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Mendivil A, Ramírez R, Morin J, Ramirez JL, Siccha-Ramirez R, Britzke R, Rivera F, Ampuero A, Oliveros N, Congrains C. Comparative Mitogenome Analysis of Two Native Apple Snail Species (Ampullariidae, Pomacea) from Peruvian Amazon. Genes (Basel) 2023; 14:1769. [PMID: 37761909 PMCID: PMC10531094 DOI: 10.3390/genes14091769] [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: 07/13/2023] [Revised: 08/22/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
Apple snails of the genus Pomacea Perry, 1810 (Mollusca: Caenogastropoda: Ampullariidae) are native to the Neotropics and exhibit high species diversity, holding cultural and ecological significance as an important protein source in Peru. However, most genetic studies in Pomacea have focused mostly on invasive species, especially in Southeast Asia, where they are considered important pests. In this study, we assembled and annotated the mitochondrial genomes of two Pomacea species native to the Peruvian Amazon: Pomacea reevei Ampuero & Ramírez, 2023 and Pomacea aulanieri (Deville & Hupé, 1850). The mitogenomes of P. reevei and P. aulanieri comprise 15,660 and 16,096 bp, respectively, and contain the typical 37 genes of the animal mitochondria with a large control region of 292 bp in P. reevei and 524 bp in P. aulanieri-which fall within the range of what is currently known in Pomacea. Comparisons with previously published mitogenomes in Pomacea revealed differences in the overlapping of adjacent genes, the size of certain protein-coding genes (PCGs) and the secondary structure of some tRNAs that are consistent with the phylogenetic relationships between these species. These findings provide valuable insights into the systematics and genomics of the genus Pomacea.
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Affiliation(s)
- Alejandro Mendivil
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Carlos Germán Amezaga 375, Lima 15081, Peru; (A.M.); (J.L.R.); (R.S.-R.); (R.B.); (F.R.); (N.O.)
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima 15046, Peru
| | - Rina Ramírez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Carlos Germán Amezaga 375, Lima 15081, Peru; (A.M.); (J.L.R.); (R.S.-R.); (R.B.); (F.R.); (N.O.)
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima 15046, Peru
| | - Jaime Morin
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Carlos Germán Amezaga 375, Lima 15081, Peru; (A.M.); (J.L.R.); (R.S.-R.); (R.B.); (F.R.); (N.O.)
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima 15046, Peru
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Erlings Skakkes gate 47B, 7012 Trondheim, Norway; (J.M.)
| | - Jorge L. Ramirez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Carlos Germán Amezaga 375, Lima 15081, Peru; (A.M.); (J.L.R.); (R.S.-R.); (R.B.); (F.R.); (N.O.)
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima 15046, Peru
| | - Raquel Siccha-Ramirez
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Carlos Germán Amezaga 375, Lima 15081, Peru; (A.M.); (J.L.R.); (R.S.-R.); (R.B.); (F.R.); (N.O.)
| | - Ricardo Britzke
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Carlos Germán Amezaga 375, Lima 15081, Peru; (A.M.); (J.L.R.); (R.S.-R.); (R.B.); (F.R.); (N.O.)
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima 15046, Peru
| | - Fátima Rivera
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Carlos Germán Amezaga 375, Lima 15081, Peru; (A.M.); (J.L.R.); (R.S.-R.); (R.B.); (F.R.); (N.O.)
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima 15046, Peru
| | - Andre Ampuero
- Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Av. Arenales 1256, Lima 15046, Peru
- Department of Marine Zoology, Senckenberg Research Institute, 60325 Frankfurt am Main, Germany; (A.A.)
| | - Nilda Oliveros
- Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Av. Carlos Germán Amezaga 375, Lima 15081, Peru; (A.M.); (J.L.R.); (R.S.-R.); (R.B.); (F.R.); (N.O.)
