scholarly journals Linked-Read Sequencing of Eight Falcons Reveals a Unique Genomic Architecture in Flux

2022 ◽  
Author(s):  
Justin Wilcox ◽  
Barbara Arca-Ruibal ◽  
Jaime Samour ◽  
Victor Mateuta ◽  
Youssef Idaghdour ◽  
...  
Keyword(s):  
Gene Conversion ◽  
Chromosomal Rearrangements ◽  
Gc Content ◽  
Chromosome Counts ◽  
Small Indels ◽  
Peregrine Falcons ◽  
Biased Gene Conversion ◽  
Saker Falcon ◽  
The Common ◽  
Interspersed Repeats

Falcons are diverse birds of cultural and economic importance. They have undergone major lineage specific chromosomal rearrangements, resulting in greatly-reduced chromosome counts relative to other birds. Here, we use 10X Genomics linked reads to provide new high-contiguity genomes for two gyrfalcons, a saker falcon, a lanner falcon, three subspecies of peregrine falcons, and the common kestrel. Assisted by a transcriptome sequenced from 22 gyrfalcon tissues, we annotate these genomes for a variety of genomic features, estimate historical demography, and then investigate genomic equilibrium in the context of falcon-specific chromosomal rearrangements. We find that falcon genomes are not in AT-GC equilibrium with a bias in mutations towards higher AT content; this bias is predominantly driven by, but not dependent on, hypermutability of CpG sites. Small indels and large structural variants were also biased towards insertions rather than deletions. Patterns of disequilibrium were linked to chromosomal rearrangements: falcons have lost GC content in regions that have fused to larger chromosomes from microchromosomes and gained GC content in regions of macrochromosomes that have translocated to microchromosomes. Inserted bases have accumulated on regions ancestrally belonging to microchromosomes, consistent with insertion-biased gene conversion. We also find an excess of interspersed repeats on regions of microchromosomes that have fused to macrochromosomes. Our results reveal that falcon genomes are in a state of flux. They further suggest that many of the key differences between microchromosomes and macrochromosomes are driven by differences in chromosome size, and indicate a clear role for recombination and biased gene conversion in determining genomic equilibrium.

scholarly journals Evidence for strong fixation bias at 4-fold degenerate sites across genes in the great tit genome

2018 ◽  
Author(s):  
Toni I. Gossmann ◽  
Mathias Bockwoldt ◽  
Lilith Diringer ◽  
Friedrich Schwarz ◽  
Vic-Fabienne Schumann
Keyword(s):  
Gene Conversion ◽  
Sequence Data ◽  
Bird Species ◽  
Gc Content ◽  
Great Tit ◽  
Genomic Features ◽  
Conversion Rates ◽  
Biased Gene Conversion ◽  
The Impact ◽  
Fixation Bias

ABSTRACTIt is well established that GC content varies across the genome in many species and that GC biased gene conversion, one form of meiotic recombination, is likely to contribute to this heterogeneity. Bird genomes provide an extraordinary system to study the impact of GC biased gene conversion owed to their specific genomic features. They are characterised by a high karyotype conservation with substantial heterogeneity in chromosome sizes, with up to a dozen large macrochromosomes and many smaller microchromosomes common across all bird species. This heterogeneity in chromosome morphology is also reflected by other genomic features, such as smaller chromosomes being gene denser, more compact and more GC rich relative to their macrochromosomal counterparts - illustrating that the intensity of GC biased gene conversion varies across the genome. Here we study whether it is possible to infer heterogeneity in GC biased gene conversion rates across the genome using a recently published method that accounts for GC biased gene conversion when estimating branch lengths in a phylogenetic context. To infer the strength of GC biased gene conversion we contrast branch length estimates across the genome both taking and not taking non-stationary GC composition into account. Using simulations we show that this approach works well when GC fixation bias is strong and note that the number of substitutions along a branch is consistently overestimated when GC biased gene conversion is not accounted for. We use this predictable feature to infer the strength of GC dynamics across the great tit genome by applying our new test statistic to data at 4-fold degenerate sites from three bird species - great tit, zebra finch and chicken - three species that are among the best annotated bird genomes to date. We show that using a simple one-dimensional binning we fail to capture a signal of fixation bias as observed in our simulations. However, using a multidimensional binning strategy, we find evidence for heterogeneity in the strength of fixation bias, including AT fixation bias. This highlights the difficulties when combining sequence data across different regions in the genome.

scholarly journals GC-biased gene conversion in X-Chromosome palindromes conserved in human, chimpanzee, and rhesus macaque

2021 ◽  
Author(s):  
Emily K Jackson ◽  
Daniel W. Bellott ◽  
Helen Skaletsky ◽  
David C. Page
Keyword(s):  
Rhesus Macaque ◽  
Gene Conversion ◽  
X Chromosome ◽  
Sex Chromosome ◽  
Gc Content ◽  
Single Copy ◽  
Flanking Sequence ◽  
X Chromosomes ◽  
Wide Range ◽  
Biased Gene Conversion

