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Tian R, Han K, Geng Y, Yang C, Shi C, Thomas PB, Pearce C, Moffatt K, Ma S, Xu S, Yang G, Zhou X, Gladyshev VN, Liu X, Fisher DO, Chopin LK, Leiner NO, Baker AM, Fan G, Seim I. A chromosome-level genome of Antechinus flavipes provides a reference for an Australian marsupial genus with male death after mating. Mol Ecol Resour 2021; 22:740-754. [PMID: 34486812 PMCID: PMC9290055 DOI: 10.1111/1755-0998.13501] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 08/16/2021] [Accepted: 08/31/2021] [Indexed: 11/30/2022]
Abstract
The 15 species of small carnivorous marsupials that comprise the genus Antechinus exhibit semelparity, a rare life-history strategy in mammals where synchronized death occurs after one breeding season. Antechinus males, but not females, age rapidly (demonstrate organismal senescence) during the breeding season and show promise as new animal models of ageing. Some antechinus species are also threatened or endangered. Here, we report a chromosome-level genome of a male yellow-footed antechinus Antechinus flavipes. The genome assembly has a total length of 3.2 Gb with a contig N50 of 51.8 Mb and a scaffold N50 of 636.7 Mb. We anchored and oriented 99.7% of the assembly on seven pseudochromosomes and found that repetitive DNA sequences occupy 51.8% of the genome. Draft genome assemblies of three related species in the subfamily Phascogalinae, two additional antechinus species (Antechinus argentus and A. arktos) and the iteroparous sister species Murexia melanurus, were also generated. Preliminary demographic analysis supports the hypothesis that climate change during the Pleistocene isolated species in Phascogalinae and shaped their population size. A transcriptomic profile across the A. flavipes breeding season allowed us to identify genes associated with aspects of the male die-off. The chromosome-level A. flavipes genome provides a steppingstone to understanding an enigmatic life-history strategy and a resource to assist the conservation of antechinuses.
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Affiliation(s)
- Ran Tian
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, China.,Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Kai Han
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Yuepan Geng
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Chen Yang
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | | | - Patrick B Thomas
- Ghrelin Research Group, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia.,Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute - Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia.,Queensland Bladder Cancer Initiative, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Woolloongabba, QLD, Australia
| | - Coral Pearce
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Kate Moffatt
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Siming Ma
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China
| | - Diana O Fisher
- School of Biological Sciences, University of Queensland, Brisbane, QLD, Australia
| | - Lisa K Chopin
- Ghrelin Research Group, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia.,Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute - Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia
| | - Natália O Leiner
- Laboratório de Ecologia de Mamíferos, Instituto de Biologia, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - Andrew M Baker
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia.,Natural Environments Program, Queensland Museum, South Brisbane, QLD, Australia
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, China.,State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China.,State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, China.,Ghrelin Research Group, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia.,Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute - Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, Australia.,School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD, Australia
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2
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Viacava P, Baker AM, Blomberg SP, Phillips MJ, Weisbecker V. Using 3D geometric morphometrics to aid taxonomic and ecological understanding of a recent speciation event within a small Australian marsupial (Antechinus: Dasyuridae). Zool J Linn Soc 2021. [DOI: 10.1093/zoolinnean/zlab048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Abstract
Taxonomic distinction of species forms the foundation of biodiversity assessments and conservation priorities. However, traditional morphological and/or genetics-based taxonomic assessments frequently miss the opportunity of elaborating on the ecological and functional context of species diversification. Here, we used 3D geometric morphometrics of the cranium to improve taxonomic differentiation and add ecomorphological characterization of a young cryptic divergence within the carnivorous marsupial genus Antechinus. Specifically, we used 168 museum specimens to characterize the recently proposed clades A. stuartii ‘south’, A. stuartii ‘north’ and A. subtropicus. Beyond slight differences attributable to overall size (and, therefore, not necessarily diagnostic), we also found clear allometry-independent shape variation. This allowed us to define new, easily measured diagnostic traits in the palate, which differentiate the three clades. Contrary to previous suggestions, we found no support for a latitudinal gradient as causing the differentiation between the clades. However, skull shape co-varied with temperature and precipitation seasonality, suggesting that the clades may be adapted to environmental variables that are likely to be impacted by climate change. Our study demonstrates the use of 3D geometric morphometrics to improve taxonomic diagnosis of cryptic mammalian species, while providing perspectives on the adaptive origins and potential future threats of mammalian diversity.
