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Sumner JT, Andrasz CL, Johnson CA, Wax S, Anderson P, Keeling EL, Davidson JM. De novo genome assembly and comparative genomics for the colonial ascidian Botrylloides violaceus. G3 (BETHESDA, MD.) 2023; 13:jkad181. [PMID: 37555394 PMCID: PMC10542563 DOI: 10.1093/g3journal/jkad181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 01/25/2023] [Accepted: 07/12/2023] [Indexed: 08/10/2023]
Abstract
Ascidians have the potential to reveal fundamental biological insights related to coloniality, regeneration, immune function, and the evolution of these traits. This study implements a hybrid assembly technique to produce a genome assembly and annotation for the botryllid ascidian, Botrylloides violaceus. A hybrid genome assembly was produced using Illumina, Inc. short and Oxford Nanopore Technologies long-read sequencing technologies. The resulting assembly is comprised of 831 contigs, has a total length of 121 Mbp, N50 of 1 Mbp, and a BUSCO score of 96.1%. Genome annotation identified 13 K protein-coding genes. Comparative genomic analysis with other tunicates reveals patterns of conservation and divergence within orthologous gene families even among closely related species. Characterization of the Wnt gene family, encoding signaling ligands involved in development and regeneration, reveals conserved patterns of subfamily presence and gene copy number among botryllids. This supports the use of genomic data from nonmodel organisms in the investigation of biological phenomena.
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Affiliation(s)
- Jack T Sumner
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Cassidy L Andrasz
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Christine A Johnson
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Sarah Wax
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Paul Anderson
- Department of Computer Science and Software Engineering, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Elena L Keeling
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Jean M Davidson
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, CA 93407, USA
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2
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Theissinger K, Fernandes C, Formenti G, Bista I, Berg PR, Bleidorn C, Bombarely A, Crottini A, Gallo GR, Godoy JA, Jentoft S, Malukiewicz J, Mouton A, Oomen RA, Paez S, Palsbøll PJ, Pampoulie C, Ruiz-López MJ, Secomandi S, Svardal H, Theofanopoulou C, de Vries J, Waldvogel AM, Zhang G, Jarvis ED, Bálint M, Ciofi C, Waterhouse RM, Mazzoni CJ, Höglund J. How genomics can help biodiversity conservation. Trends Genet 2023:S0168-9525(23)00020-3. [PMID: 36801111 DOI: 10.1016/j.tig.2023.01.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/08/2022] [Accepted: 01/19/2023] [Indexed: 02/18/2023]
Abstract
The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.
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Affiliation(s)
- Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Carlos Fernandes
- CE3C - Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal; Faculdade de Psicologia, Universidade de Lisboa, Alameda da Universidade, 1649-013 Lisboa, Portugal
| | - Giulio Formenti
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Iliana Bista
- Naturalis Biodiversity Center, Darwinweg 2, 2333, CR, Leiden, The Netherlands; Wellcome Sanger Institute, Tree of Life, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
| | - Paul R Berg
- NIVA - Norwegian Institute for Water Research, Økernveien, 94, 0579 Oslo, Norway; Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Christoph Bleidorn
- University of Göttingen, Department of Animal Evolution and Biodiversity, Untere Karspüle, 2, 37073, Göttingen, Germany
| | | | - Angelica Crottini
- CIBIO/InBio, Centro de Investigação em Biodiversidade e Recursos Genéticos, Rua Padre Armando Quintas, 7, 4485-661, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4099-002 Porto, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Guido R Gallo
- Department of Biosciences, University of Milan, Milan, Italy
| | - José A Godoy
- Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Joanna Malukiewicz
