1
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Pokrovac I, Rohner N, Pezer Ž. The prevalence of copy number increase at multiallelic copy number variants associated with cave colonization. Mol Ecol 2024; 33:e17339. [PMID: 38556927 DOI: 10.1111/mec.17339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/16/2024] [Accepted: 03/22/2024] [Indexed: 04/02/2024]
Abstract
Copy number variation is a common contributor to phenotypic diversity, yet its involvement in ecological adaptation is not easily discerned. Instances of parallelly evolving populations of the same species in a similar environment marked by strong selective pressures present opportunities to study the role of copy number variants (CNVs) in adaptation. By identifying CNVs that repeatedly occur in multiple populations of the derived ecotype and are not (or are rarely) present in the populations of the ancestral ecotype, the association of such CNVs with adaptation to the novel environment can be inferred. We used this paradigm to identify CNVs associated with recurrent adaptation of the Mexican tetra (Astyanax mexicanus) to cave environment. Using a read-depth approach, we detected CNVs from previously re-sequenced genomes of 44 individuals belonging to two ancestral surfaces and three derived cave populations. We identified 102 genes and 292 genomic regions that repeatedly diverge in copy number between the two ecotypes and occupy 0.8% of the reference genome. Functional analysis revealed their association with processes previously recognized to be relevant for adaptation, such as vision, immunity, oxygen consumption, metabolism, and neural function and we propose that these variants have been selected for in the cave or surface waters. The majority of the ecotype-divergent CNVs are multiallelic and display copy number increases in cavefish compared to surface fish. Our findings suggest that multiallelic CNVs - including gene duplications - and divergence in copy number provide a fast route to produce novel phenotypes associated with adaptation to subterranean life.
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Affiliation(s)
| | - Nicolas Rohner
- Stowers Institute for Medical Research, Kansas City, Missouri, USA
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2
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David G, Bertolotti A, Layer R, Scofield D, Hayward A, Baril T, Burnett HA, Gudmunds E, Jensen H, Husby A. Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations. Genome Biol Evol 2024; 16:evae049. [PMID: 38489588 PMCID: PMC11018544 DOI: 10.1093/gbe/evae049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/28/2024] [Accepted: 03/07/2024] [Indexed: 03/17/2024] Open
Abstract
Comprehensive characterization of structural variation in natural populations has only become feasible in the last decade. To investigate the population genomic nature of structural variation, reproducible and high-confidence structural variation callsets are first required. We created a population-scale reference of the genome-wide landscape of structural variation across 33 Nordic house sparrows (Passer domesticus). To produce a consensus callset across all samples using short-read data, we compare heuristic-based quality filtering and visual curation (Samplot/PlotCritic and Samplot-ML) approaches. We demonstrate that curation of structural variants is important for reducing putative false positives and that the time invested in this step outweighs the potential costs of analyzing short-read-discovered structural variation data sets that include many potential false positives. We find that even a lenient manual curation strategy (e.g. applied by a single curator) can reduce the proportion of putative false positives by up to 80%, thus enriching the proportion of high-confidence variants. Crucially, in applying a lenient manual curation strategy with a single curator, nearly all (>99%) variants rejected as putative false positives were also classified as such by a more stringent curation strategy using three additional curators. Furthermore, variants rejected by manual curation failed to reflect the expected population structure from SNPs, whereas variants passing curation did. Combining heuristic-based quality filtering with rapid manual curation of structural variants in short-read data can therefore become a time- and cost-effective first step for functional and population genomic studies requiring high-confidence structural variation callsets.
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Affiliation(s)
- Gabriel David
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | | | - Ryan Layer
- BioFrontiers Institute, University of Colorado, Boulder, CO, USA
- Department of Computer Science, University of Colorado, Boulder, CO, USA
| | - Douglas Scofield
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Alexander Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Tobias Baril
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, Cornwall, UK
| | - Hamish A Burnett
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Erik Gudmunds
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Henrik Jensen
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, Trondheim, Norway
| | - Arild Husby
- Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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3
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Maduna SN, Jónsdóttir ÓDB, Imsland AKD, Gíslason D, Reynolds P, Kapari L, Hangstad TA, Meier K, Hagen SB. Genomic Signatures of Local Adaptation under High Gene Flow in Lumpfish-Implications for Broodstock Provenance Sourcing and Larval Production. Genes (Basel) 2023; 14:1870. [PMID: 37895225 PMCID: PMC10606024 DOI: 10.3390/genes14101870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/20/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
Aquaculture of the lumpfish (Cyclopterus lumpus L.) has become a large, lucrative industry owing to the escalating demand for "cleaner fish" to minimise sea lice infestations in Atlantic salmon mariculture farms. We used over 10K genome-wide single nucleotide polymorphisms (SNPs) to investigate the spatial patterns of genomic variation in the lumpfish along the coast of Norway and across the North Atlantic. Moreover, we applied three genome scans for outliers and two genotype-environment association tests to assess the signatures and patterns of local adaptation under extensive gene flow. With our 'global' sampling regime, we found two major genetic groups of lumpfish, i.e., the western and eastern Atlantic. Regionally in Norway, we found marginal evidence of population structure, where the population genomic analysis revealed a small portion of individuals with a different genetic ancestry. Nevertheless, we found strong support for local adaption under high gene flow in the Norwegian lumpfish and identified over 380 high-confidence environment-associated loci linked to gene sets with a key role in biological processes associated with environmental pressures and embryonic development. Our results bridge population genetic/genomics studies with seascape genomics studies and will facilitate genome-enabled monitoring of the genetic impacts of escapees and allow for genetic-informed broodstock selection and management in Norway.
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Affiliation(s)
- Simo Njabulo Maduna
- Department of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, 9925 Svanvik, Norway;
| | | | - Albert Kjartan Dagbjartarson Imsland
- Akvaplan-Niva Iceland Office, Akralind 6, 201 Kópavogur, Iceland; (Ó.D.B.J.); (A.K.D.I.)
- Department of Biological Sciences, High Technology Centre, University of Bergen, 5020 Bergen, Norway
| | | | | | - Lauri Kapari
- Akvaplan-Niva, Framsenteret, 9296 Tromsø, Norway;
| | | | | | - Snorre B. Hagen
- Department of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, 9925 Svanvik, Norway;
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4
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Zhang F, Wang C, Xu H, Xia X, Luo X, Li K, Han J, Lei C, Chen N, Yue X. Genomic analysis reveals a KIT-related chromosomal translocation associated with the white coat phenotype in yak. J Anim Breed Genet 2023; 140:330-342. [PMID: 36789788 DOI: 10.1111/jbg.12761] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 01/25/2023] [Indexed: 02/16/2023]
Abstract
White coat pigmentation is a striking phenotype of many domesticated species and has various genetic controls. The Tianzhu White yak, an indigenous breed with a complete white coat, has fascinated Tibetans for centuries. However, the genetic basis of this trait remains unknown. Here, we conducted population genomics analysis and genome-wide association study based on the whole-genome sequencing data of 38 white and 59 non-white-coated yak. The results revealed the presence of KIT-linked Cs alleles characterized by the translocations between chromosomes 6 and 29 in all-white yak. Furthermore, structural variations showed additional duplications of the Cs alleles in white yak compared with colour-sidedness cattle. Interestingly, the Cs alleles associated with the white coat phenotype in yak were found to have introgressed from taurine cattle. Our findings unveil the shared genetic control of the white coat phenotype and its evolution in closely related bovine species.
