Immune genes are hotspots of shared positive selection across birds and mammals

eLife, Journal Year: 2019, Volume and Issue: 8

Published: Jan. 8, 2019

Consistent patterns of positive selection in functionally similar genes can suggest a common selective pressure across group species. We use alignments orthologous protein-coding from 39 species birds to estimate parameters related for 11,000 conserved birds. show that functional pathways the immune system, recombination, lipid metabolism, and phototransduction are enriched positively selected genes. By comparing our results with mammalian data, we find significant enrichment shared between taxa, these viral pathways. Using pathogen-challenge transcriptome up-regulated response pathogens also Together, pathogens, particularly viruses, consistently target same divergent clades, hotspots host-pathogen conflict over deep evolutionary time.

Language: Английский

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On the Population Dynamics of Junk: A Review on the Population Genomics of Transposable Elements

Genes, Journal Year: 2019, Volume and Issue: 10(6), P. 419 - 419

Published: May 30, 2019

Transposable elements (TEs) play an important role in shaping genomic organization and structure, may cause dramatic changes phenotypes. Despite the genetic load they impose on their host importance microevolutionary processes such as adaptation speciation, number of population genetics studies focused TEs has been rather limited so far compared to single nucleotide polymorphisms (SNPs). Here, we review current knowledge about dynamics transposable at recent evolutionary time scales, discuss mechanisms that condition abundance frequency. We first non-adaptive purifying selection variable rates transposition elimination, then focus positive balancing selection, finally conclude potential causing incompatibilities eventually speciation. also suggest possible ways better model a genomics context by incorporating advances into rich information provided SNPs demography, intrinsic properties genomes.

Language: Английский

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The Structural, Functional and Evolutionary Impact of Transposable Elements in Eukaryotes

Genes, Journal Year: 2021, Volume and Issue: 12(6), P. 918 - 918

Published: June 15, 2021

Transposable elements (TEs) are nearly ubiquitous in eukaryotes. The increase genomic data, as well progress genome annotation and molecular biology techniques, have revealed the vast number of ways mobile impacted evolution In addition to being main cause difference haploid size, TEs affected overall organization genomes by accumulating preferentially some regions, causing structural rearrangements or modifying recombination rate. Although majority insertions is neutral deleterious, been an important source evolutionary novelties played a determinant role fundamental biological processes. recruited regulation host genes implicated regulatory networks. They also served protein-coding sequences even entire genes. impact on eukaryotic only now fully appreciated they may play processes, such speciation adaptation, remains be deciphered.

Language: Английский

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What Have We Learned from the First 500 Avian Genomes?

Annual Review of Ecology Evolution and Systematics, Journal Year: 2021, Volume and Issue: 52(1), P. 611 - 639

Published: Sept. 9, 2021

The increased capacity of DNA sequencing has significantly advanced our understanding the phylogeny birds and proximate ultimate mechanisms molding their genomic diversity. In less than a decade, number available avian reference genomes to over 500—approximately 5% bird diversity—placing in privileged position advance fields phylogenomics comparative, functional, population genomics. Whole-genome sequence data, as well indels rare changes, are further resolving tree life. accumulation genomes, increasingly with long-read greatly improves resolution features such germline-restricted chromosomes W chromosome, is facilitating comparative integration genotypes phenotypes. Community-based initiatives Bird 10,000 Genomes Project Vertebrate Genome playing fundamental role amplifying coalescing vibrant international program

Language: Английский

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Remarkably High Repeat Content in the Genomes of Sparrows: The Importance of Genome Assembly Completeness for Transposable Element Discovery

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(4)

Published: April 1, 2024

Abstract Transposable elements (TE) play critical roles in shaping genome evolution. Highly repetitive TE sequences are also a major source of assembly gaps making it difficult to fully understand the impact these on host genomes. The increased capacity long-read sequencing technologies span highly regions promises provide new insights into patterns activity across diverse taxa. Here we report generation contiguous reference genomes using PacBio and Omni-C for three species Passerellidae sparrow. We compared assemblies chromosome-level sparrow nine other generated variety short- technologies. All based were longer (range: 1.12 1.41 Gb) than short-read (0.91 1.08 length was strongly correlated with amount repeat content. Repeat content Bell's (31.2% genome) highest level ever reported within order Passeriformes, which comprises over half avian diversity. levels (79.2% 93.7%) found W chromosome relative genome. Finally, show that proliferation different classes varied even among similar These support dynamic model expansion contraction clade where TEs once thought be fairly depauperate static. Our work highlights how resolution difficult-to-assemble transform our understanding

Language: Английский

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An overview of speciation and species limits in birds

Ornithology, Journal Year: 2021, Volume and Issue: 138(2)

