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Li F, Li W, Zhang Y, Wang A, Liu C, Gu Z, Yang Y. The molecular phylogeny of Caenogastropoda (Mollusca, Gastropoda) based on mitochondrial genomes and nuclear genes. Gene 2024; 928:148790. [PMID: 39053659 DOI: 10.1016/j.gene.2024.148790] [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: 04/07/2024] [Revised: 07/02/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
Comprising about 60 % of gastropod diversity, caenogastropods display almost all kinds of shell forms and include many commercially important marine groups. Although the monophyly of Caenogastropoda has been widely accepted, thier internal phylogenetic relationships remain unclear. In the present study, a total of 27 caenogastropods belonging to eight superfamilies were sequenced and used for phylogenetic reconstruction. All newly sequenced mitogenomes adhered to the consensus gene order of caenogastropods, except for those of Vanikoroidea, Vermetoidea and Cerithioidea, which involved protein-coding genes. The reconstructed mitogenomic phylogeny suggested the monophylies of Architaenioglossa, Sorbeoconcha, Hypsogastropoda and the siphonate clade. The present study also identified a close affinity among Cypraeoidea, Ficoidea, Tonnoidea, and Neogastropoda, supported by the presence of a pleurembolic proboscis. The monophyly of Neogastropoda was not supported, as Cancellariidae was found to be sister to the limpet-shaped group Calyptraeoidea, and (Tonooidea + Ficoidea) were sister to the remaining neogastropods. This study provides important information for better understanding the evolution of caenogastropods, as well as for the protection and utilization of these diverse and economically significant marine resources.
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Affiliation(s)
- Fengping Li
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China
| | - Wanying Li
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China
| | - Yu Zhang
- Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Aimin Wang
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China
| | - Chunsheng Liu
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China
| | - Zhifeng Gu
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China
| | - Yi Yang
- School of Marine Biology and Fisheries, Hainan University, Haikou 570228, China; Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China.
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2
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Wang X, Ren X, Teng X, Feng C, Xing Z, Wang S, Zheng L, Qu J, Wang L. Complete mitochondrial genome and phylogenetic analysis of Mancinella alouina. Mol Biol Rep 2024; 51:942. [PMID: 39196421 DOI: 10.1007/s11033-024-09778-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 07/04/2024] [Indexed: 08/29/2024]
Abstract
BACKGROUND The Muricidae family in the Class Gastropoda comprises numerous species with a vast range of morphological features and a worldwide presence. The phylogeny of the Muricidae has been analyzed in previous studies; however, the evolutionary relationships among the main branches of the Muricidae remain unknown. METHODS AND RESULTS In the present study, the mitochondrial genome of Mancinella alouina was sequenced. The mitochondrial genome was found to be 16,671 bp in length and made up of 37 genes (13 protein-coding genes, 22 transfer RNA and 2 ribosomal RNA genes). The genome has an A-T-rich region (66.5% A + T content) and all of the PCGs use the ATN start codon and the TAG or TAA stop codons. The mitochondrial gene arrangement of Mancinella alouina is similar to that of other Muricidae, except for Ocinebrellus inornatus and Ceratostoma burnetti. On the basis of a flexible molecular clock model, time-calibrated phylogenetic results indicate that the genus Mancinella diverged roughly 18.09 Mya, and that the family Muricidae emerged in the Late Cretaceous. CONCLUSIONS This study reveals the structural and sequence information features of the mitochondrial genome of Mancinella alouina. This study provides evidence for the relationships within the family Muricidae at the molecular level, and infer the divergence time. The results of phylogenetic analyses strongly support the current classification.
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Affiliation(s)
- Xumin Wang
- College of Life Science, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, 264005, Shandong, China
| | - Xiaoyu Ren
- College of Life Science, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, 264005, Shandong, China
| | - Xindong Teng
- Qingdao International Travel Healthcare Center, Qingdao, 266071, China
| | - Chunyu Feng
- College of Life Science, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, 264005, Shandong, China
| | - Zhikai Xing
- College of Life Science, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, 264005, Shandong, China
| | - Shuang Wang
- College of Life Science, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, 264005, Shandong, China
| | - Li Zheng
- Ministry of Natural Resources, The First Institute of Oceanography, Qingdao, 266061, Shandong, China
| | - Jiangyong Qu
- College of Life Science, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, 264005, Shandong, China.
| | - Lijun Wang
- College of Life Science, Yantai University, No.30 Qingquan Road, Laishan District, Yantai, 264005, Shandong, China.
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Ho HX, Chong TF, Ng WL, Lee SY. The complete mitochondrial genome data of Pholas orientalis (Gmelin, 1791) from Malaysia. Data Brief 2024; 55:110581. [PMID: 38966661 PMCID: PMC11222832 DOI: 10.1016/j.dib.2024.110581] [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: 11/26/2023] [Revised: 05/20/2024] [Accepted: 05/28/2024] [Indexed: 07/06/2024] Open
Abstract
Pholas orientalis (angelwing clam) is a mollusc species found in the coastal areas of Southeast Asia. Despite its economic significance, genetic information on the species is lacking. In this study, a P. orientalis specimen was collected from Kedah, Malaysia, and its complete mitochondrial genome was assembled using whole-genome sequencing data generated on an DNBSEQ-G400 platform. The circular mitochondrial genome of P. orientalis is 18,995 bp in size and contains 12 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and three control regions (D-loops). All genes are located on the heavy strand. The mitogenome has a base composition of 25.4 % A, 41.5 % T, 22.1% G, and 11 % C, exhibiting a bias towards AT content (66.9 %). The mitochondrial genomes of P. orientalis and 11 other Pholadoidea species were included in a phylogenetic analysis, which indicated that P. orientalis is closely related to Xyloredo nooi. The data reported in this study represents the first time that a Pholas mitochondrial genome has been reported. Such data will contribute to the better understanding of genetic relationships between P. orientalis and its relatives, leading to informed conservation and sustainable utilization of the species.
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Affiliation(s)
- Hao Xuan Ho
- Faculty of Health and Life Sciences, INTI International University, Nilai, Negeri Sembilan, Malaysia
| | - Teek Foh Chong
- Faculty of Health and Life Sciences, INTI International University, Nilai, Negeri Sembilan, Malaysia
| | - Wei Lun Ng
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, Selangor, Malaysia
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Shiou Yih Lee
- Faculty of Health and Life Sciences, INTI International University, Nilai, Negeri Sembilan, Malaysia
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Korábek O, Hausdorf B. Accelerated mitochondrial evolution and asymmetric fitness of hybrids contribute to the persistence of Helix thessalica in the Helix pomatia range. Mol Ecol 2024; 33:e17474. [PMID: 39031116 DOI: 10.1111/mec.17474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 06/14/2024] [Accepted: 07/08/2024] [Indexed: 07/22/2024]
Abstract
Interbreeding and introgression between recently diverged species is common. However, the processes that prevent these species from merging where they co-occur are not well understood. We studied the mechanisms that allowed an isolated group of populations of the snail Helix thessalica to persist within the range of the related Helix pomatia despite high gene flow. Using genomic cline analysis, we found that the nuclear gene flow between the two taxa across the mosaic hybrid zone was not different from that expected under neutral admixture, but that the exchange of mtDNA was asymmetric. Tests showed that there is relaxed selection in the mitochondrial genome of H. thessalica and that the substitution rate is elevated compared to that of H. pomatia. A lack of hybrids that combine the mtDNA of H. thessalica with a mainly (>46%) H. pomatia genomic background indicates that the nuclear-encoded mitochondrial proteins of H. pomatia are not well adapted to the more rapidly evolving proteins and RNAs encoded by the mitochondrion of H. thessalica. The presumed reduction of fitness of hybrids with the fast-evolving mtDNA of H. thessalica and a high H. pomatia ancestry, similar to 'Darwin's Corollary to Haldane's rule', resulted in a relative loss of H. pomatia nuclear ancestry compared to H. thessalica ancestry in the hybrid zone. This probably prevents the H. thessalica populations from merging quickly with the surrounding H. pomatia populations and supports the hypothesis that incompatibilities between rapidly evolving mitochondrial genes and nuclear genes contribute to speciation.
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Affiliation(s)
- Ondřej Korábek
- Leibniz Institute for the Analysis of Biodiversity Change, Zoological Museum, Hamburg, Germany
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Bernhard Hausdorf
- Leibniz Institute for the Analysis of Biodiversity Change, Zoological Museum, Hamburg, Germany
- Universität Hamburg, Hamburg, Germany
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Zhu Y, Yan S, Ma P, Zhang Y, Zuo C, Ma X, Zhang Z. Comparative mitochondrial genome analysis provides new insights into the classification of Modiolinae. Mol Biol Rep 2024; 51:823. [PMID: 39023631 DOI: 10.1007/s11033-024-09767-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/01/2024] [Indexed: 07/20/2024]
Abstract
BACKGROUND Mitochondrial genomes have become a powerful tool for studying molecular genetics and phylogeny of mollusks. Currently, the position of Modiolinae within Mytilidae and the taxonomic and phylogenetic relationships within Modiolinae were still controversial. This study focuses on the complete mitochondrial genomes of two species: Modiolus modulaides (Röding, 1798) and Modiolus auriculatus Krauss, 1848, which have not been sequenced before. METHODS AND RESULTS We assembled and characterized the mitochondrial genomes of M. modulaides and M. auriculatus and then analyzed the phylogenetic relationships. The mitochondrial genomes of M. modulaides and M. auriculatus were 15,422 bp and 16,027 bp, respectively. Both of them were composed of 36 functional genes, including 12 protein-coding genes, 22 transfer RNAs, and 2 ribosomal RNAs. All protein-coding genes showed A + T bias, positive GC skews, and negative AT skews in nucleotide composition. Phylogenetic analysis based on the mitochondrial genomes showed that Modiolinae and Bathymodiolinae clustered together to form a sister relationship. Seven Modiolinae species were divided into two clades: L1 (M. modulaides, M. auriculatus and Modiolus philippinarum Hanley, 1843) and L2 [Modiolus modiolus (Linnaeus, 1758), Modiolus kurilensis Bernard, 1983, Modiolus nipponicus (Oyama, 1950), and Modiolus comptus (Sowerby III, 1915)]. The divergence time of the two clades was approximately 105.75 Ma. Furthermore, the transfer RNA gene rearrangement, longer genetic distance, and greater genetic differentiation were confirmed between the L1 and L2 clades, as well as differences in the external characteristics of the shells of the two clades. CONCLUSIONS Based on the molecular data, it was speculated that species from the L1 clade might belong to other genera or new genera. This study provides molecular information for further taxonomic and phylogenetic studies of Mytilidae.