- Primate Genetics Laborator, German Primate Center, Kellnerweg 4, 37077, Göttingen, Germany
| | - Alice Mouton
- InBios - Conservation Genetics Lab, University of Liege, Chemin de la Vallée 4, 4000, Liege, Belgium
| | - Rebekah A Oomen
- Centre for Coastal Research, University of Agder, Gimlemoen 25j, 4630 Kristiansand, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO BOX 1066 Blinderm, 0316 Oslo, Norway
| | - Sadye Paez
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Per J Palsbøll
- Groningen Institute of Evolutionary Life Sciences, University of Groningen, Nijenborgh, 9747, AG, Groningen, The Netherlands; Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA 02657, USA
| | - Christophe Pampoulie
- Marine and Freshwater Research Institute, Fornubúðir, 5,220, Hanafjörður, Iceland
| | - María J Ruiz-López
- Estación Biológica de Doñana, CSIC, Calle Americo Vespucio 26, 41092, Sevillle, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), Spain
| | | | - Hannes Svardal
- Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Antwerp, Belgium
| | - Constantina Theofanopoulou
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA; Hunter College, City University of New York, NY, USA
| | - Jan de Vries
- University of Goettingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), Campus Institute Data Science (CIDAS), Goldschmidtstr. 1, 37077, Goettingen, Germany
| | - Ann-Marie Waldvogel
- Institute of Zoology, University of Cologne, Zülpicherstrasse 47b, D-50674, Cologne, Germany
| | - Guojie Zhang
- Evolutionary & Organismal Biology Research Center, Zhejiang University School of Medicine, Hangzhou, 310058, China; Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Erich D Jarvis
- The Rockefeller University, 1230 York Ave, New York, NY 10065, USA
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt/Main, Germany
| | - Claudio Ciofi
- University of Florence, Department of Biology, Via Madonna del Piano 6, Sesto Fiorentino, (FI) 50019, Italy
| | - Robert M Waterhouse
- University of Lausanne, Department of Ecology and Evolution, Le Biophore, UNIL-Sorge, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Camila J Mazzoni
- Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Str 17, 10315 Berlin, Germany; Berlin Center for Genomics in Biodiversity Research (BeGenDiv), Koenigin-Luise-Str 6-8, 14195 Berlin, Germany
| | - Jacob Höglund
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75246, Uppsala, Sweden.
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3
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Cossette ML, Stewart DT, Haghani A, Zoller JA, Shafer ABA, Horvath S. Epigenetics and island-mainland divergence in an insectivorous small mammal. Mol Ecol 2023; 32:152-166. [PMID: 36226847 DOI: 10.1111/mec.16735] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 09/20/2022] [Accepted: 09/28/2022] [Indexed: 12/29/2022]
Abstract
Geographically isolated populations, specifically island-mainland counterparts, tend to exhibit phenotypic variation in many species. The so-called island syndrome occurs when different environmental pressures lead to insular divergence from mainland populations. This phenomenon can be seen in an island population of Nova Scotia masked shrews (Sorex cinereus), which have developed a specialized feeding habit and digestive enzyme compared to their mainland counterparts. Epigenetic modifications, such as DNA methylation (DNAm), can impact phenotypes by altering gene expression without changing the DNA sequence. Here, we used a de novo masked shrew genome assembly and a mammalian methylation array profiling 37 thousand conserved CpGs to investigate morphological and DNA methylation patterns between island and mainland populations. Island shrews were morphologically and epigenetically different than their mainland counterparts, exhibiting a smaller body size. A gene ontology enrichment analyses of differentially methylated CpGs implicated developmental and digestive system related pathways. Based on our shrew epigenetic clock, island shrews might also be aging faster than their mainland counterparts. This study provides novel insight on phenotypic and epigenetic divergence in island-mainland mammal populations and suggests an underlying role of methylation in island-mainland divergence.
