Recombination suppression and selection affect local ancestries in genomes of a migratory songbird

The patterns of genetic relatedness among individuals vary along the genome, representing fluctuation of local ancestry. The factors responsible for this variation have not been well studied in wild animals with ecological and behavioural relevance. Here, we characterise the genomic architecture of genetic relatedness in the Eurasian blackcap, an iconic songbird species in ecology and quantitative genetics of migratory behaviour. We identify 23 genomic regions with deviated local relatedness patterns, using a chromosome-level de novo assembly of the blackcap genome and whole-genome resequencing data of 179 individuals from nine populations with diverse migratory phenotypes. Five genomic regions show local relatedness patterns of polymorphic inversions, three of which are syntenic to polymorphic inversions known in the zebra finch. Phylogenetic analysis reveals these three polymorphic inversions evolved independently in the blackcap and zebra finch indicating convergence of polymorphic inversions. Population genetic analyses in these three inversions in the blackcap suggest balancing selection between two haplotypes in one locus and background selection in the other two loci. One genomic region with deviated local relatedness is under selection against gene flow by population-specific reduction in recombination rate. Other genomic islands including 11 pericentromeric regions consist of evolutionarily conserved and non-conserved recombination cold-spots under background selection. Two of these regions with non-conserved recombination suppression are known to be associated with population-specific migratory phenotypes, where local relatedness patterns support additional effects of population-specific selection. These results highlight how different forms of recombination suppression and selection jointly affect heterogeneous genomic landscape of local ancestries.

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From Pan-genome to the Genomic Context of the Two Integrons of ST-111 Pseudomonas Aeruginosa AG1: A VIM-2-carrying Old-acquaintance and a Novel Imp-18-carrying Integron

10.21203/rs.3.rs-41474/v1 ◽

2020 ◽

Author(s):

Jose Arturo Molina-Mora ◽

Raquel García Batán ◽

Fernando García

Keyword(s):

Pseudomonas Aeruginosa ◽

High Risk ◽

Genome Analysis ◽

Genomic Region ◽

Genomic Islands ◽

Comparative Genomic ◽

Genomic Context ◽

Intrinsic Resistance ◽

Pan Genome ◽

Genomic Regions

Abstract Background Pseudomonas aeruginosa is an opportunist and versatile organism responsible for infections among immunocompromised hosts. This pathogen has high intrinsic resistance to most antimicrobials, including critical strains due to resistance to carbapenems, a last-resort antibiotic. P. aeruginosa AG1 (PaeAG1) is a Costa Rican high-risk ST-111 strain with resistance to multiple antibiotics, including carbapenems due to the activity of both VIM-2 and IMP-18 metallo-β-lactamases (MBLs). These genes are harbored in two class 1 integrons, belonging to one out of the 57 PaeAG1 genomic islands. However, the genomic context related to these determinants in PaeAG1 and other P. aeruginosa strains is unclear. Thus, we implemented a comparative genomic approach to define and up-date the phylogenetic relationship among complete P. aeruginosa genomes using a pan-genome analysis. We also studied the PaeAG1 genomic islands content in other strains and the architecture of genomic regions around the VIM-2- and IMP-18-carrying integrons. Results With 211 strains, the up-dated P. aeruginosa pan-genome revealed that complete genome sequences are able to separate clones by MLST profile (ST), including a clear ST-111 cluster with PaeAG1. The PaeAG1 genomic islands were found to define a diverse presence/absence pattern among related genomes, but content was related to phylogenetic relationships. Finally, landscape reconstruction of specific genomic regions showed that VIM-2-carrying integron (In59-like) is an old-acquaintance element harbored in a known genomic region completely found in other two ST-111 strains. In addition, PaeAG1 has an exclusive genomic region containing a novel IMP-18-carrying integron (registered as In1666), with an arrangement never reported before. Conclusions We provide new insights about the genomic determinants associated with the resistance to carbapenems in the high-risk PaeAG1 using comparative genomics. With the pan-genome analysis and the comparison of PaeAG1 genomic islands in other strains, it was possible to describe the genomic landscape of the two MBLs-carrying integrons, including an old-acquaintance element carrying VIM-2 and a new IMP-18-carrying integron.