Gene conversion is GC-biased across a wide range of taxa. Large palindromes on mammalian sex chromosomes undergo frequent gene conversion that maintains arm-to-arm sequence identity greater than 99%, which may increase their susceptibility to the effects of GC-biased gene conversion. Here, we demonstrate a striking history of GC-biased gene conversion in 12 palindromes conserved on the X chromosomes of human, chimpanzee, and rhesus macaque. Primate X-chromosome palindrome arms have significantly higher GC content than flanking single-copy sequences. Nucleotide replacements that occurred in human and chimpanzee palindrome arms over the past 7 million years are one-and-a-half times as GC-rich than the ancestral bases they replaced. Using simulations, we show that our observed pattern of nucleotide replacements is consistent with GC-biased gene conversion with a magnitude of 70%, similar to previously reported values based on analyses of human meioses. However, GC-biased gene conversion explains only a fraction of the observed difference in GC content between palindrome arms and flanking sequence, suggesting that additional factors are required to explain elevated GC content in palindrome arms. This work supports a greater than 2:1 preference for GC bases over AT bases during gene conversion, and demonstrates that the evolution and composition of mammalian sex chromosome palindromes is strongly influenced by GC-biased gene conversion.

scholarly journals Biased Gene Conversion and GC-Content Evolution in the Coding Sequences of Reptiles and Vertebrates

2014 ◽  
Vol 7 (1) ◽  
pp. 240-250 ◽  
Author(s):  
Emeric Figuet ◽  
Marion Ballenghien ◽  
Jonathan Romiguier ◽  
Nicolas Galtier
Keyword(s):  
Gene Conversion ◽  
Gc Content ◽  
Coding Sequences ◽  
Biased Gene Conversion

scholarly journals GC-Content Evolution in Bacterial Genomes: The Biased Gene Conversion Hypothesis Expands

PLoS Genetics ◽  
2015 ◽  
Vol 11 (2) ◽  
pp. e1004941 ◽  
Author(s):  
Florent Lassalle ◽  
Séverine Périan ◽  
Thomas Bataillon ◽  
Xavier Nesme ◽  
Laurent Duret ◽  
...  
Keyword(s):  
Gene Conversion ◽  
Gc Content ◽  
Bacterial Genomes ◽  
Biased Gene Conversion

scholarly journals GC-Biased Gene Conversion and Selection Affect GC Content in the Oryza Genus (rice)

2011 ◽  
Vol 28 (9) ◽  
pp. 2695-2706 ◽  
Author(s):  
Aline Muyle ◽  
Laurana Serres-Giardi ◽  
Adrienne Ressayre ◽  
Juan Escobar ◽  
Sylvain Glémin
Keyword(s):  
Gene Conversion ◽  
Gc Content ◽  
Biased Gene Conversion

scholarly journals GC-Content Evolution in Mammalian Genomes: The Biased Gene Conversion Hypothesis

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 907-911 ◽  
Author(s):  
N Galtier ◽  
G Piganeau ◽  
D Mouchiroud ◽  
L Duret
Keyword(s):  
Gene Conversion ◽  
Gc Content ◽  
Biased Gene Conversion ◽  
Mammalian Genomes

scholarly journals GC-biased gene conversion in X-chromosome palindromes conserved in human, chimpanzee, and rhesus macaque

2021 ◽  
Author(s):  
Emily K Jackson ◽  
Daniel W Bellott ◽  
Helen Skaletsky ◽  
David C Page
Keyword(s):  
Rhesus Macaque ◽  
Gene Conversion ◽  
X Chromosome ◽  
Sex Chromosome ◽  
Gc Content ◽  
Single Copy ◽  
Flanking Sequence ◽  
X Chromosomes ◽  
Wide Range ◽  
Biased Gene Conversion

Abstract Gene conversion is GC-biased across a wide range of taxa. Large palindromes on mammalian sex chromosomes undergo frequent gene conversion that maintains arm-to-arm sequence identity greater than 99%, which may increase their susceptibility to the effects of GC-biased gene conversion. Here, we demonstrate a striking history of GC-biased gene conversion in 12 palindromes conserved on the X chromosomes of human, chimpanzee, and rhesus macaque. Primate X-chromosome palindrome arms have significantly higher GC content than flanking single-copy sequences. Nucleotide replacements that occurred in human and chimpanzee palindrome arms over the past 7 million years are one-and-a-half times as GC-rich as the ancestral bases they replaced. Using simulations, we show that our observed pattern of nucleotide replacements is consistent with GC-biased gene conversion with a magnitude of 70%, similar to previously reported values based on analyses of human meioses. However, GC-biased gene conversion since the divergence of human and rhesus macaque explains only a fraction of the observed difference in GC content between palindrome arms and flanking sequence, suggesting that palindromes are older than 29 million years and/or had elevated GC content at the time of their formation. This work supports a greater than 2:1 preference for GC bases over AT bases during gene conversion, and demonstrates that the evolution and composition of mammalian sex chromosome palindromes is strongly influenced by GC-biased gene conversion.

scholarly journals Evidence for a force favoring GC over AT at short intronic sites in Drosophila simulans and D. melanogaster