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Affiliation(s)
- Fengwei Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chong Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Haiyue Xu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaoting Xia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiaoyu Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Kaihui Li
- Extending Station for Animal Husbandry and Veterinary Technology of Tianzhu Tibetan Autonomous County, Tianzhu, China
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xiangpeng Yue
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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5
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Martínez Sosa F, Pilot M. Molecular Mechanisms Underlying Vertebrate Adaptive Evolution: A Systematic Review. Genes (Basel) 2023; 14:416. [PMID: 36833343 PMCID: PMC9957108 DOI: 10.3390/genes14020416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/24/2023] [Accepted: 02/01/2023] [Indexed: 02/08/2023] Open
Abstract
Adaptive evolution is a process in which variation that confers an evolutionary advantage in a specific environmental context arises and is propagated through a population. When investigating this process, researchers have mainly focused on describing advantageous phenotypes or putative advantageous genotypes. A recent increase in molecular data accessibility and technological advances has allowed researchers to go beyond description and to make inferences about the mechanisms underlying adaptive evolution. In this systematic review, we discuss articles from 2016 to 2022 that investigated or reviewed the molecular mechanisms underlying adaptive evolution in vertebrates in response to environmental variation. Regulatory elements within the genome and regulatory proteins involved in either gene expression or cellular pathways have been shown to play key roles in adaptive evolution in response to most of the discussed environmental factors. Gene losses were suggested to be associated with an adaptive response in some contexts. Future adaptive evolution research could benefit from more investigations focused on noncoding regions of the genome, gene regulation mechanisms, and gene losses potentially yielding advantageous phenotypes. Investigating how novel advantageous genotypes are conserved could also contribute to our knowledge of adaptive evolution.
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Affiliation(s)
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, 80-680 Gdańsk, Poland
- Faculty of Biology, University of Gdańsk, 80-308 Gdańsk, Poland
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6
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Current advances in primate genomics: novel approaches for understanding evolution and disease. Nat Rev Genet 2023; 24:314-331. [PMID: 36599936 DOI: 10.1038/s41576-022-00554-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2022] [Indexed: 01/05/2023]
Abstract
Primate genomics holds the key to understanding fundamental aspects of human evolution and disease. However, genetic diversity and functional genomics data sets are currently available for only a few of the more than 500 extant primate species. Concerted efforts are under way to characterize primate genomes, genetic polymorphism and divergence, and functional landscapes across the primate phylogeny. The resulting data sets will enable the connection of genotypes to phenotypes and provide new insight into aspects of the genetics of primate traits, including human diseases. In this Review, we describe the existing genome assemblies as well as genetic variation and functional genomic data sets. We highlight some of the challenges with sample acquisition. Finally, we explore how technological advances in single-cell functional genomics and induced pluripotent stem cell-derived organoids will facilitate our understanding of the molecular foundations of primate biology.
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7
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Zhang J, Zhang S, Zheng Z, Lu Z, Yang Y. Genomic divergence between two sister Ostrya species through linked selection and recombination. Ecol Evol 2022; 12:e9611. [PMID: 36540075 PMCID: PMC9754895 DOI: 10.1002/ece3.9611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/16/2022] [Accepted: 11/22/2022] [Indexed: 12/23/2022] Open
Abstract
Studying the evolution of genomic divergence between lineages is a topical issue in evolutionary biology. However, the evolutionary forces that shape the heterogeneous divergence of the genomic landscape are still poorly understood. Here, two wind-pollinated sister-species (Ostrya japonica and O. chinensis) are used to explore what these potential forces might be. A total of 40 individuals from 16 populations across their main distribution areas in China were sampled for genome-wide resequencing. Population demography analyses revealed that these two sister-species diverged at 3.06-4.43 Mya. Both population contraction and increased gene flow were detected during glacial periods, suggesting secondary contact at those times. All three parameters (D XY, π, and ρ) decreased in those regions showing high levels of differentiation (F ST). These findings indicate that linked selection and recombination played a key role in the genomic heterogeneous differentiation between the two Ostrya species. Genotype-environment association analyses showed that precipitation was the most important ecological factor for speciation. Such environmentally related genes and positive selection genes may have contributed to local adaptation and the maintenance of species boundaries.
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Affiliation(s)
- Jin Zhang
- State Key Laboratory of Grassland Agro‐Ecosystems, College of EcologyLanzhou UniversityLanzhouChina
| | - Shangzhe Zhang
- State Key Laboratory of Grassland Agro‐Ecosystems, College of EcologyLanzhou UniversityLanzhouChina
| | - Zeyu Zheng
- State Key Laboratory of Grassland Agro‐Ecosystems, College of EcologyLanzhou UniversityLanzhouChina
| | - Zhiqiang Lu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglaChina
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro‐Ecosystems, College of EcologyLanzhou UniversityLanzhouChina
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8
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Pokrovac I, Pezer Ž. Recent advances and current challenges in population genomics of structural variation in animals and plants. Front Genet 2022; 13:1060898. [PMID: 36523759 PMCID: PMC9745067 DOI: 10.3389/fgene.2022.1060898] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/15/2022] [Indexed: 05/02/2024] Open
Abstract
The field of population genomics has seen a surge of studies on genomic structural variation over the past two decades. These studies witnessed that structural variation is taxonomically ubiquitous and represent a dominant form of genetic variation within species. Recent advances in technology, especially the development of long-read sequencing platforms, have enabled the discovery of structural variants (SVs) in previously inaccessible genomic regions which unlocked additional structural variation for population studies and revealed that more SVs contribute to evolution than previously perceived. An increasing number of studies suggest that SVs of all types and sizes may have a large effect on phenotype and consequently major impact on rapid adaptation, population divergence, and speciation. However, the functional effect of the vast majority of SVs is unknown and the field generally lacks evidence on the phenotypic consequences of most SVs that are suggested to have adaptive potential. Non-human genomes are heavily under-represented in population-scale studies of SVs. We argue that more research on other species is needed to objectively estimate the contribution of SVs to evolution. We discuss technical challenges associated with SV detection and outline the most recent advances towards more representative reference genomes, which opens a new era in population-scale studies of structural variation.
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Affiliation(s)
| | - Željka Pezer
- Laboratory for Evolutionary Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
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9
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Comparative analysis of microsatellites in coding regions provides insights into the adaptability of the giant panda, polar bear and brown bear. Genetica 2022; 150:355-366. [DOI: 10.1007/s10709-022-00173-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 09/13/2022] [Indexed: 11/27/2022]
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10
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Guerra‐Garcia A, Haile T, Ogutcen E, Bett KE, von Wettberg EJ. An evolutionary look into the history of lentil reveals unexpected diversity. Evol Appl 2022; 15:1313-1325. [PMID: 36051460 PMCID: PMC9423085 DOI: 10.1111/eva.13467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 07/12/2022] [Accepted: 08/01/2022] [Indexed: 11/29/2022] Open
Abstract
The characterization and preservation of genetic variation in crops is critical to meeting the challenges of breeding in the face of changing climates and markets. In recent years, the use of single nucleotide polymorphisms (SNPs) has become routine, allowing us to understand the population structure, find divergent lines for crosses, and illuminate the origin of crops. However, the focus on SNPs overlooks other forms of variation, such as copy number variation (CNVs). Lentil is the third most important cold‐season legume and was domesticated in the Fertile Crescent. We genotyped 324 accessions that represent its global diversity, and using both SNPs and CNVs, we dissected the population structure and genetic variation, and identified candidate genes. Eight clusters were detected, most of them located in or near the Fertile Crescent, even though different clusters were present in distinct regions. The cluster from South Asia was particularly differentiated and presented low diversity, contrasting with the clusters from the Mediterranean and the northern temperate. Accessions from North America were mainly assigned to one cluster and were highly diverse, reflecting the efforts of breeding programs to integrate variation. Thirty‐three genes were identified as candidates under selection and among their functions were sporopollenin synthesis in pollen, a component of chlorophyll B reductase that partially determines the antenna size, and two genes related to the import system of chloroplasts. Eleven percent of all lentil genes and 21% of lentil disease resistance genes were affected by CNVs. The gene categories overrepresented in these genes were “enzymes,” “Cell Wall Organization,” and “external stimuli response.” All the genes found in the latter were associated with pathogen response. CNVs provided information about population structure and might have played a role in adaptation. The incorporation of CNVs in diversity studies is needed for a broader understanding of how they evolve and contribute to domestication.
