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Zhou Y, Mabrouk I, Ma J, Liu Q, Song Y, Xue G, Li X, Wang S, Liu C, Hu J, Sun Y. Chromosome-level genome sequencing and multi-omics of the Hungarian White Goose (Anser anser domesticus) reveals novel miRNA-mRNA regulation mechanism of waterfowl feather follicle development. Poult Sci 2024; 103:103933. [PMID: 38943801 PMCID: PMC11261457 DOI: 10.1016/j.psj.2024.103933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/07/2024] [Accepted: 05/29/2024] [Indexed: 07/01/2024] Open
Abstract
The Hungarian White Goose (Anser anser domesticus) is an excellent European goose breed, with high feather and meat production. Despite its importance in the poultry industry, no available genome assembly information has been published. This study aimed to present Chromosome-level and functional genome sequencing of the Hungarian White Goose. The results showed that the genome assembly has a total length of 1115.82 Mb, 39 pairs of chromosomes, 92.98% of the BUSCO index, and contig N50 and scaffold N50 were up to 2.32 Mb and 60.69 Mb, respectively. Annotation of the genome assembly revealed 19550 genes, 286 miRNAs, etc. We identified 235 expanded and 1,167 contracted gene families in this breed compared with the other 16 species. We performed a positive selection analysis between this breed and four species of Anatidae to uncover the genetic information underlying feather follicle development. Further, we detected the function of miR-199-x, miR-143-y, and miR-23-z on goose embryonic skin fibroblast. In summary, we have successfully generated a highly complete genome sequence of the Hungarian white goose, which will provide a great resource to improve our understanding of gene functions and enhance the studies on feather follicle development at the genomic level.
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Affiliation(s)
- Yuxuan Zhou
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Ichraf Mabrouk
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Jingyun Ma
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Qiuyuan Liu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Yupu Song
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Guizhen Xue
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Xinyue Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Sihui Wang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Chang Liu
- Changchun Municipal People's Government, Changchun Animal Husbandry Service, Changchun, 130062, China
| | - Jingtao Hu
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Yongfeng Sun
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China; Key Laboratory of Animal Production, Product Quality and Security, Jilin Agricultural University, Ministry of Education, Changchun, 130118, China..
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Ottenburghs J, Honka J, Heikkinen ME, Madsen J, Müskens GJDM, Ellegren H. Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex. BMC Ecol Evol 2023; 23:2. [PMID: 36658479 PMCID: PMC9854053 DOI: 10.1186/s12862-023-02103-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 01/11/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Reconstructing phylogenetic relationships with genomic data remains a challenging endeavor. Numerous phylogenomic studies have reported incongruent gene trees when analyzing different genomic regions, complicating the search for a 'true' species tree. Some authors have argued that genomic regions of increased divergence (i.e. differentiation islands) reflect the species tree, although other studies have shown that these regions might produce misleading topologies due to species-specific selective sweeps or ancient introgression events. In this study, we tested the extent to which highly differentiated loci can resolve phylogenetic relationships in the Bean Goose complex, a group of goose taxa that includes the Taiga Bean Goose (Anser fabalis), the Tundra Bean Goose (Anser serrirostris) and the Pink-footed Goose (Anser brachyrhynchus). RESULTS First, we show that a random selection of genomic loci-which mainly samples the undifferentiated regions of the genome-results in an unresolved species complex with a monophyletic A. brachyrhynchus embedded within a paraphyletic cluster of A. fabalis and A. serrirostris. Next, phylogenetic analyses of differentiation islands converged upon a topology of three monophyletic clades in which A. brachyrhynchus is sister to A. fabalis, and A. serrirostris is sister to the clade uniting these two species. Close inspection of the locus trees within the differentiated regions revealed that this topology was consistently supported over other phylogenetic arrangements. As it seems unlikely that selection or introgression events have impacted all differentiation islands in the same way, we are convinced that this topology reflects the 'true' species tree. Additional analyses, based on D-statistics, revealed extensive introgression between A. fabalis and A. serrirostris, which partly explains the failure to resolve the species complex with a random selection of genomic loci. Recent introgression between these taxa has probably erased the phylogenetic branching pattern across a large section of the genome, whereas differentiation islands were unaffected by the homogenizing gene flow and maintained the phylogenetic patterns that reflect the species tree. CONCLUSIONS The evolution of the Bean Goose complex can be depicted as a simple bifurcating tree, but this would ignore the impact of introgressive hybridization. Hence, we advocate that the evolutionary relationships between these taxa are best represented as a phylogenetic network.
