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Thorburn DMJ, Sagonas K, Binzer-Panchal M, Chain FJJ, Feulner PGD, Bornberg-Bauer E, Reusch TBH, Samonte-Padilla IE, Milinski M, Lenz TL, Eizaguirre C. Origin matters: Using a local reference genome improves measures in population genomics. Mol Ecol Resour 2023; 23:1706-1723. [PMID: 37489282 DOI: 10.1111/1755-0998.13838] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/10/2023] [Accepted: 06/02/2023] [Indexed: 07/26/2023]
Abstract
Genome sequencing enables answering fundamental questions about the genetic basis of adaptation, population structure and epigenetic mechanisms. Yet, we usually need a suitable reference genome for mapping population-level resequencing data. In some model systems, multiple reference genomes are available, giving the challenging task of determining which reference genome best suits the data. Here, we compared the use of two different reference genomes for the three-spined stickleback (Gasterosteus aculeatus), one novel genome derived from a European gynogenetic individual and the published reference genome of a North American individual. Specifically, we investigated the impact of using a local reference versus one generated from a distinct lineage on several common population genomics analyses. Through mapping genome resequencing data of 60 sticklebacks from across Europe and North America, we demonstrate that genetic distance among samples and the reference genomes impacts downstream analyses. Using a local reference genome increased mapping efficiency and genotyping accuracy, effectively retaining more and better data. Despite comparable distributions of the metrics generated across the genome using SNP data (i.e. π, Tajima's D and FST ), window-based statistics using different references resulted in different outlier genes and enriched gene functions. A marker-based analysis of DNA methylation distributions had a comparably high overlap in outlier genes and functions, yet with distinct differences depending on the reference genome. Overall, our results highlight how using a local reference genome decreases reference bias to increase confidence in downstream analyses of the data. Such results have significant implications in all reference-genome-based population genomic analyses.
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Affiliation(s)
- Doko-Miles J Thorburn
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- Department of Life Sciences, Imperial College London, London, UK
| | - Kostas Sagonas
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- Department of Zoology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Mahesh Binzer-Panchal
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, National Bioinformatics Infrastructure Sweden (NBIS), Uppsala University, Uppsala, Sweden
| | - Frederic J J Chain
- Department of Biological Sciences, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Philine G D Feulner
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Erich Bornberg-Bauer
- Evolutionary Bioinformatics, Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Thorsten B H Reusch
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Irene E Samonte-Padilla
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Manfred Milinski
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
- Research Unit for Evolutionary Immunogenomics, Department of Biology, University of Hamburg, Hamburg, Germany
| | - Christophe Eizaguirre
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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2
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Liu L, Liu Q, Gao T. Genome-wide survey reveals the phylogenomic relationships of Chirolophisjaponicus Herzenstein, 1890 (Stichaeidae, Perciformes). Zookeys 2022; 1129:55-72. [PMID: 36761850 PMCID: PMC9836534 DOI: 10.3897/zookeys.1129.91543] [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: 08/11/2022] [Accepted: 10/06/2022] [Indexed: 11/13/2022] Open
Abstract
Fish are the largest vertebrate group, consisting of more than 30 000 species with important ecological and economical value, while less than 3% of fish genomes have been published. Herein, a fish, Chirolophisjaponicus, was sequenced using the next-generation sequencing. Approximately 595.7 megabase pair of the C.japonicus genome was assembled (49 901 contigs with 42.61% GC contents), leading to a prediction of 46 729 protein-coding gene models. A total of 554 136 simple sequence repeats was identified in the whole genome of C.japonicus, and dinucleotide microsatellite motifs were the most abundant, accounting for 59.49%. Phylogenomic analysis of 16 genomes based on the 694 single-copy genes suggests that C.japonicus is closely related with Anarrhichthysocellatus, Cebidichthysviolaceus, and Pholisgunnellus. The results provide more thorough genetic information of C.japonicus and a theoretical basis and reference for further genome-wide analysis.
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Affiliation(s)
- Lu Liu
- Naval Architecture and Port Engineering College, Shandong Jiaotong University, Weihai, ChinaShandong Jiaotong UniversityWeihaiChina
| | - Qi Liu
- Wuhan Onemore-tech Co., Ltd. Wuhan, Hubei, ChinaWuhan Onemore-tech Co., LtdWuhanChina
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang, ChinaZhejiang Ocean UniversityZhoushanChina,Zhejiang Provincial Key Laboratory of Mariculture and Enhancement, Zhejiang Marine Fisheries Research Institute, Zhoushan, ChinaZhejiang Marine Fisheries Research InstituteZhoushanChina
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3
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Laurentino TG, Boileau N, Ronco F, Berner D. The ectodysplasin-A receptor is a candidate gene for lateral plate number variation in stickleback fish. G3 GENES|GENOMES|GENETICS 2022; 12:6563190. [PMID: 35377433 PMCID: PMC9157104 DOI: 10.1093/g3journal/jkac077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/28/2022] [Indexed: 02/04/2023]
Abstract
Variation in lateral plating in stickleback fish represents a classical example of rapid and parallel adaptation in morphology. The underlying genetic architecture involves polymorphism at the ectodysplasin-A gene (EDA). However, lateral plate number is influenced by additional loci that remain poorly characterized. Here, we search for such loci by performing genome-wide differentiation mapping based on pooled whole-genome sequence data from a European stickleback population variable in the extent of lateral plating, while tightly controlling for the phenotypic effect of EDA. This suggests a new candidate locus, the EDA receptor gene (EDAR), for which additional support is obtained by individual-level targeted Sanger sequencing and by comparing allele frequencies among natural populations. Overall, our study illustrates the power of pooled whole-genome sequencing for searching phenotypically relevant loci and opens opportunities for exploring the population genetics and ecological significance of a new candidate locus for stickleback armor evolution.
