1
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Zaharias P, Kantor YI, Fedosov AE, Puillandre N. Coupling DNA barcodes and exon-capture to resolve the phylogeny of Turridae (Gastropoda, Conoidea). Mol Phylogenet Evol 2024; 191:107969. [PMID: 38007006 DOI: 10.1016/j.ympev.2023.107969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 11/05/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023]
Abstract
Taxon sampling in most phylogenomic studies is often based on known taxa and/or morphospecies, thus ignoring undescribed diversity and/or cryptic lineages. The family Turridae is a group of venomous snails within the hyperdiverse superfamily Conoidea that includes many undescribed and cryptic species. Therefore 'traditional' taxon sampling could constitute a strong risk of undersampling or oversampling Turridae lineages. To minimize potential biases, we establish a robust sampling strategy, from species delimitation to phylogenomics. More than 3,000 cox-1 "barcode" sequences were used to propose 201 primary species hypotheses, nearly half of them corresponding to species potentially new to science, including several cryptic species. A 110-taxa exon-capture tree, including species representatives of the diversity uncovered with the cox-1 dataset, was build using up to 4,178 loci. Our results show the polyphyly of the genus Gemmula, that is split into up to 10 separate lineages, of which half would not have been detected if the sampling strategy was based only on described species. Our results strongly suggest that the use of blind, exploratory and intensive barcode sampling is necessary to avoid sampling biases in phylogenomic studies.
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Affiliation(s)
- Paul Zaharias
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 43 rue Cuvier, CP 51, 75005 Paris, France.
| | - Yuri I Kantor
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 43 rue Cuvier, CP 51, 75005 Paris, France; A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninski prospect 33, 119071 Moscow, Russian Federation
| | - Alexander E Fedosov
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 43 rue Cuvier, CP 51, 75005 Paris, France; Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 43 rue Cuvier, CP 51, 75005 Paris, France
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2
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Farhat S, Modica MV, Puillandre N. Whole Genome Duplication and Gene Evolution in the Hyperdiverse Venomous Gastropods. Mol Biol Evol 2023; 40:msad171. [PMID: 37494290 PMCID: PMC10401626 DOI: 10.1093/molbev/msad171] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/20/2023] [Accepted: 07/17/2023] [Indexed: 07/28/2023] Open
Abstract
The diversity of venomous organisms and the toxins they produce have been increasingly investigated, but taxonomic bias remains important. Neogastropods, a group of marine predators representing almost 22% of the known gastropod diversity, evolved a wide range of feeding strategies, including the production of toxins to subdue their preys. However, whether the diversity of these compounds is at the origin of the hyperdiversification of the group and how genome evolution may correlate with both the compounds and species diversities remain understudied. Among the available gastropods genomes, only eight, with uneven quality assemblies, belong to neogastropods. Here, we generated chromosome-level assemblies of two species belonging to the Tonnoidea and Muricoidea superfamilies (Monoplex corrugatus and Stramonita haemastoma). The two obtained high-quality genomes had 3 and 2.2 Gb, respectively, and 92-89% of the total assembly conformed 35 pseudochromosomes in each species. Through the analysis of syntenic blocks, Hox gene cluster duplication, and synonymous substitutions distribution pattern, we inferred the occurrence of a whole genome duplication event in both genomes. As these species are known to release venom, toxins were annotated in both genomes, but few of them were found in homologous chromosomes. A comparison of the expression of ohnolog genes (using transcriptomes from osphradium and salivary glands in S. haemastoma), where both copies were differentially expressed, showed that most of them had similar expression profiles. The high quality of these genomes makes them valuable reference in their respective taxa, facilitating the identification of genome-level processes at the origin of their evolutionary success.