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Affiliation(s)
- Marie-Laurence Cossette
- Department of Environmental Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - Donald T Stewart
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Joseph A Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, California, USA
| | - Aaron B A Shafer
- Department of Environmental Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
- Department of Forensic Science, Trent University, Peterborough, Ontario, Canada
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, California, USA
- Altos Labs, San Diego, California, USA
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4
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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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5
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Wang L, Lei T, Han G, Yue J, Zhang X, Yang Q, Ruan H, Gu C, Zhang Q, Qian T, Zhang N, Qian W, Wang Q, Pang X, Shu Y, Gao L, Wang Y. The chromosome-scale reference genome of Rubus chingii Hu provides insight into the biosynthetic pathway of hydrolyzable tannins. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1466-1477. [PMID: 34174125 DOI: 10.1111/tpj.15394] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 06/05/2021] [Accepted: 06/21/2021] [Indexed: 05/09/2023]
Abstract
Rubus chingii Hu (Fu-Pen-Zi), a perennial woody plant in the Rosaceae family, is a characteristic traditional Chinese medicinal plant because of its unique pharmacological effects. There are abundant hydrolyzable tannin (HT) components in R. chingii that provide health benefits. Here, an R. chingii chromosome-scale genome and related functional analysis provide insights into the biosynthetic pathway of HTs. In total, sequence data of 231.21 Mb (155 scaffolds with an N50 of 8.2 Mb) were assembled into seven chromosomes with an average length of 31.4 Mb, and 33 130 protein-coding genes were predicted, 89.28% of which were functionally annotated. Evolutionary analysis showed that R. chingii was most closely related to Rubus occidentalis, from which it was predicted to have diverged 22.46 million years ago (Table S8). Comparative genomic analysis showed that there was a tandem gene cluster of UGT, carboxylesterase (CXE) and SCPL genes on chromosome 02 of R. chingii, including 11 CXE, eight UGT, and six SCPL genes, which may be critical for the synthesis of HTs. In vitro enzyme assays indicated that the proteins encoded by the CXE (LG02.4273) and UGT (LG02.4102) genes have tannin hydrolase and gallic acid glycosyltransferase functions, respectively. The genomic sequence of R. chingii will be a valuable resource for comparative genomic analysis within the Rosaceae family and will be useful for understanding the biosynthesis of HTs.
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Affiliation(s)
- Longji Wang
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
- State Key Laboratory of Tea Plant Biology, Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ting Lei
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
- State Key Laboratory of Tea Plant Biology, Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Guomin Han
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
| | - Junyang Yue
- Horticulture College, Anhui Agricultural University, Hefei, 230036, China
| | - Xueru Zhang
- GrandOmics Biosciences, Wuhan, 430073, China
| | - Qi Yang
- GrandOmics Biosciences, Wuhan, 430073, China
| | - Haixiang Ruan
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
| | - Chunyang Gu
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
| | - Qiang Zhang
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
| | - Tao Qian
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
| | - Niuniu Zhang
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
| | - Wei Qian
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
| | - Qi Wang
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
| | - Xiaojing Pang
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
| | - Yue Shu
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
| | - Liping Gao
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
- State Key Laboratory of Tea Plant Biology, Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Yunsheng Wang
- Life Science College, Anhui Agricultural University, Hefei, 230036, China
- State Key Laboratory of Tea Plant Biology, Utilization, Anhui Agricultural University, Hefei, 230036, China
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6
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Gonçalves M, Siegismund HR, Jansen van Vuuren B, Koepfli KP, Ferrand N, Godinho R. De novo whole-genome assembly and resequencing resources for the roan (Hippotragus equinus), an iconic African antelope. G3-GENES GENOMES GENETICS 2021; 11:6114458. [PMID: 33604669 PMCID: PMC8022987 DOI: 10.1093/g3journal/jkab002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 12/17/2021] [Indexed: 11/22/2022]
Abstract
Roan antelope (Hippotragus equinus) is the second-largest member of the Hippotraginae (Bovidae), and is widely distributed across sub-Saharan mesic woodlands. Despite being listed as "Least Concern" across its African range, population numbers are decreasing with many regional Red List statuses varying between Endangered and Locally Extinct. Although the roan antelope has become an economically-important game species in Southern Africa, the vast majority of wild populations are found only in fragmented protected areas, which is of conservation concern. Genomic information is crucial in devising optimal management plans. To this end, we report here the first de novo assembly and annotation of the whole-genome sequence of a male roan antelope from a captive-breeding program. Additionally, we uncover single-nucleotide variants (SNVs) through re-sequencing of five wild individuals representing five of the six described subspecies. We used 10X Genomics Chromium chemistry to produce a draft genome of 2.56 Gb consisting of 16,880 scaffolds with N50 = 8.42 Mb and a BUSCO completeness of 91.2%. The draft roan genome includes 1.1 Gbp (42.2%) repetitive sequences. De novo annotation identified 20,518 protein-coding genes. Genome synteny to the domestic cow showed an average identity of 92.7%. Re-sequencing of five wild individuals to an average sequencing depth of 9.8x resulted in the identification of a filtered set of 3.4x106 bi-allelic SNVs. The proportion of alternative homozygous SNVs for the individuals representing different subspecies, as well as differentiation as measured by PCA, were consistent with expected divergence from the reference genome and among samples. The roan antelope genome is a valuable resource for evolutionary and population genomic questions, as well as management and conservation actions.