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Affiliation(s)
- Yi Zhu
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shaojing Yan
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Peizhen Ma
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao, 266237, China
| | - Yifei Zhang
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chenxia Zuo
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- College of Life Sciences, Qingdao University, Qingdao, 266000, China
| | - Xiaojie Ma
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhen Zhang
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Sukee T, Koehler AV, Webster BL, Gauci CG, Fogarty CE, Ponder WF, Gasser RB, Young ND. Mitochondrial genome of the fluke pond snail, Austropeplea cf. brazieri (Gastropoda: Lymnaeidae). Parasit Vectors 2024; 17:283. [PMID: 38956636 PMCID: PMC11218368 DOI: 10.1186/s13071-024-06358-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 06/15/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND Lymnaeid snails of the genus Austropeplea are an important vector of the liver fluke (Fasciola hepatica), contributing to livestock production losses in Australia and New Zealand. However, the species status within Austropeplea is ambiguous due to heavy reliance on morphological analysis and a relative lack of genetic data. This study aimed to characterise the mitochondrial genome of A. cf. brazieri, an intermediate host of liver fluke in eastern Victoria. METHODS The mitochondrial genome was assembled and annotated from a combination of second- and third-generation sequencing data. For comparative purposes, we performed phylogenetic analyses of the concatenated nucleotide sequences of the mitochondrial protein-coding genes, cytochrome c oxidase subunit 1 and 16S genes. RESULTS The assembled mt genome was 13,757 base pairs and comprised 37 genes, including 13 protein-coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The mt genome length, gene order and nucleotide compositions were similar to related species of lymnaeids. Phylogenetic analyses of the mt nucleotide sequences placed A. cf. brazieri within the same clade as Orientogalba ollula with strong statistical supports. Phylogenies of the cox1 and 16S mt sequences were constructed due to the wide availability of these sequences representing the lymnaeid taxa. As expected in both these phylogenies, A. cf. brazieri clustered with other Austropeplea sequences, but the nodal supports were low. CONCLUSIONS The representative mt genome of A. cf. brazieri should provide a useful resource for future molecular, epidemiology and parasitological studies of this socio-economically important lymnaeid species.
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Affiliation(s)
- Tanapan Sukee
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Victoria, Australia
| | - Anson V Koehler
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Victoria, Australia
| | | | - Charles G Gauci
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Victoria, Australia
| | - Conor E Fogarty
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Victoria, Australia
| | | | - Robin B Gasser
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Victoria, Australia
| | - Neil D Young
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Victoria, Australia.
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Galià-Camps C, Araujo AK, Carmona L, Martín-Hervás MDR, Pola M, Palero F, Cervera JL. New mitogenomes of Runcinidae and Facelinidae: two understudied heterobranch families (Mollusca: Gastropoda). Mitochondrial DNA B Resour 2024; 9:771-776. [PMID: 38919811 PMCID: PMC11198154 DOI: 10.1080/23802359.2024.2363365] [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: 10/05/2023] [Accepted: 05/29/2024] [Indexed: 06/27/2024] Open
Abstract
Here, we present the mitochondrial sequences of two sea slugs (Heterobranchia): Runcina aurata and Facelina auriculata, the latter being the type species of the family. The mitochondrial genomes are 14,282 and 14,171bp in length, respectively, with a complete set of 13 PCGs, 2 rRNAs, and 22 tRNAs. None of the mitogenomes show gene reorganization, keeping the standard mitogenomic structure of Heterobranchia. Nucleotide composition differs significantly between them, with R. aurata showing the most AT-rich mitogenome (25.7% GC content) reported to date in Heterobranchia, and F. auriculata showing a rich GC content (35%) compared with other heterobranch mitochondrial genomes.
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Affiliation(s)
- Carles Galià-Camps
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona (UB), Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona (UB), Barcelona, Spain
| | - Ana Karla Araujo
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Campus de Excelencia Internacional del Mar (CEIMAR), Universidad de Cádiz, Puerto Real, Spain
- Instituto Universitario de Investigación Marina (INMAR), Universidad de Cádiz, Puerto Real, Spain
| | - Leila Carmona
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Campus de Excelencia Internacional del Mar (CEIMAR), Universidad de Cádiz, Puerto Real, Spain
- Instituto Universitario de Investigación Marina (INMAR), Universidad de Cádiz, Puerto Real, Spain
| | - María del Rosario Martín-Hervás
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Campus de Excelencia Internacional del Mar (CEIMAR), Universidad de Cádiz, Puerto Real, Spain
- Instituto Universitario de Investigación Marina (INMAR), Universidad de Cádiz, Puerto Real, Spain
| | - Marta Pola
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, CSIC, Madrid, Spain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), CSIC, Madrid, Spain
| | - Ferran Palero
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, Paterna, Spain
- Department of Life Sciences, The Natural History Museum, London, UK
| | - Juan Lucas Cervera
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Campus de Excelencia Internacional del Mar (CEIMAR), Universidad de Cádiz, Puerto Real, Spain
- Instituto Universitario de Investigación Marina (INMAR), Universidad de Cádiz, Puerto Real, Spain
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Gendron EMS, Qing X, Sevigny JL, Li H, Liu Z, Blaxter M, Powers TO, Thomas WK, Porazinska DL. Comparative mitochondrial genomics in Nematoda reveal astonishing variation in compositional biases and substitution rates indicative of multi-level selection. BMC Genomics 2024; 25:615. [PMID: 38890582 PMCID: PMC11184840 DOI: 10.1186/s12864-024-10500-1] [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: 02/22/2024] [Accepted: 06/05/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND Nematodes are the most abundant and diverse metazoans on Earth, and are known to significantly affect ecosystem functioning. A better understanding of their biology and ecology, including potential adaptations to diverse habitats and lifestyles, is key to understanding their response to global change scenarios. Mitochondrial genomes offer high species level characterization, low cost of sequencing, and an ease of data handling that can provide insights into nematode evolutionary pressures. RESULTS Generally, nematode mitochondrial genomes exhibited similar structural characteristics (e.g., gene size and GC content), but displayed remarkable variability around these general patterns. Compositional strand biases showed strong codon position specific G skews and relationships with nematode life traits (especially parasitic feeding habits) equal to or greater than with predicted phylogeny. On average, nematode mitochondrial genomes showed low non-synonymous substitution rates, but also high clade specific deviations from these means. Despite the presence of significant mutational saturation, non-synonymous (dN) and synonymous (dS) substitution rates could still be significantly explained by feeding habit and/or habitat. Low ratios of dN:dS rates, particularly associated with the parasitic lifestyles, suggested the presence of strong purifying selection. CONCLUSIONS Nematode mitochondrial genomes demonstrated a capacity to accumulate diversity in composition, structure, and content while still maintaining functional genes. Moreover, they demonstrated a capacity for rapid evolutionary change pointing to a potential interaction between multi-level selection pressures and rapid evolution. In conclusion, this study helps establish a background for our understanding of the potential evolutionary pressures shaping nematode mitochondrial genomes, while outlining likely routes of future inquiry.
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Affiliation(s)
- Eli M S Gendron
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA.
| | - Xue Qing
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.
| | - Joseph L Sevigny
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Hongmei Li
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Zhiyin Liu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | | | - Thomas O Powers
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, USA
| | - W Kelly Thomas
- Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
- Hubbard Center for Genome Studies, University of New Hampshire, Durham, NH, USA
| | - Dorota L Porazinska
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
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Davison A, Chowdhury M, Johansen M, Uliano-Silva M, Blaxter M. High heteroplasmy is associated with low mitochondrial copy number and selection against non-synonymous mutations in the snail Cepaea nemoralis. BMC Genomics 2024; 25:596. [PMID: 38872121 DOI: 10.1186/s12864-024-10505-w] [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: 03/01/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024] Open
Abstract
Molluscan mitochondrial genomes are unusual because they show wide variation in size, radical genome rearrangements and frequently show high variation (> 10%) within species. As progress in understanding this variation has been limited, we used whole genome sequencing of a six-generation matriline of the terrestrial snail Cepaea nemoralis, as well as whole genome sequences from wild-collected C. nemoralis, the sister species C. hortensis, and multiple other snail species to explore the origins of mitochondrial DNA (mtDNA) variation. The main finding is that a high rate of SNP heteroplasmy in somatic tissue was negatively correlated with mtDNA copy number in both Cepaea species. In individuals with under ten mtDNA copies per nuclear genome, more than 10% of all positions were heteroplasmic, with evidence for transmission of this heteroplasmy through the germline. Further analyses showed evidence for purifying selection acting on non-synonymous mutations, even at low frequency of the rare allele, especially in cytochrome oxidase subunit 1 and cytochrome b. The mtDNA of some individuals of Cepaea nemoralis contained a length heteroplasmy, including up to 12 direct repeat copies of tRNA-Val, with 24 copies in another snail, Candidula rugosiuscula, and repeats of tRNA-Thr in C. hortensis. These repeats likely arise due to error prone replication but are not correlated with mitochondrial copy number in C. nemoralis. Overall, the findings provide key insights into mechanisms of replication, mutation and evolution in molluscan mtDNA, and so will inform wider studies on the biology and evolution of mtDNA across animal phyla.
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Affiliation(s)
- Angus Davison
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
| | - Mehrab Chowdhury
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Margrethe Johansen
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Marcela Uliano-Silva
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
| | - Mark Blaxter
- Tree of Life, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, Cambridgeshire, CB10 1SA, UK
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10
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Ma P, Liu Z, Li Z, Sun X, Zhou L, Wu X, Wu B. Sequencing of the Complete Mitochondrial Genome of the Big Brown Mactra Clam, Mactra grandis (Venerida: Mactridae). Animals (Basel) 2024; 14:1376. [PMID: 38731380 PMCID: PMC11083373 DOI: 10.3390/ani14091376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/27/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024] Open
Abstract
Mitochondrial genomes are playing an increasingly important role in molluscan taxonomy, germplasm, and evolution studies. The first complete mitochondrial genome of the commercial big brown mactra clam, Mactra grandis, was characterized using Illumina next-generation sequencing in this study. The 17,289 bp circular genome has a typical gene organization of 13 protein-coding genes (PCGs), 2 rRNAs, and 22 tRNAs, with an obvious (A + T)-bias of 64.54%. All PCGs exhibited a homogeneous bias in nucleotide composition with a (A + T)-bias, a positive GC skew, and a negative AT skew. Results of phylogenetic analysis showed that Mactra grandis was most closely related to Mactra cygnus. The functional gene arrangement of the two species was identical but different from other Mactra species. The congeneric relationships among Mactra species were demonstrated by genetic distance analysis. Additionally, the selective pressure analysis suggested that cox1 was highly efficient for discriminating closely related species in genus Mactra, while nad2 was the most appropriate marker for population genetic analysis.
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Affiliation(s)
- Peizhen Ma
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (P.M.); (Z.L.); (Z.L.); (X.S.); (L.Z.)
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Zhihong Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (P.M.); (Z.L.); (Z.L.); (X.S.); (L.Z.)
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Zhuanzhuan Li
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (P.M.); (Z.L.); (Z.L.); (X.S.); (L.Z.)
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Xiujun Sun
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (P.M.); (Z.L.); (Z.L.); (X.S.); (L.Z.)
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Liqing Zhou
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (P.M.); (Z.L.); (Z.L.); (X.S.); (L.Z.)
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Xiangyu Wu
- Hainan Provincial Key Laboratory of Tropical Maricultural Technology, Hainan Academy of Ocean and Fisheries Sciences, Haikou 571126, China
| | - Biao Wu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (P.M.); (Z.L.); (Z.L.); (X.S.); (L.Z.)
