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Wang H, Zhu X, Liu Y, Luo S, Zhangsun D. Mitogenome Characterization of Four Conus Species and Comparative Analysis. Int J Mol Sci 2023; 24:ijms24119411. [PMID: 37298363 DOI: 10.3390/ijms24119411] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/19/2023] [Accepted: 05/21/2023] [Indexed: 06/12/2023] Open
Abstract
Cone snails, as a type of marine organism, have rich species diversity. Traditionally, classifications of cone snails were based mostly on radula, shell, and anatomical characters. Because of these phenotypic features' high population variability and propensity for local adaptation and convergence, identifying species can be difficult and occasionally inaccurate. In addition, mitochondrial genomes contain high phylogenetic information, so complete mitogenomes have been increasingly employed for inferring molecular phylogeny. To enrich the mitogenomic database of cone snails (Caenogastropoda: Conidae), mitogenomes of four Conus species, i.e., C. imperialis (15,505 bp), C. literatus (15,569 bp), C. virgo (15,594 bp), and C. marmoreus (15,579 bp), were characterized and compared. All 4 of these mitogenomes included 13 protein-coding genes, 2 ribosomal RNA genes, 22 tRNA genes, and non-coding regions. All the Protein Codon Genes (PCGs) of both newly sequenced mitogenomes used TAA or TAG as a terminal codon. Most PCGs used conventional start codon ATG, but an alternative initiation codon GTG was detected in a gene (NADH dehydrogenase subunit 4 (nad4)) of C. imperialis. In addition, the phylogenetic relationships were reconstructed among 20 Conus species on the basis of PCGs, COX1, and the complete mitogenome using both Bayesian Inference (BI) and Maximum Likelihood (ML). The phylogenetic results supported that C. litteratus, C. quercinus, and C. virgo were clustered together as a sister group (PP = 1, BS = 99), but they did not support the phylogenetic relation of C. imperialis and C. tribblei (PP = 0.79, BS = 50). In addition, our study established that PCGs and complete mitogenome are the two useful markers for phylogenetic inference of Conus species. These results enriched the data of the cone snail's mitochondrion in the South China Sea and provided a reliable basis for the interpretation of the phylogenetic relationship of the cone snail based on the mitochondrial genome.
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Affiliation(s)
- Hao Wang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou 570228, China
| | - Xiaopeng Zhu
- School of Medicine, Guangxi University, Nanning 530004, China
| | - Yuepeng Liu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou 570228, China
| | - Sulan Luo
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou 570228, China
- School of Medicine, Guangxi University, Nanning 530004, China
| | - Dongting Zhangsun
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Hainan University, Haikou 570228, China
- School of Medicine, Guangxi University, Nanning 530004, China
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Lee Y, Park JK. Complete mitochondrial genome of Conus lischkeanus Weinkauff, 1875 (Neogastropoda, Conidae) and phylogenetic implications of the evolutionary diversification of dietary types of Conus species. Zookeys 2022; 1088:173-185. [PMID: 35437368 PMCID: PMC8930903 DOI: 10.3897/zookeys.1088.78990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/11/2022] [Indexed: 11/17/2022] Open
Abstract
The family Conidae, commonly known as cone snails, is one of the most intriguing gastropod groups owing to their diverse array of feeding behaviors (diets) and toxin peptides (conotoxins). Conuslischkeanus Weinkauff, 1875 is a worm-hunting species widely distributed from Africa to the Northwest Pacific. In this study, we report the mitochondrial genome sequence of C.lischkeanus and inferred its phylogenetic relationship with other Conus species. Its mitochondrial genome is a circular DNA molecule (16,120 bp in size) composed of 37 genes: 13 protein-coding genes (PCGs), 22 transfer RNA genes, and two ribosomal RNA genes. Phylogenetic analyses of concatenated nucleotide sequences of 13 PCGs and two ribosomal RNA genes showed that C.lischkeanus belongs to the subgenus Lividoconus group, which is grouped with species of the subgenus Virgiconus, and a member of the largest assemblage of worm-hunting (vermivorous) species at the most basal position in this group. Mitochondrial genome phylogeny supports the previous hypothesis that the ancestral diet of cone snails was worm-hunting, and that other dietary types (molluscivous or piscivorous) have secondarily evolved multiple times from different origins. This new, complete mitochondrial genome information provides valuable insights into the mitochondrial genome diversity and molecular phylogeny of Conus species.
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Du L, Cai S, Liu J, Liu R, Zhang H. The complete mitochondrial genome of a cold seep gastropod Phymorhynchus buccinoides (Neogastropoda: Conoidea: Raphitomidae). PLoS One 2020; 15:e0242541. [PMID: 33253261 PMCID: PMC7703994 DOI: 10.1371/journal.pone.0242541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 11/04/2020] [Indexed: 11/18/2022] Open
Abstract
Phymorhynchus is a genus of deep-sea snails that are most distributed in hydrothermal vent or cold seep environments. In this study, we presented the complete mitochondrial genome of P. buccinoides, a cold seep snail from the South China Sea. It is the first mitochondrial genome of a cold seep member of the superfamily Conoidea. The mitochondrial genome is 15,764 bp in length, and contains 13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes. These genes are encoded on the positive strand, except for 8 tRNA genes that are encoded on the negative strand. The start codon ATG and 3 types of stop codons, TAA, TAG and the truncated termination codon T, are used in the 13 PCGs. All 13 PCGs in the 26 species of Conoidea share the same gene order, while several tRNA genes have been translocated. Phylogenetic analysis revealed that P. buccinoides clustered with Typhlosyrinx sp., Eubela sp., and Phymorhynchus sp., forming the Raphitomidae clade, with high support values. Positive selection analysis showed that a residue located in atp6 (18 S) was identified as the positively selected site with high posterior probabilities, suggesting potential adaption to the cold seep environment. Overall, our data will provide a useful resource on the evolutionary adaptation of cold seep snails for future studies.
