Fine-Scale Map Reveals Highly Variable Recombination Rates Associated with Genomic Features in the Eurasian Blackcap

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(1)

Published: Jan. 1, 2024

Abstract Recombination is responsible for breaking up haplotypes, influencing genetic variability, and the efficacy of selection. Bird genomes lack protein PR domain-containing 9, a key determinant recombination dynamics in most metazoans. Historical maps birds show an apparent stasis positioning events. This highly conserved pattern over long timescales may constrain evolution birds. At same time, extensive variation rate observed across genome between different species Here, we characterize fine-scale historical map iconic migratory songbird, Eurasian blackcap (Sylvia atricapilla), using linkage disequilibrium–based approach that accounts population demography. Our results reveal variable rates among within chromosomes, which associate positively with nucleotide diversity GC content negatively chromosome size. increased significantly at regulatory regions but not necessarily gene bodies. CpG islands are associated strongly rates, though their specific position local DNA methylation patterns likely influence this relationship. The association retrotransposons varied according to family location. also provide evidence heterogeneous intrachromosomal conservation its closest sister taxon, garden warbler. These findings highlight considerable variability scales role genomic features shaping variation. study opens possibility further investigating impact on population-genomic features.

Language: Английский

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Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise

Molecular Ecology Resources, Journal Year: 2020, Volume and Issue: 21(1), P. 263 - 286

Published: Sept. 16, 2020

Abstract Genome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs increasing efficiency of sequencing technologies now enable assembling genomes unprecedented quality contiguity. However, the difficulty in repeat‐rich GC‐rich regions (genomic “dark matter”) limits insights into evolution genome structure regulatory networks. Here, we compare available (short/linked/long reads proximity ligation maps) combinations thereof genomic dark matter. By adopting different de novo assembly strategies, draft to a curated multiplatform reference identify features that cause gaps within each assembly. We show implementing long‐read, linked‐read performs best recovering transposable elements, multicopy MHC genes, microchromosomes W chromosome. Telomere‐to‐telomere not reality yet for most organisms, but leveraging technology choice it is possible minimize downstream analysis. provide roadmap tailor projects optimized completeness both coding noncoding parts nonmodel genomes.

Language: Английский

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From molecules to populations: appreciating and estimating recombination rate variation

Nature Reviews Genetics, Journal Year: 2020, Volume and Issue: 21(8), P. 476 - 492

Published: May 29, 2020

Language: Английский

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Fourth Report on Chicken Genes and Chromosomes 2022

Cytogenetic and Genome Research, Journal Year: 2022, Volume and Issue: 162(8-9), P. 405 - 528

Published: Jan. 1, 2022

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Language: Английский

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Chromosome-length genome assembly and linkage map of a critically endangered Australian bird: the helmeted honeyeater

GigaScience, Journal Year: 2022, Volume and Issue: 11

Published: Jan. 1, 2022

Abstract Background The helmeted honeyeater (Lichenostomus melanops cassidix) is a Critically Endangered bird endemic to Victoria, Australia. To aid its conservation, the population subject of genetic rescue. understand, monitor, and modulate effects rescue on genome, chromosome-length genome high-density linkage map are required. Results We used combination Illumina, Oxford Nanopore, Hi-C sequencing technologies assemble honeyeater, comprising 906 scaffolds, with length 1.1 Gb scaffold N50 63.8 Mb. Annotation comprised 57,181 gene models. Using pedigree 257 birds 53,111 single-nucleotide polymorphisms, we obtained recombination maps for 25 autosomes Z chromosome. total sex-averaged was 1,347 cM long, male being 6.7% longer than female map. Recombination revealed sexually dimorphic rates (overall higher in males), average rate 1.8 cM/Mb. Comparative analyses high synteny that 3 passerine species (e.g., 32 scaffolds mapped 30 zebra finch chromosome). assembly suggest exhibits fission chromosome 1A into 2 chromosomes relative finch. PSMC analysis showed ∼15-fold decline effective size ∼60,000 from mid- late Pleistocene. Conclusions annotated provide rich resources evolutionary studies will be fundamental guiding conservation efforts honeyeater.

Language: Английский

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Genomic Architecture Predicts Tree Topology, Population Structuring, and Demographic History in Amazonian Birds

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(1)

Published: Jan. 1, 2024

Abstract Geographic barriers are frequently invoked to explain genetic structuring across the landscape. However, inferences on spatial and temporal origins of population variation have been largely limited evolutionary neutral models, ignoring potential role natural selection intrinsic genomic processes known as architecture in producing heterogeneity differentiation genome. To test how characteristics (e.g. recombination rate) impacts our ability reconstruct general patterns between species that cooccur geographic barriers, we sequenced whole genomes multiple bird populations distributed rivers southeastern Amazonia. We found phylogenetic relationships within demographic parameters varied genome predictable ways. Genetic diversity was positively associated with rate negatively tree support. Gene flow less pervasive regions low recombination, making these windows more likely retain matched tree. further approximately a third showed evidence selective sweeps linked selection, skewing genome-wide estimates effective sizes gene toward lower values. In sum, effects can be disentangled from elucidate differentiation.