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Affiliation(s)
- Telma G Laurentino
- Department of Environmental Sciences, Zoology, University of Basel, 4051 Basel, Switzerland
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
| | - Nicolas Boileau
- Department of Environmental Sciences, Zoology, University of Basel, 4051 Basel, Switzerland
| | - Fabrizia Ronco
- Department of Environmental Sciences, Zoology, University of Basel, 4051 Basel, Switzerland
| | - Daniel Berner
- Department of Environmental Sciences, Zoology, University of Basel, 4051 Basel, Switzerland
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4
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Nath S, Shaw DE, White MA. Improved contiguity of the threespine stickleback genome using long-read sequencing. G3-GENES GENOMES GENETICS 2021; 11:6114463. [PMID: 33598708 PMCID: PMC8022941 DOI: 10.1093/g3journal/jkab007] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 12/27/2020] [Indexed: 12/28/2022]
Abstract
While the cost and time for assembling a genome has drastically decreased, it still remains a challenge to assemble a highly contiguous genome. These challenges are rapidly being overcome by the integration of long-read sequencing technologies. Here, we use long-read sequencing to improve the contiguity of the threespine stickleback fish (Gasterosteus aculeatus) genome, a prominent genetic model species. Using Pacific Biosciences sequencing, we assembled a highly contiguous genome of a freshwater fish from Paxton Lake. Using contigs from this genome, we were able to fill over 76.7% of the gaps in the existing reference genome assembly, improving contiguity over fivefold. Our gap filling approach was highly accurate, validated by 10X Genomics long-distance linked-reads. In addition to closing a majority of gaps, we were able to assemble segments of telomeres and centromeres throughout the genome. This highlights the power of using long sequencing reads to assemble highly repetitive and difficult to assemble regions of genomes. This latest genome build has been released through a newly designed community genome browser that aims to consolidate the growing number of genomics datasets available for the threespine stickleback fish.
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Affiliation(s)
- Shivangi Nath
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Daniel E Shaw
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Michael A White
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
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5
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Kivikoski M, Rastas P, Löytynoja A, Merilä J. Automated improvement of stickleback reference genome assemblies with Lep-Anchor software. Mol Ecol Resour 2021; 21:2166-2176. [PMID: 33955177 DOI: 10.1111/1755-0998.13404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 01/06/2023]
Abstract
We describe an integrative approach to improve contiguity and haploidy of a reference genome assembly and demonstrate its impact with practical examples. With two novel features of Lep-Anchor software and a combination of dense linkage maps, overlap detection and bridging long reads, we generated an improved assembly of the nine-spined stickleback (Pungitius pungitius) reference genome. We were able to remove a significant number of haplotypic contigs, detect more genetic variation and improve the contiguity of the genome, especially that of X chromosome. However, improved scaffolding cannot correct for mosaicism of erroneously assembled contigs, demonstrated by a de novo assembly of a 1.6-Mbp inversion. Qualitatively similar gains were obtained with the genome of three-spined stickleback (Gasterosteus aculeatus). Since the utility of genome-wide sequencing data in biological research depends heavily on the quality of the reference genome, the improved and fully automated approach described here should be helpful in refining reference genome assemblies.
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Affiliation(s)
- Mikko Kivikoski
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Pasi Rastas
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ari Löytynoja
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Juha Merilä
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Division of Ecology and Biodiversity, The University of Hong Kong, Hong Kong, Hong Kong, SAR
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6
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Bissegger M, Laurentino TG, Roesti M, Berner D. Widespread intersex differentiation across the stickleback genome – The signature of sexually antagonistic selection? Mol Ecol 2019; 29:262-271. [DOI: 10.1111/mec.15255] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 09/18/2019] [Accepted: 09/25/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Mirjam Bissegger
- Department of Environmental Sciences, Zoology University of Basel Basel Switzerland
| | - Telma G. Laurentino
- Department of Environmental Sciences, Zoology University of Basel Basel Switzerland
| | - Marius Roesti
- Institute of Ecology and Evolution University of Bern Bern Switzerland
| | - Daniel Berner
- Department of Environmental Sciences, Zoology University of Basel Basel Switzerland
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7
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Guo L, Yao H, Shepherd B, Sepulveda-Villet OJ, Zhang DC, Wang HP. Development of a Genomic Resource and Identification of Nucleotide Diversity of Yellow Perch by RAD Sequencing. Front Genet 2019; 10:992. [PMID: 31681426 PMCID: PMC6802114 DOI: 10.3389/fgene.2019.00992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 09/18/2019] [Indexed: 01/28/2023] Open
Affiliation(s)
- Liang Guo
- Aquatic Genetics and Breeding Laboratory, Ohio State University South Centers, Piketon, OH, United States.,Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institutes, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Hong Yao
- Aquatic Genetics and Breeding Laboratory, Ohio State University South Centers, Piketon, OH, United States
| | - Brian Shepherd
- USDA-ARS-School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States
| | - Osvaldo J Sepulveda-Villet
- USDA-ARS-School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States.,School of Freshwater Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States
| | - Dian-Chang Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institutes, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Han-Ping Wang
- Aquatic Genetics and Breeding Laboratory, Ohio State University South Centers, Piketon, OH, United States
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