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Affiliation(s)
- Jente Ottenburghs
- Department of Evolutionary Biology, University of Uppsala, Uppsala, Sweden.
| | - Johanna Honka
- grid.10858.340000 0001 0941 4873Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Marja E. Heikkinen
- grid.10858.340000 0001 0941 4873Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, 90014 Oulu, Finland
| | - Jesper Madsen
- grid.7048.b0000 0001 1956 2722Department of Ecoscience, Aarhus University, C. F. Møllers Allé 8, 8000 Aarhus C, Denmark
| | - Gerhard J. D. M. Müskens
- grid.4818.50000 0001 0791 5666Team Animal Ecology, Wageningen Environmental Research, Wageningen University & Research, Droevendaalsesteeg 3-3A, 6708 PB Wageningen, The Netherlands
| | - Hans Ellegren
- grid.8993.b0000 0004 1936 9457Department of Evolutionary Biology, University of Uppsala, Uppsala, Sweden
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Kong HK, Chan Z, Yan SW, Lo PY, Wong WT, Wong KH, Lo CL. Revealing the species-specific genotype of the edible bird’s nest-producing swiftlet, Aerodramus fuciphagus and the proteome of edible bird’s nest. Food Res Int 2022; 160:111670. [DOI: 10.1016/j.foodres.2022.111670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/23/2022] [Accepted: 07/07/2022] [Indexed: 11/16/2022]
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4
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Mitochondrial dysfunction in follicles is associated with broodiness in Zhedong white goose. Anim Reprod Sci 2022; 243:107032. [DOI: 10.1016/j.anireprosci.2022.107032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/29/2022] [Accepted: 07/03/2022] [Indexed: 11/29/2022]
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5
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Piórkowska K, Żukowski K, Połtowicz K, Witarski W, Nowak J, Potocka P, Ropka-Molik K. Hypothalamus-pituitary axis transcriptomic modification dependent on growth rate in geese (Anser anser domesticus). Anim Genet 2021; 52:834-847. [PMID: 34595762 DOI: 10.1111/age.13140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2021] [Indexed: 11/28/2022]
Abstract
The hypothalamus-pituitary axis is involved in digest processing, stress response, energy storage and many other processes. In birds, this control differs from in mammals, such as regulation of appetite and satiety centre. The transcriptomics analyses of both brain structures can explain and identify the molecular processes related to body growth and development and nutritional status. Many reports describe chicken transcriptome in literature, but gene expression studies in the other poultry species are extremely rare. Therefore, the present research undertook the attempt to explain hypothalamus-pituitary processes in domestic geese-Polish White Kołuda®, main Polish line. After 16 weeks of fattening, significant differences in geese weight were observed. Therefore, transcriptome of pituitary and hypothalamus profiles could be compared between low and high growth rate geese groups. Due to the lack of domestic geese genome assembly in the public databases, we used three mapping approaches: de novo analysis, mapping to two other pink-footed and swan geese genomes. The functional examination showed that the most enriched biological process in the geese hypothalamus covered the immune response. Moreover, in the hypothalamus, proteins typical for the pituitary such as PRL and GH were differentially expressed (DE). Our study recommends one gene as a candidate for growth rate in geese-the FOS gene, which encodes Fos proto-oncogene-DE in both analysed tissues. The FOS gene is involved in regulating feeding behaviour, immune regulation, stimulating cellular proliferation and controlling growth hormone synthesis. Moreover, the present investigation indicates DE genes involved in gene expression regulation. The study delivers new information about the changes in the pituitary-hypothalamic axis in geese dependent on growth rate differences.
