species of interest for studying the early stages of sex chromosome evolution. We have obtained a large expressed sequence tag data set containing more than 1,608 sequence fragments by 454 sequencing. Using three different methods, we conservatively define 21 preferred codons. Interestingly, the preferred codons in S. latifolia are almost identical to those in Arabidopsis thaliana, despite their long divergence time (we estimate average nonsynonymous site divergence to be 0.216, and synonymous sites are saturated). The agreement suggests that the nature of selection on codon usage has not changed significantly during the long evolutionary time separating the two species. As in many other organisms, the frequency of preferred codons is negatively correlated with protein length. For the 43 genes with both exon and intron sequences, we find a positive correlation between gene expression levels and GC content at third codon positions, but a strong negative correlation between expression and intron GC content, suggesting that the CUB we detect in S. latifolia is more likely to be due to natural selection than to mutational bias. Using polymorphism data, we detect evidence of ongoing natural selection on CUB, but we find little support for effects of biased gene conversion. An analysis of ten sex-linked genes reveals that the X chromosome has experienced significantly more unpreferred to preferred than preferred to unpreferred substitutions, suggesting that it may be evolving higher CUB. In contrast, numbers of substitutions between preferred and unpreferred codons are similar in both directions in the Y-linked genes, contrary to the expectation of genetic degeneration.
Genetics, 2007
Despite its recent evolutionary origin, the sex chromosome system of the plant Silene latifolia s... more Despite its recent evolutionary origin, the sex chromosome system of the plant Silene latifolia shows signs of progressive suppression of recombination having created evolutionary strata of different X–Y divergence on sex chromosomes. However, even after 8 years of effort, this result is based on analyses of five sex-linked gene sequences, and the maximum divergence (and thus the age of this plant's sex chromosome system) has remained uncertain. More genes are therefore needed. Here, by segregation analysis of intron size variants (ISVS) and single nucleotide polymorphisms (SNPs), we identify three new Y-linked genes, one being duplicated on the Y chromosome, and test for evolutionary strata. All the new genes have homologs on the X and Y chromosomes. Synonymous divergence estimated between the X and Y homolog pairs is within the range of those already reported. Genetic mapping of the new X-linked loci shows that the map is the same in all three families that have been studied s...
Genetics, 2008
Mechanisms involved in eroding fitness of evolving Y chromosomes have been the focus of much theo... more Mechanisms involved in eroding fitness of evolving Y chromosomes have been the focus of much theoretical and empirical work. Evolving Y chromosomes are expected to accumulate transposable elements (TEs), but it is not known whether such accumulation contributes to their genetic degeneration. Among TEs, miniature inverted-repeat transposable elements are nonautonomous DNA transposons, often inserted in introns and untranslated regions of genes. Thus, if they invade Y-linked genes and selection against their insertion is ineffective, they could contribute to genetic degeneration of evolving Y chromosomes. Here, we examine the population dynamics of active MITEs in the young Y chromosomes of the plant Silene latifolia and compare their distribution with those in recombining genomic regions. To isolate active MITEs, we developed a straightforward approach on the basis of the assumption that recent transposon insertions or excisions create singleton or low-frequency size polymorphisms th...
PLOS Genetics, 2021
The sex chromosome pairs of many species do not undergo genetic recombination, unlike the autosom... more The sex chromosome pairs of many species do not undergo genetic recombination, unlike the autosomes. It has been proposed that the suppressed recombination results from natural selection favouring close linkage between sex-determining genes and mutations on this chromosome with advantages in one sex, but disadvantages in the other (these are called sexually antagonistic mutations). No example of such selection leading to suppressed recombination has been described, but populations of the guppy display sexually antagonistic mutations (affecting male coloration), and would be expected to evolve suppressed recombination. In extant close relatives of the guppy, the Y chromosomes have suppressed recombination, and have lost all the genes present on the X (this is called genetic degeneration). However, the guppy Y occasionally recombines with its X, despite carrying sexually antagonistic mutations. We describe evidence that a new Y evolved recently in the guppy, from an X chromosome like ...
Biological Reviews
The version in the Kent Academic Repository may differ from the final published version. Users ar... more The version in the Kent Academic Repository may differ from the final published version. Users are advised to check http://kar.kent.ac.uk for the status of the paper. Users should always cite the published version of record.
Genome Biology and Evolution
Theory predicts that the sexes can achieve greater fitness if loci with sexually antagonistic pol... more 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 assembl...
Summary/Genetic and physical mapping of the guppy (P. reticulata) have shown that recombination p... more Summary/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, 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 cro...
G3: Genes|Genomes|Genetics
Despite over 100 years of study, the location of the fully sex-linked region of the guppy (Poecil... more Despite over 100 years of study, the location of the fully sex-linked region of the guppy (Poecilia reticulata) carrying the male-determining locus, and the regions where the XY pair recombine, remain unclear. Previous population genomics studies to determine these regions used small samples from recently bottlenecked captive populations, which increase the false positive rate of associations between individuals' sexes and SNPs. Using new data from multiple natural populations, we show that a recently proposed candidate for this species' male-determining gene is probably not completely sex-linked, leaving the maleness factor still unidentified. Variants in the chromosome 12 region carrying the candidate gene sometimes show linkage disequilibrium with the sex-determining factor, but no consistently male-specific variant has yet been found. Our genetic mapping with molecular markers spread across chromosome 12 confirms that this is the guppy XY pair. We describe two families w...
We describe new genetic mapping results from 6 full-sib families in the guppy (Poecilia reticulat... more 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 an...
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Papers by Roberta Bergero