2021 ◽  
Author(s):  
Ben Jackson ◽  
Brian Charlesworth
Keyword(s):  
Gene Conversion ◽  
Direct Evidence ◽  
Natural Populations ◽  
Gc Content ◽  
Spontaneous Mutations ◽  
Selective Pressures ◽  
Use Of Data ◽  
Large Numbers ◽  
Biased Gene Conversion ◽  
Long Timescales

Abstract Population genetics studies often make use of a class of nucleotide site free from selective pressures, in order to make inferences about population size changes or natural selection at other sites. If such neutral sites can be identified, they offer the opportunity to avoid any confounding effects of selection. Here we investigate evolution at putatively neutrally evolving short intronic sites in natural populations of Drosophila melanogaster and D. simulans, in order to understand the properties of spontaneous mutations and the extent of GC-biased gene conversion in these species. Use of data on the genetics of natural populations is advantageous because it integrates information from large numbers of individuals over long timescales. In agreement with direct evidence from observations of spontaneous mutations in Drosophila, we find a bias in the spectrum of mutations towards AT basepairs. In addition, we find that this bias is stronger in the D. melanogaster lineage than in the D. simulans lineage. The evidence for GC-biased gene conversion in Drosophila has been equivocal. Here we provide evidence for a weak force favoring GC in both species, which is correlated with the GC content of introns and is stronger in D. simulans than in D. melanogaster.

scholarly journals The effects of GC-biased gene conversion on patterns of genetic diversity among and across butterfly genomes

2020 ◽  
Author(s):  
Jesper Boman ◽  
Carina F. Mugal ◽  
Niclas Backström
Keyword(s):  
Genetic Diversity ◽  
Gene Conversion ◽  
Gc Content ◽  
Butterfly Species ◽  
Substantial Variation ◽  
Mutation Bias ◽  
Diversity Pattern ◽  
Main Determinant ◽  
Biased Gene Conversion ◽  
Linked Selection

AbstractRecombination reshuffles the alleles of a population through crossover and gene conversion. These mechanisms have considerable consequences on the evolution and maintenance of genetic diversity. Crossover, for example, can increase genetic diversity by breaking the linkage between selected and nearby neutral variants. Bias in favor of G or C alleles during gene conversion may instead promote the fixation of one allele over the other, thus decreasing diversity. Mutation bias from G or C to A and T opposes GC-biased gene conversion (gBGC). Less recognized is that these two processes may –when balanced– promote genetic diversity. Here we investigate how gBGC and mutation bias shape genetic diversity patterns in wood white butterflies (Leptidea sp.). This constitutes the first in-depth investigation of gBGC in butterflies. Using 60 re-sequenced genomes from six populations of three species, we find substantial variation in the strength of gBGC across lineages. When modeling the balance of gBGC and mutation bias and comparing analytical results with empirical data, we reject gBGC as the main determinant of genetic diversity in these butterfly species. As alternatives, we consider linked selection and GC content. We find evidence that high values of both reduce diversity. We also show that the joint effects of gBGC and mutation bias can give rise to a diversity pattern which resembles the signature of linked selection. Consequently, gBGC should be considered when interpreting the effects of linked selection on levels of genetic diversity.

scholarly journals Evolutionary Consequences of DNA Methylation on the GC Content in Vertebrate Genomes

2015 ◽  
Vol 5 (3) ◽  
pp. 441-447 ◽  
Author(s):  
Carina F Mugal ◽  
Peter F Arndt ◽  
Lena Holm ◽  
Hans Ellegren
Keyword(s):  
Dna Methylation ◽  
Gene Conversion ◽  
Local Equilibrium ◽  
Gc Content ◽  
Strong Impact ◽  
Whole Genome ◽  
Cpg Dinucleotides ◽  
Genome Methylation ◽  
Biased Gene Conversion ◽  
The Impact

Abstract The genomes of many vertebrates show a characteristic variation in GC content. To explain its origin and evolution, mainly three mechanisms have been proposed: selection for GC content, mutation bias, and GC-biased gene conversion. At present, the mechanism of GC-biased gene conversion, i.e., short-scale, unidirectional exchanges between homologous chromosomes in the neighborhood of recombination-initiating double-strand breaks in favor for GC nucleotides, is the most widely accepted hypothesis. We here suggest that DNA methylation also plays an important role in the evolution of GC content in vertebrate genomes. To test this hypothesis, we investigated one mammalian (human) and one avian (chicken) genome. We used bisulfite sequencing to generate a whole-genome methylation map of chicken sperm and made use of a publicly available whole-genome methylation map of human sperm. Inclusion of these methylation maps into a model of GC content evolution provided significant support for the impact of DNA methylation on the local equilibrium GC content. Moreover, two different estimates of equilibrium GC content, one that neglects and one that incorporates the impact of DNA methylation and the concomitant CpG hypermutability, give estimates that differ by approximately 15% in both genomes, arguing for a strong impact of DNA methylation on the evolution of GC content. Thus, our results put forward that previous estimates of equilibrium GC content, which neglect the hypermutability of CpG dinucleotides, need to be reevaluated.

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