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Affiliation(s)
- Pietro Viacava
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Andrew M Baker
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
- Natural Environments Program, Queensland Museum, South Brisbane, Queensland, Australia
| | - Simone P Blomberg
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Matthew J Phillips
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Vera Weisbecker
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
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Tian R, Han K, Geng Y, Yang C, Guo H, Shi C, Xu S, Yang G, Zhou X, Gladyshev VN, Liu X, Chopin LK, Fisher DO, Baker AM, Leiner NO, Fan G, Seim I. A Chromosome-Level Genome of the Agile Gracile Mouse Opossum (Gracilinanus agilis). Genome Biol Evol 2021; 13:evab162. [PMID: 34247236 PMCID: PMC8390783 DOI: 10.1093/gbe/evab162] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2021] [Indexed: 12/27/2022] Open
Abstract
There are more than 100 species of American didelphid marsupials (opossums and mouse opossums). Limited genomic resources for didelphids exists, with only two publicly available genome assemblies compared with dozens in the case of their Australasian counterparts. This discrepancy impedes evolutionary and ecological research. To address this gap, we assembled a high-quality chromosome-level genome of the agile gracile mouse opossum (Gracilinanus agilis) using a combination of stLFR sequencing, polishing with mate-pair data, and anchoring onto pseudochromosomes using Hi-C. This species employs a rare life-history strategy, semelparity, and all G. agilis males and most females die at the end of their first breeding season after succumbing to stress and exhaustion. The 3.7-Gb chromosome-level assembly, with 92.6% anchored onto pseudochromosomes, has a scaffold N50 of 683.5 Mb and a contig N50 of 56.9 kb. The genome assembly shows high completeness, with a mammalian BUSCO score of 88.1%. Around 49.7% of the genome contains repetitive elements. Gene annotation yielded 24,425 genes, of which 83.9% were functionally annotated. The G. agilis genome is an important resource for future studies of marsupial biology, evolution, and conservation.
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Affiliation(s)
- Ran Tian
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Jiangsu, China
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Jiangsu, China
| | - Kai Han
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, China
| | - Yuepan Geng
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Jiangsu, China
| | - Chen Yang
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Jiangsu, China
| | - Han Guo
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Jiangsu, China
| | | | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Jiangsu, China
| | - Guang Yang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Jiangsu, China
| | - Xuming Zhou
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, China
| | - Lisa K Chopin
- Ghrelin Research Group, Translational Research Institute, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Diana O Fisher
- School of Biological Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Andrew M Baker
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
- Natural Environments Program, Queensland Museum, South Brisbane, Queensland, Australia
| | - Natália O Leiner
- Laboratório de Ecologia de Mamíferos, Instituto de Biologia, Universidade Federal de Uberlândia, MG, Brazil
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong, China
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, China
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Jiangsu, China
- Ghrelin Research Group, Translational Research Institute, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute, Queensland University of Technology, Brisbane, Queensland, Australia
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
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4
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Geng Y, Yang C, Guo H, Thomas PB, Jeffery PL, Chopin LK, Baker AM, Tian R, Seim I. The mitochondrial genome of the black-tailed dusky antechinus ( Antechinus arktos). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:3835-3837. [PMID: 33426294 PMCID: PMC7759261 DOI: 10.1080/23802359.2020.1840940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In this study, we report the mitochondrial genome of the black-tailed antechinus (Antechinus arktos), a recently-discovered, endangered carnivorous marsupial inhabiting a caldera that straddles the border of Australia’s mid-east coast. The circular A. arktos genome is 17,334 bp in length and has an AT content of 63.3%. Its gene content and arrangement are consistent with reported marsupial mitogenome assemblies.