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Affiliation(s)
- Margarida Gonçalves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus de Vairão, 4485-661 Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Hans R Siegismund
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Bettine Jansen van Vuuren
- Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, 2006 Johannesburg, South Africa
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, Front Royal, VA 22630, USA.,Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, Washington, DC 20008, USA
| | - Nuno Ferrand
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus de Vairão, 4485-661 Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal.,Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, 2006 Johannesburg, South Africa
| | - Raquel Godinho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus de Vairão, 4485-661 Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal.,Department of Zoology, Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, 2006 Johannesburg, South Africa
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7
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Lopes M, Louzada S, Gama-Carvalho M, Chaves R. Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time. Int J Mol Sci 2021; 22:4707. [PMID: 33946766 PMCID: PMC8125562 DOI: 10.3390/ijms22094707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/24/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022] Open
Abstract
(Peri)centromeric repetitive sequences and, more specifically, satellite DNA (satDNA) sequences, constitute a major human genomic component. SatDNA sequences can vary on a large number of features, including nucleotide composition, complexity, and abundance. Several satDNA families have been identified and characterized in the human genome through time, albeit at different speeds. Human satDNA families present a high degree of sub-variability, leading to the definition of various subfamilies with different organization and clustered localization. Evolution of satDNA analysis has enabled the progressive characterization of satDNA features. Despite recent advances in the sequencing of centromeric arrays, comprehensive genomic studies to assess their variability are still required to provide accurate and proportional representation of satDNA (peri)centromeric/acrocentric short arm sequences. Approaches combining multiple techniques have been successfully applied and seem to be the path to follow for generating integrated knowledge in the promising field of human satDNA biology.
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Affiliation(s)
- Mariana Lopes
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.L.); (S.L.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal;
| | - Sandra Louzada
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.L.); (S.L.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal;
| | - Margarida Gama-Carvalho
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal;
| | - Raquel Chaves
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.L.); (S.L.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal;
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8
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Allio R, Tilak MK, Scornavacca C, Avenant NL, Kitchener AC, Corre E, Nabholz B, Delsuc F. High-quality carnivoran genomes from roadkill samples enable comparative species delineation in aardwolf and bat-eared fox. eLife 2021; 10:e63167. [PMID: 33599612 PMCID: PMC7963486 DOI: 10.7554/elife.63167] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 02/16/2021] [Indexed: 12/26/2022] Open
Abstract
In a context of ongoing biodiversity erosion, obtaining genomic resources from wildlife is essential for conservation. The thousands of yearly mammalian roadkill provide a useful source material for genomic surveys. To illustrate the potential of this underexploited resource, we used roadkill samples to study the genomic diversity of the bat-eared fox (Otocyon megalotis) and the aardwolf (Proteles cristatus), both having subspecies with similar disjunct distributions in Eastern and Southern Africa. First, we obtained reference genomes with high contiguity and gene completeness by combining Nanopore long reads and Illumina short reads. Then, we showed that the two subspecies of aardwolf might warrant species status (P. cristatus and P. septentrionalis) by comparing their genome-wide genetic differentiation to pairs of well-defined species across Carnivora with a new Genetic Differentiation index (GDI) based on only a few resequenced individuals. Finally, we obtained a genome-scale Carnivora phylogeny including the new aardwolf species.