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Affiliation(s)
- Katarzyna Piórkowska
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland
| | - Kacper Żukowski
- Department of Cattle Breeding, National Research Institute of Animal Production, Balice, Poland
| | - Katarzyna Połtowicz
- Department of Poultry Breeding, National Research Institute of Animal Production, Balice, Poland
| | - Wojciech Witarski
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland
| | - Joanna Nowak
- Department of Poultry Breeding, National Research Institute of Animal Production, Balice, Poland
| | - Paulina Potocka
- National Research Institute of Animal Production, Experimental Station Kołuda Wielka, Janikowo, Poland
| | - Katarzyna Ropka-Molik
- Department of Animal Molecular Biology, National Research Institute of Animal Production, Balice, Poland
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6
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Wesołowski W, Domnicz B, Augustynowicz J, Szklarczyk M. VCF2CAPS-A high-throughput CAPS marker design from VCF files and its test-use on a genotyping-by-sequencing (GBS) dataset. PLoS Comput Biol 2021; 17:e1008980. [PMID: 34014924 PMCID: PMC8186816 DOI: 10.1371/journal.pcbi.1008980] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 06/08/2021] [Accepted: 04/18/2021] [Indexed: 11/21/2022] Open
Abstract
Next-generation sequencing (NGS) is a powerful tool for massive detection of DNA sequence variants such as single nucleotide polymorphisms (SNPs), multi-nucleotide polymorphisms (MNPs) and insertions/deletions (indels). For routine screening of numerous samples, these variants are often converted into cleaved amplified polymorphic sequence (CAPS) markers which are based on the presence versus absence of restriction sites within PCR products. Current computational tools for SNP to CAPS conversion are limited and usually infeasible to use for large datasets as those generated with NGS. Moreover, there is no available tool for massive conversion of MNPs and indels into CAPS markers. Here, we present VCF2CAPS–a new software for identification of restriction endonucleases that recognize SNP/MNP/indel-containing sequences from NGS experiments. Additionally, the program contains filtration utilities not available in other SNP to CAPS converters–selection of markers with a single polymorphic cut site within a user-specified sequence length, and selection of markers that differentiate up to three user-defined groups of individuals from the analyzed population. Performance of VCF2CAPS was tested on a thoroughly analyzed dataset from a genotyping-by-sequencing (GBS) experiment. A selection of CAPS markers picked by the program was subjected to experimental verification. CAPS markers, also referred to as PCR-RFLPs, belong to basic tools exploited in plant, animal and human genetics. Our new software–VCF2CAPS–fills the gap in the current inventory of genetic software by high-throughput CAPS marker design from next-generation sequencing (NGS) data. The program should be of interest to geneticists involved in molecular diagnostics. In this paper we show a successful exemplary application of VCF2CAPS and we believe that its usefulness is guaranteed by the growing availability of NGS services.
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Affiliation(s)
- Wojciech Wesołowski
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Krakow, Poland
| | - Beata Domnicz
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Krakow, Poland
| | - Joanna Augustynowicz
- Department of Botany, Physiology and Plant Protection, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Krakow, Poland
| | - Marek Szklarczyk
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Krakow, Poland
- * E-mail:
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7
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Martini D, Dussex N, Robertson BC, Gemmell NJ, Knapp M. Evolution of the "world's only alpine parrot": Genomic adaptation or phenotypic plasticity, behaviour and ecology? Mol Ecol 2021; 30:6370-6386. [PMID: 33973288 DOI: 10.1111/mec.15978] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/19/2021] [Accepted: 04/28/2021] [Indexed: 02/06/2023]
Abstract
Climate warming, in particular in island environments, where opportunities for species to disperse are limited, may become a serious threat to cold adapted alpine species. In order to understand how alpine species may respond to a warming world, we need to understand the drivers that have shaped their habitat specialisation and the evolutionary adaptations that allow them to utilize alpine habitats. The endemic, endangered New Zealand kea (Nestor notabilis) is considered the only alpine parrot in the world. As a species commonly found in the alpine zone it may be highly susceptible to climate warming. But is it a true alpine specialist? Is its evolution driven by adaptation to the alpine zone, or is the kea an open habitat generalist that simply uses the alpine zone to, for example, avoid lower lying anthropogenic landscapes? We use whole genome data of the kea and its close, forest adapted sister species, the kākā (Nestor meridionalis) to reconstruct the evolutionary history of both species and identify the functional genomic differences that underlie their habitat specialisations. Our analyses do not identify major functional genomic differences between kea and kākā in pathways associated with high-altitude. Rather, we found evidence that selective pressures on adaptations commonly found in alpine species are present in both Nestor species, suggesting that selection for alpine adaptations has not driven their divergence. Strongly divergent demographic responses to past climate warming between the species nevertheless highlight potential future threats to kea survival in a warming world.