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Affiliation(s)
- Sarah Farhat
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Maria Vittoria Modica
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Roma, Italy
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
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3
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Abalde S, Crocetta F, Tenorio MJ, D'Aniello S, Fassio G, Rodríguez-Flores PC, Uribe JE, M L Afonso C, Oliverio M, Zardoya R. Hidden species diversity and mito-nuclear discordance within the Mediterranean cone snail, Lautoconus ventricosus. Mol Phylogenet Evol 2023:107838. [PMID: 37286063 DOI: 10.1016/j.ympev.2023.107838] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 05/15/2023] [Accepted: 05/31/2023] [Indexed: 06/09/2023]
Abstract
The Mediterranean cone snail, Lautoconus ventricosus, is currently considered a single species inhabiting the whole Mediterranean basin and the adjacent Atlantic coasts. Yet, no population genetic study has assessed its taxonomic status. Here, we collected 245 individuals from 75 localities throughout the Mediterranean Sea and used cox1 barcodes, complete mitochondrial genomes, and genome skims to test whether L. ventricosus represents a complex of cryptic species. The maximum likelihood phylogeny based on complete mitochondrial genomes recovered six main clades (hereby named blue, brown, green, orange, red, and violet) with sufficient sequence divergence to be considered putative species. On the other hand, phylogenomic analyses based on 437 nuclear genes only recovered four out of the six clades: blue and orange clades were thoroughly mixed and the brown one was not recovered. This mito-nuclear discordance revealed instances of incomplete lineage sorting and introgression, and may have caused important differences in the dating of main cladogenetic events. Species delimitation tests proposed the existence of at least three species: green, violet, and red+blue+orange (i.e., cyan). Green plus cyan (with sympatric distributions) and violet, had West and East Mediterranean distributions, respectively, mostly separated by the Siculo-Tunisian biogeographical barrier. Morphometric analyses of the shell using species hypotheses as factor and shell length as covariate showed that the discrimination power of the studied parameters was only 70.2%, reinforcing the cryptic nature of the uncovered species, and the importance of integrative taxonomic approaches considering morphology, ecology, biogeography, and mitochondrial and nuclear population genetic variation.
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Affiliation(s)
- Samuel Abalde
- Department of Zoology, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden; Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain.
| | - Fabio Crocetta
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy
| | - Manuel J Tenorio
- Departamento CMIM y Q. Inorgánica-INBIO, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real, Cádiz, Spain
| | - Salvatore D'Aniello
- Department of Biology and Evolution of Marine Organisms (BEOM), Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121 Napoli, Italy
| | - Giulia Fassio
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Zoology-Viale dell'Università 32, 00185 Rome, Italy
| | - Paula C Rodríguez-Flores
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain; Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge MA 02138, USA
| | - Juan E Uribe
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Carlos M L Afonso
- Centre of Marine Sciences (CCMAR), Universidade do Algarve, Campus de Gambelas, 8005 - 139 Faro, Portugal
| | - Marco Oliverio
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Zoology-Viale dell'Università 32, 00185 Rome, Italy
| | - 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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4
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Koch TL, Ramiro IBL, Flórez Salcedo P, Engholm E, Jensen KJ, Chase K, Olivera BM, Bjørn-Yoshimoto WE, Safavi-Hemami H. Reconstructing the Origins of the Somatostatin and Allatostatin-C Signaling Systems Using the Accelerated Evolution of Biodiverse Cone Snail Toxins. Mol Biol Evol 2022; 39:msac075. [PMID: 35383850 PMCID: PMC9048919 DOI: 10.1093/molbev/msac075] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Somatostatin and its related peptides (SSRPs) form an important family of hormones with diverse physiological roles. The ubiquitous presence of SSRPs in vertebrates and several invertebrate deuterostomes suggests an ancient origin of the SSRP signaling system. However, the existence of SSRP genes outside of deuterostomes has not been established, and the evolutionary history of this signaling system remains poorly understood. Our recent discovery of SSRP-like toxins (consomatins) in venomous marine cone snails (Conus) suggested the presence of a related signaling system in mollusks and potentially other protostomes. Here, we identify the molluscan SSRP-like signaling gene that gave rise to the consomatin family. Following recruitment into venom, consomatin genes experienced strong positive selection and repeated gene duplications resulting in the formation of a hyperdiverse family of venom peptides. Intriguingly, the largest number of consomatins was found in worm-hunting species (>400 sequences), indicating a homologous system in annelids, another large protostome phylum. Consistent with this, comprehensive sequence mining enabled the identification of SSRP-like sequences (and their corresponding orphan receptor) in annelids and several other protostome phyla. These results established the existence of SSRP-like peptides in many major branches of bilaterians and challenge the prevailing hypothesis that deuterostome SSRPs and protostome allatostatin-C are orthologous peptide families. Finally, having a large set of predator-prey SSRP sequences available, we show that although the cone snail's signaling SSRP-like genes are under purifying selection, the venom consomatin genes experience rapid directional selection to target receptors in a changing mix of prey.