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Background selection as baseline for nucleotide variation across the Drosophila genome

10.1101/005017 ◽

2014 ◽

Author(s):

Josep M Comeron

Keyword(s):

Balancing Selection ◽

Genetic Maps ◽

Drosophila Genome ◽

Background Selection ◽

Deleterious Mutations ◽

Entire Genome ◽

Genome Wide ◽

Intergenic Regions ◽

Selection Parameters ◽

Genomic Regions

The constant removal of deleterious mutations by natural selection causes a reduction in neutral diversity and efficacy of selection at genetically linked sites (a process called Background Selection, BGS). Population genetic studies, however, often ignore BGS effects when investigating demographic events or the presence of other types of selection. To obtain a more realistic evolutionary expectation that incorporates the unavoidable consequences of deleterious mutations, we generated high-resolution landscapes of variation across the Drosophila melanogaster genome under a BGS scenario independent of polymorphism data. We find that BGS plays a significant role in shaping levels of variation across the entire genome, including long introns and intergenic regions distant from annotated genes. We also find that a very large percentage of the observed variation in diversity across autosomes can be explained by BGS alone, up to 70% across individual chromosome arms, thus indicating that BGS predictions can be used as baseline to infer additional types of selection and demographic events. This approach allows detecting several outlier regions with signal of recent adaptive events and selective sweeps. The use of a BGS baseline, however, is particularly appropriate to investigate the presence of balancing selection and our study exposes numerous genomic regions with the predicted signature of higher polymorphism than expected when a BGS context is taken into account. Importantly, we show that these conclusions are robust to the mutation and selection parameters of the BGS model. Finally, analyses of protein evolution together with previous comparisons of genetic maps between Drosophila species, suggest temporally variable recombination landscapes and thus, local BGS effects that may differ between extant and past phases. Because genome-wide BGS and temporal changes in linkage effects can skew approaches to estimate demographic and selective events, future analyses should incorporate BGS predictions and capture local recombination variation across genomes and along lineages.

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Genomic Context of the Two Integrons of ST-111 Pseudomonas aeruginosa AG1: A VIM-2-carrying Old-acquaintance and a Novel Imp-18-carrying Integron

10.21203/rs.3.rs-41474/v2 ◽

2020 ◽

Author(s):

Jose Arturo Molina-Mora ◽

Diana Chinchilla-Montero ◽

Raquel García Batán ◽

Fernando García

Keyword(s):

Pseudomonas Aeruginosa ◽

Comparative Genomics ◽

High Risk ◽

Genomic Region ◽

Genomic Islands ◽

Genomic Context ◽

Intrinsic Resistance ◽

Pan Genome ◽

Class 1 ◽

Genomic Regions

Abstract Pseudomonas aeruginosa is an opportunist and versatile organism responsible for infections mainly in immunocompromised hosts. This pathogen has high intrinsic resistance to most antimicrobials. P. aeruginosa AG1 (PaeAG1) is a Costa Rican high-risk ST-111 strain with resistance to multiple antibiotics, including carbapenems, due to the activity of VIM-2 and IMP-18 metallo-β-lactamases (MBLs). These genes are harbored in two class 1 integrons located inone out of the 57 PaeAG1 genomic islands. However, the genomic context associated to these determinants in PaeAG1 and other P. aeruginosa strains is unclear. Thus, we first assessed the transcriptional activity of VIM-2 and IMP-18 genes when exposed to imipenem (a carbapenem) by RT-qPCR. To select related genomes to PaeAG1, we implemented a pan-genome analysis to define and up-date the phylogenetic relationship among complete P. aeruginosa genomes. We also studied the PaeAG1 genomic islands content in the related strains and finally we described the architecture and possible evolutionary steps of the genomic regions around the VIM-2- and IMP-18-carrying integrons.Expression of VIM-2 and IMP-18 genes was demonstrated to be induced after imipenem exposure. In a subsequent comparative genomics analysis with 211 strains, the P. aeruginosa pan-genome revealed that complete genome sequences are able to separate clones by MLST profile, including a clear ST-111 cluster with PaeAG1. The PaeAG1 genomic islands were found to define a diverse presence/absence pattern among related genomes. Finally, landscape reconstruction of genomic regions showed that VIM-2-carrying integron (In59-like) is an old-acquaintance element harbored in the same known region found in other two ST-111 strains. Also, PaeAG1 has an exclusive genomic region containing a novel IMP-18-carrying integron (registered as In1666), with an arrangement never reported before. Altogether, we provide new insights about the genomic determinants associated with the resistance to carbapenems in this high-risk P. aeruginosa using comparative genomics.

