Chromosome-Level Genome Assembly of the Common Chaffinch (Aves: Fringilla coelebs): A Valuable Resource for Evolutionary Biology

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

Published: Feb. 17, 2021

The common chaffinch, Fringilla coelebs, is one of the most common, widespread, and well-studied passerines in Europe, with a broad distribution encompassing Western Europe parts Asia, North Africa, Macaronesian archipelagos. We present high-quality genome assembly chaffinch generated using Illumina shotgun sequencing combination Chicago Hi-C libraries. final 994.87-Mb chromosome-level assembly, 98% sequence data located chromosome scaffolds N50 statistic 69.73 Mb. Our shows high completeness, complete BUSCO score 93.9% avian set. Around 7.8% contains interspersed repetitive elements. structural annotation yielded 17,703 genes, 86.5% which have functional annotation, including 7,827 universal single-copy orthologs out 8,338 genes represented This new annotated will be valuable resource as reference for comparative population genomic analyses passerine, avian, vertebrate evolution.

Language: Английский

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A high-density linkage map reveals broad- and fine-scale sex differences in recombination in the hihi (stitchbird; Notiomystis cincta)

Heredity, Journal Year: 2024, Volume and Issue: 133(4), P. 262 - 275

Published: Aug. 2, 2024

Abstract Recombination, the process of DNA exchange between homologous chromosomes during meiosis, plays a major role in genomic diversity and evolutionary change. Variation recombination rate is widespread despite often being essential for progression meiosis. One such variation heterochiasmy, where rates differ sexes. Heterochiasmy has been observed across broad taxonomic groups, yet it remains an enigma. We used Lep-MAP3, pedigree-based software that efficient handling large datasets, to generate linkage maps hihi or stitchbird ( Notiomystis cincta) , utilising information from >36 K SNPs 36 families. constructed 29 maps, including previously unscaffolded Z chromosome. The endangered passerine endemic Aotearoa New Zealand sexually dimorphic exhibits high levels sexual conflict, sperm competition. Patterns are consistent with those other birds, higher micro-chromosomes. male-biased, line predictions Haldane-Huxley rule, male map 15% longer. Micro-chromosomes exhibit heterochiasmy greater extent, contrary reported birds. At intra-chromosomal level, nearer chromosome ends gene-rich regions. Regions extreme enriched genes implicated cell structure. This study adds important contribution assessing theories provides framework future studies investigating fine-scale heterochiasmy.

Language: Английский

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Beyond genes‐for‐behaviour: The potential for genomics to resolve long‐standing questions in avian brood parasitism

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(11), P. 1 - 20

Published: Nov. 1, 2024

Abstract Behavioural ecology by definition of its founding ‘Tinbergian framework’ is an integrative field, however, it lags behind in incorporating genomic methods. ‘Finding the gene/s for a behaviour’ still rarely feasible or cost‐effective wild but as we show here, data can be used to address broader questions. Here use avian brood parasitism, model system behavioural case study highlight how ecologists could full potential state‐of‐the‐art tools. Brood parasite–host interactions are one most easily observable and amenable natural laboratories antagonistic coevolution, such have intrigued evolutionary biologists decades. Using worked examples, demonstrate causes mechanisms (co)evolutionary adaptation answer three key questions field: (i) Where when should parasitism evolve?, (ii) When hosts defend?, (iii) Will coevolution persist with ecological change? In doing so, discuss molecular collaborate integrate Tinbergen's achieve coherent science that he promoted solve mysteries nature.

Language: Английский

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The First Genome of the Balearic Shearwater (Puffinus mauretanicus) Provides a Valuable Resource for Conservation Genomics and Sheds Light on Adaptation to a Pelagic lifestyle

Genome Biology and Evolution, Journal Year: 2022, Volume and Issue: 14(5)

Published: May 1, 2022

The Balearic shearwater (Puffinus mauretanicus) is the most threatened seabird in Europe and a member of speciose group pelagic seabirds, order Procellariiformes, which exhibit extreme adaptations to lifestyle. fossil record suggests that human colonisation Islands resulted sharp decrease population size. Currently, populations species continue be decimated mainly due predation by introduced mammals bycatch longline fisheries, with some studies predicting its extinction 2070. Here, using combination short long reads, we generate first high-quality reference genome for shearwater, completeness amongst highest across available avian species. We used this study critical aspects relevant conservation status gain insights into adaptation lifestyle Procellariiformes. detected relatively high levels genome-wide heterozygosity despite reduced However, reconstruction historical demography uncovered an abrupt decline potentially linked reduction neritic zone during Penultimate Glacial Period (∼194-135 ka). Comparative genomics analyses uncover set candidate genes may have played important role including those enhancement fishing capabilities, night vision, development natriuresis. obtained will crucial future genetic tools efforts Critically Endangered