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture and Rural Affairs, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
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11
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Fields PD, Jalinsky JR, Bankers L, McElroy KE, Sharbrough J, Higgins C, Morgan-Richards M, Boore JL, Neiman M, Logsdon JM. Genome Evolution and Introgression in the New Zealand mud Snails Potamopyrgus estuarinus and Potamopyrgus kaitunuparaoa. Genome Biol Evol 2024; 16:evae091. [PMID: 38776329 PMCID: PMC11110935 DOI: 10.1093/gbe/evae091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2024] [Indexed: 05/24/2024] Open
Abstract
We have sequenced, assembled, and analyzed the nuclear and mitochondrial genomes and transcriptomes of Potamopyrgus estuarinus and Potamopyrgus kaitunuparaoa, two prosobranch snail species native to New Zealand that together span the continuum from estuary to freshwater. These two species are the closest known relatives of the freshwater species Potamopyrgus antipodarum-a model for studying the evolution of sex, host-parasite coevolution, and biological invasiveness-and thus provide key evolutionary context for understanding its unusual biology. The P. estuarinus and P. kaitunuparaoa genomes are very similar in size and overall gene content. Comparative analyses of genome content indicate that these two species harbor a near-identical set of genes involved in meiosis and sperm functions, including seven genes with meiosis-specific functions. These results are consistent with obligate sexual reproduction in these two species and provide a framework for future analyses of P. antipodarum-a species comprising both obligately sexual and obligately asexual lineages, each separately derived from a sexual ancestor. Genome-wide multigene phylogenetic analyses indicate that P. kaitunuparaoa is likely the closest relative to P. antipodarum. We nevertheless show that there has been considerable introgression between P. estuarinus and P. kaitunuparaoa. That introgression does not extend to the mitochondrial genome, which appears to serve as a barrier to hybridization between P. estuarinus and P. kaitunuparaoa. Nuclear-encoded genes whose products function in joint mitochondrial-nuclear enzyme complexes exhibit similar patterns of nonintrogression, indicating that incompatibilities between the mitochondrial and the nuclear genome may have prevented more extensive gene flow between these two species.
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Affiliation(s)
- Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel 4051, Switzerland
| | | | - Laura Bankers
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Kyle E McElroy
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Joel Sharbrough
- Department of Biology, New Mexico Institute of Mining and Technology, Socorro, NM, USA
| | - Chelsea Higgins
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Mary Morgan-Richards
- School of Natural Sciences, Massey University Manawatū, Palmerston North, New Zealand
| | - Jeffrey L Boore
- Phenome Health, Seattle, WA, USA
- Institute for Systems Biology, Seattle, WA, USA
| | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, IA, USA
- Department of Gender, Women's, and Sexuality Studies, University of Iowa, Iowa City, IA, USA
| | - John M Logsdon
- Department of Biology, University of Iowa, Iowa City, IA, USA
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12
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Stelbrink B, von Rintelen T, Marwoto RM, Salzburger W. Mitogenomes do not substantially improve phylogenetic resolution in a young non-model adaptive radiation of freshwater gastropods. BMC Ecol Evol 2024; 24:42. [PMID: 38589809 PMCID: PMC11000327 DOI: 10.1186/s12862-024-02235-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/01/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND Species flocks in ancient lakes, and particularly those arising from adaptive radiation, make up the bulk of overall taxonomic and morphological diversity in these insular ecosystems. For these mostly young species assemblages, classical mitochondrial barcoding markers have so far been key to disentangle interspecific relationships. However, with the rise and further development of next-generation sequencing (NGS) methods and mapping tools, genome-wide data have become an increasingly important source of information even for non-model groups. RESULTS Here, we provide, for the first time, a comprehensive mitogenome dataset of freshwater gastropods endemic to Sulawesi and thus of an ancient lake invertebrate species flock in general. We applied low-coverage whole-genome sequencing for a total of 78 individuals including 27 out of the 28 Tylomelania morphospecies from the Malili lake system as well as selected representatives from Lake Poso and adjacent catchments. Our aim was to assess whether mitogenomes considerably contribute to the phylogenetic resolution within this young species flock. Interestingly, we identified a high number of variable and parsimony-informative sites across the other 'non-traditional' mitochondrial loci. However, although the overall support was very high, the topology obtained was largely congruent with previously published single-locus phylogenies. Several clades remained unresolved and a large number of species was recovered polyphyletic, indicative of both rapid diversification and mitochondrial introgression. CONCLUSIONS This once again illustrates that, despite the higher number of characters available, mitogenomes behave like a single locus and thus can only make a limited contribution to resolving species boundaries, particularly when introgression events are involved.
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Affiliation(s)
- Björn Stelbrink
- Justus Liebig University Giessen, Giessen, Germany.
- University of Basel, Basel, Switzerland.
| | - Thomas von Rintelen
- Museum für Naturkunde - Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Ristiyanti M Marwoto
- Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, BRIN Gedung Widyasatwaloka, Cibinong, Indonesia
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13
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Dumidae A, Subkrasae C, Ardpairin J, Pansri S, Homkaew C, Gordon CN, Mangkit B, Thanwisai A, Vitta A. Assessment of the genetic diversity of lymnaeid (Gastropoda: Pulmonata) snails and their infection status with trematode cercariae in different regions of Thailand. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 119:105576. [PMID: 38408586 DOI: 10.1016/j.meegid.2024.105576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 02/01/2024] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
Abstract
Lymnaeid snails are some of the most widespread snails and are the first intermediate host of trematode parasites that affect human and livestock health. A full understanding of the genetic relationship of hosts and parasites is of paramount importance for effective parasite management. The present study assessed the prevalence of trematode larvae in lymnaeid snails and examined the genetic diversity of these snails collected across Thailand. We collected 672 lymnaeid snails from 39 locations in 22 provinces of six regions in Thailand. Subsequently, cercarial infection in the snails was observed by using the shedding method. Lymnaeid snails released 5 types of trematode cercariae, namely, xiphidiocercariae, echinostome cercariae I, echinostome cercariae II, furcocercous cercariae, and strigea cercariae. The phylogenetic analysis based on ITS2 and 28S rDNA sequences revealed 5 cercaria types assigned to four trematode families, of which two belong to the group of human intestinal flukes. Combination of shell morphology and sequence analysis of the mitochondrial COI and 16S rDNA genes, the lymnaeid snails were classified into two species, Radix rubiginosa and Orientogalba viridis. Moreover, the combined dataset of mtDNA genes (COI + 16S rDNA) from R. rubiginosa and O. viridis revealed 32 and 15 different haplotypes, respectively, of which only a few haplotypes were infected with cercariae. The genetic diversity and genetic structure revealed that R. rubiginosa and O. viridis experienced a bottleneck phenomenon, and showed limited gene flow between populations. Population demographic history analyses revealed that R. rubiginosa and O. viridis experienced population reductions followed by recent population expansion. These findings may improve our understanding of parasite-lymnaeid evolutionary relationships, as well as the underlying molecular genetic basis, which is information that can be used for further effective control of the spread of trematode disease.
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Affiliation(s)
- Abdulhakam Dumidae
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Chanakan Subkrasae
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Jiranun Ardpairin
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Supawan Pansri
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Chanatinat Homkaew
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Chadaporn Nuchjangreed Gordon
- Department of Medical Sciences, Faculty of Allied Health Sciences, Burapha University, Chonburi Province 20131, Thailand
| | - Bandid Mangkit
- Department of Veterinary Technology, Faculty of Veterinary Technology, Kasetsart University, Bangkok, Thailand, 10900
| | - Aunchalee Thanwisai
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand; Centre of Excellence in Medical Biotechnology (CEMB), Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand; Center of Excellence for Biodiversity, Faculty of Sciences, Naresuan University, Phitsanulok 65000, Thailand
| | - Apichat Vitta
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand; Centre of Excellence in Medical Biotechnology (CEMB), Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand; Center of Excellence for Biodiversity, Faculty of Sciences, Naresuan University, Phitsanulok 65000, Thailand.
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14
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Plazzi F, Le Cras Y, Formaggioni A, Passamonti M. Mitochondrially mediated RNA interference, a retrograde signaling system affecting nuclear gene expression. Heredity (Edinb) 2024; 132:156-161. [PMID: 37714959 PMCID: PMC10923801 DOI: 10.1038/s41437-023-00650-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 09/17/2023] Open
Abstract
Several functional classes of short noncoding RNAs are involved in manifold regulatory processes in eukaryotes, including, among the best characterized, miRNAs. One of the most intriguing regulatory networks in the eukaryotic cell is the mito-nuclear crosstalk: recently, miRNA-like elements of mitochondrial origin, called smithRNAs, were detected in a bivalve species, Ruditapes philippinarum. These RNA molecules originate in the organelle but were shown in vivo to regulate nuclear genes. Since miRNA genes evolve easily de novo with respect to protein-coding genes, in the present work we estimate the probability with which a newly arisen smithRNA finds a suitable target in the nuclear transcriptome. Simulations with transcriptomes of 12 bivalve species suggest that this probability is high and not species specific: one in a hundred million (1 × 10-8) if five mismatches between the smithRNA and the 3' mRNA are allowed, yet many more are allowed in animals. We propose that novel smithRNAs may easily evolve as exaptation of the pre-existing mitochondrial RNAs. In turn, the ability of evolving novel smithRNAs may have played a pivotal role in mito-nuclear interactions during animal evolution, including the intriguing possibility of acting as speciation trigger.
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Affiliation(s)
- Federico Plazzi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3 - 40126, Bologna, BO, Italy.
| | - Youn Le Cras
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3 - 40126, Bologna, BO, Italy
- Magistère Européen de Génétique, Université Paris Cité, 85 Boulevard Saint Germain, 75006, Paris, Italy
| | - Alessandro Formaggioni
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3 - 40126, Bologna, BO, Italy
| | - Marco Passamonti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3 - 40126, Bologna, BO, Italy
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15
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Breton S. Comparative mitogenomics of Brachiopods reveals conservatism in articulate species and unusualness in inarticulate species. Mol Biol Rep 2024; 51:298. [PMID: 38341808 DOI: 10.1007/s11033-024-09270-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 01/18/2024] [Indexed: 02/13/2024]
Abstract
BACKGROUND Brachiopods are a phylum of marine invertebrates with over 10,000 fossil species. Today, there are fewer than 500 extant species assigned to the class Articulata or Inarticulata and for which knowledge of evolutionary genetics and genomics is still poor. Until now, complete mitogenome sequences of two inarticulate species and four articulate species were available. METHODS AND RESULTS The complete mitogenome of the inarticulate brachiopod species Lingula reevii (20,778 bp) was obtained by using next generation sequencing. It contains 12 protein-coding genes (the annotation of atp8 is unsure), two ribosomal RNA genes, 26 transfer RNA genes, and one supernumerary ORF that is also conserved in the inarticulate species Lingula anatina. It is hypothesized that this ORF could represent a Lingula-specific mtORFan gene (without obvious homology to other genes). Comparative mitogenomics indicate the mitochondrial gene order of L. reevii is unique among brachiopods, and that compared to articulate species, inarticulate species exhibit massive mitogenome rearrangements, deviant ATP8 protein sequences and supernumerary ORFs, possibly representing species- or lineage-specific mtORFan genes. CONCLUSION The results of this study enrich genetics knowledge of extant brachiopods, which may eventually help to test hypotheses about their decline.
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Affiliation(s)
- Sophie Breton
- Department of Biological Sciences, University of Montreal, Montreal, Canada.