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Identification of genomic islands in Synechococcus sp. WH8102 using genomic barcode and whole-genome microarray analyses

Current Bioinformatics ◽

10.2174/1574893615666200121160615 ◽

2020 ◽

Vol 15 ◽

Author(s):

Jiahui Pan ◽

Xizi Luo ◽

Tong Shao ◽

Chaoying Li ◽

Tingting Zhao ◽

...

Keyword(s):

Genomic Islands ◽

Whole Genome ◽

Photosynthetic Organisms ◽

Depth Study ◽

Whole Genome Microarray ◽

Integrated Methods ◽

Synechococcus Sp ◽

Intuitive View ◽

Genomic Regions ◽

Different Origins

Background: Synechococcus sp. WH8102 is one of the most abundant photosynthetic organisms in many ocean regions. Objective: The aim of this study is to identify genomic islands (GIs) in Synechococcus sp. WH8102 with integrated methods. Methods: We have applied genomic barcode to identify the GIs in Synechococcus sp. WH8102, which could make genomic regions of different origins visually apparent. The gene expression data of the predicted GIs was analyzed through microarray data which was collected for functional analysis of the relevant genes. Results: Seven GIs were identified in Synechococcus sp. WH8102. Most of them are involved in cell surface modification, photosynthesis and drug resistance. In addition, our analysis also revealed the functions of these GIs, which could be used for in-depth study on the evolution of this strain. Conclusion: Genomic barcodes provide us with a comprehensive and intuitive view of the target genome. We can use it to understand the intrinsic characteristics of the whole genome and identify GIs or other similar elements.

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panRGP: a pangenome-based method to predict genomic islands and explore their diversity

Bioinformatics ◽

10.1093/bioinformatics/btaa792 ◽

2020 ◽

Vol 36 (Supplement_2) ◽

pp. i651-i658 ◽

Cited By ~ 1

Author(s):

Adelme Bazin ◽

Guillaume Gautreau ◽

Claudine Médigue ◽

David Vallenet ◽

Alexandra Calteau

Keyword(s):

Escherichia Coli ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Species Level ◽

Genomic Islands ◽

Genome Plasticity ◽

Reference Dataset ◽

Prokaryotic Genomes ◽

Ideal Approach ◽

Genomic Regions

Abstract Motivation Horizontal gene transfer (HGT) is a major source of variability in prokaryotic genomes. Regions of genome plasticity (RGPs) are clusters of genes located in highly variable genomic regions. Most of them arise from HGT and correspond to genomic islands (GIs). The study of those regions at the species level has become increasingly difficult with the data deluge of genomes. To date, no methods are available to identify GIs using hundreds of genomes to explore their diversity. Results We present here the panRGP method that predicts RGPs using pangenome graphs made of all available genomes for a given species. It allows the study of thousands of genomes in order to access the diversity of RGPs and to predict spots of insertions. It gave the best predictions when benchmarked along other GI detection tools against a reference dataset. In addition, we illustrated its use on metagenome assembled genomes by redefining the borders of the leuX tRNA hotspot, a well-studied spot of insertion in Escherichia coli. panRPG is a scalable and reliable tool to predict GIs and spots making it an ideal approach for large comparative studies. Availability and implementation The methods presented in the current work are available through the following software: https://github.com/labgem/PPanGGOLiN. Detailed results and scripts to compute the benchmark metrics are available at https://github.com/axbazin/panrgp_supdata.