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Affiliation(s)
| | - Teketel Haile
- Department of Plant Sciences University of Saskatchewan Saskatoon SK Canada
| | - Ezgi Ogutcen
- Conservatoire et Jardin Botaniques de la Ville de Genève Geneva Switzerland
| | - Kirstin E. Bett
- Department of Plant Sciences University of Saskatchewan Saskatoon SK Canada
| | - Eric J. von Wettberg
- Plant and Soil Science and Gund Institute for the Environment University of Vermont Burlington VT USA
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11
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Wong ATC, Lam DK, Poon ESK, Chan DTC, Sin SYW. Intra-specific copy number variation of MHC class II genes in the Siamese fighting fish. Immunogenetics 2022; 74:327-346. [PMID: 35229174 DOI: 10.1007/s00251-022-01255-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 02/04/2022] [Indexed: 11/28/2022]
Abstract
Duplicates of genes for major histocompatibility complex (MHC) molecules can be subjected to selection independently and vary markedly in their evolutionary rates, sequence polymorphism, and functional roles. Therefore, without a thorough understanding of their copy number variation (CNV) in the genome, the MHC-dependent fitness consequences within a species could be misinterpreted. Studying the intra-specific CNV of this highly polymorphic gene, however, has long been hindered by the difficulties in assigning alleles to loci and the lack of high-quality genomic data. Here, using the high-quality genome of the Siamese fighting fish (Betta splendens), a model for mate choice studies, and the whole-genome sequencing (WGS) data of 17 Betta species, we achieved locus-specific amplification of their three classical MHC class II genes - DAB1, DAB2, and DAB3. By performing quantitative PCR and depth-of-coverage analysis using the WGS data, we revealed intra-specific CNV at the DAB3 locus. We identified individuals that had two allelic copies (i.e., heterozygous or homozygous) or one allele (i.e., hemizygous) and individuals without this gene. The CNV was due to the deletion of a 20-kb-long genomic region harboring both the DAA3 and DAB3 genes. We further showed that the three DAB genes were under different modes of selection, which also applies to their corresponding DAA genes that share similar pattern of polymorphism. Our study demonstrates a combined approach to study CNV within a species, which is crucial for the understanding of multigene family evolution and the fitness consequences of CNV.
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Affiliation(s)
- Anson Tsz Chun Wong
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - Derek Kong Lam
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - Emily Shui Kei Poon
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - David Tsz Chung Chan
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China
| | - Simon Yung Wa Sin
- School of Biological Sciences, The University of Hong Kong, Pok Fu Lam Road, Hong Kong SAR, China.
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12
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Derežanin L, Blažytė A, Dobrynin P, Duchêne DA, Grau JH, Jeon S, Kliver S, Koepfli KP, Meneghini D, Preick M, Tomarovsky A, Totikov A, Fickel J, Förster DW. Multiple types of genomic variation contribute to adaptive traits in the mustelid subfamily Guloninae. Mol Ecol 2022; 31:2898-2919. [PMID: 35334142 DOI: 10.1111/mec.16443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 03/06/2022] [Accepted: 03/14/2022] [Indexed: 11/28/2022]
Abstract
Species of the mustelid subfamily Guloninae inhabit diverse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra (Eira barbara), the earliest diverging species in the subfamily, and compared this with the genomes available for the wolverine (Gulo gulo) and the sable (Martes zibellina). Our comparative genomic analyses included searching for signs of positive selection, examining changes in gene family sizes, as well as searching for species-specific structural variants (SVs). Among candidate loci associated with phenotypic traits, we observed many related to diet, body condition and reproduction. For example, for the tayra, which has an atypical gulonine reproductive strategy of aseasonal breeding, we observe species-specific changes in many pregnancy-related genes. For the wolverine, a circumpolar hypercarnivore that must cope with seasonal food scarcity, we observed many changes in genes associated with diet and body condition. All types of genomic variation examined (single nucleotide polymorphisms, gene family expansions, structural variants) contributed substantially to the identification of candidate loci. This strongly argues for consideration of variation other than single nucleotide polymorphisms in comparative genomics studies aiming to identify loci of adaptive significance.
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Affiliation(s)
- Lorena Derežanin
- Leibniz Institute for Zoo and Wildlife Research (IZW, Alfred Kowalke Straße 17, 10315, Berlin, Germany
| | - Asta Blažytė
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST, Ulsan, 44919, Republic of Korea
| | - Pavel Dobrynin
- Computer Technologies Laboratory, ITMO University, 49 Kronverkskiy Pr, 197101, Saint Petersburg, Russia
| | - David A Duchêne
- Center for Evolutionary Hologenomics, The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark
| | - José Horacio Grau
- amedes Genetics, amedes Medizinische Dienstleistungen GmbH, Jägerstr. 61, 10117, Berlin, Germany
| | - Sungwon Jeon
- Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST, Ulsan, 44919, Republic of Korea.,Clinomics Inc, Ulsan, 44919, Republic of Korea
| | - Sergei Kliver
- Institute of Molecular and Cellular Biology, SB RAS, 8/2 Acad. Lavrentiev Ave, Novosibirsk, 630090, Russia
| | - Klaus-Peter Koepfli
- Computer Technologies Laboratory, ITMO University, 49 Kronverkskiy Pr, 197101, Saint Petersburg, Russia.,Smithsonian-Mason School of Conservation, 1500 Remount Road, Front Royal, VA, 22630, USA.,Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, 1500 Remount Road, Front Royal, VA, 22630, USA
| | - Dorina Meneghini
- Leibniz Institute for Zoo and Wildlife Research (IZW, Alfred Kowalke Straße 17, 10315, Berlin, Germany
| | - Michaela Preick
- Institute for Biochemistry and Biology, Faculty of Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, OT, Germany
| | - Andrey Tomarovsky
- Computer Technologies Laboratory, ITMO University, 49 Kronverkskiy Pr, 197101, Saint Petersburg, Russia.,Institute of Molecular and Cellular Biology, SB RAS, 8/2 Acad. Lavrentiev Ave, Novosibirsk, 630090, Russia.,Novosibirsk State University, 1 Pirogova str, Novosibirsk, 630090, Russia
| | - Azamat Totikov
- Computer Technologies Laboratory, ITMO University, 49 Kronverkskiy Pr, 197101, Saint Petersburg, Russia.,Institute of Molecular and Cellular Biology, SB RAS, 8/2 Acad. Lavrentiev Ave, Novosibirsk, 630090, Russia.,Novosibirsk State University, 1 Pirogova str, Novosibirsk, 630090, Russia
| | - Jörns Fickel
- Leibniz Institute for Zoo and Wildlife Research (IZW, Alfred Kowalke Straße 17, 10315, Berlin, Germany.,Institute for Biochemistry and Biology, Faculty of Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, OT, Germany
| | - Daniel W Förster
- Leibniz Institute for Zoo and Wildlife Research (IZW, Alfred Kowalke Straße 17, 10315, Berlin, Germany
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13
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Prunier J, Carrier A, Gilbert I, Poisson W, Albert V, Taillon J, Bourret V, Côté SD, Droit A, Robert C. CNVs with adaptive potential in Rangifer tarandus: genome architecture and new annotated assembly. Life Sci Alliance 2021; 5:5/3/e202101207. [PMID: 34911809 PMCID: PMC8711850 DOI: 10.26508/lsa.202101207] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/29/2021] [Accepted: 11/29/2021] [Indexed: 01/13/2023] Open
Abstract
Rangifer tarandus has experienced recent drastic population size reductions throughout its circumpolar distribution and preserving the species implies genetic diversity conservation. To facilitate genomic studies of the species populations, we improved the genome assembly by combining long read and linked read and obtained a new highly accurate and contiguous genome assembly made of 13,994 scaffolds (L90 = 131 scaffolds). Using de novo transcriptome assembly of RNA-sequencing reads and similarity with annotated human gene sequences, 17,394 robust gene models were identified. As copy number variations (CNVs) likely play a role in adaptation, we additionally investigated these variations among 20 genomes representing three caribou ecotypes (migratory, boreal and mountain). A total of 1,698 large CNVs (length > 1 kb) showing a genome distribution including hotspots were identified. 43 large CNVs were particularly distinctive of the migratory and sedentary ecotypes and included genes annotated for functions likely related to the expected adaptations. This work includes the first publicly available annotation of the caribou genome and the first assembly allowing genome architecture analyses, including the likely adaptive CNVs reported here.
