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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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Katyal G, Ebanks B, Lucassen M, Papetti C, Chakrabarti L. Sequence and structure comparison of ATP synthase F0 subunits 6 and 8 in notothenioid fish. PLoS One 2021; 16:e0245822. [PMID: 34613983 PMCID: PMC8494342 DOI: 10.1371/journal.pone.0245822] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 09/09/2021] [Indexed: 11/20/2022] Open
Abstract
Mitochondrial changes such as tight coupling of the mitochondria have facilitated sustained oxygen and respiratory activity in haemoglobin-less icefish of the Channichthyidae family. We aimed to characterise features in the sequence and structure of the proteins directly involved in proton transport, which have potential physiological implications. ATP synthase subunit a (ATP6) and subunit 8 (ATP8) are proteins that function as part of the F0 component (proton pump) of the F0F1complex. Both proteins are encoded by the mitochondrial genome and involved in oxidative phosphorylation. To explore mitochondrial sequence variation for ATP6 and ATP8 we analysed sequences from C. gunnari and C. rastrospinosus and compared them with their closely related red-blooded species and eight other vertebrate species. Our comparison of the amino acid sequence of these proteins reveals important differences that could underlie aspects of the unique physiology of the icefish. In this study we find that changes in the sequence of subunit a of the icefish C. gunnari at position 35 where there is a hydrophobic alanine which is not seen in the other notothenioids we analysed. An amino acid change of this type is significant since it may have a structural impact. The biology of the haemoglobin-less icefish is necessarily unique and any insights about these animals will help to generate a better overall understanding of important physiological pathways.
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Affiliation(s)
- Gunjan Katyal
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | - Brad Ebanks
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
| | | | | | - Lisa Chakrabarti
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, United Kingdom
- MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, Nottingham, United Kingdom
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Yang T, Xu G, Gu B, Shi Y, Mzuka HL, Shen H. The Complete Mitochondrial Genome Sequences of the Philomycus bilineatus (Stylommatophora: Philomycidae) and Phylogenetic Analysis. Genes (Basel) 2019; 10:E198. [PMID: 30841657 PMCID: PMC6471268 DOI: 10.3390/genes10030198] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/27/2019] [Accepted: 02/27/2019] [Indexed: 01/22/2023] Open
Abstract
The mitochondrial genome (mitogenome) can provide information for phylogenetic analyses and evolutionary biology. We first sequenced, annotated, and characterized the mitogenome of Philomycus bilineatus in this study. The complete mitogenome was 14,347 bp in length, containing 13 protein-coding genes (PCGs), 23 transfer RNA genes, two ribosomal RNA genes, and two non-coding regions (A + T-rich region). There were 15 overlap locations and 18 intergenic spacer regions found throughout the mitogenome of P. bilineatus. The A + T content in the mitogenome was 72.11%. All PCGs used a standard ATN as a start codon, with the exception of cytochrome c oxidase 1 (cox1) and ATP synthase F0 subunit 8 (atp8) with TTG and GTG. Additionally, TAA or TAG was identified as the typical stop codon. All transfer RNA (tRNA) genes had a typical clover-leaf structure, except for trnS1 (AGC), trnS2 (TCA), and trnK (TTT). A phylogenetic analysis with another 37 species of gastropods was performed using Bayesian inference, based on the amino acid sequences of 13 mitochondrial PCGs. The results indicated that P. bilineatus shares a close ancestry with Meghimatium bilineatum. It seems more appropriate to reclassify it as Arionoidea rather than Limacoidea, as previously thought. Our research may provide a new meaningful insight into the evolution of P. bilineatus.
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Affiliation(s)
- Tiezhu Yang
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai OceanUniversity, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai OceanUniversity, Ministry of Education, China.
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution,Shanghai 201306, China.
| | - Guolyu Xu
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai OceanUniversity, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai OceanUniversity, Ministry of Education, China.
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution,Shanghai 201306, China.
| | - Bingning Gu
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai OceanUniversity, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai OceanUniversity, Ministry of Education, China.
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution,Shanghai 201306, China.
| | - Yanmei Shi
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai OceanUniversity, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai OceanUniversity, Ministry of Education, China.
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution,Shanghai 201306, China.
| | - Hellen Lucas Mzuka
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai OceanUniversity, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai OceanUniversity, Ministry of Education, China.
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution,Shanghai 201306, China.
| | - Heding Shen
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai OceanUniversity, China.
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai OceanUniversity, Ministry of Education, China.
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution,Shanghai 201306, China.
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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 H, Zhang JE, Deng Z, Luo H, Guo J, Zhang C, Wu Y, Luo M, Zhao B. The complete mitochondrial genome of the apple snail Pomacea maculate (Gastropoda: Ampullariidae). Mitochondrial DNA B Resour 2018; 3:1064-1066. [PMID: 33474416 PMCID: PMC7800453 DOI: 10.1080/23802359.2018.1511841] [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: 07/19/2018] [Accepted: 08/10/2018] [Indexed: 11/05/2022] Open
Abstract
We present the complete mitochondrial genome of Pomacea maculate in this study. The mitochondrial genome is 15,512 bp in length, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes. Overall nucleotide compositions of the light strand are 41.13% of A, 30.81% of T, 15.25% of C and 12.81% of G. Its gene arrangement and distribution are different from the typical vertebrates. The absence of D-loop is consistent with the Gastropoda, but at least one lengthy non-coding region is essential regulatory element for the initiation of transcription and replication. Phylogenetic tree is constructed by the maximum-likelihood method based on the complete mitochondrial genomes of 15 species of Caenogastropoda, using Helix aspersa as outgroup to assess their actual phylogenetic relationship and evolution. The result provides fundamental data for resolving phylogenetic and genetic problems related to effective management strategies.
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Affiliation(s)
- Huirong Yang
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Jia-En Zhang
- Institute of Tropical and Subtropical Ecology, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture P.R. China, Guangzhou, China
- Guangdong Engineering Research Center for Modern Eco-Agriculture and Circular Agriculture, Guangzhou, China
| | - Zhixin Deng
- Institute of Tropical and Subtropical Ecology, South China Agricultural University, Guangzhou, China
| | - Hao Luo
- Institute of Tropical and Subtropical Ecology, South China Agricultural University, Guangzhou, China
| | - Jing Guo
- Institute of Tropical and Subtropical Ecology, South China Agricultural University, Guangzhou, China
| | - Chunxia Zhang
- Institute of Tropical and Subtropical Ecology, South China Agricultural University, Guangzhou, China
| | - Yuanyuan Wu
- College of Marine Sciences, South China Agricultural University, Guangzhou, China
| | - Mingzhu Luo
- Institute of Tropical and Subtropical Ecology, South China Agricultural University, Guangzhou, China
| | - Benliang Zhao
- Institute of Tropical and Subtropical Ecology, South China Agricultural University, Guangzhou, China
- Key Laboratory of Agro-Environment in the Tropics, Ministry of Agriculture P.R. China, Guangzhou, China
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