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Publisher Correction: Germline de novo mutation clusters arise during oocyte aging in genomic regions with high double-strand-break incidence

Nature Genetics ◽

10.1038/s41588-021-00905-z ◽

2021 ◽

Author(s):

Jakob M. Goldmann ◽

Vladimir B. Seplyarskiy ◽

Wendy S. W. Wong ◽

Thierry Vilboux ◽

Pieter B. Neerincx ◽

...

Keyword(s):

De Novo ◽

Strand Break ◽

Double Strand Break ◽

De Novo Mutation ◽

Oocyte Aging ◽

Genomic Regions

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3D reconstruction of genomic regions from sparse interaction data

NAR Genomics and Bioinformatics ◽

10.1093/nargab/lqab017 ◽

2021 ◽

Vol 3 (1) ◽

Author(s):

Julen Mendieta-Esteban ◽

Marco Di Stefano ◽

David Castillo ◽

Irene Farabella ◽

Marc A Marti-Renom

Keyword(s):

3D Models ◽

Genomic Region ◽

Gene Promoters ◽

Chromosome Conformation ◽

The Matrix ◽

Chromatin Structural ◽

A Cell ◽

Similar Accuracy ◽

Genomic Regions ◽

Interaction Matrices

Abstract Chromosome conformation capture (3C) technologies measure the interaction frequency between pairs of chromatin regions within the nucleus in a cell or a population of cells. Some of these 3C technologies retrieve interactions involving non-contiguous sets of loci, resulting in sparse interaction matrices. One of such 3C technologies is Promoter Capture Hi-C (pcHi-C) that is tailored to probe only interactions involving gene promoters. As such, pcHi-C provides sparse interaction matrices that are suitable to characterize short- and long-range enhancer–promoter interactions. Here, we introduce a new method to reconstruct the chromatin structural (3D) organization from sparse 3C-based datasets such as pcHi-C. Our method allows for data normalization, detection of significant interactions and reconstruction of the full 3D organization of the genomic region despite of the data sparseness. Specifically, it builds, with as low as the 2–3% of the data from the matrix, reliable 3D models of similar accuracy of those based on dense interaction matrices. Furthermore, the method is sensitive enough to detect cell-type-specific 3D organizational features such as the formation of different networks of active gene communities.

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Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C

Nature Communications ◽

10.1038/s41467-020-20536-y ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Zev N. Kronenberg ◽

Arang Rhie ◽

Sergey Koren ◽

Gregory T. Concepcion ◽

Paul Peluso ◽

...

Keyword(s):

Zebra Finch ◽

Cultured Cells ◽

De Novo ◽

Single Cells ◽

Variant Calling ◽

Chromatin Interaction ◽

Extended Haplotype ◽

Benchmark Datasets ◽

And Performance ◽

Genome Assemblies

AbstractHaplotype-resolved genome assemblies are important for understanding how combinations of variants impact phenotypes. To date, these assemblies have been best created with complex protocols, such as cultured cells that contain a single-haplotype (haploid) genome, single cells where haplotypes are separated, or co-sequencing of parental genomes in a trio-based approach. These approaches are impractical in most situations. To address this issue, we present FALCON-Phase, a phasing tool that uses ultra-long-range Hi-C chromatin interaction data to extend phase blocks of partially-phased diploid assembles to chromosome or scaffold scale. FALCON-Phase uses the inherent phasing information in Hi-C reads, skipping variant calling, and reduces the computational complexity of phasing. Our method is validated on three benchmark datasets generated as part of the Vertebrate Genomes Project (VGP), including human, cow, and zebra finch, for which high-quality, fully haplotype-resolved assemblies are available using the trio-based approach. FALCON-Phase is accurate without having parental data and performance is better in samples with higher heterozygosity. For cow and zebra finch the accuracy is 97% compared to 80–91% for human. FALCON-Phase is applicable to any draft assembly that contains long primary contigs and phased associate contigs.

