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Teeling EC, Vernes SC, Dávalos LM, Ray DA, Gilbert MTP, Myers E. Bat Biology, Genomes, and the Bat1K Project: To Generate Chromosome-Level Genomes for All Living Bat Species. Annu Rev Anim Biosci 2017; 6:23-46. [PMID: 29166127 DOI: 10.1146/annurev-animal-022516-022811] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bats are unique among mammals, possessing some of the rarest mammalian adaptations, including true self-powered flight, laryngeal echolocation, exceptional longevity, unique immunity, contracted genomes, and vocal learning. They provide key ecosystem services, pollinating tropical plants, dispersing seeds, and controlling insect pest populations, thus driving healthy ecosystems. They account for more than 20% of all living mammalian diversity, and their crown-group evolutionary history dates back to the Eocene. Despite their great numbers and diversity, many species are threatened and endangered. Here we announce Bat1K, an initiative to sequence the genomes of all living bat species (n∼1,300) to chromosome-level assembly. The Bat1K genome consortium unites bat biologists (>148 members as of writing), computational scientists, conservation organizations, genome technologists, and any interested individuals committed to a better understanding of the genetic and evolutionary mechanisms that underlie the unique adaptations of bats. Our aim is to catalog the unique genetic diversity present in all living bats to better understand the molecular basis of their unique adaptations; uncover their evolutionary history; link genotype with phenotype; and ultimately better understand, promote, and conserve bats. Here we review the unique adaptations of bats and highlight how chromosome-level genome assemblies can uncover the molecular basis of these traits. We present a novel sequencing and assembly strategy and review the striking societal and scientific benefits that will result from the Bat1K initiative.
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Affiliation(s)
- Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland;
| | - Sonja C Vernes
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, 6500 AH, The Netherlands.,Donders Centre for Cognitive Neuroimaging, Nijmegen, 6525 EN, The Netherlands
| | - Liliana M Dávalos
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York 11794-5245, USA
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas 79409, USA
| | - M Thomas P Gilbert
- Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark.,University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Eugene Myers
- Max Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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- *Full list of Bat1K Consortium members in Supplemental Appendix
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Chromosomal Evolution in Chiroptera. Genes (Basel) 2017; 8:genes8100272. [PMID: 29027987 PMCID: PMC5664122 DOI: 10.3390/genes8100272] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 10/05/2017] [Accepted: 10/06/2017] [Indexed: 01/05/2023] Open
Abstract
Chiroptera is the second largest order among mammals, with over 1300 species in 21 extant families. The group is extremely diverse in several aspects of its natural history, including dietary strategies, ecology, behavior and morphology. Bat genomes show ample chromosome diversity (from 2n = 14 to 62). As with other mammalian orders, Chiroptera is characterized by clades with low, moderate and extreme chromosomal change. In this article, we will discuss trends of karyotypic evolution within distinct bat lineages (especially Phyllostomidae, Hipposideridae and Rhinolophidae), focusing on two perspectives: evolution of genome architecture, modes of chromosomal evolution, and the use of chromosome data to resolve taxonomic problems.