| | - Carlos Congrains
- Department of Plant and Environmental Protection Services, University of Hawaii at Manoa, Honolulu, HI 96822, USA;
- U.S. Department of Agriculture-Agricultural Research Service, Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Tropical Pest Genetics and Molecular Biology Research Unit, Hilo, HI 96720, USA
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Yang H, Zhang JE, Xia J, Yang J, Guo J, Deng Z, Luo M. Comparative Characterization of the Complete Mitochondrial Genomes of the Three Apple Snails (Gastropoda: Ampullariidae) and the Phylogenetic Analyses. Int J Mol Sci 2018; 19:E3646. [PMID: 30463257 PMCID: PMC6274680 DOI: 10.3390/ijms19113646] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 10/31/2018] [Accepted: 11/02/2018] [Indexed: 01/07/2023] Open
Abstract
The apple snails Pomacea canaliculata, Pomacea diffusa and Pomacea maculate (Gastropoda: Caenogastropoda: Ampullariidae) are invasive pests causing massive economic losses and ecological damage. We sequenced and characterized the complete mitochondrial genomes of these snails to conduct phylogenetic analyses based on comparisons with the mitochondrial protein coding sequences of 47 Caenogastropoda species. The gene arrangements, distribution and content were canonically identical and consistent with typical Mollusca except for the tRNA-Gln absent in P. diffusa. An identifiable control region (d-loop) was absent. Bayesian phylogenetic analysis indicated that all the Ampullariidae species clustered on the same branch. The genus Pomacea clustered together and then with the genus Marisa. The orders Architaenioglossa and Sorbeoconcha clustered together and then with the order Hypsogastropoda. Furthermore, the intergenic and interspecific taxonomic positions were defined. Unexpectedly, Ceraesignum maximum, Dendropoma gregarium, Eualetes tulipa and Thylacodes squamigerus, traditionally classified in order Hypsogastropoda, were isolated from the order Hypsogastropoda in the most external branch of the Bayesian inference tree. The divergence times of the Caenogastropoda indicated that their evolutionary process covered four geological epochs that included the Quaternary, Neogene, Paleogene and Cretaceous periods. This study will facilitate further investigation of species identification to aid in the implementation of effective management and control strategies of these invasive species.
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Affiliation(s)
- Huirong Yang
- College of Marine Sciences, South China Agricultural University, Guangzhou 510640, China.
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
| | - Jia-En Zhang
- Institute of Tropical and Subtropical Ecology, South China Agricultural University, Guangzhou 510642, China.
| | - Jun Xia
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
- Xinjiang Acadamy of Animal Sciences, Institute of Veterinary Medicine (Research Center of Animal Clinical), Urumqi 830000, China.
| | - Jinzeng Yang
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
| | - Jing Guo
- Institute of Tropical and Subtropical Ecology, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Engineering Research Center for Modern Eco-Agriculture and Circular Agriculture, Guangzhou 510642, China.
| | - Zhixin Deng
- Institute of Tropical and Subtropical Ecology, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Engineering Research Center for Modern Eco-Agriculture and Circular Agriculture, Guangzhou 510642, China.
| | - Mingzhu Luo
- Institute of Tropical and Subtropical Ecology, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Engineering Research Center for Modern Eco-Agriculture and Circular Agriculture, Guangzhou 510642, China.
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Yang QQ, Liu SW, Song F, Liu GF, Yu XP. Comparative mitogenome analysis on species of four apple snails (Ampullariidae: Pomacea). Int J Biol Macromol 2018; 118:525-533. [PMID: 29935238 DOI: 10.1016/j.ijbiomac.2018.06.092] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 11/16/2022]
Abstract
The genus Pomacea contains most of the economically important Ampullariid apple snails. Five Pomacea species were reported introduced out of their native ranges, including three highly invasive species, i.e. P. maculata, P. canaliculata and an unidentified species, Pomacea sp. In this study, the mitogenome of P. maculata was determined, which carried typical gene set of metazoan mitogenomes and shared the same gene rearrangement of Ampullariidae mitogenomes. The control region of the P. maculata has a 13-bp inverted repeat unit. We compared the mitogenome of P. maculata with P. canaliculata, Pomacea sp. and the aquatic pet species, P. diffusa. The three highly invasive species showed high sequence similarity of PCGs and RNAs. atp8 and nad2 showed the lowest similarity and the highest Ka/Ks ratios, indicating that both genes have potential for studying species identification and populations genetics in apple snails. All PCGs have the Ka/Ks ratios <1, indicating the existence of purifying selection in Pomacea species. We reconstructed phylogenetic trees using 14 Caenogastropda species based on sequences of PCGs and rRNAs using Bayesian inference. Pomacea maculata grouped with other Ampullariids and was most closely related to Pomacea sp. The mitogenome of P. maculata provides useful genetic resource for exploring the genetics and evolution of P. maculata and other apple snails.
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Affiliation(s)
- Qian-Qian Yang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Su-Wen Liu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Fan Song
- Department of Entomology, China Agricultural University, Beijing 100193, China
| | - Guang-Fu Liu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Xiao-Ping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China.