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Elucidation of Early Evolution of HIV-1 Group M in the Congo Basin Using Computational Methods

Genes ◽

10.3390/genes12040517 ◽

2021 ◽

Vol 12 (4) ◽

pp. 517

Author(s):

Marcel Tongo ◽

Darren P. Martin ◽

Jeffrey R. Dorfman

Keyword(s):

Genetic Relatedness ◽

Early Evolution ◽

Congo Basin ◽

Global Epidemic ◽

The Past ◽

History Of ◽

Cold Spots ◽

Genomic Regions ◽

Basin Region ◽

Hiv 1

The Congo Basin region is believed to be the site of the cross-species transmission event that yielded HIV-1 group M (HIV-1M). It is thus likely that the virus has been present and evolving in the region since that cross-species transmission. As HIV-1M was only discovered in the early 1980s, our directly observed record of the epidemic is largely limited to the past four decades. Nevertheless, by exploiting the genetic relatedness of contemporary HIV-1M sequences, phylogenetic methods provide a powerful framework for investigating simultaneously the evolutionary and epidemiologic history of the virus. Such an approach has been taken to find that the currently classified HIV-1 M subtypes and Circulating Recombinant Forms (CRFs) do not give a complete view of HIV-1 diversity. In addition, the currently identified major HIV-1M subtypes were likely genetically predisposed to becoming a major component of the present epidemic, even before the events that resulted in the global epidemic. Further efforts have identified statistically significant hot- and cold-spots of HIV-1M subtypes sequence inheritance in genomic regions of recombinant forms. In this review we provide ours and others recent findings on the emergence and spread of HIV-1M variants in the region, which have provided insights into the early evolution of this virus.

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Evolutionary strata on young mating-type chromosomes despite the lack of sexual antagonism

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1701658114 ◽

2017 ◽

Vol 114 (27) ◽

pp. 7067-7072 ◽

Cited By ~ 47

Author(s):

Sara Branco ◽

Hélène Badouin ◽

Ricardo C. Rodríguez de la Vega ◽

Jérôme Gouzy ◽

Fantin Carpentier ◽

...

Keyword(s):

Mating Type ◽

Balancing Selection ◽

Smut Fungi ◽

Mating Types ◽

Sexual Antagonism ◽

Recombination Suppression ◽

Ancestral Gene ◽

Anther Smut ◽

Mating Type Genes ◽

Suppressed Recombination

Sex chromosomes can display successive steps of recombination suppression known as “evolutionary strata,” which are thought to result from the successive linkage of sexually antagonistic genes to sex-determining genes. However, there is little evidence to support this explanation. Here we investigate whether evolutionary strata can evolve without sexual antagonism using fungi that display suppressed recombination extending beyond loci determining mating compatibility despite lack of male/female roles associated with their mating types. By comparing full-length chromosome assemblies from five anther-smut fungi with or without recombination suppression in their mating-type chromosomes, we inferred the ancestral gene order and derived chromosomal arrangements in this group. This approach shed light on the chromosomal fusion underlying the linkage of mating-type loci in fungi and provided evidence for multiple clearly resolved evolutionary strata over a range of ages (0.9–2.1 million years) in mating-type chromosomes. Several evolutionary strata did not include genes involved in mating-type determination. The existence of strata devoid of mating-type genes, despite the lack of sexual antagonism, calls for a unified theory of sex-related chromosome evolution, incorporating, for example, the influence of partially linked deleterious mutations and the maintenance of neutral rearrangement polymorphism due to balancing selection on sexes and mating types.

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