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Affiliation(s)
- Thomas Lund Koch
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen-N 2200, Denmark
| | - Iris Bea L. Ramiro
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen-N 2200, Denmark
| | | | - Ebbe Engholm
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen-N 2200, Denmark
- Department of Chemistry, University of Copenhagen, Frederiksberg 1871, Denmark
| | - Knud Jørgen Jensen
- Department of Chemistry, University of Copenhagen, Frederiksberg 1871, Denmark
| | - Kevin Chase
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Baldomero M. Olivera
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Helena Safavi-Hemami
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen-N 2200, Denmark
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
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5
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Fedosov A, Zaharias P, Puillandre N. A phylogeny-aware approach reveals unexpected venom components in divergent lineages of cone snails. Proc Biol Sci 2021; 288:20211017. [PMID: 34229491 PMCID: PMC8261202 DOI: 10.1098/rspb.2021.1017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/11/2021] [Indexed: 12/31/2022] Open
Abstract
Marine gastropods of the genus Conus are renowned for their remarkable diversity and deadly venoms. While Conus venoms are increasingly well studied for their biomedical applications, we know surprisingly little about venom composition in other lineages of Conidae. We performed comprehensive venom transcriptomic profiling for Conasprella coriolisi and Pygmaeconus traillii, first time for both respective genera. We complemented reference-based transcriptome annotation by a de novo toxin prediction guided by phylogeny, which involved transcriptomic data on two additional 'divergent' cone snail lineages, Profundiconus, and Californiconus. We identified toxin clusters (SSCs) shared among all or some of the four analysed genera based on the identity of the signal region-a molecular tag present in toxins. In total, 116 and 98 putative toxins represent 29 and 28 toxin gene superfamilies in Conasprella and Pygmaeconus, respectively; about quarter of these only found by semi-manual annotation of the SSCs. Two rare gene superfamilies, originally identified from fish-hunting cone snails, were detected outside Conus rather unexpectedly, so we further investigated their distribution across Conidae radiation. We demonstrate that both these, in fact, are ubiquitous in Conidae, sometimes with extremely high expression. Our findings demonstrate how a phylogeny-aware approach circumvents methodological caveats of similarity-based transcriptome annotation.
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Affiliation(s)
- Alexander Fedosov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russian Federation
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 26, 75005 Paris, France
| | - Paul Zaharias
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 26, 75005 Paris, France
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Nicolas Puillandre
- Institut Systématique Evolution Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 26, 75005 Paris, France
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6
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Wood AW, Duda TF. Reticulate evolution in Conidae: Evidence of nuclear and mitochondrial introgression. Mol Phylogenet Evol 2021; 161:107182. [PMID: 33892099 DOI: 10.1016/j.ympev.2021.107182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 04/07/2021] [Accepted: 04/15/2021] [Indexed: 10/21/2022]
Abstract
Conidae is a hyperdiverse family of marine snails that has many hallmarks of adaptive radiation. Hybridization and introgression may contribute to such instances of rapid diversification by generating novel gene combinations that facilitate exploitation of distinct niches. Here we evaluated whether or not these mechanisms may have contributed to the evolutionary history of a subgenus of Conidae (Virroconus). Several observations hint at evidence of past introgression for members of this group, including incongruence between phylogenetic relationships inferred from mitochondrial gene sequences and morphology and widespread sympatry of many Virroconus species in the Indo-West Pacific. We generated and analyzed transcriptome data of Virroconus species to (i) infer a robust nuclear phylogeny, (ii) assess mitochondrial and nuclear gene tree discordance, and (iii) formally test for introgression of nuclear loci. We identified introgression of mitochondrial genomes and nuclear gene regions between ancestors of one pair of Virroconus species, and mitochondrial introgression between another pair. We also found evidence of adaptive introgression of conotoxin venom loci between a third pair of species. Together, our results demonstrate that hybridization and introgression impacted the evolutionary history of Virroconus and hence may have contributed to the adaptive radiation of Conidae.
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Affiliation(s)
- Andrew W Wood
- University of Michigan, Department of Ecology & Evolutionary Biology, 1105 North University Avenue, Biological Sciences Building, Ann Arbor, MI 48109-1085, USA.
| | - Thomas F Duda
- University of Michigan, Department of Ecology & Evolutionary Biology, 1105 North University Avenue, Biological Sciences Building, Ann Arbor, MI 48109-1085, USA.