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Affiliation(s)
- Julien Prunier
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Quebec City, Canada
| | - Alexandra Carrier
- Département des sciences animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Quebec City, Canada
| | - Isabelle Gilbert
- Département des sciences animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Quebec City, Canada
| | - William Poisson
- Département des sciences animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Quebec City, Canada
| | - Vicky Albert
- Ministère des Forêts, de la Faune et des Parcs du Québec, Quebec City, Canada
| | - Joëlle Taillon
- Ministère des Forêts, de la Faune et des Parcs du Québec, Quebec City, Canada
| | - Vincent Bourret
- Ministère des Forêts, de la Faune et des Parcs du Québec, Quebec City, Canada
| | - Steeve D Côté
- Caribou Ungava, département de biologie, Faculté des Sciences et de Génie, Université Laval, Quebec City, Canada
| | - Arnaud Droit
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Quebec City, Canada
| | - Claude Robert
- Département des sciences animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Quebec City, Canada
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14
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Igoshin AV, Deniskova TE, Yurchenko AA, Yudin NS, Dotsev AV, Selionova MI, Zinovieva NA, Larkin DM. Copy number variants in genomes of local sheep breeds from Russia. Anim Genet 2021; 53:119-132. [PMID: 34904242 DOI: 10.1111/age.13163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2021] [Indexed: 01/21/2023]
Abstract
Copy number variants (CNVs) are genomic structural variations that contribute to many adaptive and economically important traits in livestock. In this study, we detected CNVs in 354 animals from 16 Russian indigenous sheep breeds and analysed their possible functional roles. Our analysis of the entire sample set resulted in 4527 CNVs forming 1450 CNV regions (CNVRs). When constructing CNVRs for individual breeds, a total of 2715 regions ranging from 88 in Groznensk to 337 in Osetin breeds were identified. To make interbreed CNVR frequency comparison possible, we also identified core CNVRs using CNVs with overlapping chromosomal locations found in different breeds. This resulted in 137 interbreed CNVRs with frequency >15% in at least one breed. Functional enrichment analysis of genes affected by CNVRs in individual breeds revealed 12 breeds with significant enrichments in olfactory perception, PRAME family proteins, and immune response. Function of genes affected by interbreed and breed-specific CNVRs revealed candidates related to domestication, adaptation to high altitudes and cold climates, reproduction, parasite resistance, milk and meat qualities, wool traits, fat storage, and fat metabolism. Our work is the first attempt to uncover and characterise the CNV makeup of Russian indigenous sheep breeds. Further experimental and functional validation of CNVRs would help in developing new and improving existing sheep breeds.
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Affiliation(s)
- A V Igoshin
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia
| | - T E Deniskova
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia
| | - A A Yurchenko
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia
| | - N S Yudin
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - A V Dotsev
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia
| | - M I Selionova
- Russian State Agrarian University, Moscow Timiryazev Agricultural Academy, Moscow, 127550, Russia
| | - N A Zinovieva
- L.K. Ernst Federal Research Center for Animal Husbandry, Podolsk, 142132, Russia
| | - D M Larkin
- The Federal Research Center Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia.,Royal Veterinary College, University of London, London, NW1 0TU, UK
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15
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Saremi NF, Oppenheimer J, Vollmers C, O'Connell B, Milne SA, Byrne A, Yu L, Ryder OA, Green RE, Shapiro B. An Annotated Draft Genome for the Andean Bear, Tremarctos ornatus. J Hered 2021; 112:377-384. [PMID: 33882130 PMCID: PMC8280923 DOI: 10.1093/jhered/esab021] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 04/20/2021] [Indexed: 12/18/2022] Open
Abstract
The Andean bear is the only extant member of the Tremarctine subfamily and the only extant ursid species to inhabit South America. Here, we present an annotated de novo assembly of a nuclear genome from a captive-born female Andean bear, Mischief, generated using a combination of short and long DNA and RNA reads. Our final assembly has a length of 2.23 Gb, and a scaffold N50 of 21.12 Mb, contig N50 of 23.5 kb, and BUSCO score of 88%. The Andean bear genome will be a useful resource for exploring the complex phylogenetic history of extinct and extant bear species and for future population genetics studies of Andean bears.
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Affiliation(s)
- Nedda F Saremi
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA
| | - Jonas Oppenheimer
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA
| | - Christopher Vollmers
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA
| | - Brendan O'Connell
- Department of Medical and Molecular Genetics, Oregon Health & Science University, Portland, OR
| | - Shard A Milne
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Ashley Byrne
- Department of Molecular, Cellular, Developmental Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | | | - Richard E Green
- Department of Biomolecular Engineering and Bioinformatics, University of California Santa Cruz, Santa Cruz, CA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA
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16
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Chacón-Vargas K, McCarthy CO, Choi D, Wang L, Yu JH, Gibbons JG. Comparison of Two Aspergillus oryzae Genomes From Different Clades Reveals Independent Evolution of Alpha-Amylase Duplication, Variation in Secondary Metabolism Genes, and Differences in Primary Metabolism. Front Microbiol 2021; 12:691296. [PMID: 34326825 PMCID: PMC8313989 DOI: 10.3389/fmicb.2021.691296] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/22/2021] [Indexed: 12/02/2022] Open
Abstract
Microbes (bacteria, yeasts, molds), in addition to plants and animals, were domesticated for their roles in food preservation, nutrition and flavor. Aspergillus oryzae is a domesticated filamentous fungal species traditionally used during fermentation of Asian foods and beverage, such as sake, soy sauce, and miso. To date, little is known about the extent of genome and phenotypic variation of A. oryzae isolates from different clades. Here, we used long-read Oxford Nanopore and short-read Illumina sequencing to produce a highly accurate and contiguous genome assemble of A. oryzae 14160, an industrial strain from China. To understand the relationship of this isolate, we performed phylogenetic analysis with 90 A. oryzae isolates and 1 isolate of the A. oryzae progenitor, Aspergillus flavus. This analysis showed that A. oryzae 14160 is a member of clade A, in comparison to the RIB 40 type strain, which is a member of clade F. To explore genome variation between isolates from distinct A. oryzae clades, we compared the A. oryzae 14160 genome with the complete RIB 40 genome. Our results provide evidence of independent evolution of the alpha-amylase gene duplication, which is one of the major adaptive mutations resulting from domestication. Synteny analysis revealed that both genomes have three copies of the alpha-amylase gene, but only one copy on chromosome 2 was conserved. While the RIB 40 genome had additional copies of the alpha-amylase gene on chromosomes III, and V, 14160 had a second copy on chromosome II and an third copy on chromosome VI. Additionally, we identified hundreds of lineage specific genes, and putative high impact mutations in genes involved in secondary metabolism, including several of the core biosynthetic genes. Finally, to examine the functional effects of genome variation between strains, we measured amylase activity, proteolytic activity, and growth rate on several different substrates. RIB 40 produced significantly higher levels of amylase compared to 14160 when grown on rice and starch. Accordingly, RIB 40 grew faster on rice, while 14160 grew faster on soy. Taken together, our analyses reveal substantial genome and phenotypic variation within A. oryzae.
