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Pardos-Blas JR, Irisarri I, Abalde S, Afonso CML, Tenorio MJ, Zardoya R. The genome of the venomous snail Lautoconus ventricosus sheds light on the origin of conotoxin diversity. Gigascience 2021; 10:giab037. [PMID: 34037232 PMCID: PMC8152183 DOI: 10.1093/gigascience/giab037] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/23/2021] [Accepted: 04/30/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Venoms are deadly weapons to subdue prey or deter predators that have evolved independently in many animal lineages. The genomes of venomous animals are essential to understand the evolutionary mechanisms involved in the origin and diversification of venoms. RESULTS Here, we report the chromosome-level genome of the venomous Mediterranean cone snail, Lautoconus ventricosus (Caenogastropoda: Conidae). The total size of the assembly is 3.59 Gb; it has high contiguity (N50 = 93.53 Mb) and 86.6 Mb of the genome assembled into the 35 largest scaffolds or pseudochromosomes. On the basis of venom gland transcriptomes, we annotated 262 complete genes encoding conotoxin precursors, hormones, and other venom-related proteins. These genes were scattered in the different pseudochromosomes and located within repetitive regions. The genes encoding conotoxin precursors were normally structured into 3 exons, which did not necessarily coincide with the 3 structural domains of the corresponding proteins. Additionally, we found evidence in the L. ventricosus genome for a past whole-genome duplication event by means of conserved gene synteny with the Pomacea canaliculata genome, the only one available at the chromosome level within Caenogastropoda. The whole-genome duplication event was further confirmed by the presence of a duplicated hox gene cluster. Key genes for gastropod biology including those encoding proteins related to development, shell formation, and sex were located in the genome. CONCLUSIONS The new high-quality L. ventricosus genome should become a reference for assembling and analyzing new gastropod genomes and will contribute to future evolutionary genomic studies among venomous animals.
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Affiliation(s)
- José Ramón Pardos-Blas
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Iker Irisarri
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, D-37077 Goettingen, Germany
- Campus Institute Data Science (CIDAS), Goettingen, Wilhelmsplatz 1, D-37073, Germany
| | - Samuel Abalde
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain
- Department of Zoology, Swedish Museum of Natural History, Frescativägen 40, 11418 Stockholm, Sweden
| | - Carlos M L Afonso
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, 8005–139 Faro, Portugal
| | - Manuel J Tenorio
- Departamento CMIM y Q. Inorgánica-INBIO, Facultad de Ciencias, Universidad de Cadiz, 11510 Puerto Real, Cádiz, Spain
| | - Rafael Zardoya
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain
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Bino G, Kingsford RT, Archer M, Connolly JH, Day J, Dias K, Goldney D, Gongora J, Grant T, Griffiths J, Hawke T, Klamt M, Lunney D, Mijangos L, Munks S, Sherwin W, Serena M, Temple-Smith P, Thomas J, Williams G, Whittington C. The platypus: evolutionary history, biology, and an uncertain future. J Mammal 2019; 100:308-327. [PMID: 31043761 PMCID: PMC6479513 DOI: 10.1093/jmammal/gyz058] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 02/25/2019] [Indexed: 12/21/2022] Open
Abstract
The platypus (Ornithorhynchus anatinus) is one of the world's most evolutionarily distinct mammals, one of five extant species of egg-laying mammals, and the only living species within the family Ornithorhynchidae. Modern platypuses are endemic to eastern mainland Australia, Tasmania, and adjacent King Island, with a small introduced population on Kangaroo Island, South Australia, and are widely distributed in permanent river systems from tropical to alpine environments. Accumulating knowledge and technological advancements have provided insights into many aspects of its evolutionary history and biology but have also raised concern about significant knowledge gaps surrounding distribution, population sizes, and trends. The platypus' distribution coincides with many of Australia's major threatening processes, including highly regulated and disrupted rivers, intensive habitat destruction, and fragmentation, and they were extensively hunted for their fur until the early 20th century. Emerging evidence of local population declines and extinctions identifies that ecological thresholds have been crossed in some populations and, if threats are not addressed, the species will continue to decline. In 2016, the IUCN Red Listing for the platypus was elevated to "Near Threatened," but the platypus remains unlisted on threatened species schedules of any Australian state, apart from South Australia, or nationally. In this synthesis, we review the evolutionary history, genetics, biology, and ecology of this extraordinary mammal and highlight prevailing threats. We also outline future research directions and challenges that need to be met to help conserve the species.