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Liu S, Yang Q, He C, Yu X. The complete mitochondrial genome of Pomacea diffusa (Gastropoda: Ampullariidae). MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:491-492. [PMID: 33473873 PMCID: PMC7800231 DOI: 10.1080/23802359.2017.1361348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In this study, we analyzed the complete mitochondrial genome of the spike-topped apple snail, Pomacea diffusa Blume, 1957 (Gastropoda: Ampullariidae). The mitochondrial genome of P. diffusa was 16,373 bp, consisting 13 protein-coding genes, 2 rRNAs, and 22 tRNAs and a non-coding region with a 12 bp repeat unit. There were 29 mitochondrial genes of P. diffusa are distributed on the H-strand, and the other eight tRNA genes encoded on the L-strand. The average AT content of 13 protein-coding genes was 68.7%. A phylogenetic analysis showed that there was a close relationship between P. diffusa and invasive apple snail species, Pomacea canaliculata and Pomacea aff. maculata.
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Affiliation(s)
- Suwen Liu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Qianqian Yang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Chao He
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China
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Wang JG, Zhang D, Jakovlić I, Wang WM. Sequencing of the complete mitochondrial genomes of eight freshwater snail species exposes pervasive paraphyly within the Viviparidae family (Caenogastropoda). PLoS One 2017; 12:e0181699. [PMID: 28742843 PMCID: PMC5526530 DOI: 10.1371/journal.pone.0181699] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 07/04/2017] [Indexed: 11/21/2022] Open
Abstract
Phylogenetic relationships among snails (Caenogastropoda) are still unresolved, and many taxonomic categories remain non-monophyletic. Paraphyly has been reported within a large family of freshwater snails, Viviparidae, where the taxonomic status of several species remains questionable. As many endemic Chinese viviparid species have become endangered during the last few decades, this presents a major obstacle for conservation efforts. Mitochondrial genomes (mitogenomes) carry a large amount of data, so they can often provide a much higher resolution for phylogenetic analyses in comparison to the traditionally used molecular markers. To help resolve their phylogenetic relationships, the complete mitogenomes of eight Chinese viviparid snails, Viviparus chui, Cipangopaludina chinensis, C. ussuriensis, C. dianchiensis (endangered), Margarya melanioides (endangered), M. monodi (critically endangered), Bellamya quadrata and B. aeruginosa, were sequenced and compared to almost all of the available caenogastropod mitogenomes. Viviparidae possess the largest mitogenomes (16 392 to 18 544 bp), exhibit the highest A+T bias (72.5% on average), and some exhibit unique gene orders (a rearrangement of the standard MYCWQGE box), among the Caenogastropoda. Apart from the Vermetidae family and Cerithioidea superfamily, which possessed unique gene orders, the remaining studied caenogastropod mitogenomes exhibited highly conserved gene order, with minimal variations. Maximum likelihood and Bayesian inference analyses, used to reconstruct the phylogenetic relationships among 49 almost complete (all 37 genes) caenogastropod mitogenomes, produced almost identical tree topologies. Viviparidae were divided into three clades: a) Margarya and Cipangopaludina (except C. ussuriensis), b) Bellamya and C. ussuriensis, c) Viviparus chui. Our results present evidence that some Cipangopaludina species (dianchiensis and cathayensis) should be renamed into the senior genus Margarya. The phylogenetic resolution obtained in this study is insufficient to fully resolve the relationships within the 'b' clade, but if C. chinensis proves to be a valid representative of the genus, C. ussuriensis may have to be reassigned a different genus (possibly Bellamya, or even a new genus). Non-monophyly also remains pervasive among the higher (above the family-level) Caenogastropod taxonomic classes. Gene order distance matrix produced a different phylogenetic signal from the nucleotide sequences, which indicates a limited usability of this approach for inferring caenogastropod phylogenies. As phenotypic homoplasy appears to be widespread among some viviparid genera, in order to effectively protect the rapidly diminishing endemic Viviparid populations in China, further detailed molecular phylogenetic studies are urgently needed to resolve the taxonomic status of several species.
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Affiliation(s)
- Ju-Guang Wang
- Key Lab of Freshwater Animal Breeding of the Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, PR China
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, PR China
| | - Dong Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Wuhan Institute of Biotechnology, Wuhan, PR China
| | - Wei-Min Wang
- Key Lab of Freshwater Animal Breeding of the Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, PR China
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, PR China
- Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde, China
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