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Affiliation(s)
- Katherine Chacón-Vargas
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, United States.,Department of Food Science, University of Massachusetts, Amherst, MA, United States
| | - Colin O McCarthy
- Department of Food Science, University of Massachusetts, Amherst, MA, United States
| | - Dasol Choi
- Deapertment of Food Science, University of Wisconsin-Madison, Madison, WI, United States.,Department of Bacteriology, and Food Research Institute, University of Wisconsin-Madison, Madison, WI, United States
| | - Long Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jae-Hyuk Yu
- Department of Bacteriology, and Food Research Institute, University of Wisconsin-Madison, Madison, WI, United States.,Department of Systems Biotechnology, Konkuk University, Seoul, South Korea
| | - John G Gibbons
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, United States.,Department of Food Science, University of Massachusetts, Amherst, MA, United States.,Organismic & Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, MA, United States
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17
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Cai Z, He Y, Liu S, Xue Y, Quan H, Zhang L, Gao YQ. Hierarchical dinucleotide distribution in genome along evolution and its effect on chromatin packing. Life Sci Alliance 2021; 4:4/8/e202101028. [PMID: 34168075 PMCID: PMC8321668 DOI: 10.26508/lsa.202101028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 11/29/2022] Open
Abstract
It describes how hierarchical CpG distribution on the genomes of species change in the evolution and the correlation with the chromatin structure. Dinucleotide densities and their distribution patterns vary significantly among species. Previous studies revealed that CpG is susceptible to methylation, enriched at topologically associating domain boundaries and its distribution along the genome correlates with chromatin compartmentalization. However, the multi-scale organizations of CpG in the linear genome, their role in chromatin organization, and how they change along the evolution are only partially understood. By comparing the CpG distribution at different genomic length scales, we quantify the difference between the CpG distributions of different species and evaluate how the hierarchical uneven CpG distribution appears in evolution. The clustering of species based on the CpG distribution is consistent with the phylogenetic tree. Interestingly, we found the CpG distribution and chromatin structure to be correlated in many different length scales, especially for mammals and avians, consistent with the mosaic CpG distribution in the genomes of these species.
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Affiliation(s)
- Zhicheng Cai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Biomedical Pioneering Innovation Center, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Yueying He
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Biomedical Pioneering Innovation Center, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Sirui Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Biomedical Pioneering Innovation Center, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Yue Xue
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Biomedical Pioneering Innovation Center, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Hui Quan
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Biomedical Pioneering Innovation Center, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Ling Zhang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.,Biomedical Pioneering Innovation Center, Peking University, Beijing, China
| | - Yi Qin Gao
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China .,Biomedical Pioneering Innovation Center, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
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18
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Kess T, Dempson JB, Lehnert SJ, Layton KKS, Einfeldt A, Bentzen P, Salisbury SJ, Messmer AM, Duffy S, Ruzzante DE, Nugent CM, Ferguson MM, Leong JS, Koop BF, O'Connell MF, Bradbury IR. Genomic basis of deep-water adaptation in Arctic Charr (Salvelinus alpinus) morphs. Mol Ecol 2021; 30:4415-4432. [PMID: 34152667 DOI: 10.1111/mec.16033] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/28/2021] [Accepted: 06/03/2021] [Indexed: 12/30/2022]
Abstract
The post-glacial colonization of Gander Lake in Newfoundland, Canada, by Arctic Charr (Salvelinus alpinus) provides the opportunity to study the genomic basis of adaptation to extreme deep-water environments. Colonization of deep-water (>50 m) habitats often requires extensive adaptation to cope with novel environmental challenges from high hydrostatic pressure, low temperature, and low light, but the genomic mechanisms underlying evolution in these environments are rarely known. Here, we compare genomic divergence between a deep-water morph adapted to depths of up to 288 m and a larger, piscivorous pelagic morph occupying shallower depths. Using both a SNP array and resequencing of whole nuclear and mitochondrial genomes, we find clear genetic divergence (FST = 0.11-0.15) between deep and shallow water morphs, despite an absence of morph divergence across the mitochondrial genome. Outlier analyses identified many diverged genomic regions containing genes enriched for processes such as gene expression and DNA repair, cardiac function, and membrane transport. Detection of putative copy number variants (CNVs) uncovered 385 genes with CNVs distinct to piscivorous morphs, and 275 genes with CNVs distinct to deep-water morphs, enriched for processes associated with synapse assembly. Demographic analyses identified evidence for recent and local morph divergence, and ongoing reductions in diversity consistent with postglacial colonization. Together, these results show that Arctic Charr morph divergence has occurred through genome-wide differentiation and elevated divergence of genes underlying multiple cellular and physiological processes, providing insight into the genomic basis of adaptation in a deep-water habitat following postglacial recolonization.
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Affiliation(s)
- Tony Kess
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - J Brian Dempson
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - Sarah J Lehnert
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - Kara K S Layton
- School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Anthony Einfeldt
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Paul Bentzen
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | | | - Amber M Messmer
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - Steven Duffy
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | | | - Cameron M Nugent
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Moira M Ferguson
- Department of Integrative Biology, University of Guelph, Guelph, ON, Canada
| | - Jong S Leong
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Ben F Koop
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Michael F O'Connell
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
| | - Ian R Bradbury
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, St. John's, NL, Canada
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19
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Strillacci MG, Moradi-Shahrbabak H, Davoudi P, Ghoreishifar SM, Mokhber M, Masroure AJ, Bagnato A. A genome-wide scan of copy number variants in three Iranian indigenous river buffaloes. BMC Genomics 2021; 22:305. [PMID: 33902439 PMCID: PMC8077898 DOI: 10.1186/s12864-021-07604-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 04/11/2021] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND In Iran, river buffalo is of great importance. It plays an important role in the economy of the Country, because its adaptation to harsh climate conditions and long productive lifespan permitting its farming across the Country and to convert low-quality feed into valuable milk. The genetic variability in Iranian buffalo breeds have been recently studied using SNPs genotyping data, but a whole genome Copy Number Variants (CNVs) mapping was not available. The aim of this study was to perform a genome wide CNV scan in 361 buffaloes of the three Iranian river breeds (Azeri, Khuzestani and Mazandarani) through the analysis of data obtained using the Axiom® Buffalo Genotyping Array 90 K. RESULTS CNVs detection resulted in a total of 9550 CNVs and 302 CNVRs identified in at least 5% of samples within breed, covering around 1.97% of the buffalo genome. and A total of 22 CNVRs were identified in all breeds and a different proportion of regions were in common among the three populations. Within the more represented CNVRs (n = 302) mapped a total of 409 buffalo genes, some of which resulted associated with morphological, healthy, milk, meat and reproductive traits, according to Animal Genome Cattle database. CONCLUSIONS This work provides a step forward in the interpretation of genomic variation within and among the buffalo populations, releasing a first map of CNVs and providing insights about their recent selection and adaptation to environment. The presence of the set of genes and QTL traits harbored in the CNVRs could be possibly linked with the buffalo's natural adaptive history together to a recent selection for milk used as primary food source from this species.