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Affiliation(s)
- Rémi Allio
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Marie-Ka Tilak
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Celine Scornavacca
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
| | - Nico L Avenant
- National Museum and Centre for Environmental Management, University of the Free StateBloemfonteinSouth Africa
| | - Andrew C Kitchener
- Department of Natural Sciences, National Museums ScotlandEdinburghUnited Kingdom
| | - Erwan Corre
- CNRS, Sorbonne Université, CNRS, ABiMS, Station Biologique de RoscoffRoscoffFrance
| | - Benoit Nabholz
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
- Institut Universitaire de France (IUF)ParisFrance
| | - Frédéric Delsuc
- Institut des Sciences de l’Evolution de Montpellier (ISEM), CNRS, IRD, EPHE, Université de MontpellierMontpellierFrance
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9
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Pischedda E, Crava C, Carlassara M, Zucca S, Gasmi L, Bonizzoni M. ViR: a tool to solve intrasample variability in the prediction of viral integration sites using whole genome sequencing data. BMC Bioinformatics 2021; 22:45. [PMID: 33541262 PMCID: PMC7863434 DOI: 10.1186/s12859-021-03980-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 01/27/2021] [Indexed: 12/16/2022] Open
Abstract
Background Several bioinformatics pipelines have been developed to detect sequences from viruses that integrate into the human genome because of the health relevance of these integrations, such as in the persistence of viral infection and/or in generating genotoxic effects, often progressing into cancer. Recent genomics and metagenomics analyses have shown that viruses also integrate into the genome of non-model organisms (i.e., arthropods, fish, plants, vertebrates). However, rarely studies of endogenous viral elements (EVEs) in non-model organisms have gone beyond their characterization from reference genome assemblies. In non-model organisms, we lack a thorough understanding of the widespread occurrence of EVEs and their biological relevance, apart from sporadic cases which nevertheless point to significant roles of EVEs in immunity and regulation of expression. The concomitance of repetitive DNA, duplications and/or assembly fragmentations in a genome sequence and intrasample variability in whole-genome sequencing (WGS) data could determine misalignments when mapping data to a genome assembly. This phenomenon hinders our ability to properly identify integration sites. Results To fill this gap, we developed ViR, a pipeline which solves the dispersion of reads due to intrasample variability in sequencing data from both single and pooled DNA samples thus ameliorating the detection of integration sites. We tested ViR to work with both in silico and real sequencing data from a non-model organism, the arboviral vector Aedes albopictus. Potential viral integrations predicted by ViR were molecularly validated supporting the accuracy of ViR results. Conclusion ViR will open new venues to explore the biology of EVEs, especially in non-model organisms. Importantly, while we generated ViR with the identification of EVEs in mind, its application can be extended to detect any lateral transfer event providing an ad-hoc sequence to interrogate.
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Affiliation(s)
- Elisa Pischedda
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy
| | - Cristina Crava
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy.,ERI BIOTECMED, Universitat de Valencia, 46010, Valencia, Spain
| | - Martina Carlassara
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy
| | | | - Leila Gasmi
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy
| | - Mariangela Bonizzoni
- Department of Biology and Biotechnology, University of Pavia, 27100, Pavia, Italy.
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10
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Peona V, Blom MPK, Xu L, Burri R, Sullivan S, Bunikis I, Liachko I, Haryoko T, Jønsson KA, Zhou Q, Irestedt M, Suh A. Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise. Mol Ecol Resour 2021; 21:263-286. [PMID: 32937018 PMCID: PMC7757076 DOI: 10.1111/1755-0998.13252] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 01/09/2023]
Abstract
Genome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies now enable assembling genomes at unprecedented quality and contiguity. However, the difficulty in assembling repeat-rich and GC-rich regions (genomic "dark matter") limits insights into the evolution of genome structure and regulatory networks. Here, we compare the efficiency of currently available sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter. By adopting different de novo assembly strategies, we compare individual draft assemblies to a curated multiplatform reference assembly and identify the genomic features that cause gaps within each assembly. We show that a multiplatform assembly implementing long-read, linked-read and proximity sequencing technologies performs best at recovering transposable elements, multicopy MHC genes, GC-rich microchromosomes and the repeat-rich W chromosome. Telomere-to-telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is now possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects for optimized completeness of both the coding and noncoding parts of nonmodel genomes.