Language: Английский

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The genetic architecture of recombination rates is polygenic and differs between the sexes in wild house sparrows (Passer domesticus)

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(9)

Published: Aug. 24, 2024

Abstract Meiotic recombination through chromosomal crossing-over is a fundamental feature of sex and an important driver genomic diversity. It ensures proper disjunction, allows increased selection responses, prevents mutation accumulation; however, it also mutagenic can break up favorable haplotypes. This cost–benefit dynamic likely to vary depending on mechanistic evolutionary contexts, indeed, rates show huge variation in nature. Identifying the genetic architecture this key understanding its causes consequences. Here, we investigate individual rate wild house sparrows (Passer domesticus). We integrate pedigree data identify autosomal crossover counts (ACCs) intrachromosomal allelic shuffling (r¯intra) 13,056 gametes transmitted from 2,653 individuals their offspring. Females had 1.37 times higher ACC, 1.55 r¯intra than males. ACC were heritable females males (ACC h2 = 0.23 0.11; 0.12 0.14), but cross-sex additive correlations low (rA 0.29 0.32 for r¯intra). Conditional bivariate analyses showed that all measures remained after accounting values opposite sex, indicating sex-specific evolve somewhat independently. Genome-wide models are polygenic driven by many small-effect loci, which act trans as global modifiers. Our findings have different potential birds, providing compelling mechanism evolution sexual dimorphism recombination.

Language: Английский

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Mating system and the evolution of recombination rates in seed plants

Journal of Evolutionary Biology, Journal Year: 2025, Volume and Issue: unknown

Published: May 5, 2025

Abstract Meiotic recombination is a central mechanism underlying sexual reproduction among eukaryotes. In many species, the rate strongly constrained by chromosome size, as number of crossovers per generally ranges between one and no more than few (around three to five). Yet, rates are variable can evolve in particular when they differ their reproductive system. According theory, indirect selection towards higher expected be stronger inbred populations, such selfing species compared with randomly mating species. To test for impact system on evolution rates, we leveraged dataset genetic maps, genome sizes, numbers, life history traits 200 seed plant After controlling size effect, phylogeny, map quality, found joint positive effect longevity mixed-mating We also that had significantly larger chromosomes outcrossing suggesting relaxed crossover interference these former Our results point an important factor potentially shaping despite mechanical constraints acting chromosome.

Language: Английский

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Analysis of Paralogons, Origin of the Vertebrate Karyotype, and Ancient Chromosomes Retained in Extant Species

Genome Biology and Evolution, Journal Year: 2021, Volume and Issue: 13(4)

Published: March 3, 2021

A manually curated set of ohnolog families has been assembled, for seven species bony vertebrates, that includes 255 four-member and 631 three-member families, encompassing over 2,900 ohnologs. Across species, the patterns chromosomes upon which ohnologs reside fall into 17 distinct categories. These paralogons reflect ancestral existed in our chordate ancestor immediately prior to two rounds whole-genome duplication (2R-WGD) occurred around 600 Ma. Within each paralogon, it now possible assign those pairs diverged from other at first round duplication, through analysis molecular phylogeny families. Comparison with another recent identified four apparently incorrect assignments pairings following 2R, along several omissions, study. By comparison between paralogons, also identify nine chromosomal fusions 1R three after generated an bony-vertebrate karyotype comprising 47 chromosomes. At least 27 can, some extant be shown not have undergone any fusion or fission events. Such are here termed "archeochromosomes," survived essentially unchanged their content genes 400 Myr. Their utility lies potential tracking various events different lineages throughout expansion vertebrates.

Language: Английский

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The genetic architecture of recombination rates is polygenic and differs between the sexes in wild house sparrows (Passer domesticus)

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Jan. 27, 2023

Abstract Meiotic recombination through chromosomal crossing-over is a fundamental feature of sex and an important driver genomic diversity. It ensures proper disjunction, allows increased selection responses, prevents mutation accumulation; however, it also mutagenic can break up favourable haplotypes. This cost/benefit dynamic likely to vary depending on mechanistic evolutionary contexts, indeed, rates show huge variation in nature. Identifying the genetic architecture this key understanding its causes consequences. Here, we investigate individual rate wild house sparrows ( Passer domesticus ). We integrate pedigree data identify autosomal crossover counts (ACC) intra-chromosomal allelic shuffling r̅ intra ) 13,056 gametes. Females had 1.37 times higher ACC, 1.55 than males. ACC were heritable females males (ACC h 2 = 0.23 0.11; 0.12 0.14), but cross-sex additive correlations low (r A 0.29 0.32 for Conditional bivariate analyses showed that all measures remained after accounting values opposite sex, indicating sex-specific evolve somewhat independently. Genome-wide models are polygenic driven by many small-effect loci, which act trans as global modifiers. Our findings have different potential birds, providing compelling mechanism evolution sexual dimorphism recombination.

Language: Английский

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