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Affiliation(s)
- Yuepan Geng
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, PR China
| | - Chen Yang
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, PR China
| | - Han Guo
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, PR China
| | - Patrick B Thomas
- Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute - Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
| | - Penny L Jeffery
- Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute - Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
| | - Lisa K Chopin
- Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute - Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia.,Ghrelin Research Group, Translational Research Institute -Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Andrew M Baker
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Australia.,Natural Environments Program, Queensland Museum, Queensland, Australia
| | - Ran Tian
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, PR China
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, PR China.,Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute - Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia.,Ghrelin Research Group, Translational Research Institute -Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia.,School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Australia
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5
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Brandies PA, Tang S, Johnson RSP, Hogg CJ, Belov K. The first Antechinus reference genome provides a resource for investigating the genetic basis of semelparity and age-related neuropathologies. GIGABYTE 2020; 2020:gigabyte7. [PMID: 36824596 PMCID: PMC9631953 DOI: 10.46471/gigabyte.7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/04/2020] [Indexed: 12/14/2022] Open
Abstract
Antechinus are a genus of mouse-like marsupials that exhibit a rare reproductive strategy known as semelparity and also naturally develop age-related neuropathologies similar to those in humans. We provide the first annotated antechinus reference genome for the brown antechinus (Antechinus stuartii). The reference genome is 3.3 Gb in size with a scaffold N50 of 73Mb and 93.3% complete mammalian BUSCOs. Using bioinformatic methods we assign scaffolds to chromosomes and identify 0.78 Mb of Y-chromosome scaffolds. Comparative genomics revealed interesting expansions in the NMRK2 gene and the protocadherin gamma family, which have previously been associated with aging and age-related dementias respectively. Transcriptome data displayed expression of common Alzheimer's related genes in the antechinus brain and highlight the potential of utilising the antechinus as a future disease model. The valuable genomic resources provided herein will enable future research to explore the genetic basis of semelparity and age-related processes in the antechinus.
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Affiliation(s)
- Parice A. Brandies
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Simon Tang
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Robert S. P. Johnson
- Zoologica: Veterinary and Zoological Consulting, Millthorpe, New South Wales, Australia
| | - Carolyn J. Hogg
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, Faculty of Science, University of Sydney, Sydney, New South Wales, Australia, Corresponding author. E-mail:
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Tian R, Geng Y, Thomas PB, Jeffery PL, Mutton TY, Chopin LK, Baker AM, Seim I. The mitochondrial genome of the black-tailed dasyure ( Murexia melanurus). MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:3598-3600. [PMID: 33366102 PMCID: PMC7707616 DOI: 10.1080/23802359.2019.1677526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In this study, we report the mitochondrial genome of the black-tailed dasyure (Murexia melanurus) of New Guinea. The circular genome is 17,736 bp in length and has an AT content of 60.5%. Its gene content – 13 protein-coding genes (PCGs), 2 ribosomal (rRNA) genes, 21 transfer RNA (tRNA) genes, a tRNA pseudogene (tRNALys), and a non-coding control region (CR) – and gene arrangement are consistent with previous marsupial mitogenome assemblies.
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Affiliation(s)
- Ran Tian
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Yuepan Geng
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China
| | - Patrick B Thomas
- Ghrelin Research Group, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia.,Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute - Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia.,Queensland Bladder Cancer Initiative, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Woolloongabba, Queensland, Australia
| | - Penny L Jeffery
- Ghrelin Research Group, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia.,Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute - Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Thomas Y Mutton
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Lisa K Chopin
- Ghrelin Research Group, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia.,Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute - Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Andrew M Baker
- School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia.,Natural Environments Program, Queensland Museum, South Brisbane, Queensland, Australia
| | - Inge Seim
- Integrative Biology Laboratory, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, China.,Ghrelin Research Group, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia.,Australian Prostate Cancer Research Centre-Queensland, Translational Research Institute - Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, Australia.,Comparative and Endocrine Biology Laboratory, Translational Research Institute-Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Woolloongabba, Queensland, Australia
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