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7
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Lu A, Watkins M, Li Q, Robinson SD, Concepcion GP, Yandell M, Weng Z, Olivera BM, Safavi-Hemami H, Fedosov AE. Transcriptomic Profiling Reveals Extraordinary Diversity of Venom Peptides in Unexplored Predatory Gastropods of the Genus Clavus. Genome Biol Evol 2020; 12:684-700. [PMID: 32333764 PMCID: PMC7259678 DOI: 10.1093/gbe/evaa083] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2020] [Indexed: 12/21/2022] Open
Abstract
Predatory gastropods of the superfamily Conoidea number over 12,000 living species. The evolutionary success of this lineage can be explained by the ability of conoideans to produce complex venoms for hunting, defense, and competitive interactions. Whereas venoms of cone snails (family Conidae) have become increasingly well studied, the venoms of most other conoidean lineages remain largely uncharacterized. In the present study, we present the venom gland transcriptomes of two species of the genus Clavus that belong to the family Drilliidae. Venom gland transcriptomes of two specimens of Clavus canalicularis and two specimens of Clavus davidgilmouri were analyzed, leading to the identification of a total of 1,176 putative venom peptide toxins (drillipeptides). Based on the combined evidence of secretion signal sequence identity, entire precursor similarity search (BLAST), and the orthology inference, putative Clavus toxins were assigned to 158 different gene families. The majority of identified transcripts comprise signal, pro-, mature peptide, and post-regions, with a typically short (<50 amino acids) and cysteine-rich mature peptide region. Thus, drillipeptides are structurally similar to conotoxins. However, convincing homology with known groups of Conus toxins was only detected for very few toxin families. Among these are Clavus counterparts of Conus venom insulins (drillinsulins), porins (drilliporins), and highly diversified lectins (drillilectins). The short size of most drillipeptides and structural similarity to conotoxins were unexpected, given that most related conoidean gastropod families (Terebridae and Turridae) possess longer mature peptide regions. Our findings indicate that, similar to conotoxins, drillipeptides may represent a valuable resource for future pharmacological exploration.
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Affiliation(s)
- Aiping Lu
- Department of Central Laboratory, Shanghai Tenth People’s Hospital of Tongji University, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | | | - Qing Li
- Eccles Institute of Human Genetics, University of Utah
- High-Throughput Genomics and Bioinformatic Analysis Shared Resource, Huntsman Cancer Institute, University of Utah
| | | | - Gisela P Concepcion
- Marine Science Institute, University of the Philippines-Diliman, Quezon City, Philippines
| | - Mark Yandell
- Eccles Institute of Human Genetics, University of Utah
- Utah Center for Genetic Discovery, University of Utah
| | - Zhiping Weng
- Department of Central Laboratory, Shanghai Tenth People’s Hospital of Tongji University, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School
| | | | - Helena Safavi-Hemami
- Department of Biochemistry, University of Utah
- Department of Biology, University of Copenhagen, Denmark
| | - Alexander E Fedosov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Science, Moscow, Russia
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8
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Data, time and money: evaluating the best compromise for inferring molecular phylogenies of non-model animal taxa. Mol Phylogenet Evol 2020; 142:106660. [DOI: 10.1016/j.ympev.2019.106660] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/17/2019] [Accepted: 10/17/2019] [Indexed: 12/15/2022]
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9
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Sudewi AA, Susilawathi NM, Mahardika BK, Mahendra AN, Pharmawati M, Phuong MA, Mahardika GN. Selecting Potential Neuronal Drug Leads from Conotoxins of Various Venomous Marine Cone Snails in Bali, Indonesia. ACS OMEGA 2019; 4:19483-19490. [PMID: 31763573 PMCID: PMC6868881 DOI: 10.1021/acsomega.9b03122] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 10/23/2019] [Indexed: 06/10/2023]
Abstract
Many conotoxins, natural peptides of marine cone snails, have been identified to target neurons. Here, we provide data on pharmacological families of the conotoxins of 11 species of cone snails collected in Bali. The identified definitive pharmacological families possibly targeting neuronal tissues were α (alpha), ι (iota), κ (kappa), and ρ (rho). These classes shall target nicotinic acetylcholine receptors, voltage-gated Na channels, voltage-gated K channels, and α1-adrenoceptors, respectively. The VI/VII-O3 conotoxins might be prospected as an inhibitor of N-methyl-d-aspartate. Con-ikot-ikot could be applied as an α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptor blocker medicine. The definitive pharmacology classes of conotoxins as well as those yet to be elucidated need to be further established and verified.
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Affiliation(s)
- Anak A.