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16
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Zhou Z, Song Y, Zheng Z, Liu Y, Yao H, Rao X, Lin G. The Complete Mitochondrial Genome and Phylogenetic Analysis of the Freshwater Shellfish Novaculina chinensis (Bivalvia: Pharidae). Int J Mol Sci 2023; 25:67. [PMID: 38203240 PMCID: PMC10778892 DOI: 10.3390/ijms25010067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Razor clams, belonging to the Pharidae and Solenidae families, are ecologically and economically important; however, very little research has been conducted on the Pharidae family. The genus Novaculina is a marine-derived freshwater lineage, and Novaculina chinensis is a rare freshwater species of the Pharidae family. In order to understand the phylogenetic relationships of N. chinensis, we sequenced the mitochondrial genome of the genus Novaculina, which is 16,262 bp in length and consists of 12 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs). The phylogenetic relationships of 69 Imparidentian mitochondrial genomes (mitogenomes) indicated that N. chineisis is closely related to Sinonovacula constricta of the order Adapedonta. Our study also found that the Ka/Ks ratios of 12 protein-coding genes in the Pharidae family are lower than one, indicating the occurrence of negative purification selection. Morphological observations of the siphons of N. chinensis, Novaculina myanmarensis, and Novaculina gangetica indicate that N. chinensis may be the ancestral clade of the genus Novaculina, which has not been proposed in previous studies. Our study provides useful molecular information on the phylogenetic and evolutionary relationships of Pharidae and also contributes to the conservation and management of the germplasm resources of N. chinensis.
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Affiliation(s)
| | | | | | | | | | - Xiaozhen Rao
- Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China; (Z.Z.); (Y.S.); (Z.Z.); (Y.L.); (H.Y.)
| | - Gang Lin
- Fujian Key Laboratory of Special Marine Bioresource Sustainable Utilization, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China; (Z.Z.); (Y.S.); (Z.Z.); (Y.L.); (H.Y.)
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17
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Gomes-dos-Santos A, Vilas-Arrondo N, Machado AM, Román-Marcote E, Del Río Iglesias JL, Baldó F, Pérez M, Fonseca MM, Castro LFC, Froufe E. Mitochondrial replication's role in vertebrate mtDNA strand asymmetry. Open Biol 2023; 13:230181. [PMID: 38113934 PMCID: PMC10730292 DOI: 10.1098/rsob.230181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 11/21/2023] [Indexed: 12/21/2023] Open
Abstract
Mitogenomes are defined as compact and structurally stable over aeons. This perception results from a vertebrate-centric vision, where few types of mtDNA rearrangements are described. Here, we bring a new light to the involvement of mitochondrial replication in the strand asymmetry of the vertebrate mtDNA. Using several species of deep-sea hatchetfish (Sternoptychidae) displaying distinct mtDNA structural arrangements, we unravel the inversion of the coding direction of protein-coding genes (PCGs). This unexpected change is coupled with a strand asymmetry nucleotide composition reversal and is shown to be directly related to the strand location of the Control Region (CR). An analysis of the fourfold redundant sites of the PCGs (greater than 6000 vertebrates), revealed the rarity of this phenomenon, found in nine fish species (five deep-sea hatchetfish). Curiously, in Antarctic notothenioid fishes (Trematominae), where a single PCG inversion (the only other record in fish) is coupled with the inversion of the CR, the standard asymmetry is disrupted for the remaining PCGs but not yet reversed, suggesting a transitory state. Our results hint that a relaxation of the classic vertebrate mitochondrial structural stasis promotes disruption of the natural balance of asymmetry of the mtDNA. These findings support the long-lasting hypothesis that replication is the main molecular mechanism promoting the strand-specific compositional bias of this unique and indispensable molecule.
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Affiliation(s)
- André Gomes-dos-Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Nair Vilas-Arrondo
- Programa de Doctorado ‘Ciencias marinas, Tecnología y Gestión’ (Do*MAR), Universidad de Vigo, Vigo, Spain
- Centro Oceanográfico de Vigo (COV), Instituto Español de Oceanografía (IEO-CSIC), Subida a Radio Faro, 50, Vigo (Pontevedra), 36390, Spain
| | - André M. Machado
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Esther Román-Marcote
- Centro Oceanográfico de Vigo (COV), Instituto Español de Oceanografía (IEO-CSIC), Subida a Radio Faro, 50, Vigo (Pontevedra), 36390, Spain
| | - Jose Luís Del Río Iglesias
- Centro Oceanográfico de Vigo (COV), Instituto Español de Oceanografía (IEO-CSIC), Subida a Radio Faro, 50, Vigo (Pontevedra), 36390, Spain
| | - Francisco Baldó
- Centro Oceanográfico de Cádiz (COCAD), Instituto Español de Oceanografía (IEO-CSIC), Puerto Pesquero, Muelle de Levante s/n, Cádiz, 11006, Spain
| | - Montse Pérez
- Centro Oceanográfico de Vigo (COV), Instituto Español de Oceanografía (IEO-CSIC), Subida a Radio Faro, 50, Vigo (Pontevedra), 36390, Spain
| | - Miguel M. Fonseca
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - L. Filipe C. Castro
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Porto, Portugal
| | - Elsa Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
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18
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Selifanova M, Demianchenko O, Noskova E, Pitikov E, Skvortsov D, Drozd J, Vatolkina N, Apel P, Kolodyazhnaya E, Ezhova MA, Tzetlin AB, Neretina TV, Knorre DA. ORFans in Mitochondrial Genomes of Marine Polychaete Polydora. Genome Biol Evol 2023; 15:evad219. [PMID: 38019573 PMCID: PMC10721130 DOI: 10.1093/gbe/evad219] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 11/18/2023] [Accepted: 11/24/2023] [Indexed: 11/30/2023] Open
Abstract
Most characterized metazoan mitochondrial genomes are compact and encode a small set of proteins that are essential for oxidative phosphorylation, as well as rRNA and tRNA for their expression. However, in rare cases, invertebrate taxa have additional open reading frames (ORFs) in their mtDNA sequences. Here, we sequenced and analyzed the mitochondrial genome of a polychaete worm, Polydora cf. ciliata, part of whose life cycle takes place in low-oxygen conditions. In the mitogenome, we found three "ORFan" regions (544, 1,060, and 427 bp) that have no resemblance to any standard metazoan mtDNA gene but lack stop codons in one of the reading frames. Similar regions are found in the mitochondrial genomes of three other Polydora species and Bocardiella hamata. All five species share the same gene order in their mitogenomes, which differ from that of other known Spionidae mitogenomes. By analyzing the ORFan sequences, we found that they are under purifying selection pressure and contain conservative regions. The codon adaptation indices (CAIs) of the ORFan genes were in the same range of values as the CAI of conventional protein-coding genes in corresponding mitochondrial genomes. The analysis of the P. cf. ciliata mitochondrial transcriptome showed that ORFan-544, ORFan-427, and a portion of the ORFan-1060 are transcribed. Together, this suggests that ORFan-544 and ORFan-427 encode functional proteins. It is likely that the ORFans originated when the Polydora/Bocardiella species complex separated from the rest of the Spionidae, and this event coincided with massive gene rearrangements in their mitochondrial genomes and tRNA-Met duplication.
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Affiliation(s)
- Maria Selifanova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Oleg Demianchenko
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Elizaveta Noskova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Egor Pitikov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Denis Skvortsov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Jana Drozd
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Nika Vatolkina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Polina Apel
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina Kolodyazhnaya
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Margarita A Ezhova
- Pertsov White Sea Biological Station, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alexander B Tzetlin
- Pertsov White Sea Biological Station, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Tatiana V Neretina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Pertsov White Sea Biological Station, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Science, Moscow, Russia
| | - Dmitry A Knorre
- Pertsov White Sea Biological Station, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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19
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Yan S, Ma P, Zuo C, Zhu Y, Ma X, Zhang Z. Genetic Analysis Based on Mitochondrial nad2 Gene Reveals a Recent Population Expansion of the Invasive Mussel, Mytella strigata, in China. Genes (Basel) 2023; 14:2038. [PMID: 38002981 PMCID: PMC10671778 DOI: 10.3390/genes14112038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
Mytella strigata is a highly adaptable invasive alien species that has been established in coastal China since 2014. Mitochondrial DNA (mtDNA) is an important tool for studying the evolution and population genetics of invasive species. In this study, the mitochondrial genome of M. strigata from China was sequenced by Illumina high-throughput sequencing and characterized with 13 protein-coding genes (PCGs). By assessing the selective pressure of 13 PCGs, the nad2 gene had the fastest evolutionary rate and was finally selected for population genetic analysis. A total of 285 nad2 sequences from seven M. strigata populations in China were analyzed and showed obviously T-rich and C-rich characteristics. According to population genetic diversity analysis, all the seven populations had haplotype (gene) diversity (Hd) ≥ 0.5 and nucleotide diversity (Pi) < 0.005. Haplotype networks showed a "star" distribution. Population historical dynamic analyses showed that Fu's Fs and Tajima's D values of all populations were negative except the Qukou (QK) and Beihai (BH) populations. The Zhangzhou (ZJ) and Xiamen (XM) populations were unimodal while the other populations were multimodal. These results suggested that the population of M. strigata in China may have passed the bottleneck period and is currently in a state of population expansion.
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Affiliation(s)
- Shaojing Yan
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (S.Y.)
| | - Peizhen Ma
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (S.Y.)
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
| | - Chenxia Zuo
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (S.Y.)
- College of Life Sciences, Qingdao University, Qingdao 266000, China
| | - Yi Zhu
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (S.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaojie Ma
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (S.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Zhang
- Laboratory of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (S.Y.)
- University of Chinese Academy of Sciences, Beijing 100049, China
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20
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Liu X, Sigwart JD, Sun J. Phylogenomic analyses shed light on the relationships of chiton superfamilies and shell-eye evolution. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:525-537. [PMID: 38045544 PMCID: PMC10689665 DOI: 10.1007/s42995-023-00207-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 11/01/2023] [Indexed: 12/05/2023]
Abstract
Mollusca is the second-largest animal phylum with over 100,000 extant species representing eight classes. Across 1000 extant species in the class Polyplacophora, chitons have a relatively constrained morphology but with some notable deviations. Several genera possess "shell eyes", i.e., true eyes with a lens and retina that are embedded within the dorsal shells. The phylogeny of the major chiton clades is mostly well established, in a set of superfamily-level and higher level taxa supported by various approaches, including morphological studies, multiple gene markers, mitogenome-phylogeny, and phylotranscriptomic approaches. However, one critical lineage has remained unclear, namely Schizochiton which was controversially suggested as being the potential independent origin of chiton shell eyes. Here, with the draft genome sequencing of Schizochiton incisus (superfamily Schizochitonoidea) plus assemblies of transcriptome data from other polyplacophorans, we present phylogenetic reconstructions using both mitochondrial genomes and phylogenomic approaches with multiple methods. We found that phylogenetic trees from mitogenomic data are inconsistent, reflecting larger scale confounding factors in molluscan mitogenomes. However, a consistent and robust topology was generated with protein-coding genes using different models and methods. Our results support Schizochitonoidea as the sister group to other Chitonoidea in Chitonina, in agreement with the established classification. Combined with evidence from fossils, our phylogenetic results suggest that the earliest origin of shell eyes is in Schizochitonoidea, and that these structures were also gained secondarily in other genera in Chitonoidea. Our results have generated a holistic review of the internal relationship within Polyplacophora, and a better understanding of the evolution of Polyplacophora.