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Affiliation(s)
- Denise Martini
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Nicolas Dussex
- Centre for Palaeogenetics, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.,Department of Zoology, Stockholm University, Stockholm, Sweden
| | | | - Neil J Gemmell
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - Michael Knapp
- Department of Anatomy, University of Otago, Dunedin, New Zealand
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8
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Moodley Y, Westbury MV, Russo IRM, Gopalakrishnan S, Rakotoarivelo A, Olsen RA, Prost S, Tunstall T, Ryder OA, Dalén L, Bruford MW. Interspecific Gene Flow and the Evolution of Specialization in Black and White Rhinoceros. Mol Biol Evol 2021; 37:3105-3117. [PMID: 32585004 DOI: 10.1093/molbev/msaa148] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Africa's black (Diceros bicornis) and white (Ceratotherium simum) rhinoceros are closely related sister-taxa that evolved highly divergent obligate browsing and grazing feeding strategies. Although their precursor species Diceros praecox and Ceratotherium mauritanicum appear in the fossil record ∼5.2 Ma, by 4 Ma both were still mixed feeders, and were even spatiotemporally sympatric at several Pliocene sites in what is today Africa's Rift Valley. Here, we ask whether or not D. praecox and C. mauritanicum were reproductively isolated when they came into Pliocene secondary contact. We sequenced and de novo assembled the first annotated black rhinoceros reference genome and compared it with available genomes of other black and white rhinoceros. We show that ancestral gene flow between D. praecox and C. mauritanicum ceased sometime between 3.3 and 4.1 Ma, despite conventional methods for the detection of gene flow from whole genome data returning false positive signatures of recent interspecific migration due to incomplete lineage sorting. We propose that ongoing Pliocene genetic exchange, for up to 2 My after initial divergence, could have potentially hindered the development of obligate feeding strategies until both species were fully reproductively isolated, but that the more severe and shifting paleoclimate of the early Pleistocene was likely the ultimate driver of ecological specialization in African rhinoceros.
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Affiliation(s)
- Yoshan Moodley
- Department of Zoology, University of Venda, Thohoyandou, Republic of South Africa
| | - Michael V Westbury
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Isa-Rita M Russo
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andrinajoro Rakotoarivelo
- Department of Zoology, University of Venda, Thohoyandou, Republic of South Africa.,Natiora Ahy Madagasikara, Ampahibe, Antananarivo, Madagascar
| | - Remi-Andre Olsen
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Stefan Prost
- LOEWE-Centre for Translational Biodiversity Genomics, Senckenberg Museum, Frankfurt, Germany.,South African National Biodiversity Institute, National Zoological Gardens, Pretoria, Republic of South Africa
| | - Tate Tunstall
- San Diego Zoo Institute for Conservation Research, San Diego Zoo Global, Escondido, CA
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, San Diego Zoo Global, Escondido, CA
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Michael W Bruford
- School of Biosciences, Cardiff University, Cardiff, United Kingdom.,Sustainable Places Research Institute, Cardiff University, Cardiff, United Kingdom
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9
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Díez-Del-Molino D, von Seth J, Gyllenstrand N, Widemo F, Liljebäck N, Svensson M, Sjögren-Gulve P, Dalén L. Population genomics reveals lack of greater white-fronted introgression into the Swedish lesser white-fronted goose. Sci Rep 2020; 10:18347. [PMID: 33110153 PMCID: PMC7591532 DOI: 10.1038/s41598-020-75315-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 09/21/2020] [Indexed: 11/09/2022] Open
Abstract
Interspecific introgression is considered a potential threat to endangered taxa. One example where this has had a major impact on conservation policy is the lesser white-fronted goose (LWfG). After a dramatic decline in Sweden, captive breeding birds were released between 1981-1999 with the aim to reinforce the population. However, the detection of greater white-fronted goose (GWfG) mitochondrial DNA in the LWfG breeding stock led to the release program being dismantled, even though the presence of GWfG introgression in the actual wild Swedish LWfG population was never documented. To examine this, we sequenced the complete genomes of 21 LWfG birds from the Swedish, Russian and Norwegian populations, and compared these with genomes from other goose species, including the GWfG. We found no evidence of interspecific introgression into the wild Swedish LWfG population in either nuclear genomic or mitochondrial data. Moreover, Swedish LWfG birds are genetically distinct from the Russian and Norwegian populations and display comparatively low genomic diversity and high levels of inbreeding. Our findings highlight the utility of genomic approaches in providing scientific evidence that can help improve conservation management as well as policies for breeding and reinforcement programmes.