R. Sudewi
- Neurology
Department of the Faculty of Medicine and Pharmacology Department of the Faculty
of Medicine, Udayana University, Jl. Sudirman, Denpasar 80226, Bali, Indonesia
| | - Ni M. Susilawathi
- Neurology
Department of the Faculty of Medicine and Pharmacology Department of the Faculty
of Medicine, Udayana University, Jl. Sudirman, Denpasar 80226, Bali, Indonesia
| | - Bayu K. Mahardika
- The
Animal Biomedical and Molecular Biology Laboratory, Udayana University of Bali, Jl. Sesetan-Markisa 6, Denpasar 80223, Bali, Indonesia
| | - Agung N. Mahendra
- Neurology
Department of the Faculty of Medicine and Pharmacology Department of the Faculty
of Medicine, Udayana University, Jl. Sudirman, Denpasar 80226, Bali, Indonesia
| | - Made Pharmawati
- Faculty
of Mathematic and Natural Sciences, Udayana
University of Bali, Kampus
Bukit Jimbaran, Badung 80361, Bali, Indonesia
| | - Mark A. Phuong
- Department
of Ecology and Evolutionary Biology, University
of California, Los Angeles, Los
Angeles 90095, California, United States
| | - Gusti N. Mahardika
- The
Animal Biomedical and Molecular Biology Laboratory, Udayana University of Bali, Jl. Sesetan-Markisa 6, Denpasar 80223, Bali, Indonesia
- The Indonesian
Biodiversity Research Center, Jl. Sudirman, Denpasar 80225, Bali, Indonesia
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10
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Venom Diversity and Evolution in the Most Divergent Cone Snail Genus Profundiconus. Toxins (Basel) 2019; 11:toxins11110623. [PMID: 31661832 PMCID: PMC6891753 DOI: 10.3390/toxins11110623] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 10/24/2019] [Accepted: 10/24/2019] [Indexed: 01/02/2023] Open
Abstract
Profundiconus is the most divergent cone snail genus and its unique phylogenetic position, sister to the rest of the family Conidae, makes it a key taxon for examining venom evolution and diversity. Venom gland and foot transcriptomes of Profundiconus cf. vaubani and Profundiconus neocaledonicus were de novo assembled, annotated, and analyzed for differential expression. One hundred and thirty-seven venom components were identified from P. cf. vaubani and 82 from P. neocaledonicus, with only four shared by both species. The majority of the transcript diversity was composed of putative peptides, including conotoxins, profunditoxins, turripeptides, insulin, and prohormone-4. However, there were also a significant percentage of other putative venom components such as chymotrypsin and L-rhamnose-binding lectin. The large majority of conotoxins appeared to be from new gene superfamilies, three of which are highly different from previously reported venom peptide toxins. Their low conotoxin diversity and the type of insulin found suggested that these species, for which no ecological information are available, have a worm or molluscan diet associated with a narrow dietary breadth. Our results indicate that Profundiconus venom is highly distinct from that of other cone snails, and therefore important for examining venom evolution in the Conidae family.
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11
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Conotoxin Diversity in the Venom Gland Transcriptome of the Magician's Cone, Pionoconus magus. Mar Drugs 2019; 17:md17100553. [PMID: 31569823 PMCID: PMC6835573 DOI: 10.3390/md17100553] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 09/24/2019] [Indexed: 12/14/2022] Open
Abstract
The transcriptomes of the venom glands of two individuals of the magician’s cone, Pionoconus magus, from Okinawa (Japan) were sequenced, assembled, and annotated. In addition, RNA-seq raw reads available at the SRA database from one additional specimen of P. magus from the Philippines were also assembled and annotated. The total numbers of identified conotoxin precursors and hormones per specimen were 118, 112, and 93. The three individuals shared only five identical sequences whereas the two specimens from Okinawa had 30 sequences in common. The total number of distinct conotoxin precursors and hormones for P. magus was 275, and were assigned to 53 conotoxin precursor and hormone superfamilies, two of which were new based on their divergent signal region. The superfamilies that had the highest number of precursors were M (42), O1 (34), T (27), A (18), O2 (17), and F (13), accounting for 55% of the total diversity. The D superfamily, previously thought to be exclusive of vermivorous cones was found in P. magus and contained a highly divergent mature region. Similarly, the A superfamily alpha 4/3 was found in P. magus despite the fact that it was previously postulated to be almost exclusive of the genus Rhombiconus. Differential expression analyses of P. magus compared to Chelyconus ermineus, the only fish-hunting cone from the Atlantic Ocean revealed that M and A2 superfamilies appeared to be more expressed in the former whereas the O2 superfamily was more expressed in the latter.
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