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Affiliation(s)
- Lvpei Du
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shanya Cai
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Jun Liu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Ruoyu Liu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Haibin Zhang
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
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Affiliation(s)
- Samuel Abalde
- Departamento de Biodiversidad y Biología Evolutiva; Museo Nacional de Ciencias Naturales (MNCN-CSIC); Madrid Spain
| | - Manuel J. Tenorio
- Departamento CMIM y Q. Inorgánica-INBIO, Facultad de Ciencias; Universidad de Cádiz; Puerto Real Spain
| | - Juan E. Uribe
- Departamento de Biodiversidad y Biología Evolutiva; Museo Nacional de Ciencias Naturales (MNCN-CSIC); Madrid Spain
- Department of Invertebrate Zoology, Smithsonian Institution; National Museum of Natural History; Washington District of Columbia USA
- Grupo de Evolución, Sistemática y Ecología Molecular; Universidad del Magdalena; Santa Marta Colombia
| | - Rafael Zardoya
- Departamento de Biodiversidad y Biología Evolutiva; Museo Nacional de Ciencias Naturales (MNCN-CSIC); Madrid Spain
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Gao B, Peng C, Chen Q, Zhang J, Shi Q. Mitochondrial genome sequencing of a vermivorous cone snail Conus quercinus supports the correlative analysis between phylogenetic relationships and dietary types of Conus species. PLoS One 2018; 13:e0193053. [PMID: 30059499 PMCID: PMC6066214 DOI: 10.1371/journal.pone.0193053] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 02/02/2018] [Indexed: 12/15/2022] Open
Abstract
Complete mitochondrial genome (mitogenome) sequence of a worm-hunting cone snail, Conus quercinus, was reported in this study. Its mitogenome, the longest one (16,460 bp) among reported Conus specie, is composed of 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and one D-loop region. The mitochondrial gene arrangement is highly-conserved and identical to other reported. However, the D-loop region of C. quercinus is the longest (943 bp) with the higher A+T content (71.3%) and a long AT tandem repeat stretch (68 bp). Subsequent phylogenetic analysis demonstrated that three different dietary types (vermivorous, molluscivorous and piscivorous) of cone snails are clustered separately, suggesting that the phylogenetics of cone snails is related to their dietary types. In conclusion, our current work improves our understanding of the mitogenomic structure and evolutionary status of the vermivorous C. quercinus, which support the putative hypothesis that the Conus ancestor was vermivorous.
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Affiliation(s)
- Bingmiao Gao
- Hainan Provincial Key Laboratory of Research and Development of Tropical Medicinal Plants, Hainan Medical University, Haikou, China
| | - Chao Peng
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
| | - Qin Chen
- School of Agricultural and Forestry Science and Technology, Hainan Radio & TV University, Haikou, China
| | - Junqing Zhang
- Hainan Provincial Key Laboratory of Research and Development of Tropical Medicinal Plants, Hainan Medical University, Haikou, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen, China
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Gao B, Peng C, Yang J, Yi Y, Zhang J, Shi Q. Cone Snails: A Big Store of Conotoxins for Novel Drug Discovery. Toxins (Basel) 2017; 9:E397. [PMID: 29215605 PMCID: PMC5744117 DOI: 10.3390/toxins9120397] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/28/2017] [Accepted: 12/04/2017] [Indexed: 12/11/2022] Open
Abstract
Marine drugs have developed rapidly in recent decades. Cone snails, a group of more than 700 species, have always been one of the focuses for new drug discovery. These venomous snails capture prey using a diverse array of unique bioactive neurotoxins, usually named as conotoxins or conopeptides. These conotoxins have proven to be valuable pharmacological probes and potential drugs due to their high specificity and affinity to ion channels, receptors, and transporters in the nervous systems of target prey and humans. Several research groups, including ours, have examined the venom gland of cone snails using a combination of transcriptomic and proteomic sequencing, and revealed the existence of hundreds of conotoxin transcripts and thousands of conopeptides in each Conus species. Over 2000 nucleotide and 8000 peptide sequences of conotoxins have been published, and the number is still increasing quickly. However, more than 98% of these sequences still lack 3D structural and functional information. With the rapid development of genomics and bioinformatics in recent years, functional predictions and investigations on conotoxins are making great progress in promoting the discovery of novel drugs. For example, ω-MVIIA was approved by the U.S. Food and Drug Administration in 2004 to treat chronic pain, and nine more conotoxins are at various stages of preclinical or clinical evaluation. In short, the genus Conus, the big family of cone snails, has become an important genetic resource for conotoxin identification and drug development.
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Affiliation(s)
- Bingmiao Gao
- Hainan Provincial Key Laboratory of Research and Development of Tropical Medicinal Plants, Hainan Medical University, Haikou 571199, China.
| | - Chao Peng
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Jiaan Yang
- Micro Pharmtech, Ltd., Wuhan 430075, China.
| | - Yunhai Yi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
| | - Junqing Zhang
- Hainan Provincial Key Laboratory of Research and Development of Tropical Medicinal Plants, Hainan Medical University, Haikou 571199, China.
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
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