Language: Английский

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Whole‐genome phylogeography of the blue‐faced honeyeater (Entomyzon cyanotis) and discovery and characterization of a neo‐Z chromosome

Molecular Ecology, Journal Year: 2022, Volume and Issue: 32(6), P. 1248 - 1270

Published: July 7, 2022

Whole-genome surveys of genetic diversity and geographic variation often yield unexpected discoveries novel structural variation, which long-read DNA sequencing can help clarify. Here, we report on whole-genome phylogeography a bird exhibiting classic vicariant geographies across Australia New Guinea, the blue-faced honeyeater (Entomyzon cyanotis), discovery characterization neo-Z chromosome by sequencing. Using short-read genome-wide SNPs, inferred population divergence events within E. cyanotis Carpentarian other biogeographic barriers during Pleistocene (~0.3-1.7 Ma). Evidence for introgression between nonsister populations supports hypothesis reticulate evolution around triad dynamic Lake Carpentaria Guinea. During this phylogeographic survey, discovered large (134 Mbp) explored its diversity, landscape. We show that, as in some sylvioid passerine birds, fusion occurred 5 Z to form chromosome; cyanotis, ancestral pseudoautosomal region (PAR) appears nonrecombinant W, along with most fused 5. The added recombination-suppressed portion (~37.2 displays reduced faster differentiation compared ancestral-Z. Yet, new PAR (~17.4 shows elevated autosomes, potentially resulting from introgression. In our case, helped clarify genomic landscape autosomes sex chromosomes species where prior knowledge genome structure was still incomplete.

Language: Английский

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Geogenomic Predictors of Genetree Heterogeneity Explain Phylogeographic and Introgression History: A Case Study in an Amazonian Bird (Thamnophilus aethiops)

Systematic Biology, Journal Year: 2023, Volume and Issue: 73(1), P. 36 - 52

Published: Oct. 6, 2023

Abstract Can knowledge about genome architecture inform biogeographic and phylogenetic inference? Selection, drift, recombination, gene flow interact to produce a genomic landscape of divergence wherein patterns differentiation genealogy vary nonrandomly across the genomes diverging populations. For instance, genealogical that arise due should be more likely occur on smaller chromosomes, which experience high whereas those tracking histories geographic isolation (reduced caused by barrier) larger sex chromosomes. In Amazonia, populations many bird species diverge introgress rivers, resulting in reticulated signals. Herein, we used reduced representation data disentangle evolutionary history 4 an Amazonian antbird, Thamnophilus aethiops, whose was associated with dynamic evolution Madeira River Basin. Specifically, evaluate whether large river capture event ca. 200 Ka, gave rise genealogies making spatially explicit predictions based processes. We first estimated chromosome-level phylogenies recovered 2 primary topologies genome. The topology (T1) most consistent population for Z-chromosome. second (T2), upon secondary contact. To support these topologies, trained convolutional neural network classify our into alternative diversification models estimate demographic parameters. best-fit model concordant T1 included between non-sister taxa. Finally, modeled levels introgression as functions chromosome length found chromosomes experienced higher flow. Given (1) genetrees supporting T2 were (2) lower (and especially Z-chromosome), argue represents rivers contact barrier loss. Our results suggest significant portion heterogeneity arises extrinsic processes such interacting intrinsic architecture. Future phylogeographic studies would benefit from accounting processes, different parts reveal contrasting, albeit complementary histories, all are relevant disentangling intricate geogenomic mechanisms biotic diversification. [Amazonia; biogeography; modeling; flow; tree; architecture; geogenomics; introgression; linked selection; network; phylogenomic; phylogeography; reproductive isolation; speciation; tree.]