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Affiliation(s)
- David Díez-Del-Molino
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405, Stockholm, Sweden. .,Department of Zoology, Stockholm University, 10691, Stockholm, Sweden.
| | - Johanna von Seth
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405, Stockholm, Sweden.,Department of Zoology, Stockholm University, 10691, Stockholm, Sweden
| | - Niclas Gyllenstrand
- Centre for Genetic Identification, Department of Environmental Research and Monitoring, Swedish Museum of Natural History, Box 50007, 10405, Stockholm, Sweden
| | - Fredrik Widemo
- Department of Wildlife, Fish and Environmental Studies, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Niklas Liljebäck
- Grimsö Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences, 73091, Riddarhyttan, Sweden
| | - Mikael Svensson
- Swedish Species Information Centre, SLU ArtDatabanken, Box 7007, 750 07, Uppsala, Sweden
| | - Per Sjögren-Gulve
- The Wildlife Analysis Unit, Swedish Environmental Protection Agency, 106 48, Stockholm, Sweden
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405, Stockholm, Sweden.
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Long-Term Reciprocal Gene Flow in Wild and Domestic Geese Reveals Complex Domestication History. G3-GENES GENOMES GENETICS 2020; 10:3061-3070. [PMID: 32680852 PMCID: PMC7466990 DOI: 10.1534/g3.120.400886] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Hybridization has frequently been observed between wild and domestic species and can substantially impact genetic diversity of both counterparts. Geese show some of the highest levels of interspecific hybridization across all bird orders, and two of the goose species in the genus Anser have been domesticated providing an excellent opportunity for a joint study of domestication and hybridization. Until now, knowledge of the details of the goose domestication process has come from archaeological findings and historical writings supplemented with a few studies based on mitochondrial DNA. Here, we used genome-wide markers to make the first genome-based inference of the timing of European goose domestication. We also analyzed the impact of hybridization on the genome-wide genetic variation in current populations of the European domestic goose and its wild progenitor: the graylag goose (Anser anser). Our dataset consisted of 58 wild graylags sampled around Eurasia and 75 domestic geese representing 14 breeds genotyped for 33,527 single nucleotide polymorphisms. Demographic reconstruction and clustering analysis suggested that divergence between wild and domestic geese around 5,300 generations ago was followed by long-term genetic exchange, and that graylag populations have 3.2–58.0% admixture proportions with domestic geese, with distinct geographic patterns. Surprisingly, many modern European breeds share considerable (> 10%) ancestry with the Chinese domestic geese that is derived from the swan goose Anser cygnoid. We show that the domestication process can progress despite continued and pervasive gene flow from the wild form.
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11
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Recent introgression between Taiga Bean Goose and Tundra Bean Goose results in a largely homogeneous landscape of genetic differentiation. Heredity (Edinb) 2020; 125:73-84. [PMID: 32451423 PMCID: PMC7413267 DOI: 10.1038/s41437-020-0322-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 02/06/2023] Open
Abstract
Several studies have uncovered a highly heterogeneous landscape of genetic differentiation across the genomes of closely related species. Specifically, genetic differentiation is often concentrated in particular genomic regions (“islands of differentiation”) that might contain barrier loci contributing to reproductive isolation, whereas the rest of the genome is homogenized by introgression. Alternatively, linked selection can produce differentiation islands in allopatry without introgression. We explored the influence of introgression on the landscape of genetic differentiation in two hybridizing goose taxa: the Taiga Bean Goose (Anser fabalis) and the Tundra Bean Goose (A. serrirostris). We re-sequenced the whole genomes of 18 individuals (9 of each taxon) and, using a combination of population genomic summary statistics and demographic modeling, we reconstructed the evolutionary history of these birds. Next, we quantified the impact of introgression on the build-up and maintenance of genetic differentiation. We found evidence for a scenario of allopatric divergence (about 2.5 million years ago) followed by recent secondary contact (about 60,000 years ago). Subsequent introgression events led to high levels of gene flow, mainly from the Tundra Bean Goose into the Taiga Bean Goose. This scenario resulted in a largely undifferentiated genomic landscape (genome-wide FST = 0.033) with a few notable differentiation peaks that were scattered across chromosomes. The summary statistics indicated that some peaks might contain barrier loci while others arose in allopatry through linked selection. Finally, based on the low genetic differentiation, considerable morphological variation and incomplete reproductive isolation, we argue that the Taiga and the Tundra Bean Goose should be treated as subspecies.