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Affiliation(s)
- Maria G. Strillacci
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell’Università 6, 26900 Lodi, Italy
| | - Hossein Moradi-Shahrbabak
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167 Iran
| | - Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N5E3 Canada
| | - Seyed Mohammad Ghoreishifar
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167 Iran
| | - Mahdi Mokhber
- Department of Animal Science, Faculty of Agriculture and Natural resources, Urmia University, 11Km Sero Road, P. O. Box: 165, Urmia, 57561-51818 Iran
| | - Anoar Jamai Masroure
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell’Università 6, 26900 Lodi, Italy
| | - Alessandro Bagnato
- Department of Veterinary Medicine, Università degli Studi di Milano, Via dell’Università 6, 26900 Lodi, Italy
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20
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Seixas FA, Edelman NB, Mallet J. Synteny-Based Genome Assembly for 16 Species of Heliconius Butterflies, and an Assessment of Structural Variation across the Genus. Genome Biol Evol 2021; 13:6207971. [PMID: 33792688 PMCID: PMC8290116 DOI: 10.1093/gbe/evab069] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/29/2021] [Indexed: 12/11/2022] Open
Abstract
Heliconius butterflies (Lepidoptera: Nymphalidae) are a group of 48 neotropical species widely studied in evolutionary research. Despite the wealth of genomic data generated in past years, chromosomal level genome assemblies currently exist for only two species, Heliconius melpomene and Heliconius erato, each a representative of one of the two major clades of the genus. Here, we use these reference genomes to improve the contiguity of previously published draft genome assemblies of 16 Heliconius species. Using a reference-assisted scaffolding approach, we place and order the scaffolds of these genomes onto chromosomes, resulting in 95.7-99.9% of their genomes anchored to chromosomes. Genome sizes are somewhat variable among species (270-422 Mb) and in one small group of species (Heliconius hecale, Heliconius elevatus, and Heliconius pardalinus) expansions in genome size are driven mainly by repetitive sequences that map to four small regions in the H. melpomene reference genome. Genes from these repeat regions show an increase in exon copy number, an absence of internal stop codons, evidence of constraint on nonsynonymous changes, and increased expression, all of which suggest that at least some of the extra copies are functional. Finally, we conducted a systematic search for inversions and identified five moderately large inversions fixed between the two major Heliconius clades. We infer that one of these inversions was transferred by introgression between the lineages leading to the erato/sara and burneyi/doris clades. These reference-guided assemblies represent a major improvement in Heliconius genomic resources that enable further genetic and evolutionary discoveries in this genus.
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Affiliation(s)
- Fernando A Seixas
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Nathaniel B Edelman
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA.,Yale Institute for Biospheric Studies, Yale University, New Haven, Connecticut, USA
| | - James Mallet
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
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21
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Sui Y, Peng S. A Mechanism Leading to Changes in Copy Number Variations Affected by Transcriptional Level Might Be Involved in Evolution, Embryonic Development, Senescence, and Oncogenesis Mediated by Retrotransposons. Front Cell Dev Biol 2021; 9:618113. [PMID: 33644055 PMCID: PMC7905054 DOI: 10.3389/fcell.2021.618113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/11/2021] [Indexed: 01/05/2023] Open
Abstract
In recent years, more and more evidence has emerged showing that changes in copy number variations (CNVs) correlated with the transcriptional level can be found during evolution, embryonic development, and oncogenesis. However, the underlying mechanisms remain largely unknown. The success of the induced pluripotent stem cell suggests that genome changes could bring about transformations in protein expression and cell status; conversely, genome alterations generated during embryonic development and senescence might also be the result of genome changes. With rapid developments in science and technology, evidence of changes in the genome affected by transcriptional level has gradually been revealed, and a rational and concrete explanation is needed. Given the preference of the HIV-1 genome to insert into transposons of genes with high transcriptional levels, we propose a mechanism based on retrotransposons facilitated by specific pre-mRNA splicing style and homologous recombination (HR) to explain changes in CNVs in the genome. This mechanism is similar to that of the group II intron that originated much earlier. Under this proposed mechanism, CNVs on genome are dynamically and spontaneously extended in a manner that is positively correlated with transcriptional level or contract as the cell divides during evolution, embryonic development, senescence, and oncogenesis, propelling alterations in them. Besides, this mechanism explains several critical puzzles in these processes. From evidence collected to date, it can be deduced that the message contained in genome is not just three-dimensional but will become four-dimensional, carrying more genetic information.
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Affiliation(s)
- Yunpeng Sui
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
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22
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Zheng Z, Li Y, Li M, Li G, Du X, Hongyin H, Yin M, Lu Z, Zhang X, Shrestha N, Liu J, Yang Y. Whole-Genome Diversification Analysis of the Hornbeam Species Reveals Speciation and Adaptation Among Closely Related Species. FRONTIERS IN PLANT SCIENCE 2021; 12:581704. [PMID: 33643339 PMCID: PMC7902934 DOI: 10.3389/fpls.2021.581704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
Speciation is the key evolutionary process for generating biological diversity and has a central place in evolutionary and ecological research. How species diverge and adapt to different habitats is one of the most exciting areas in speciation studies. Here, we sequenced 55 individuals from three closely related species in the genus Carpinus: Carpinus tibetana, Carpinus monbeigiana, and Carpinus mollicoma to understand the strength and direction of gene flow and selection during the speciation process. We found low genetic diversity in C. tibetana, which reflects its extremely small effective population size. The speciation analysis between C. monbeigiana and C. mollicoma revealed that both species diverged ∼1.2 Mya with bidirectional gene flow. A total of 291 highly diverged genes, 223 copy number variants genes, and 269 positive selected genes were recovered from the two species. Genes associated with the diverged and positively selected regions were mainly involved in thermoregulation, plant development, and response to stress, which included adaptations to their habitats. We also found a great population decline and a low genetic divergence of C. tibetana, which suggests that this species is extremely vulnerable. We believe that the current diversification and adaption study and the important genomic resource sequenced herein will facilitate the speciation studies and serve as an important methodological reference for future research.