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Carr M, Gonzalez G, Sasaki M, Dool SE, Ito K, Ishii A, Hang'ombe BM, Mweene AS, Teeling EC, Hall WW, Orba Y, Sawa H. Identification of the same polyomavirus species in different African horseshoe bat species is indicative of short-range host-switching events. J Gen Virol 2017; 98:2771-2785. [PMID: 28984241 DOI: 10.1099/jgv.0.000935] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Polyomaviruses (PyVs) are considered to be highly host-specific in different mammalian species, with no well-supported evidence for host-switching events. We examined the species diversity and host specificity of PyVs in horseshoe bats (Rhinolophus spp.), a broadly distributed and highly speciose mammalian genus. We annotated six PyV genomes, comprising four new PyV species, based on pairwise identity within the large T antigen (LTAg) coding region. Phylogenetic comparisons revealed two instances of highly related PyV species, one in each of the Alphapolyomavirus and Betapolyomavirus genera, present in different horseshoe bat host species (Rhinolophus blasii and R. simulator), suggestive of short-range host-switching events. The two pairs of Rhinolophus PyVs in different horseshoe bat host species were 99.9 and 88.8 % identical with each other over their respective LTAg coding sequences and thus constitute the same virus species. To corroborate the species identification of the bat hosts, we analysed mitochondrial cytb and a large nuclear intron dataset derived from six independent and neutrally evolving loci for bat taxa of interest. Bayesian estimates of the ages of the most recent common ancestors suggested that the near-identical and more distantly related PyV species diverged approximately 9.1E4 (5E3-2.8E5) and 9.9E6 (4E6-18E6) years before the present, respectively, in contrast to the divergence times of the bat host species: 12.4E6 (10.4E6-15.4E6). Our findings provide evidence that short-range host-switching of PyVs is possible in horseshoe bats, suggesting that PyV transmission between closely related mammalian species can occur.
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Affiliation(s)
- Michael Carr
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan.,National Virus Reference Laboratory, University College Dublin, Belfield, Dublin 4, Ireland
| | - Gabriel Gonzalez
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Michihito Sasaki
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Serena E Dool
- Zoological Institute and Museum, University of Greifswald, Anklamer Street 20, D-17489 Greifswald, Germany
| | - Kimihito Ito
- Division of Bioinformatics, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Akihiro Ishii
- Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, Lusaka, Zambia
| | - Bernard M Hang'ombe
- Department of Para-clinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Aaron S Mweene
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Emma C Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - William W Hall
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan.,Global Virus Network, Baltimore, MD 21201, USA
| | - Yasuko Orba
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
| | - Hirofumi Sawa
- Global Virus Network, Baltimore, MD 21201, USA.,Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan.,Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia.,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan
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Shahabi S, Akmali V, Sharifi M. Taxonomic Evaluation of the Greater Horseshoe Bat Rhinolophus ferrumequinum (Chiroptera: Rhinolophidae) in Iran Inferred from the Mitochondrial D-Loop Gene. Zoolog Sci 2017; 34:361-367. [DOI: 10.2108/zs170001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Saeed Shahabi
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
| | - Vahid Akmali
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
| | - Mozafar Sharifi
- Department of Biology, Faculty of Science, Razi University, Kermanshah, Iran
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Volleth M, Son NT, Wu Y, Li Y, Yu W, Lin LK, Arai S, Trifonov V, Liehr T, Harada M. Comparative Chromosomal Studies inRhinolophus formosaeandR. luctusfrom China and Vietnam: Elevation ofR. l. lanosusto Species Rank. ACTA CHIROPTEROLOGICA 2017. [DOI: 10.3161/15081109acc2017.19.1.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Marianne Volleth
- Department of Human Genetics, Otto von Guericke University, Leipziger Strasse 44, 39120 Magdeburg, Germany
| | - Nguyen Truong Son
- Department of Vertebrate Zoology, Institute of Ecology and Biological Resources and Graduate University of Sciences and Technology, Vietnam Academy of Sciences and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, Vietnam
| | - Yi Wu
- College of Life Sciences, Guangzhou University, 230 Wei Huan Xi Road, Guangzhou, 510006, China
| | - Yuchun Li
- Marine College, Shandong University, Weihai, 264209, China
| | - Wenhua Yu