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Affiliation(s)
- Valentina Peona
- Department of Ecology and Genetics—Evolutionary BiologyScience for Life LaboratoriesUppsala UniversityUppsalaSweden
- Department of Organismal Biology—Systematic BiologyScience for Life LaboratoriesUppsala UniversityUppsalaSweden
| | - Mozes P. K. Blom
- Department of Bioinformatics and GeneticsSwedish Museum of Natural HistoryStockholmSweden
- Museum für NaturkundeLeibniz Institut für Evolutions‐ und BiodiversitätsforschungBerlinGermany
| | - Luohao Xu
- Department of Neurosciences and Developmental BiologyUniversity of ViennaViennaAustria
| | - Reto Burri
- Department of Population EcologyInstitute of Ecology and EvolutionFriedrich‐Schiller‐University JenaJenaGermany
| | | | - Ignas Bunikis
- Department of Immunology, Genetics and PathologyScience for Life LaboratoryUppsala Genome CenterUppsala UniversityUppsalaSweden
| | | | - Tri Haryoko
- Research Centre for BiologyMuseum Zoologicum BogorienseIndonesian Institute of Sciences (LIPI)CibinongIndonesia
| | - Knud A. Jønsson
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagenDenmark
| | - Qi Zhou
- Department of Neurosciences and Developmental BiologyUniversity of ViennaViennaAustria
- MOE Laboratory of Biosystems Homeostasis & ProtectionLife Sciences InstituteZhejiang UniversityHangzhouChina
- Center for Reproductive MedicineThe 2nd Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouChina
| | - Martin Irestedt
- Department of Bioinformatics and GeneticsSwedish Museum of Natural HistoryStockholmSweden
| | - Alexander Suh
- Department of Ecology and Genetics—Evolutionary BiologyScience for Life LaboratoriesUppsala UniversityUppsalaSweden
- Department of Organismal Biology—Systematic BiologyScience for Life LaboratoriesUppsala UniversityUppsalaSweden
- School of Biological Sciences—Organisms and the EnvironmentUniversity of East AngliaNorwichUK
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11
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Jung H, Ventura T, Chung JS, Kim WJ, Nam BH, Kong HJ, Kim YO, Jeon MS, Eyun SI. Twelve quick steps for genome assembly and annotation in the classroom. PLoS Comput Biol 2020; 16:e1008325. [PMID: 33180771 PMCID: PMC7660529 DOI: 10.1371/journal.pcbi.1008325] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Eukaryotic genome sequencing and de novo assembly, once the exclusive domain of well-funded international consortia, have become increasingly affordable, thus fitting the budgets of individual research groups. Third-generation long-read DNA sequencing technologies are increasingly used, providing extensive genomic toolkits that were once reserved for a few select model organisms. Generating high-quality genome assemblies and annotations for many aquatic species still presents significant challenges due to their large genome sizes, complexity, and high chromosome numbers. Indeed, selecting the most appropriate sequencing and software platforms and annotation pipelines for a new genome project can be daunting because tools often only work in limited contexts. In genomics, generating a high-quality genome assembly/annotation has become an indispensable tool for better understanding the biology of any species. Herein, we state 12 steps to help researchers get started in genome projects by presenting guidelines that are broadly applicable (to any species), sustainable over time, and cover all aspects of genome assembly and annotation projects from start to finish. We review some commonly used approaches, including practical methods to extract high-quality DNA and choices for the best sequencing platforms and library preparations. In addition, we discuss the range of potential bioinformatics pipelines, including structural and functional annotations (e.g., transposable elements and repetitive sequences). This paper also includes information on how to build a wide community for a genome project, the importance of data management, and how to make the data and results Findable, Accessible, Interoperable, and Reusable (FAIR) by submitting them to a public repository and sharing them with the research community.
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Affiliation(s)
- Hyungtaek Jung
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Centre for Agriculture and Bioeconomy, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Tomer Ventura
- Genecology Research Centre, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - J. Sook Chung
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, United States of America
| | - Woo-Jin Kim
- Genetics and Breeding Research Center, National Institute of Fisheries Science, Geoje, Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Hee Jeong Kong
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Young-Ok Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Min-Seung Jeon
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Seong-il Eyun
- Department of Life Science, Chung-Ang University, Seoul, Korea
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12
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Kraft F, Kurth I. Long-read sequencing to understand genome biology and cell function. Int J Biochem Cell Biol 2020; 126:105799. [PMID: 32629027 DOI: 10.1016/j.biocel.2020.105799] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 06/29/2020] [Accepted: 07/02/2020] [Indexed: 02/08/2023]
Abstract
Determining the sequence of DNA and RNA molecules has a huge impact on the understanding of cell biology and function. Recent advancements in next-generation short-read sequencing (NGS) technologies, drops in cost and a resolution down to the single-cell level shaped our current view on genome structure and function. Third-generation sequencing (TGS) methods further complete the knowledge about these processes based on long reads and the ability to analyze DNA or RNA at single molecule level. Long-read sequencing provides additional possibilities to study genome architecture and the composition of highly complex regions and to determine epigenetic modifications of nucleotide bases at a genome-wide level. We discuss the principles and advancements of long-read sequencing and its applications in genome biology.
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Affiliation(s)
- Florian Kraft
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany.