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Affiliation(s)
- Gilad Bino
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Richard T Kingsford
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Michael Archer
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Joanne H Connolly
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia.,Graham Centre for Agricultural Innovation, Wagga Wagga, New South Wales, Australia
| | - Jenna Day
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Kimberly Dias
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - David Goldney
- Charles Sturt University, Wagga Wagga, New South Wales, Australia
| | - Jaime Gongora
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Tom Grant
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | | | - Tahneal Hawke
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Melissa Klamt
- Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Daniel Lunney
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia.,Office of Environment and Heritage, Hurstville, New South Wales, Australia
| | - Luis Mijangos
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Sarah Munks
- School of Biological Sciences, University of Tasmania, Tasmania, Australia.,Forest Practices Authority, Hobart, Tasmania, Australia
| | - William Sherwin
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Melody Serena
- Australian Platypus Conservancy, Wiseleigh, Victoria, Australia
| | - Peter Temple-Smith
- Department of Obstetrics and Gynaecology, Southern Clinical School, Monash University, Clayton, Victoria, Australia
| | | | - Geoff Williams
- Australian Platypus Conservancy, Wiseleigh, Victoria, Australia
| | - Camilla Whittington
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Sydney, New South Wales, Australia.,School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
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Junqueira-de-Azevedo ILM, Bastos CMV, Ho PL, Luna MS, Yamanouye N, Casewell NR. Venom-related transcripts from Bothrops jararaca tissues provide novel molecular insights into the production and evolution of snake venom. Mol Biol Evol 2014; 32:754-66. [PMID: 25502939 PMCID: PMC4327157 DOI: 10.1093/molbev/msu337] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Attempts to reconstruct the evolutionary history of snake toxins in the context of their co-option to the venom gland rarely account for nonvenom snake genes that are paralogous to toxins, and which therefore represent important connectors to ancestral genes. In order to reevaluate this process, we conducted a comparative transcriptomic survey on body tissues from a venomous snake. A nonredundant set of 33,000 unigenes (assembled transcripts of reference genes) was independently assembled from six organs of the medically important viperid snake Bothrops jararaca, providing a reference list of 82 full-length toxins from the venom gland and specific products from other tissues, such as pancreatic digestive enzymes. Unigenes were then screened for nontoxin transcripts paralogous to toxins revealing 1) low level coexpression of approximately 20% of toxin genes (e.g., bradykinin-potentiating peptide, C-type lectin, snake venom metalloproteinase, snake venom nerve growth factor) in body tissues, 2) the identity of the closest paralogs to toxin genes in eight classes of toxins, 3) the location and level of paralog expression, indicating that, in general, co-expression occurs in a higher number of tissues and at lower levels than observed for toxin genes, and 4) strong evidence of a toxin gene reverting back to selective expression in a body tissue. In addition, our differential gene expression analyses identify specific cellular processes that make the venom gland a highly specialized secretory tissue. Our results demonstrate that the evolution and production of venom in snakes is a complex process that can only be understood in the context of comparative data from other snake tissues, including the identification of genes paralogous to venom toxins.
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Affiliation(s)
- Inácio L M Junqueira-de-Azevedo
- Laboratório Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Carolina Mancini Val Bastos
- Laboratório Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling (CeTICS), Instituto Butantan, São Paulo, Brazil Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Paulo Lee Ho
- Centro de Biotecnologia, Instituto Butantan, São Paulo, Brazil
| | | | - Norma Yamanouye
- Laboratório de Farmacologia, Instituto Butantan, São Paulo-SP, Brazil
| | - Nicholas R Casewell
- Alistair Reid Venom Research Unit, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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Whittington CM, Belov K. Tracing monotreme venom evolution in the genomics era. Toxins (Basel) 2014; 6:1260-73. [PMID: 24699339 PMCID: PMC4014732 DOI: 10.3390/toxins6041260] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/17/2014] [Accepted: 03/27/2014] [Indexed: 01/07/2023] Open
Abstract
The monotremes (platypuses and echidnas) represent one of only four extant venomous mammalian lineages. Until recently, monotreme venom was poorly understood. However, the availability of the platypus genome and increasingly sophisticated genomic tools has allowed us to characterize platypus toxins, and provides a means of reconstructing the evolutionary history of monotreme venom. Here we review the physiology of platypus and echidna crural (venom) systems as well as pharmacological and genomic studies of monotreme toxins. Further, we synthesize current ideas about the evolution of the venom system, which in the platypus is likely to have been retained from a venomous ancestor, whilst being lost in the echidnas. We also outline several research directions and outstanding questions that would be productive to address in future research. An improved characterization of mammalian venoms will not only yield new toxins with potential therapeutic uses, but will also aid in our understanding of the way that this unusual trait evolves.
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Affiliation(s)
- Camilla M Whittington
- School of Biological Sciences, The University of Sydney, Camperdown, NSW 2006, Australia.
| | - Katherine Belov
- Faculty of Veterinary Science, The University of Sydney, Camperdown, NSW 2006, Australia.
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Ligabue-Braun R, Verli H, Carlini CR. Venomous mammals: a review. Toxicon 2012; 59:680-95. [PMID: 22410495 DOI: 10.1016/j.toxicon.2012.02.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Revised: 01/19/2012] [Accepted: 02/21/2012] [Indexed: 01/09/2023]
Abstract
The occurrence of venom in mammals has long been considered of minor importance, but recent fossil discoveries and advances in experimental techniques have cast new light into this subject. Mammalian venoms form a heterogeneous group having different compositions and modes of action and are present in three classes of mammals, Insectivora, Monotremata, and Chiroptera. A fourth order, Primates, is proposed to have venomous representatives. In this review we highlight recent advances in the field while summarizing biochemical characteristics of these secretions and their effects upon humans and other animals. Historical aspects of venom discovery and evolutionary hypothesis regarding their origin are also discussed.
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Affiliation(s)
- Rodrigo Ligabue-Braun
- Graduate Program in Cellular and Molecular Biology, Center of Biotechnology, Department of Biophysics-IB, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
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