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Affiliation(s)
- Xu Liu
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laoshan Laboratory, Qingdao, 266237 China
| | - Julia D. Sigwart
- Department of Marine Zoology, Senckenberg Research Institute and Natural History Museum Frankfurt, 60325 Frankfurt Am Main, Germany
| | - Jin Sun
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education) and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
- Laoshan Laboratory, Qingdao, 266237 China
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21
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Ma P, Liu Y, Wang J, Chen Y, Zhang Z, Zhang T, Wang H. Comparative analysis of the mitochondrial genomes of the family Mactridae (Mollusca: Venerida) and their phylogenetic implications. Int J Biol Macromol 2023; 249:126081. [PMID: 37536404 DOI: 10.1016/j.ijbiomac.2023.126081] [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: 01/27/2023] [Revised: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/05/2023]
Abstract
Taxonomy and phylogenetic relationships within the family Mactridae have remained debatable because of the plasticity of morphological characteristics and the lack of accurate molecular data, thereby resulting in abundant synonyms and taxa rearrangements. Mitochondrial genomes (mitogenomes) have been widely used as powerful tools to reconstruct phylogenies of various groups of mollusks; however, they have not been used for studying the phylogeny of mactrids specifically. In the present study, mitogenomes of seven Mactridae species, namely Mactra chinensis, Mactra cygnus, Mactra quadrangularis, Mactra cumingii, Mactrinula dolabrata, Raeta pulchella, and Raeta sp., were sequenced by Illumina high-throughput sequencing, and a comparative mitochondrial genomic analysis was conducted. The newly sequenced mitogenomes were double-stranded circular molecules, with all functional genes encoded on the heavy strand. All the new mactrid mitogenomes had two rRNA genes (12S and 16S), 13 protein-coding genes (PCGs) (atp6, cox1, cox2, cox3, cytb, nad1, nad2, nad3, nad4, nad4l, nad5, nad6, and atp8), and 22 tRNAs. The mitogenomes showed considerable variation in AT content, GC skew, and AT skew. The results of the phylogenetic analysis confirmed monophyly of the family Mactridae and suggested that genera Mactrinula, Spisula, Rangia, and Mulinia should not be placed under subfamily Mactrinae. Our results supported that potential cryptic species existed in Mactra antiquata. We also proposed subfamily Kymatoxinae should belong to the family Mactridae rather than Anatinellidae and Mactra alta in China should be Mactra cygnus. Additionally, conservation in functional gene arrangement was found in genera Mactra, Raeta, and Lutraria. But gene orders in S. sachalinensis and S. solida were quite different, questioning their congeneric relationship. Our results further suggested that the taxonomy within the family Mactridae requires an integrative revision.
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Affiliation(s)
- Peizhen Ma
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Yumeng Liu
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jiahui Wang
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Ya Chen
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Zhang
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Zhang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Haiyan Wang
- Department of Marine Organism Taxonomy & Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
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22
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Li F, Zhang Y, Zhong T, Heng X, Ao T, Gu Z, Wang A, Liu C, Yang Y. The Complete Mitochondrial Genomes of Two Rock Scallops (Bivalvia: Spondylidae) Indicate Extensive Gene Rearrangements and Adaptive Evolution Compared with Pectinidae. Int J Mol Sci 2023; 24:13844. [PMID: 37762147 PMCID: PMC10531248 DOI: 10.3390/ijms241813844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Different from the diverse family Pectinidae, the Spondylidae is a small group with a single genus that shares the sedentary life habit of cementing themselves to the substrate. However, little information related to the genetic diversity of Spondylidae has been reported. In the present study, the complete mitochondrial genomes of Spondylus versicolor and S. spinosus were sequenced and compared with those of pectinids. The mtDNA of S. versicolor and S. spinosus show similar patterns with respect to genome size, AT content, AT skew, GC skew, and codon usage, and their mitogenomic sizes are longer than most pectinid species. The mtDNA of S. spinosus is 27,566 bp in length, encoding 13 protein-coding genes, 22 transfer RNA genes, and 2 ribosomal RNA genes, while an additional tRNA-Met was found in the mtDNA of S. versicolor, which is 28,600 bp in length. The monophylies of Spondylidae and Pectinidae were well supported, but the internal relationships within Pectinidae remain unresolved due to the paraphyly of the genus Mimachlamy and the controversial position of the tribe Aequipectinini. The gene orders of S. versicolor and S. spinosus are almost identical but differ greatly from species of the Pectinidae, indicating extensive gene rearrangements compared with Pectinidae. Positive selection analysis revealed evidence of adaptive evolution in the branch of Spondylidae. The present study could provide important information with which to understand the evolutionary progress of the diverse and economically significant marine bivalve Pectinoidea.
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Affiliation(s)
- Fengping Li
- School of Marine Biology and Aquaculture, Hainan University, Haikou 570228, China; (F.L.); (Z.G.); (A.W.); (C.L.)
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China
| | - Yu Zhang
- Sanya Oceanographic Institution, Ocean University of China, Sanya 572000, China
| | - Tao Zhong
- School of Marine Biology and Aquaculture, Hainan University, Haikou 570228, China; (F.L.); (Z.G.); (A.W.); (C.L.)
| | - Xin Heng
- School of Marine Biology and Aquaculture, Hainan University, Haikou 570228, China; (F.L.); (Z.G.); (A.W.); (C.L.)
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China
| | - Tiancheng Ao
- School of Marine Biology and Aquaculture, Hainan University, Haikou 570228, China; (F.L.); (Z.G.); (A.W.); (C.L.)
| | - Zhifeng Gu
- School of Marine Biology and Aquaculture, Hainan University, Haikou 570228, China; (F.L.); (Z.G.); (A.W.); (C.L.)
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China
| | - Aimin Wang
- School of Marine Biology and Aquaculture, Hainan University, Haikou 570228, China; (F.L.); (Z.G.); (A.W.); (C.L.)
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China
| | - Chunsheng Liu
- School of Marine Biology and Aquaculture, Hainan University, Haikou 570228, China; (F.L.); (Z.G.); (A.W.); (C.L.)
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China
| | - Yi Yang
- School of Marine Biology and Aquaculture, Hainan University, Haikou 570228, China; (F.L.); (Z.G.); (A.W.); (C.L.)
- Sanya Nanfan Research Institute, Hainan University, Sanya 572025, China
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23
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Cai LN, Zhang LH, Lin YJ, Wang JY, Storey KB, Zhang JY, Yu DN. Two-Fold ND5 Genes, Three-Fold Control Regions, lncRNA, and the "Missing" ATP8 Found in the Mitogenomes of Polypedates megacephalus (Rhacophridae: Polypedates). Animals (Basel) 2023; 13:2857. [PMID: 37760257 PMCID: PMC10525163 DOI: 10.3390/ani13182857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/03/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
In prior research on the mitochondrial genome (mitogenome) of Polypedates megacephalus, the one copy of ND5 gene was translocated to the control region (CR) and the ATP8 gene was not found. Gene loss is uncommon among vertebrates. However, in this study, we resequenced the mitogenomes of P. megacephalus from different regions using a "primer bridging" approach with Sanger sequencing technologies, which revealed the "missing" ATP8 gene in P. megacephalus as well as three other previously published Polypedates. The mitogenome of this species was found to contain two copies of the ND5 genes and three copies of the control regions. Furthermore, multiple tandem repeats were identified in the control regions. Notably, we observed that there was no correlation between genetic divergence and geographic distance. However, using the mitogenome, gene expression analysis was performed via RT-qPCR of liver samples and it was thus determined that COIII, ND2, ND4, and ND6 were reduced to 0.64 ± 0.24, 0.55 ± 0.34, 0.44 ± 0.21 and 0.65 ± 0.17, respectively, under low-temperature stress (8 °C) as compared with controls (p < 0.05). Remarkably, the transcript of long non-coding RNA (lncRNA) between positions 8029 and 8612 decreased significantly with exposure to low-temperature stress (8 °C). Antisense ND6 gene expression showed a downward trend, but this was not significant. These results reveal that modulations of protein-coding mitochondrial genes and lncRNAs of P. megacephalus play a crucial role in the molecular response to cold stress.
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Affiliation(s)
- Ling-Na Cai
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (L.-N.C.); (Y.-J.L.); (J.-Y.W.)
| | - Li-Hua Zhang
- Taishun County Forestry Bureau, Wenzhou 325200, China;
| | - Yi-Jie Lin
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (L.-N.C.); (Y.-J.L.); (J.-Y.W.)
| | - Jing-Yan Wang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (L.-N.C.); (Y.-J.L.); (J.-Y.W.)
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada;
| | - Jia-Yong Zhang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (L.-N.C.); (Y.-J.L.); (J.-Y.W.)
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Dan-Na Yu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (L.-N.C.); (Y.-J.L.); (J.-Y.W.)
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
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24
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Shen W, Wu M. Complete mitochondrial genome of Laeocathaica amdoana Möllendorff, 1899 and phylogenetic analysis of Camaenidae (Gastropoda: Stylommatophora: Helicoidea). Mitochondrial DNA B Resour 2023; 8:731-736. [PMID: 37426573 PMCID: PMC10327522 DOI: 10.1080/23802359.2023.2231253] [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: 01/10/2023] [Accepted: 06/10/2023] [Indexed: 07/11/2023] Open
Abstract
The first complete mitochondrial genome of the dart sac-bearing camaenid Laeocathaica Möllendorff, 1899 was sequenced and analyzed in this study. The whole mitogenome of Laeocathaica amdoana Möllendorff, 1899 was 14,660 bp in length and its nucleotide composition showed high AT-content of 67.45%. It had 37 genes, including 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. The phylogeny yielded by both Bayesian inference and maximum-likelihood method suggested that Laeocathaica was closely related to the other dart sac-bearing camaenids with known complete mitochondrial genome. These genetic data are expected to provide fundamental resources for further genetic studies on the camaenids.
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Affiliation(s)
- Wang Shen
- School of Life Sciences, Nanjing University, Nanjing, China
| | - Min Wu
- School of Life Sciences, Nanjing University, Nanjing, China
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25
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Kobayashi G, Itoh H, Nakajima N. Molecular Phylogeny of Thoracotreme Crabs Including Nine Newly Determined Mitochondrial Genomes. Zoolog Sci 2023; 40:224-234. [PMID: 37256570 DOI: 10.2108/zs220063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 01/02/2023] [Indexed: 06/01/2023]
Abstract
Mitochondrial genomes are used widely for the molecular phylogenetic analysis of animals. Although phylogenetic analyses based on the mitogenomes of brachyurans often yield well-resolved phylogenies, most interfamilial phylogenetic relationships in Thoracotremata remain unclear. We determined nine new mitogenomes of Thoracotremata, including mitogenomes of Camptandriidae (Deiratonotus japonicus), Dotillidae (Ilyoplax integra, Ilyoplax pusilla, and Tmethypocoelis choreutes), Macrophthalmidae (Ilyograpsus nodulosus), Pinnotheridae (Arcotheres sp. and Indopinnixa haematosticta), Plagusiidae (Guinusia dentipes), and Percnidae (Percnon planissimum). Interestingly, Percnon planissimum (Percnidae) was found to possess ≥ 19 repeated sequences in the control region. The gene orders of Il. nodulosus, Arcotheres sp., and In. haematosticta were revealed to be unique among thoracotreme crabs. Although the results of Bayesian and maximum likelihood (ML) phylogenetic analyses of three datasets were incongruent, highly supported clades (PP ≥ 0.99 or BS ≥ 99%) were not contradictory among the analyses. All analyses suggested the paraphyly of Grapsoidea and Ocypodoidea, corroborating the findings of previous studies based on molecular phylogenies of thoracotreme crabs. The phylogenetic positions of symbiotic thoracotreme crabs, Pinnotheridae and Cryptochiridae, were highly supported (Pinnotheridae + Ocypodidae and Cryptochiridae + Grapsidae, respectively) for the Bayesian analyses but not for the ML analyses. Analyses of more thoracotreme species' mitogenome sequences in additional studies will further strengthen the framework for thoracotreme evolution.