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Affiliation(s)
- Zeyu Zheng
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Ying Li
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Minjie Li
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Guiting Li
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xin Du
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Hu Hongyin
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Mou Yin
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Zhiqiang Lu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, China
| | - Xu Zhang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Nawal Shrestha
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology and School of Life Sciences, Lanzhou University, Lanzhou, China
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Copy Number Variants in Four Italian Turkey Breeds. Animals (Basel) 2021; 11:ani11020391. [PMID: 33546454 PMCID: PMC7913726 DOI: 10.3390/ani11020391] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 01/31/2021] [Indexed: 12/15/2022] Open
Abstract
Simple Summary Hybrid Turkey selection is focusing on meat production traits characterized by high genetic heritability; the strong directional selection is well known to produce a constant loss in genetic diversity. Genetic characterization is one of the essential activities in the management of populations at risk of extinction. In addition, the genetic structure at the population level and the relationships between individuals are nowadays analysable at the genomic level. In this paper, the genome of 4 different Italian turkey breeds included in the Autochthonous Italian Poultry Breeds Register are analysed in order to obtain a genome-wide Copy Number Variant scan to ameliorate the existing knowledge of the genomic structure of Italian local turkey breeds. Differences have been described at genomic level for physiological, reproductive, and behavioral traits. The analyzed breeds are clearly distinguishable at the genomic level, and their relationships are clearly linked to their geographical origin and to the history of the rural structure of their developing regions. Genome information based on Copy Number Variant (CNV) detection has generated important information in this study concerning the uniqueness of the Italian local turkey breeds. Abstract Heritage breeds can be considered a genetic reservoir of genetic variability to be conserved and valorized considering their historical, cultural, and adaptive characteristics and possibly for their high potential in commercial hybrid genetic improvement by gene introgression. The aim of the present research is to investigate via Copy Number Variant (CNVs) the genomic makeup of 4 Italian autochthonous turkey breeds (Bronzato Comune—BrCI, 24; Ermellinato di Rovigo—ErRo, 24; Parma e Piacenza—PrPc, 25; Romagnolo—RoMa, 29). CNVs detection was performed using two different software and an interbreed CNVs comparison was carried out. A total of 1077 CNVs were identified in 102 turkeys, summarized into 519 CNV regions (CNVRs), which resulted after merging in 101 and 18 breed and shared regions. Biodiversity was analyzed using the effective information supplied by CNVs analysis, and BrCI and ErRo were characterized by a low mapped CNV number. Differences were described at a genomic level related to physiological, reproductive, and behavioral traits. The comparison with other three Italian turkey breeds (Brianzolo, Colle Euganei, and Nero Italiano) using a CNV data set available in the literature showed high clustering properties at the genomic level, and their relationships are strictly linked to the geographical origin and to the history of the rural structure of their native regions.
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24
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Molecular signatures of sexual communication in the phlebotomine sand flies. PLoS Negl Trop Dis 2020; 14:e0008967. [PMID: 33370303 PMCID: PMC7793272 DOI: 10.1371/journal.pntd.0008967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 01/08/2021] [Accepted: 11/09/2020] [Indexed: 12/21/2022] Open
Abstract
Phlebotomine sand flies employ an elaborate system of pheromone communication wherein males produce pheromones that attract other males to leks (thus acting as an aggregation pheromone) and females to the lekking males (sex pheromone). In addition, the type of pheromone produced varies among populations. Despite the numerous studies on sand fly chemical communication, little is known of their chemosensory genome. Chemoreceptors interact with chemicals in an organism’s environment to elicit essential behaviors such as the identification of suitable mates and food sources. Thus, they play important roles during adaptation and speciation. Major chemoreceptor gene families, odorant receptors (ORs), gustatory receptors (GRs) and ionotropic receptors (IRs) together detect and discriminate the chemical landscape. Here, we annotated the chemoreceptor repertoire in the genomes of Lutzomyia longipalpis and Phlebotomus papatasi, major phlebotomine vectors in the New World and Old World, respectively. Comparison with other sequenced Diptera revealed a large and unique expansion where over 80% of the ~140 ORs belong to a single, taxonomically restricted clade. We next conducted a comprehensive analysis of the chemoreceptors in 63 L. longipalpis individuals from four different locations in Brazil representing allopatric and sympatric populations and three sex-aggregation pheromone types (chemotypes). Population structure based on single nucleotide polymorphisms (SNPs) and gene copy number in the chemoreceptors corresponded with their putative chemotypes, and corroborate previous studies that identified multiple populations. Our work provides genomic insights into the underlying behavioral evolution of sexual communication in the L. longipalpis species complex in Brazil, and highlights the importance of accounting for the ongoing speciation in central and South American Lutzomyia that could have important implications for vectorial capacity. Phlebotomine sand flies are the primary vectors of Leishmania parasites, the causative agents of cutaneous and visceral leishmaniasis. Due to the lack of vaccines, control of leishmaniasis relies upon reducing human exposure to sand flies. Sand flies produce sex-aggregation pheromones that elicit robust olfactory behaviors, and the molecular targets for pheromone detection remain unknown. We identified chemoreceptors in the genomes of L. longipalpis and P. papatasi, and used these gene models to explore chemoreceptor evolution in 63 L. longipalpis individuals representing different pheromone types. These analyses identified genomic loci underlying chemosensory behavior in sand flies. This paves the way for understanding the sand fly species diversity at the molecular level, and functional characterization of these candidate genes will isolate and identify chemostimuli that can directly be tested as potential attractants for odor-baited traps.
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25
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Dorant Y, Cayuela H, Wellband K, Laporte M, Rougemont Q, Mérot C, Normandeau E, Rochette R, Bernatchez L. Copy number variants outperform SNPs to reveal genotype–temperature association in a marine species. Mol Ecol 2020; 29:4765-4782. [DOI: 10.1111/mec.15565] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Yann Dorant
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Hugo Cayuela
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Kyle Wellband
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Martin Laporte
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Quentin Rougemont
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Claire Mérot
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Eric Normandeau
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
| | - Rémy Rochette
- Department of Biology University of New Brunswick Saint John NB Canada
| | - Louis Bernatchez
- Institut de Biologie Intégrative des Systèmes (IBIS) Université Laval Québec QC Canada
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26
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Guan D, Martínez A, Castelló A, Landi V, Luigi-Sierra MG, Fernández-Álvarez J, Cabrera B, Delgado JV, Such X, Jordana J, Amills M. A genome-wide analysis of copy number variation in Murciano-Granadina goats. Genet Sel Evol 2020; 52:44. [PMID: 32770942 PMCID: PMC7414533 DOI: 10.1186/s12711-020-00564-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/28/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND In this work, our aim was to generate a map of the copy number variations (CNV) segregating in a population of Murciano-Granadina goats, the most important dairy breed in Spain, and to ascertain the main biological functions of the genes that map to copy number variable regions. RESULTS Using a dataset that comprised 1036 Murciano-Granadina goats genotyped with the Goat SNP50 BeadChip, we were able to detect 4617 and 7750 autosomal CNV with the PennCNV and QuantiSNP software, respectively. By applying the EnsembleCNV algorithm, these CNV were assembled into 1461 CNV regions (CNVR), of which 486 (33.3% of the total CNVR count) were consistently called by PennCNV and QuantiSNP and used in subsequent analyses. In this set of 486 CNVR, we identified 78 gain, 353 loss and 55 gain/loss events. The total length of all the CNVR (95.69 Mb) represented 3.9% of the goat autosomal genome (2466.19 Mb), whereas their size ranged from 2.0 kb to 11.1 Mb, with an average size of 196.89 kb. Functional annotation of the genes that overlapped with the CNVR revealed an enrichment of pathways related with olfactory transduction (fold-enrichment = 2.33, q-value = 1.61 × 10-10), ABC transporters (fold-enrichment = 5.27, q-value = 4.27 × 10-04) and bile secretion (fold-enrichment = 3.90, q-value = 5.70 × 10-03). CONCLUSIONS A previous study reported that the average number of CNVR per goat breed was ~ 20 (978 CNVR/50 breeds), which is much smaller than the number we found here (486 CNVR). We attribute this difference to the fact that the previous study included multiple caprine breeds that were represented by small to moderate numbers of individuals. Given the low frequencies of CNV (in our study, the average frequency of CNV is 1.44%), such a design would probably underestimate the levels of the diversity of CNV at the within-breed level. We also observed that functions related with sensory perception, metabolism and embryo development are overrepresented in the set of genes that overlapped with CNV, and that these loci often belong to large multigene families with tens, hundreds or thousands of paralogous members, a feature that could favor the occurrence of duplications or deletions by non-allelic homologous recombination.