Language: Английский

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

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2019, Volume and Issue: unknown

Published: Dec. 20, 2019

Abstract Genome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs increasing efficiency of sequencing technologies have opened up a whole new world genomic biodiversity. Although these generate high-quality genome assemblies, there still regions difficult to assemble, like repetitive elements GC-rich (genomic “dark matter”). In this study, we compare the used (short/linked/long reads proximity ligation maps) combinations thereof in assembling dark matter starting from same sample. By adopting different de-novo assembly strategies, were able each draft curated multiplatform one identify nature previously missing with particular focus on transposable elements, multi-copy MHC genes, regions. Thanks approach, demonstrate feasibility producing chromosome-level for non-model organism (paradise crow) which only suboptimal samples available. Our approach was reconstruct complex chromosomes repeat-rich W sex chromosome several microchromosomes. Telomere-to-telomere not reality yet most organisms, but leveraging technology choice it is possible minimize gaps downstream analysis. We provide roadmap tailor projects around completeness both coding non-coding parts genomes.

Language: Английский

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Genome-wide analyses of the relict gull (Larus relictus): insights and evolutionary implications

BMC Genomics, Journal Year: 2021, Volume and Issue: 22(1)

Published: April 29, 2021

Abstract Background The relict gull ( Larus relictus ), was classified as vulnerable on the IUCN Red List and is a first-class national protected bird in China. Genomic resources for L. are lacking, which limits study of its evolution conservation. Results In this study, based Illumina PacBio sequencing platforms, we successfully assembled genome , one few known reference genomes genus . size final 1.21 Gb, with contig N50 8.11 Mb. A total 18,454 genes were predicted from assembly results, 16,967 (91.94%) these annotated. contained 92.52 Mb repeat sequence, accounting 7.63% assembly. phylogenetic tree constructed using 4902 single-copy orthologous genes, showed had closest relative smithsonianus divergence time 14.7 Mya estimated between them. PSMC analyses indicated that been undergoing long-term population decline during 0.01-0.1 small effective fom 8800 to 2200 individuals. Conclusions This will be valuable genomic resource range conservation studies help establish foundation further investigating whether breeding complex population. As species threatened by habitat loss fragmentation, actions protect suggested alleviate fragmentation populations.

Language: Английский

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Assembly of female and male hihi genomes (stitchbird; Notiomystis cincta) enables characterization of the W chromosome and resources for conservation genomics

Molecular Ecology Resources, Journal Year: 2023, Volume and Issue: unknown

Published: June 18, 2023

A high-quality reference genome can be a valuable resource for threatened species by providing foundation to assess their evolutionary potential adapt future pressures such as environmental change. We assembled the of female hihi (Notiomysits cincta), passerine bird endemic Aotearoa New Zealand. The is 1.06 Gb, and high quality highly contiguous, with contig N50 7.0 Mb, estimated QV 44 BUSCO completeness 96.8%. male assembly comparable was generated in parallel. population linkage map used scaffold autosomal contigs into chromosomes. Female sequence coverage comparative genomics analyses were identify Z-, W-linked contigs. In total, 94.6% length assigned putative nuclear chromosome scaffolds. Native DNA methylation correlated between sexes, W more methylated than chromosomes Z 43 differentially regions identified, these may represent interesting candidates establishment or maintenance sex differences. By generating heterogametic sex, we have created that enables characterization genome-wide diversity facilitates investigation female-specific processes. genomes will form basis fine-scale assessment impacts low genetic inbreeding on adaptive therefore enable tailored informed conservation management this taonga (treasured) species.

Language: Английский

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The recombination landscape of the barn owl, from families to populations

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 16, 2024

Abstract Homologous recombination is a meiotic process that generates diversity along the genome and interacts with all evolutionary forces. Despite its importance, studies of landscapes are lacking due to methodological limitations dearth appropriate data. Linkage mapping based on familial data gives unbiased sex-specific broad-scale estimates while linkage disequilibrium (LD) inference population provides finer resolution albeit depending effective size acting selective In this study, we use combination these two methods, using dataset whole sequences elucidate landscape for Afro-European barn owl ( Tyto alba ). allows us refine assembly chromosome-level quality. We find subtle differences in crossover placement between sexes leads differential shuffling alleles. LD concordant family-based identify large variation rates within among groups. Larger chromosomes show smaller have universally high rate which shapes landscape. also local hotspots accordance other birds PRDM9 gene. However very little stability when compared populations shallow genetic differentiation. Overall, comprehensive analysis enhances our understanding dynamics, genomic architecture, owl, contributing valuable insights broader field avian genomics. Article summary To study events look either family or data, each method having advantages over other. both approaches quantify exist sexes, chromosomes.

Language: Английский

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