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Affiliation(s)
- Genki Kobayashi
- Ishinomaki Senshu University, Minamisakai, Ishinomaki, Miyagi 986-8580, Japan,
| | - Hajime Itoh
- National Institute for Environmental Studies, Tsukuba, Ibaraki 305-8506, Japan
| | - Nobuyoshi Nakajima
- National Institute for Environmental Studies, Tsukuba, Ibaraki 305-8506, Japan
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26
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Smith CH, Pinto BJ, Kirkpatrick M, Hillis DM, Pfeiffer JM, Havird JC. A tale of two paths: The evolution of mitochondrial recombination in bivalves with doubly uniparental inheritance. J Hered 2023; 114:199-206. [PMID: 36897956 PMCID: PMC10212130 DOI: 10.1093/jhered/esad004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 01/19/2023] [Indexed: 03/12/2023] Open
Abstract
In most animals, mitochondrial DNA is strictly maternally inherited and non-recombining. One exception to this pattern is called doubly uniparental inheritance (DUI), a phenomenon involving the independent transmission of female and male mitochondrial genomes. DUI is known only from the molluskan class Bivalvia. The phylogenetic distribution of male-transmitted mitochondrial DNA (M mtDNA) in bivalves is consistent with several evolutionary scenarios, including multiple independent gains, losses, and varying degrees of recombination with female-transmitted mitochondrial DNA (F mtDNA). In this study, we use phylogenetic methods to test M mtDNA origination hypotheses and infer the prevalence of mitochondrial recombination in bivalves with DUI. Phylogenetic modeling using site concordance factors supported a single origin of M mtDNA in bivalves coupled with recombination acting over long evolutionary timescales. Ongoing mitochondrial recombination is present in Mytilida and Venerida, which results in a pattern of concerted evolution of F mtDNA and M mtDNA. Mitochondrial recombination could be favored to offset the deleterious effects of asexual inheritance and maintain mitonuclear compatibility across tissues. Cardiida and Unionida have gone without recent recombination, possibly due to an extension of the COX2 gene in male mitochondrial DNA. The loss of recombination could be connected to the role of M mtDNA in sex determination or sexual development. Our results support that recombination events may occur throughout the mitochondrial genomes of DUI species. Future investigations may reveal more complex patterns of inheritance of recombinants, which could explain the retention of signal for a single origination of M mtDNA in protein-coding genes.
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Affiliation(s)
- Chase H Smith
- Department of Integrative Biology, University of Texas, Austin, TX, United States
| | - Brendan J Pinto
- Center for Evolutionary Medicine & Public Health, Arizona State University, Tempe, AZ, United States
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI, United States
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas, Austin, TX, United States
| | - David M Hillis
- Department of Integrative Biology, University of Texas, Austin, TX, United States
| | - John M Pfeiffer
- Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, United States
- Department of Integrative Biology, University of Texas, Austin, TX, United States
| | - Justin C Havird
- Department of Integrative Biology, University of Texas, Austin, TX, United States
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27
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Li F, Liu H, Heng X, Zhang Y, Fan M, Wang S, Liu C, Gu Z, Wang A, Yang Y. The complete mitochondrial genome of Hyotissasinensis (Bivalvia, Ostreoidea) indicates the genetic diversity within Gryphaeidae. Biodivers Data J 2023; 11:e101333. [PMID: 38327347 PMCID: PMC10848854 DOI: 10.3897/bdj.11.e101333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/12/2023] [Indexed: 03/22/2023] Open
Abstract
Different from the true oyster (family Ostreidae), the molecular diversity of the gryphaeid oyster (family Gryphaeidae) has never been sufficiently investigated. In the present study, the complete mitochondrial (mt) genome of Hyotissasinensis was sequenced and compared with those of other ostreoids. The total length of H.sinensis mtDNA is 30,385 bp, encoding 12 protein-coding-genes (PCGs), 26 transfer RNA (tRNA) genes and two ribosomal RNA (rRNA) genes. The nucleotide composition and codon usage preference of H.sinensis mtDNA is similar to that of H.hyotis within the same genus. On the other hand, the presence of three trnM and three trnL genes of H.sinensis was not detected neither in H.hyotis nor other ostroid species. Another unique character of H.sinensis mtDNA is that both rrnS and rrnL have a nearly identical duplication. The PCG order of H.sinensis is identical to H.hyotis and the two congener species also share an identical block of 12 tRNA genes. The tRNA rearrangements mostly happen in the region from Cox1 to Nad3, the same area where the duplicated genes are located. The rearrangements within Gryphaeidae could be explained by a "repeat-random loss model". Phylogenetic analyses revealed Gryphaeidae formed by H.sinensis + H.hyotis as sister to Ostreidae, whereas the phylogenetic relationship within the latter group remains unresolved. The present study indicated the mitogenomic diversity within Gryphaeidae and could also provide important data for future better understanding the gene order rearrangements within superfamily Ostreoidea.
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Affiliation(s)
- Fengping Li
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, ChinaState Key Laboratory of Marine Resource Utilization in South China Sea, Hainan UniversityHaikouChina
- College of Marine Science, Hainan University, Haikou, ChinaCollege of Marine Science, Hainan UniversityHaikouChina
| | - Hongyue Liu
- Institute of Marine Science and Technology, Shandong University, Qingdao, ChinaInstitute of Marine Science and Technology, Shandong UniversityQingdaoChina
| | - Xin Heng
- College of Marine Science, Hainan University, Haikou, ChinaCollege of Marine Science, Hainan UniversityHaikouChina
| | - Yu Zhang
- Sanya Oceanographic Institution, Ocean University of China, Sanya, ChinaSanya Oceanographic Institution, Ocean University of ChinaSanyaChina
| | - Mingfu Fan
- College of Marine Science, Hainan University, Haikou, ChinaCollege of Marine Science, Hainan UniversityHaikouChina
| | - Shunshun Wang
- College of Marine Science, Hainan University, Haikou, ChinaCollege of Marine Science, Hainan UniversityHaikouChina
| | - Chunsheng Liu
- College of Marine Science, Hainan University, Haikou, ChinaCollege of Marine Science, Hainan UniversityHaikouChina
| | - Zhifeng Gu
- College of Marine Science, Hainan University, Haikou, ChinaCollege of Marine Science, Hainan UniversityHaikouChina
| | - Aimin Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, ChinaState Key Laboratory of Marine Resource Utilization in South China Sea, Hainan UniversityHaikouChina
| | - Yi Yang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, ChinaState Key Laboratory of Marine Resource Utilization in South China Sea, Hainan UniversityHaikouChina
- College of Marine Science, Hainan University, Haikou, ChinaCollege of Marine Science, Hainan UniversityHaikouChina
- Sanya Nanfan Research Institute, Hainan University, Sanya, ChinaSanya Nanfan Research Institute, Hainan UniversitySanyaChina
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28
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Li H, Li C, Ma P, Wang H, Zhang Z. The complete mitochondrial genome of a fouling mussel, Xenostrobus atratus (Mollusca: Mytilidae), and its phylogenetic implication. Mitochondrial DNA B Resour 2023; 8:301-304. [PMID: 36860475 PMCID: PMC9970215 DOI: 10.1080/23802359.2023.2179354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023] Open
Abstract
In this study, we report the female-lineage mitochondrial genome of Xenostrobus atratus for the first time. The circular mitochondrial genome is 14,806 bp in length and contains 12 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes. All genes are encoded on the heavy strand. The genome composition is A + T biased (66.6%), with 25.2% A, 41.4% T, 21.7% G and 11.7% C. A Bayesian inference (BI) phylogenetic tree was constructed based on the mitochondrial genomes of X. atratus and 46 other Mytilidae species. Our results demonstrate that X. atratus and Limnoperna fortunei have distinct lineages, opposing synonymizing Xenostrobus within Limnoperna. According to this study, the validity of the subfamily Limnoperninae and genus Xenostrobus is strongly supported. However, there is still an urgent need for more mitochondrial data to decide to which subfamily X. atratus belongs.
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Affiliation(s)
- Houmei Li
- School of Marine Sciences, Ningbo University, Ningbo, P. R. China,Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Chenghua Li
- School of Marine Sciences, Ningbo University, Ningbo, P. R. China
| | - Peizhen Ma
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Haiyan Wang
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, P. R. China
| | - Zhen Zhang
- Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, P. R. China,University of Chinese Academy of Sciences, Beijing, P. R. China,CONTACT Zhen Zhang Laboratory of Marine Organism Taxonomy and Phylogeny, Qingdao Key Laboratory of Marine Biodiversity and Conservation, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, P. R. China
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29
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Zhang T, Wang Y, Song H. The Complete Mitochondrial Genome and Gene Arrangement of the Enigmatic Scaphopod Pictodentalium vernedei. Genes (Basel) 2023; 14:210. [PMID: 36672951 PMCID: PMC9859601 DOI: 10.3390/genes14010210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/10/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
The enigmatic scaphopods, or tusk shells, are a small and rare group of molluscs whose phylogenomic position among the Conchifera is undetermined, and the taxonomy within this class also needs revision. Such work is hindered by there only being a very few mitochondrial genomes in this group that are currently available. Here, we present the assembly and annotation of the complete mitochondrial genome from Dentaliida Pictodentalium vernedei, whose mitochondrial genome is 14,519 bp in size, containing 13 protein-coding genes, 22 tRNA genes and two rRNA genes. The nucleotide composition was skewed toward A-T, with a 71.91% proportion of AT content. Due to the mitogenome-based phylogenetic analysis, we defined P. vernedei as a sister to Graptacme eborea in Dentaliida. Although a few re-arrangements occurred, the mitochondrial gene order showed deep conservation within Dentaliida. Yet, such a gene order in Dentaliida largely diverges from Gadilida and other molluscan classes, suggesting that scaphopods have the highest degree of mitogenome arrangement compared to other molluscs.
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Affiliation(s)
- Tianzhe Zhang
- School of Energy and Environmental Engineering, Hebei University of Technology, Tianjin 300401, China
| | - Yunan Wang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 101400, China
| | - Hao Song
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 101400, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
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30
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Sharbrough J, Bankers L, Cook E, Fields PD, Jalinsky J, McElroy KE, Neiman M, Logsdon JM, Boore JL. Single-molecule Sequencing of an Animal Mitochondrial Genome Reveals Chloroplast-like Architecture and Repeat-mediated Recombination. Mol Biol Evol 2023; 40:6980790. [PMID: 36625177 PMCID: PMC9874032 DOI: 10.1093/molbev/msad007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/28/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Recent advances in long-read sequencing technology have allowed for single-molecule sequencing of entire mitochondrial genomes, opening the door for direct investigation of the mitochondrial genome architecture and recombination. We used PacBio sequencing to reassemble mitochondrial genomes from two species of New Zealand freshwater snails, Potamopyrgus antipodarum and Potamopyrgus estuarinus. These assemblies revealed a ∼1.7 kb structure within the mitochondrial genomes of both species that was previously undetected by an assembly of short reads and likely corresponding to a large noncoding region commonly present in the mitochondrial genomes. The overall architecture of these Potamopyrgus mitochondrial genomes is reminiscent of the chloroplast genomes of land plants, harboring a large single-copy (LSC) region and a small single-copy (SSC) region separated by a pair of inverted repeats (IRa and IRb). Individual sequencing reads that spanned across the Potamopyrgus IRa-SSC-IRb structure revealed the occurrence of a "flip-flop" recombination. We also detected evidence for two distinct IR haplotypes and recombination between them in wild-caught P. estuarinus, as well as extensive intermolecular recombination between single-nucleotide polymorphisms in the LSC region. The chloroplast-like architecture and repeat-mediated mitochondrial recombination we describe here raise fundamental questions regarding the origins and commonness of inverted repeats in cytoplasmic genomes and their role in mitochondrial genome evolution.
