1
|
Lee Y, Kim KB, Choi EH, Hwang UW. Complete mitochondrial genome of the worm snail Thylacodes adamsii (Littorinimorpha: Vermetidae) from South Korea. Mitochondrial DNA B Resour 2024; 9:753-757. [PMID: 38895513 PMCID: PMC11185085 DOI: 10.1080/23802359.2024.2368209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024] Open
Abstract
The worm snail Thylacodes adamsii (Mörch, 1859) (Littorinimorpha: Vermetidae) is a sessile gastropod that mainly inhabits rocky shores along the warm temperate to tropical ocean. Herein, the complete mitochondrial genome (mitogenome) of T. adamsii from South Korea was characterized. The genome is 14,913 bp in length and contains 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes. The genome organization and base composition of T. adamsii are similar to those of other vermetids. A phylogenetic tree was reconstructed using maximum likelihood based on the nucleotide sequences of the 13 PCGs; this tree supported the monophyly of Vermetidae. The complete mitogenome of T. adamsii can assist with molecular species identification and vermetid phylogenetic research in the future.
Collapse
Affiliation(s)
- Yumin Lee
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
| | - Ki Beom Kim
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
- Institute for Korean Herb-Bio Convergence Promotion, Kyungpook National University, Daegu, South Korea
| | - Eun Hwa Choi
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
- Phylomics Inc., Daegu, South Korea
| | - Ui Wook Hwang
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
- Institute for Korean Herb-Bio Convergence Promotion, Kyungpook National University, Daegu, South Korea
- Phylomics Inc., Daegu, South Korea
- Department of Biomedical Convergence Science and Technology, School of Industrial Technology Advances, Kyungpook National University, Daegu, South Korea
| |
Collapse
|
2
|
Ma Y, Zheng B, Li J, Meng W, Xu K, Ye Y. Characterization of the complete mitochondrial genome of Desmaulus extinctorium (Littorinimorpha, Calyptraeoidea, Calyptraeidae) and molecular phylogeny of Littorinimorpha. PLoS One 2024; 19:e0301389. [PMID: 38547307 PMCID: PMC10977763 DOI: 10.1371/journal.pone.0301389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/12/2024] [Indexed: 04/02/2024] Open
Abstract
For the purpose of determining the placement of Calyptraeidae within the Littorinimorpha, we hereby furnish a thorough analysis of the mitochondrial genome (mitogenome) sequence of Desmaulus extinctorium. This mitogenome spans 16,605 base pairs and encompasses the entire set of 37 genes, including 13 PCGs, 22 tRNAs and two rRNAs, with an evident AT bias. Notably, tRNASer1 and tRNASer2 lack dihydrouracil (DHU) arms, resulting in an inability to form a secondary structure. Similarly, tRNAAla lacks a TΨC arm, rendering it incapable of forming a secondary structure. In contrast, the remaining tRNAs demonstrate a characteristic secondary structure reminiscent of a cloverleaf. A comparison with ancestral gastropods reveals distinct differences in three gene clusters (or genes), encompassing 15 tRNAs and eight PCGs. Notably, inversions and translocations represent the major types of rearrangements observed in D. extinctorium. Phylogenetic analysis demonstrates robust support for a monophyletic grouping of all Littorinimorpha species, with D. extinctorium representing a distinct Calyptraeoidea clade. In summary, this investigation provides the first complete mitochondrial dataset for a species of the Calyptraeidae, thus providing novel insights into the phylogenetic relationships within the Littorinimorpha.
Collapse
Affiliation(s)
- Yanwen Ma
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Biqi Zheng
- Department of Natural Resources, Ningde Marine Center, Ningde, 352000, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Wei Meng
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of China, Zhoushan, 316021, China
| | - Kaida Xu
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of China, Zhoushan, 316021, China
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| |
Collapse
|
3
|
The queen conch mitogenome: intra- and interspecific mitogenomic variability in Strombidae and phylogenetic considerations within the Hypsogastropoda. Sci Rep 2021; 11:11972. [PMID: 34099752 PMCID: PMC8184947 DOI: 10.1038/s41598-021-91224-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/24/2021] [Indexed: 02/05/2023] Open
Abstract
Aliger gigas is an economically important and vulnerable marine species. We present a new mitogenome of A. gigas from the Mexican Caribbean and use the eight publicly available Strombidae mitogenomes to analyze intra- and interspecific variation. We present the most complete phylogenomic understanding of Hypsogastropoda to date (17 superfamilies, 39 families, 85 genera, 109 species) to revisit the phylogenetic position of the Stromboidea and evaluate divergence times throughout the phylogeny. The A. gigas mitogenome comprises 15,460 bp including 13 PCGs, 22 tRNAs, and two rRNAs. Nucleotide diversity suggested divergence between the Mexican and Colombian lineages of A. gigas. Interspecific divergence showed high differentiation among Strombidae species and demonstrated a close relationship between A. gigas and Strombus pugilis, between Lambis lambis and Harpago chiragra, and among Tridentarius dentatus/Laevistrombus canarium/Ministrombus variabilis. At the intraspecific level, the gene showing the highest differentiation is ATP8 and the lowest is NAD4L, whereas at the interspecific level the NAD genes show the highest variation and the COX genes the lowest. Phylogenomic analyses confirm that Stromboidea belongs in the non-Latrogastropoda clade and includes Xenophoridea. The phylogenomic position of other superfamilies, including those of previously uncertain affiliation, is also discussed. Finally, our data indicated that Stromboidea diverged into two principal clades in the early Cretaceous while Strombidae diversified in the Paleocene, and lineage diversification within A. gigas took place in the Pleistocene.
