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Mei X, Liu G, Yan J, Zhao C, Wang X, Zhou S, Wei Q, Zhao S, Liu Z, Sha W, Zhang H. A chromosome-level genome assembly of the yellow-throated marten (Martes flavigula). Sci Data 2023; 10:216. [PMID: 37069236 PMCID: PMC10110515 DOI: 10.1038/s41597-023-02120-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 03/29/2023] [Indexed: 04/19/2023] Open
Abstract
The yellow-throated marten (Martes flavigula) is a medium-sized carnivore that is widely distributed across much of Asia and occupies an extensive variety of habitats. We reported a high-quality genome assembly of this organism that was generated using Oxford Nanopore and Hi-C technologies. The final genome sequences contained 215 contigs with a total size of 2,449.15 Mb and a contig N50 length of 68.60 Mb. Using Hi-C analysis, 2,419.20 Mb (98.78%) of the assembled sequences were anchored onto 21 linkage groups. Merqury evaluation suggested that the genome was 94.95% complete with a QV value of 43.75. Additionally, the genome was found to comprise approximately 39.74% repeat sequences, of which long interspersed elements (LINE) that accounted for 26.13% of the entire genome, were the most abundant. Of the 20,464 protein-coding genes, prediction and functional annotation was successfully performed for 20,322 (99.31%) genes. The high-quality, chromosome-level genome of the marten reported in this study will serve as a reference for future studies on genetic diversity, evolution, and conservation biology.
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Affiliation(s)
- Xuesong Mei
- School of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Guangshuai Liu
- School of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Jiakuo Yan
- School of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Chao Zhao
- School of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Xibao Wang
- School of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Shengyang Zhou
- School of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Qinguo Wei
- School of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Shihu Zhao
- School of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Zhao Liu
- School of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Weilai Sha
- School of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China
| | - Honghai Zhang
- School of Life Sciences, Qufu Normal University, Qufu, 273165, Shandong, China.
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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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