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Affiliation(s)
| | - Laura Bankers
- Department of Biology, University of Iowa, Iowa City, IA
| | - Emily Cook
- Department of Biology, New Mexico Institute of Mining and Technology, Socorro, NM 87801
| | - Peter D Fields
- Zoologisches Institut, University of Basel, Basel, Switzerland
| | | | - Kyle E McElroy
- Department of Biology, University of Iowa, Iowa City, IA,Department of Ecology, Evolution, and Organismal Biology, Iowa State University, IA
| | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, IA
| | - John M Logsdon
- Department of Biology, University of Iowa, Iowa City, IA
| | - Jeffrey L Boore
- Phenome Health and Institute for Systems Biology, Seattle, WA
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31
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Xu R, Martelossi J, Smits M, Iannello M, Peruzza L, Babbucci M, Milan M, Dunham JP, Breton S, Milani L, Nuzhdin SV, Bargelloni L, Passamonti M, Ghiselli F. Multi-tissue RNA-Seq Analysis and Long-read-based Genome Assembly Reveal Complex Sex-specific Gene Regulation and Molecular Evolution in the Manila Clam. Genome Biol Evol 2022; 14:6889380. [PMID: 36508337 PMCID: PMC9803972 DOI: 10.1093/gbe/evac171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 11/26/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
The molecular factors and gene regulation involved in sex determination and gonad differentiation in bivalve molluscs are unknown. It has been suggested that doubly uniparental inheritance (DUI) of mitochondria may be involved in these processes in species such as the ubiquitous and commercially relevant Manila clam, Ruditapes philippinarum. We present the first long-read-based de novo genome assembly of a Manila clam, and a RNA-Seq multi-tissue analysis of 15 females and 15 males. The highly contiguous genome assembly was used as reference to investigate gene expression, alternative splicing, sequence evolution, tissue-specific co-expression networks, and sexual contrasting SNPs. Differential expression (DE) and differential splicing (DS) analyses revealed sex-specific transcriptional regulation in gonads, but not in somatic tissues. Co-expression networks revealed complex gene regulation in gonads, and genes in gonad-associated modules showed high tissue specificity. However, male gonad-associated modules showed contrasting patterns of sequence evolution and tissue specificity. One gene set was related to the structural organization of male gametes and presented slow sequence evolution but high pleiotropy, whereas another gene set was enriched in reproduction-related processes and characterized by fast sequence evolution and tissue specificity. Sexual contrasting SNPs were found in genes overrepresented in mitochondrial-related functions, providing new candidates for investigating the relationship between mitochondria and sex in DUI species. Together, these results increase our understanding of the role of DE, DS, and sequence evolution of sex-specific genes in an understudied taxon. We also provide resourceful genomic data for studies regarding sex diagnosis and breeding in bivalves.
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Affiliation(s)
- Ran Xu
- Corresponding authors: E-mail: (R.X.); E-mail: (F.G.)
| | | | | | | | - Luca Peruzza
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
| | - Massimo Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
| | - Joseph P Dunham
- Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA,SeqOnce Biosciences Inc., Pasadena, CA, USA
| | - Sophie Breton
- Department of Biological Sciences, University of Montreal, Montreal, Canada
| | - Liliana Milani
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Sergey V Nuzhdin
- Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Padova, Italy
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32
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Zhang N, Li Y, Halanych KM, Kong L, Li Q. A comparative analysis of mitochondrial ORFs provides new insights on expansion of mitochondrial genome size in Arcidae. BMC Genomics 2022; 23:809. [PMID: 36474182 PMCID: PMC9727918 DOI: 10.1186/s12864-022-09040-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Arcidae, comprising about 260 species of ark shells, is an ecologically and economically important lineage of bivalve mollusks. Interestingly, mitochondrial genomes of several Arcidae species are 2-3 times larger than those of most bilaterians, and are among the largest bilaterian mitochondrial genomes reported to date. The large mitochondrial genome size is mainly due to expansion of unassigned regions (regions that are functionally unassigned). Previous work on unassigned regions of Arcidae mtDNA genomes has focused on nucleotide-level analyses to observe sequence characteristics, however the origin of expansion remains unclear. RESULTS We assembled six new mitogenomes and sequenced six transcriptomes of Scapharca broughtonii to identify conserved functional ORFs that are transcribed in unassigned regions. Sixteen lineage-specific ORFs with different copy numbers were identified from seven Arcidae species, and 11 of 16 ORFs were expressed and likely biologically active. Unassigned regions of 32 Arcidae mitogenomes were compared to verify the presence of these novel mitochondrial ORFs and their distribution. Strikingly, multiple structural analyses and functional prediction suggested that these additional mtDNA-encoded proteins have potential functional significance. In addition, our results also revealed that the ORFs have a strong connection to the expansion of Arcidae mitochondrial genomes and their large-scale duplication play an important role in multiple expansion events. We discussed the possible origin of ORFs and hypothesized that these ORFs may originate from duplication of mitochondrial genes. CONCLUSIONS The presence of lineage-specific mitochondrial ORFs with transcriptional activity and potential functional significance supports novel features for Arcidae mitochondrial genomes. Given our observation and analyses, these ORFs may be products of mitochondrial gene duplication. These findings shed light on the origin and function of novel mitochondrial genes in bivalves and provide new insights into evolution of mitochondrial genome size in metazoans.
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Affiliation(s)
- Ning Zhang
- grid.4422.00000 0001 2152 3263Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Yuanning Li
- grid.27255.370000 0004 1761 1174Shandong University, Qingdao, China
| | - Kenneth M. Halanych
- grid.217197.b0000 0000 9813 0452Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC 28409 USA
| | - Lingfeng Kong
- grid.4422.00000 0001 2152 3263Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qi Li
- grid.4422.00000 0001 2152 3263Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China ,grid.484590.40000 0004 5998 3072Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Zhao B, Gao S, Zhao M, Lv H, Song J, Wang H, Zeng Q, Liu J. Mitochondrial genomic analyses provide new insights into the "missing" atp8 and adaptive evolution of Mytilidae. BMC Genomics 2022; 23:738. [PMID: 36324074 PMCID: PMC9628169 DOI: 10.1186/s12864-022-08940-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022] Open
Abstract
Background Mytilidae, also known as marine mussels, are widely distributed in the oceans worldwide. Members of Mytilidae show a tremendous range of ecological adaptions, from the species distributed in freshwater to those that inhabit in deep-sea. Mitochondria play an important role in energy metabolism, which might contribute to the adaptation of Mytilidae to different environments. In addition, some bivalve species are thought to lack the mitochondrial protein-coding gene ATP synthase F0 subunit 8. Increasing studies indicated that the absence of atp8 may be caused by annotation difficulties for atp8 gene is characterized by highly divergent, variable length. Results In this study, the complete mitochondrial genomes of three marine mussels (Xenostrobus securis, Bathymodiolus puteoserpentis, Gigantidas vrijenhoeki) were newly assembled, with the lengths of 14,972 bp, 20,482, and 17,786 bp, respectively. We annotated atp8 in the sequences that we assembled and the sequences lacking atp8. The newly annotated atp8 sequences all have one predicted transmembrane domain, a similar hydropathy profile, as well as the C-terminal region with positively charged amino acids. Furthermore, we reconstructed the phylogenetic trees and performed positive selection analysis. The results showed that the deep-sea bathymodiolines experienced more relaxed evolutionary constraints. And signatures of positive selection were detected in nad4 of Limnoperna fortunei, which may contribute to the survival and/or thriving of this species in freshwater. Conclusions Our analysis supported that atp8 may not be missing in the Mytilidae. And our results provided evidence that the mitochondrial genes may contribute to the adaptation of Mytilidae to different environments. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08940-8.
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Affiliation(s)
- Baojun Zhao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Shengtao Gao
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanog Inst, Ocean University of China, Sanya, 572000, China
| | - Mingyang Zhao
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanog Inst, Ocean University of China, Sanya, 572000, China
| | - Hongyu Lv
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanog Inst, Ocean University of China, Sanya, 572000, China
| | - Jingyu Song
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanog Inst, Ocean University of China, Sanya, 572000, China
| | - Hao Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
| | - Qifan Zeng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China. .,Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanog Inst, Ocean University of China, Sanya, 572000, China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Jing Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China.
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34
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Lubośny M, Śmietanka B, Lasota R, Burzyński A. Confirmation of the first intronic sequence in the bivalvian mitochondrial genome of Macoma balthica (Linnaeus, 1758). Biol Lett 2022; 18:20220275. [PMID: 36196553 PMCID: PMC9532982 DOI: 10.1098/rsbl.2022.0275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In 2020, the first male-type mitochondrial genome from the clam Macoma balthica was published. Apart from the unusual doubly uniparental inheritance of mtDNA, scientists observed a unique (over 4k bp long) extension in the middle of the cox2 gene. We have attempted to replicate these data by NGS DNA sequencing and explore further the expression of the long cox2 gene. In our study, we report an even longer cox2 gene (over 5.5 kbp) with no stop codon separating conserved cox2 domains, as well as, based on the rtPCR, a lower relative gene expression pattern of the middle part of the gene (5' = 1; mid = 0.46; 3' = 0.89). Lastly, we sequenced the cox2 gene transcript proving the excision of the intronic sequence.
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Affiliation(s)
- Marek Lubośny
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot 81-712, Poland
| | - Beata Śmietanka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot 81-712, Poland
| | - Rafał Lasota
- Faculty of Oceanography and Geography, Division of Marine Ecosystems Functioning, University of Gdańsk, Gdynia 81-378, Poland
| | - Artur Burzyński
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot 81-712, Poland
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35
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Complete mitochondrial genome of freshwater pearl mussel Lamellidens marginalis (Lamarck, 1819) and its phylogenetic relation within unionidae family. Mol Biol Rep 2022; 49:9593-9603. [DOI: 10.1007/s11033-022-07857-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 08/11/2022] [Indexed: 10/15/2022]
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36
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Mito-nuclear coevolution and phylogenetic artifacts: the case of bivalve mollusks. Sci Rep 2022; 12:11040. [PMID: 35773462 PMCID: PMC9247169 DOI: 10.1038/s41598-022-15076-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 06/17/2022] [Indexed: 11/08/2022] Open
Abstract
Mito-nuclear phylogenetic discordance in Bivalvia is well known. In particular, the monophyly of Amarsipobranchia (Heterodonta + Pteriomorphia), retrieved from mitochondrial markers, contrasts with the monophyly of Heteroconchia (Heterodonta + Palaeoheterodonta), retrieved from nuclear markers. However, since oxidative phosphorylation nuclear markers support the Amarsipobranchia hypothesis instead of the Heteroconchia one, interacting subunits of the mitochondrial complexes ought to share the same phylogenetic signal notwithstanding the genomic source, which is different from the signal obtained from other nuclear markers. This may be a clue of coevolution between nuclear and mitochondrial genes. In this work we inferred the phylogenetic signal from mitochondrial and nuclear oxidative phosphorylation markers exploiting different phylogenetic approaches and added two more datasets for comparison: genes of the glycolytic pathway and genes related to the biogenesis of regulative small noncoding RNAs. All trees inferred from mitochondrial and nuclear subunits of the mitochondrial complexes support the monophyly of Amarsipobranchia, regardless of the phylogenetic pipeline. However, not every single marker agrees with this topology: this is clearly visible in nuclear subunits that do not directly interact with the mitochondrial counterparts. Overall, our data support the hypothesis of a coevolution between nuclear and mitochondrial genes for the oxidative phosphorylation. Moreover, we suggest a relationship between mitochondrial topology and different nucleotide composition between clades, which could be associated to the highly variable gene arrangement in Bivalvia.