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Affiliation(s)
- Dailu Guan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Amparo Martínez
- Departamento de Genética, Universidad de Córdoba, 14071, Córdoba, Spain
| | - Anna Castelló
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Vincenzo Landi
- Departamento de Genética, Universidad de Córdoba, 14071, Córdoba, Spain.,Department of Veterinary Medicine, University of Bari "Aldo Moro", SP. 62 per Casamassima km. 3, 70010, Valenzano, BA, Italy
| | - María Gracia Luigi-Sierra
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Javier Fernández-Álvarez
- Asociación Nacional de Criadores de Caprino de Raza Murciano-Granadina (CAPRIGRAN), 18340, Granada, Spain
| | - Betlem Cabrera
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | | | - Xavier Such
- Group of Research in Ruminants (G2R), Department of Animal and Food Science, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona, Spain
| | - Jordi Jordana
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain. .,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
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Samaniego Castruita JA, Westbury MV, Lorenzen ED. Analyses of key genes involved in Arctic adaptation in polar bears suggest selection on both standing variation and de novo mutations played an important role. BMC Genomics 2020; 21:543. [PMID: 32758141 PMCID: PMC7430819 DOI: 10.1186/s12864-020-06940-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/22/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Polar bears are uniquely adapted to an Arctic existence. Since their relatively recent divergence from their closest living relative, brown bears, less than 500,000 years ago, the species has evolved an array of novel traits suited to its Arctic lifestyle. Previous studies sought to uncover the genomic underpinnings of these unique characteristics, and disclosed the genes showing the strongest signal of positive selection in the polar bear lineage. Here, we survey a comprehensive dataset of 109 polar bear and 33 brown bear genomes to investigate the genomic variants within these top genes present in each species. Specifically, we investigate whether fixed homozygous variants in polar bears derived from selection on standing variation in the ancestral gene pool or on de novo mutation in the polar bear lineage. RESULTS We find that a large number of sites fixed in polar bears are biallelic in brown bears, suggesting selection on standing variation. Moreover, we uncover sites in which polar bears are fixed for a derived allele while brown bears are fixed for the ancestral allele, which we suggest may be a signal of de novo mutation in the polar bear lineage. CONCLUSIONS Our findings suggest that, among other mechanisms, natural selection acting on changes in genes derived from a combination of variation already in the ancestral gene pool, and from de novo missense mutations in the polar bear lineage, may have enabled the rapid adaptation of polar bears to their new Arctic environment.
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28
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Zhang Y, Hu Y, Wang X, Jiang Q, Zhao H, Wang J, Ju Z, Yang L, Gao Y, Wei X, Bai J, Zhou Y, Huang J. Population Structure, and Selection Signatures Underlying High-Altitude Adaptation Inferred From Genome-Wide Copy Number Variations in Chinese Indigenous Cattle. Front Genet 2020; 10:1404. [PMID: 32117428 PMCID: PMC7033542 DOI: 10.3389/fgene.2019.01404] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 12/23/2019] [Indexed: 12/12/2022] Open
Abstract
Copy number variations (CNVs) have been demonstrated as crucial substrates for evolution, adaptation and breed formation. Chinese indigenous cattle breeds exhibit a broad geographical distribution and diverse environmental adaptability. Here, we analyzed the population structure and adaptation to high altitude of Chinese indigenous cattle based on genome-wide CNVs derived from the high-density BovineHD SNP array. We successfully detected the genome-wide CNVs of 318 individuals from 24 Chinese indigenous cattle breeds and 37 yaks as outgroups. A total of 5,818 autosomal CNV regions (683 bp-4,477,860 bp in size), covering ~14.34% of the bovine genome (UMD3.1), were identified, showing abundant CNV resources. Neighbor-joining clustering, principal component analysis (PCA), and population admixture analysis based on these CNVs support that most Chinese cattle breeds are hybrids of Bos taurus taurus (hereinafter to be referred as Bos taurus) and Bos taurus indicus (Bos indicus). The distribution patterns of the CNVs could to some extent be related to the geographical backgrounds of the habitat of the breeds, and admixture among cattle breeds from different districts. We analyzed the selective signatures of CNVs positively involved in high-altitude adaptation using pairwise Fst analysis within breeds with a strong Bos taurus background (taurine-type breeds) and within Bos taurus×Bos indicus hybrids, respectively. CNV-overlapping genes with strong selection signatures (at top 0.5% of Fst value), including LETM1 (Fst = 0.490), TXNRD2 (Fst = 0.440), and STUB1 (Fst = 0.420) within taurine-type breeds, and NOXA1 (Fst = 0.233), RUVBL1 (Fst = 0.222), and SLC4A3 (Fst=0.154) within hybrids, were potentially involved in the adaptation to hypoxia. Thus, we provide a new profile of population structure from the CNV aspects of Chinese indigenous cattle and new insights into high-altitude adaptation in cattle.
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Affiliation(s)
- Yaran Zhang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yan Hu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiuge Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Qiang Jiang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Han Zhao
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jinpeng Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Zhihua Ju
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yaping Gao
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xiaochao Wei
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jiachen Bai
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jinming Huang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, Jinan, China.,Engineering Center of Animal Breeding and Reproduction, Jinan, China
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Myers EA, McKelvy AD, Burbrink FT. Biogeographic barriers, Pleistocene refugia, and climatic gradients in the southeastern Nearctic drive diversification in cornsnakes (Pantherophis guttatus complex). Mol Ecol 2020; 29:797-811. [PMID: 31955477 DOI: 10.1111/mec.15358] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 01/08/2020] [Accepted: 01/13/2020] [Indexed: 12/21/2022]
Abstract
The southeastern Nearctic is a biodiversity hotspot that is also rich in cryptic species. Numerous hypotheses (e.g., vicariance, local adaptation, and Pleistocene speciation in glacial refugia) have been tested in an attempt to explain diversification and the observed pattern of extant biodiversity. However, previous phylogeographic studies have both supported and refuted these hypotheses. Therefore, while data support one or more of these diversification hypotheses, it is likely that taxa are forming within this region in species-specific ways. Here, we generate a genomic data set for the cornsnakes (Pantherophis guttatus complex), which are widespread across this region, spanning both biogeographic barriers and climatic gradients. We use phylogeographic model selection combined with hindcast ecological niche models to determine regions of habitat stability through time. This combined approach suggests that numerous drivers of population differentiation explain the current diversity of this group of snakes. The Mississippi River caused initial speciation in this species complex, with more recent divergence events linked to adaptations to ecological heterogeneity and allopatric Pleistocene refugia. Lastly, we discuss the taxonomy of this group and suggest there may be additional cryptic species in need of formal recognition.
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Affiliation(s)
- Edward A Myers
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA.,Department of Herpetology, The American Museum of Natural History, New York, NY, USA
| | - Alexander D McKelvy
- Department of Biology, The Graduate School and Center, City University of New York, New York, NY, USA
| | - Frank T Burbrink
- Department of Herpetology, The American Museum of Natural History, New York, NY, USA
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30
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Signatures of Relaxed Selection in the CYP8B1 Gene of Birds and Mammals. J Mol Evol 2019; 87:209-220. [DOI: 10.1007/s00239-019-09903-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 07/25/2019] [Indexed: 01/26/2023]
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