- College of Life Sciences, Guangzhou University, 230 Wei Huan Xi Road, Guangzhou, 510006, China
| | - Liang-Kong Lin
- Laboratory of Wildlife Ecology, Department of Biology, Tunghai University, No. 1727, Sec. 4. Taiwan Boulevard, Xitun District, Taichung 40704, Taiwan
| | - Satoru Arai
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Toyama 1-23-1, Shinjuku, Tokyo 162-8640, Japan
| | - Vladimir Trifonov
- Institute of Human Genetics, Jena University Hospital, Friedrich-Schiller University, Kollegiengasse 10, 07743 Jena, Germany
| | - Thomas Liehr
- Institute of Molecular and Cellular Biology, Siberian Branch of RAS, 8 Ac. Lavrentieva Avenue, Novosibirsk 630090, Russia
| | - Masashi Harada
- Laboratory Animal Center, Graduate School of Medicine, Osaka City University, Abeno, Osaka 545-8585, Japan
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Foley NM, Goodman SM, Whelan CV, Puechmaille SJ, Teeling E. Towards Navigating the Minotaur's Labyrinth: Cryptic Diversity and Taxonomic Revision within the Speciose Genus Hipposideros (Hipposideridae). ACTA CHIROPTEROLOGICA 2017. [DOI: 10.3161/15081109acc2017.19.1.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Nicole M. Foley
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Steven M. Goodman
- Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, IL, USA
- Association Vahatra, BP 3972, Antananarivo 101, Madagascar
| | - Conor V. Whelan
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Sebastien J. Puechmaille
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
- Applied Zoology and Nature Conservation, Greifswald University, Greifswald, Germany
| | - Emma Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
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Dool SE, Puechmaille SJ, Kelleher C, McAney K, Teeling EC. The Effects of Human-Mediated Habitat Fragmentation on a Sedentary Woodland-Associated Species (Rhinolophus hipposideros) at Its Range Margin. ACTA CHIROPTEROLOGICA 2016. [DOI: 10.3161/15081109acc2016.18.2.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Serena E. Dool
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Sébastien J. Puechmaille
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Conor Kelleher
- Spring Lane, Carrigagulla, Ballinagree, Macroom, County Cork, Ireland
| | - Kate McAney
- The Vincent Wildlife Trust, Donaghpatrick, Headford, County Galway, Ireland
| | - Emma C. Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
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58
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Kacprzyk J, Teeling EC, Kelleher C, Volleth M. Wing Membrane Biopsies for Bat Cytogenetics: Finding of 2n = 54 in Irish Rhinolophushipposideros (Rhinolophidae, Chiroptera, Mammalia) Supports Two Geographically Separated Chromosomal Variants in Europe. Cytogenet Genome Res 2016; 148:279-83. [PMID: 27333200 DOI: 10.1159/000447111] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2016] [Indexed: 11/19/2022] Open
Abstract
In Europe, 2 different diploid chromosome numbers, 2n = 54 and 2n = 56, have been described in the lesser horseshoe bat (Rhinolophushipposideros). The eastern form with 2n = 56 extends from the Czech Republic to Greece. To date, specimens with 54 chromosomes have been reported only from Spain and Germany. This study expands the distributional area of the western variant to Ireland. Strikingly, this distribution of European chromosomal variants is in contrast to the available molecular data that indicate little genetic differentiation of R. hipposideros populations spanning Northwestern to Central Europe. Further, we have developed an optimized protocol for establishing fibroblast cell cultures, suitable for karyotype analyses, from 3-mm wing membrane biopsies. This is a useful technique for cytogenetic studies of endangered bat species, as this non-lethal sampling method imposes only minimum stress to the animal without lasting adverse effects and is routinely used to sample tissue probes for molecular genetic studies in bats.
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Affiliation(s)
- Joanna Kacprzyk
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
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Dool SE, O’Donnell CFJ, Monks JM, Puechmaille SJ, Kerth G. Phylogeographic-based conservation implications for the New Zealand long-tailed bat, (Chalinolobus tuberculatus): identification of a single ESU and a candidate population for genetic rescue. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0844-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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60
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Jacobs DS, Mutumi GL, Maluleke T, Webala PW. Convergence as an Evolutionary Trade-off in the Evolution of Acoustic Signals: Echolocation in Horseshoe Bats as a Case Study. Evol Biol 2016. [DOI: 10.1007/978-3-319-41324-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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