Published: April 6, 2021

Abstract Accurately determining avian species limits has been a challenge and work in progress for most of century. It is fascinating but difficult problem. Under the biological concept, only lineages that remain essentially independent when they are sympatry clearly species. Otherwise, there no clear line yet found marks pair diverging (e.g., allopatry) become different enough to warrant full status. Also, with more data, often require reevaluation. The process divergence speciation itself very complex focus intense research. Translating what we understand into taxonomic names can be challenging. A series issues important. Single-locus criteria unlikely convincing. Genetic independence not requirement, degree (gene flow) needs considered opportunity gene flow complete. Time-based (limits determined by time separation) unsatisfactory, though integrating effectively our datasets warranted. We need disentangle data signal due neutral processes vs. selection prioritize latter as main driver speciation. Assortative mating also likely an adequate criterion limits. Hybridization important than ever, condition being treated evenly taxonomy: evolutionary trysts 2 or stuck together through just short over long periods. Comparative methods use occurs between good contact infer among allopatric forms gold standard, inaccurate controversial. Species-level taxonomy birds unsettled some time. While study never exciting dynamic, silver bullet delimitation, nor it will ever one. Careful using integrative comparative framework promising way forward.

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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Identification and Characterization of LINE and SINE Retrotransposons in the African Hedgehog (Atelerix albiventris, Erinaceidae) and Their Association with 3D Genome Organization and Gene Expression

Genes, Journal Year: 2025, Volume and Issue: 16(4), P. 397 - 397

Published: March 29, 2025

Background: The African hedgehog (Atelerix albiventris) exhibits specialized skin differentiation leading to spine formation, yet its regulatory mechanisms remain unclear. Transposable elements (TEs), particularly LINEs (long interspersed nuclear elements) and SINEs (short elements), are known influence genome organization gene regulation. Objectives: Given the high proportion of in genome, this study aims characterize distribution, evolutionary dynamics, potential roles SINEs, focusing on their associations with chromatin architecture, DNA methylation, expression. Methods: We analyzed LINE SINE distribution using HiFi sequencing classified TE families through phylogenetic reconstruction. Hi-C data were used explore interactions while whole-genome 5mCpG methylation was inferred from PacBio reads muscle tissue a deep-learning-based approach. RNA-seq tissues assess expression genes linked development. Results: form distinct genomic blocks GC-rich highly methylated regions, whereas enriched AT-rich, hypomethylated regions. associated differently A/B compartments, euchromatin heterochromatin. Methylation analysis suggests that younger TEs tend have higher levels, indicates some differentially expressed may be involved epidermal skeletal Conclusions: This provides genome-wide perspective patterns, A. albiventris. While not establishing direct causal link, findings suggest development, offering basis for future functional studies.

Language: Английский

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Reactivation of transposable elements following hybridization in fission yeast

Genome Research, Journal Year: 2021, Volume and Issue: 32(2), P. 324 - 336

Published: Dec. 14, 2021

Hybridization is thought to reactivate transposable elements (TEs) that were efficiently suppressed in the genomes of parental hosts. Here, we provide evidence for this "genomic shock hypothesis" fission yeast Schizosaccharomyces pombe In species, two divergent lineages (Sp and Sk) have experienced recent, likely human-induced, hybridization. We used long-read sequencing data assemble 37 samples derived from 31 S. strains spanning a wide range ancestral admixture proportions. A comprehensive TE inventory revealed exclusive presence long terminal repeat (LTR) retrotransposons. Sequence analysis active full-length elements, as well solo LTRs, complex history homologous recombination. Population genetic analyses syntenic sequences placed insertion many LTRs before split Sp Sk lineages. Most inserted more recently, after With exception single element with signs positive selection, both and, particular, carry signatures purifying selection indicating effective removal by host. Consistent reactivation upon hybridization, number LTR retrotransposons, varying extensively zero 87 among strains, significantly increases degree genomic admixture. This study gives detailed account global diversity pombe, documents recombination histories within provides hypothesis."

Language: Английский

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The State of Squamate Genomics: Past, Present, and Future of Genome Research in the Most Speciose Terrestrial Vertebrate Order

Genes, Journal Year: 2023, Volume and Issue: 14(7), P. 1387 - 1387

Published: July 1, 2023

Squamates include more than 11,000 extant species of lizards, snakes, and amphisbaenians, display a dazzling diversity phenotypes across their over 200-million-year evolutionary history on Earth. Here, we introduce define squamates (Order Squamata) review the promise genomic investigations into patterns processes governing squamate evolution, given recent technological advances in DNA sequencing, genome assembly, analysis. We survey most recently available whole assemblies for squamates, including taxonomic distribution genomes, assess quality metrics usefulness research. then focus disagreements phylogenetic inference, how methods high-throughput phylogenomics affect these inferences, demonstrate genomes to settle or sustain persistent arguments squamates. role transposable elements play vertebrate element annotation analysis, further that through understanding diversity, abundance, activity can be an ideal model evolution size structure vertebrates. discuss contribute other areas biological research such as venom systems, studies phenotypic sex determination. Because they represent 30% living amniote, deserve consortium par with efforts amniotes (i.e., mammals birds) aim sequence families clade.

Language: Английский

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