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12
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Wang W, Wang F, Hao R, Wang A, Sharshov K, Druzyaka A, Lancuo Z, Shi Y, Feng S. First de novo whole genome sequencing and assembly of the bar-headed goose. PeerJ 2020; 8:e8914. [PMID: 32292659 PMCID: PMC7144584 DOI: 10.7717/peerj.8914] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 03/15/2020] [Indexed: 12/23/2022] Open
Abstract
Background The bar-headed goose (Anser indicus) mainly inhabits the plateau wetlands of Asia. As a specialized high-altitude species, bar-headed geese can migrate between South and Central Asia and annually fly twice over the Himalayan mountains along the central Asian flyway. The physiological, biochemical and behavioral adaptations of bar-headed geese to high-altitude living and flying have raised much interest. However, to date, there is still no genome assembly information publicly available for bar-headed geese. Methods In this study, we present the first de novo whole genome sequencing and assembly of the bar-headed goose, along with gene prediction and annotation. Results 10X Genomics sequencing produced a total of 124 Gb sequencing data, which can cover the estimated genome size of bar-headed goose for 103 times (average coverage). The genome assembly comprised 10,528 scaffolds, with a total length of 1.143 Gb and a scaffold N50 of 10.09 Mb. Annotation of the bar-headed goose genome assembly identified a total of 102 Mb (8.9%) of repetitive sequences, 16,428 protein-coding genes, and 282 tRNAs. In total, we determined that there were 63 expanded and 20 contracted gene families in the bar-headed goose compared with the other 15 vertebrates. We also performed a positive selection analysis between the bar-headed goose and the closely related low-altitude goose, swan goose (Anser cygnoides), to uncover its genetic adaptations to the Qinghai-Tibetan Plateau. Conclusion We reported the currently most complete genome sequence of the bar-headed goose. Our assembly will provide a valuable resource to enhance further studies of the gene functions of bar-headed goose. The data will also be valuable for facilitating studies of the evolution, population genetics and high-altitude adaptations of the bar-headed geese at the genomic level.
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Affiliation(s)
- Wen Wang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xi'ning, Qinghai, China
| | - Fang Wang
- Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xi'ning, Qinghai, China
| | - Rongkai Hao
- Novogene Bioinformatics Institute, Beijing, China
| | - Aizhen Wang
- College of Eco-Environmental Engineering, Qinghai University, Xi'ning, Qinghai, China
| | - Kirill Sharshov
- Research Institute of Experimental and Clinical Medicine, Novosibirsk, Russia
| | - Alexey Druzyaka
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Zhuoma Lancuo
- School of Finance and Economics, Qinghai University, Xi'ning, Qinghai, China
| | - Yuetong Shi
- KunLun College of Qinghai University, Xi'ning, Qinghai, China
| | - Shuo Feng
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xi'ning, Qinghai, China
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Nilsson P, Solbakken MH, Schmid BV, Orr RJS, Lv R, Cui Y, Song Y, Zhang Y, Baalsrud HT, Tørresen OK, Stenseth NC, Yang R, Jakobsen KS, Easterday WR, Jentoft S. The Genome of the Great Gerbil Reveals Species-Specific Duplication of an MHCII Gene. Genome Biol Evol 2020; 12:3832-3849. [PMID: 31971556 PMCID: PMC7046166 DOI: 10.1093/gbe/evaa008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2020] [Indexed: 12/13/2022] Open
Abstract
The great gerbil (Rhombomys opimus) is a social rodent living in permanent, complex burrow systems distributed throughout Central Asia, where it serves as the main host of several important vector-borne infectious pathogens including the well-known plague bacterium (Yersinia pestis). Here, we present a continuous annotated genome assembly of the great gerbil, covering over 96% of the estimated 2.47-Gb genome. Taking advantage of the recent genome assemblies of the sand rat (Psammomys obesus) and the Mongolian gerbil (Meriones unguiculatus), comparative immunogenomic analyses reveal shared gene losses within TLR gene families (i.e., TLR8, TLR10, and the entire TLR11-subfamily) for Gerbillinae, accompanied with signs of diversifying selection of TLR7 and TLR9. Most notably, we find a great gerbil-specific duplication of the MHCII DRB locus. In silico analyses suggest that the duplicated gene provides high peptide binding affinity for Yersiniae epitopes as well as Leishmania and Leptospira epitopes, putatively leading to increased capability to withstand infections by these pathogens. Our study demonstrates the power of whole-genome sequencing combined with comparative genomic analyses to gain deeper insight into the immunogenomic landscape of the great gerbil and its close relatives.