Collapse
|
4
|
Choi EH, Choi NR, Hwang UW. The mitochondrial genome of an Endangered freshwater snail Koreoleptoxis nodifila (Caenogastropoda: Semisulcospiridae) from South Korea. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:1120-1123. [PMID: 33796761 PMCID: PMC7995809 DOI: 10.1080/23802359.2021.1901626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
The mitochondrial genome of the Endangered freshwater snail Koreoleptoxis nodifila (Caenogastropoda: Semisulcospiridae) from South Korea is determined and characterized in detail. It is 15,737 bp in length being composed of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs), and one control region. It has a base composition of 31.23% for A, 16.29% for G, 17.84% for C, and 34.64% for T. The phylogenetic trees reconstructed based on the maximum-likelihood (ML) method and Bayesian inference (BI) confirmed that K. nodifila belongs to the Semisulcospiridae clade in the monophyletic caeonogastropod superfamily Cerithioidea.
Collapse
Affiliation(s)
- Eun Hwa Choi
- Department of Biology Education, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
| | - Na Rae Choi
- Department of Biology Education, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
| | - Ui Wook Hwang
- Department of Biology Education, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea.,Institute for Korean Herb-Bio Convergence Promotion, Kyungpook National University, Daegu, South Korea.,Biomedical Convergence Science and Technology, Kyungpook National University, Daegu, South Korea
| |
Collapse
|
5
|
Choi EH, Hwang UW. The complete mitochondrial genome of an endangered triton snail Charonia lampas (Littorinimorpha: Charoniidae) from South Korea. Mitochondrial DNA B Resour 2021; 6:956-958. [PMID: 33796697 PMCID: PMC7995882 DOI: 10.1080/23802359.2021.1889416] [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] [Indexed: 12/03/2022] Open
Abstract
The complete mitochondrial genome of an endangered triton snail Charonia lampas (Littorinimorpha: Charoniidae) from South Korea was determined with the size of 15,330 bp, which contained 13 protein-coding genes, 22 tRNAs, and two rRNAs. The overall features of the mitochondrial genome are similar to those of typical gastropod mitochondrial genomes, except for the absence of a control region (CR): a conserved gene order, a high A + T content (67.45% for C. lampas), preference for AT-rich codons, etc. It is the second mitochondrial genome reported from this species after Cho et al. (2017), and there is ca. 98% sequence similarity between those of the species. According to the maximum-likelihood tree, C. lampas placed within the monophyletic Tonnoidea, forming a monoclade with Cypraeoidea and Stromboidea within Littorinimorpha. Interestingly, we confirmed that Vermetoidea is placed at the basal position of the monophyletic Littorinimorpha.
Collapse
Affiliation(s)
- Eun Hwa Choi
- Department of Biology Education, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
| | - Ui Wook Hwang
- Department of Biology Education, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
- Institute for Korean Herb-Bio Convergence Promotion, Kyungpook National University, Daegu, South Korea
- Biomedical Convergence Science and Technology, Kyungpook National University, Daegu, South Korea
| |
Collapse
|
6
|
Irwin AR, Strong EE, Kano Y, Harper EM, Williams ST. Eight new mitogenomes clarify the phylogenetic relationships of Stromboidea within the caenogastropod phylogenetic framework. Mol Phylogenet Evol 2021; 158:107081. [PMID: 33482382 DOI: 10.1016/j.ympev.2021.107081] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/18/2020] [Accepted: 01/12/2021] [Indexed: 01/24/2023]
Abstract
Members of the gastropod superfamily Stromboidea (Littorinimorpha) are characterised by their elaborate shell morphologies, distinctive mode of locomotion, and often large and colourful eyes. This iconic group comprises over 130 species, including many large and charismatic species. The family Strombidae is of particular interest, largely due to its commercial importance and wide distribution in tropical and subtropical waters. Although a few strombid mitochondrial genomes have been sequenced, data for the other four Recent families in Stromboidea are lacking. In this study we report seven new stromboid mitogenomes obtained from transcriptomic and genomic data, with taxonomic representation from each Recent stromboid family, including the first mitogenomes for Aporrhaidae, Rostellariidae, Seraphsidae and Struthiolariidae. We also report a new mitogenome for the family Xenophoridae. We use these data, along with published sequences, to investigate the relationships among these and other caenogastropod groups. All analyses undertaken in this study support monophyly of Stromboidea as redefined here to include Xenophoridae, a finding consistent with morphological and behavioural data. Consistent with previous morphological and molecular analyses, including those based on mitogenomes, monophyly of Hypsogastropoda is confirmed but monophyly of Littorinimorpha is again rejected.
Collapse
Affiliation(s)
- Alison R Irwin
- Department of Life Sciences, Natural History Museum, Cromwell Rd, London SW7 5BD, United Kingdom; School of Biological Sciences, University of Bristol, 24 Tyndall Ave, Bristol BS8 1TQ, United Kingdom.
| | - Ellen E Strong
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, 10th St. & Constitution Ave. NW, Washington, D.C. 20560, United States.
| | - Yasunori Kano
- Department of Marine Ecosystems Dynamics, Atmosphere and Ocean Research Institute, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan.
| | - Elizabeth M Harper
- Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EQ, United Kingdom.
| | - Suzanne T Williams
- Department of Life Sciences, Natural History Museum, Cromwell Rd, London SW7 5BD, United Kingdom.
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|