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany.
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13
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Etherington GJ, Heavens D, Baker D, Lister A, McNelly R, Garcia G, Clavijo B, Macaulay I, Haerty W, Di Palma F. Sequencing smart: De novo sequencing and assembly approaches for a non-model mammal. Gigascience 2020; 9:5836134. [PMID: 32396200 PMCID: PMC7216774 DOI: 10.1093/gigascience/giaa045] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 02/28/2020] [Accepted: 04/15/2020] [Indexed: 01/05/2023] Open
Abstract
Background Whilst much sequencing effort has focused on key mammalian model organisms such as mouse and human, little is known about the relationship between genome sequencing techniques for non-model mammals and genome assembly quality. This is especially relevant to non-model mammals, where the samples to be sequenced are often degraded and of low quality. A key aspect when planning a genome project is the choice of sequencing data to generate. This decision is driven by several factors, including the biological questions being asked, the quality of DNA available, and the availability of funds. Cutting-edge sequencing technologies now make it possible to achieve highly contiguous, chromosome-level genome assemblies, but rely on high-quality high molecular weight DNA. However, funding is often insufficient for many independent research groups to use these techniques. Here we use a range of different genomic technologies generated from a roadkill European polecat (Mustela putorius) to assess various assembly techniques on this low-quality sample. We evaluated different approaches for de novo assemblies and discuss their value in relation to biological analyses. Results Generally, assemblies containing more data types achieved better scores in our ranking system. However, when accounting for misassemblies, this was not always the case for Bionano and low-coverage 10x Genomics (for scaffolding only). We also find that the extra cost associated with combining multiple data types is not necessarily associated with better genome assemblies. Conclusions The high degree of variability between each de novo assembly method (assessed from the 7 key metrics) highlights the importance of carefully devising the sequencing strategy to be able to carry out the desired analysis. Adding more data to genome assemblies does not always result in better assemblies, so it is important to understand the nuances of genomic data integration explained here, in order to obtain cost-effective value for money when sequencing genomes.
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Affiliation(s)
| | - Darren Heavens
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - David Baker
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Ashleigh Lister
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Rose McNelly
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Gonzalo Garcia
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Bernardo Clavijo
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Iain Macaulay
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | - Wilfried Haerty
- The Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
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14
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Colella JP, Tigano A, MacManes MD. A linked-read approach to museomics: Higher quality de novo genome assemblies from degraded tissues. Mol Ecol Resour 2020; 20:856-870. [PMID: 32153100 PMCID: PMC7496956 DOI: 10.1111/1755-0998.13155] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 03/03/2020] [Accepted: 03/06/2020] [Indexed: 12/20/2022]
Abstract
High-throughput sequencing technologies are a proposed solution for accessing the molecular data in historical specimens. However, degraded DNA combined with the computational demands of short-read assemblies has posed significant laboratory and bioinformatics challenges for de novo genome assembly. Linked-read or "synthetic long-read" sequencing technologies, such as 10× Genomics, may provide a cost-effective alternative solution to assemble higher quality de novo genomes from degraded tissue samples. Here, we compare assembly quality (e.g., genome contiguity and completeness, presence of orthogroups) between four new deer mouse (Peromyscus spp.) genomes assembled using linked-read technology and four published genomes assembled from a single shotgun library. At a similar price-point, these approaches produce vastly different assemblies, with linked-read assemblies having overall higher contiguity and completeness, measured by larger N50 values and greater number of genes assembled, respectively. As a proof-of-concept, we used annotated genes from the four Peromyscus linked-read assemblies and eight additional rodent taxa to generate a phylogeny, which reconstructed the expected relationships among species with 100% support. Although not without caveats, our results suggest that linked-read sequencing approaches are a viable option to build de novo genomes from degraded tissues, which may prove particularly valuable for taxa that are extinct, rare or difficult to collect.
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Affiliation(s)
- Jocelyn P Colella
- Molecular, Cellular, and Biomedical Sciences Department, University of New Hampshire, Durham, NH, USA.,Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Anna Tigano
- Molecular, Cellular, and Biomedical Sciences Department, University of New Hampshire, Durham, NH, USA.,Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Matthew D MacManes
- Molecular, Cellular, and Biomedical Sciences Department, University of New Hampshire, Durham, NH, USA.,Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
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