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Affiliation(s)
- Pernille Nilsson
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Monica H Solbakken
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Boris V Schmid
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | | | - Ruichen Lv
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yujiang Zhang
- Xinjiang Center for Disease Control and Prevention, Urumqi, China
| | - Helle T Baalsrud
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Ole K Tørresen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Nils Chr Stenseth
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - William Ryan Easterday
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
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Wright B, Farquharson KA, McLennan EA, Belov K, Hogg CJ, Grueber CE. From reference genomes to population genomics: comparing three reference-aligned reduced-representation sequencing pipelines in two wildlife species. BMC Genomics 2019; 20:453. [PMID: 31159724 PMCID: PMC6547446 DOI: 10.1186/s12864-019-5806-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 05/17/2019] [Indexed: 11/13/2022] Open
Abstract
Background Recent advances in genomics have greatly increased research opportunities for non-model species. For wildlife, a growing availability of reference genomes means that population genetics is no longer restricted to a small set of anonymous loci. When used in conjunction with a reference genome, reduced-representation sequencing (RRS) provides a cost-effective method for obtaining reliable diversity information for population genetics. Many software tools have been developed to process RRS data, though few studies of non-model species incorporate genome alignment in calling loci. A commonly-used RRS analysis pipeline, Stacks, has this capacity and so it is timely to compare its utility with existing software originally designed for alignment and analysis of whole genome sequencing data. Here we examine population genetic inferences from two species for which reference-aligned reduced-representation data have been collected. Our two study species are a threatened Australian marsupial (Tasmanian devil Sarcophilus harrisii; declining population) and an Arctic-circle migrant bird (pink-footed goose Anser brachyrhynchus; expanding population). Analyses of these data are compared using Stacks versus two widely-used genomics packages, SAMtools and GATK. We also introduce a custom R script to improve the reliability of single nucleotide polymorphism (SNP) calls in all pipelines and conduct population genetic inferences for non-model species with reference genomes. Results Although we identified orders of magnitude fewer SNPs in our devil dataset than for goose, we found remarkable symmetry between the two species in our assessment of software performance. For both datasets, all three methods were able to delineate population structure, even with varying numbers of loci. For both species, population structure inferences were influenced by the percent of missing data. Conclusions For studies of non-model species with a reference genome, we recommend combining Stacks output with further filtering (as included in our R pipeline) for population genetic studies, paying particular attention to potential impact of missing data thresholds. We recognise SAMtools as a viable alternative for researchers more familiar with this software. We caution against the use of GATK in studies with limited computational resources or time. Electronic supplementary material The online version of this article (10.1186/s12864-019-5806-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Belinda Wright
- Faculty of Science, The University of Sydney, School of Life and Environmental Sciences, Sydney, Australia
| | - Katherine A Farquharson
- Faculty of Science, The University of Sydney, School of Life and Environmental Sciences, Sydney, Australia
| | - Elspeth A McLennan
- Faculty of Science, The University of Sydney, School of Life and Environmental Sciences, Sydney, Australia
| | - Katherine Belov
- Faculty of Science, The University of Sydney, School of Life and Environmental Sciences, Sydney, Australia
| | - Carolyn J Hogg
- Faculty of Science, The University of Sydney, School of Life and Environmental Sciences, Sydney, Australia
| | - Catherine E Grueber
- Faculty of Science, The University of Sydney, School of Life and Environmental Sciences, Sydney, Australia. .,San Diego Zoo Global, San Diego, USA.
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15
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Affiliation(s)
- Jonathan Flint
- Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
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