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37
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Li Y, Altamia MA, Shipway JR, Brugler MR, Bernardino AF, de Brito TL, Lin Z, da Silva Oliveira FA, Sumida P, Smith CR, Trindade-Silva A, Halanych KM, Distel DL. Contrasting modes of mitochondrial genome evolution in sister taxa of wood-eating marine bivalves (Teredinidae and Xylophagaidae). Genome Biol Evol 2022; 14:evac089. [PMID: 35714221 PMCID: PMC9226539 DOI: 10.1093/gbe/evac089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/19/2022] [Accepted: 06/05/2022] [Indexed: 11/14/2022] Open
Abstract
The bivalve families Teredinidae and Xylophagaidae include voracious consumers of wood in shallow and deep-water marine environments, respectively. The taxa are sister clades whose members consume wood as food with the aid of intracellular cellulolytic endosymbionts housed in their gills. This combination of adaptations is found in no other group of animals and was likely present in the common ancestor of both families. Despite these commonalities, the two families have followed dramatically different evolutionary paths with respect to anatomy, life history and distribution. Here we present 42 new mitochondrial genome sequences from Teredinidae and Xylophagaidae and show that distinct trajectories have also occurred in the evolution and organization of their mitochondrial genomes. Teredinidae display significantly greater rates of amino acid substitution but absolute conservation of protein-coding gene order, whereas Xylophagaidae display significantly less amino acid change but have undergone numerous and diverse changes in genome organization since their divergence from a common ancestor. As with many bivalves, these mitochondrial genomes encode two ribosomal RNAs, 12 protein coding genes, and 22 tRNAs; atp8 was not detected. We further show that their phylogeny, as inferred from amino acid sequences of 12 concatenated mitochondrial protein-coding genes, is largely congruent with those inferred from their nuclear genomes based on 18S and 28S ribosomal RNA sequences. Our results provide a robust phylogenetic framework to explore the tempo and mode of mitochondrial genome evolution and offer directions for future phylogenetic and taxonomic studies of wood-boring bivalves.
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Affiliation(s)
- Yuanning Li
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Marvin A Altamia
- Ocean Genome Legacy Center, Department of Marine and Environmental Science, Northeastern University, Nahant, Massachusetts 01908, USA
| | - J Reuben Shipway
- Marine Biology and Ecology Research Centre, School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, United Kingdom
| | - Mercer R Brugler
- Department of Natural Sciences, University of South Carolina Beaufort, 801 Carteret Street, Beaufort, South Carolina 29902, USA
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024, USA
| | | | - Thaís Lima de Brito
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Ceará, Brazil
| | - Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, USA
| | | | - Paulo Sumida
- Departamento de Oceanografia Biológica, Instituto Oceanográfico da Universidade de São Paulo, São Paulo, SP, Brazil
| | - Craig R Smith
- Department of Oceanography, University of Hawai’i at Mãnoa, Hawaii, USA
| | - Amaro Trindade-Silva
- Drug Research and Development Center, Department of Physiology and Pharmacology, Federal University of Ceará, Ceará, Brazil
| | - Kenneth M Halanych
- Center for Marine Science, University of North Carolina Wilmington, North Carolina, USA
| | - Daniel L Distel
- Ocean Genome Legacy Center, Department of Marine and Environmental Science, Northeastern University, Nahant, Massachusetts 01908, USA
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38
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De Vivo M, Lee HH, Huang YS, Dreyer N, Fong CL, de Mattos FMG, Jain D, Wen YHV, Mwihaki JK, Wang TY, Machida RJ, Wang J, Chan BKK, Tsai IJ. Utilisation of Oxford Nanopore sequencing to generate six complete gastropod mitochondrial genomes as part of a biodiversity curriculum. Sci Rep 2022; 12:9973. [PMID: 35705661 PMCID: PMC9200733 DOI: 10.1038/s41598-022-14121-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
High-throughput sequencing has enabled genome skimming approaches to produce complete mitochondrial genomes (mitogenomes) for species identification and phylogenomics purposes. In particular, the portable sequencing device from Oxford Nanopore Technologies (ONT) has the potential to facilitate hands-on training from sampling to sequencing and interpretation of mitogenomes. In this study, we present the results from sampling and sequencing of six gastropod mitogenomes (Aplysia argus, Cellana orientalis, Cellana toreuma, Conus ebraeus, Conus miles and Tylothais aculeata) from a graduate level biodiversity course. The students were able to produce mitogenomes from sampling to annotation using existing protocols and programs. Approximately 4 Gb of sequence was produced from 16 Flongle and one MinION flow cells, averaging 235 Mb and N50 = 4.4 kb per flow cell. Five of the six 14.1-18 kb mitogenomes were circlised containing all 13 core protein coding genes. Additional Illumina sequencing revealed that the ONT assemblies spanned over highly AT rich sequences in the control region that were otherwise missing in Illumina-assembled mitogenomes, but still contained a base error of one every 70.8-346.7 bp under the fast mode basecalling with the majority occurring at homopolymer regions. Our findings suggest that the portable MinION device can be used to rapidly produce low-cost mitogenomes onsite and tailored to genomics-based training in biodiversity research.
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Affiliation(s)
- Mattia De Vivo
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Hsin-Han Lee
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Bioinformatics Program, Taiwan International Graduate Program, National Taiwan University, Taipei, Taiwan
- Bioinformatics Program, Institute of Information Science, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
| | - Yu-Sin Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Niklas Dreyer
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
- Natural History Museum of Denmark, University of Copenhagen, Faculty of Science, Copenhagen, Denmark
| | - Chia-Ling Fong
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Felipe Monteiro Gomes de Mattos
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Dharmesh Jain
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
- Molecular and Biological Agricultural Sciences, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, Taiwan
| | - Yung-Hui Victoria Wen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taipei, Taiwan
| | - John Karichu Mwihaki
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
- Biodiversity Program, Taiwan International Graduate Program, Academia Sinica and National Taiwan Normal University, Taipei, Taiwan
| | - Tzi-Yuan Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ryuji J Machida
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - John Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Benny K K Chan
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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Tassé M, Choquette T, Angers A, Stewart DT, Pante E, Breton S. The longest mitochondrial protein in metazoans is encoded by the male-transmitted mitogenome of the bivalve Scrobicularia plana. Biol Lett 2022; 18:20220122. [PMID: 35673874 PMCID: PMC9174706 DOI: 10.1098/rsbl.2022.0122] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Cytochrome c oxidase subunit II (COX2) is one of the three mitochondrially encoded proteins of the complex IV of the respiratory chain that catalyses the reduction of oxygen to water. The cox2 gene spans about 690 base pairs in most animal species and produces a protein composed of approximately 230 amino acids. We discovered an extreme departure from this pattern in the male-transmitted mitogenome of the bivalve Scrobicularia plana with doubly uniparental inheritance (DUI) of mitochondrial DNA (mtDNA), which possesses an important in-frame insertion of approximately 4.8 kb in its cox2 gene. This feature—an enlarged male cox2 gene—is found in many species with DUI; the COX2 protein can be up to 420 amino acids long. Through RT-PCRs, immunoassays and comparative genetics, the evolution and functionality of this insertion in S. plana were characterized. The in-frame insertion is conserved among individuals from different populations and bears the signature of purifying selection seemingly indicating maintenance of functionality. Its transcription and translation were confirmed: this gene produces a polypeptide of 1892 amino acids, making it the largest metazoan COX2 protein known to date. We hypothesize that these extreme modifications in the COX2 protein affect the metabolism of mitochondria containing the male-transmitted mtDNA in Scrobicularia plana.
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Affiliation(s)
- Mélanie Tassé
- Département de sciences biologiques, Université de Montréal, Montréal, QC, Canada
| | - Thierry Choquette
- Département de sciences biologiques, Université de Montréal, Montréal, QC, Canada
| | - Annie Angers
- Département de sciences biologiques, Université de Montréal, Montréal, QC, Canada
| | | | - Eric Pante
- Littoral, Environnement et Sociétés (LIENSs), UMR 7266 CNRS-La Rochelle Université, 2 rue Olympe de Gouges, 17000 La Rochelle, France
| | - Sophie Breton
- Département de sciences biologiques, Université de Montréal, Montréal, QC, Canada
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Adaptive mitochondrial genome functioning in ecologically different farm-impacted natural seedbeds of the endemic blue mussel Mytilus chilensis. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 42:100955. [PMID: 35065314 DOI: 10.1016/j.cbd.2021.100955] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 12/16/2021] [Accepted: 12/16/2021] [Indexed: 11/22/2022]
Abstract
We assessed the adaptive contribution of the mitochondrial genes involved with the respiratory chain and oxidative phosphorylation of the blue mussel Mytilus chilensis, a native and heavily exploited species in the inner sea of Chiloé Island, southern Chile. The assembled mitochondrial transcriptome of individuals from two ecologically different farm-impacted natural seedbeds, Cochamó (41°S) and Yaldad (42°S), represented about 4.5% of the whole de novo transcriptome of the species and showed location and tissue (gills, mantle) specific expression differences in 13 protein-coding mitochondrial genes. The RNA-Seq analysis detected differences in the number of up-regulated mitogenes between individuals from Cochamó (7) and Yaldad (11), some being tissue-specific (ND4L and COX2). However, the analysis did not detect transcripts-per-million (TPM = 0) of ND2 and ND5 in gills and ATP6 in mantle samples from Cochamó. Likewise, for ND6 and ATP8 in any sample. Several monomorphic location-specific mitochondrial genetic variants were detected in samples from Cochamó (78) and Yaldad (207), representing standing genetic variability to optimize mitochondrial functioning under local habitats. Overall, these mitochondrial transcriptomic differences reflect the impact of environmental conditions on the mitochondrial genome functioning and offer new markers to assess the effects on mussel fitness of habitat translocations, a routine industry practice. Likewise, these mitochondrial markers should help monitor and maintain adaptive population differences in this keystone and heavily exploited native species.
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Comparative mitogenomics of freshwater snails of the genus Bulinus, obligatory vectors of Schistosoma haematobium, causative agent of human urogenital schistosomiasis. Sci Rep 2022; 12:5357. [PMID: 35354876 PMCID: PMC8967911 DOI: 10.1038/s41598-022-09305-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 03/10/2022] [Indexed: 02/05/2023] Open
Abstract
AbstractAmong the snail genera most responsible for vectoring human-infecting schistosomes, Bulinus, Biomphalaria, and Oncomelania, the former is in many respects the most important. Bulinid snails host the most common human blood fluke, Schistosoma haematobium, responsible for approximately two-thirds of the estimated 237 million cases of schistosomiasis. They also support transmission of schistosomes to millions of domestic and wild animals. Nonetheless, our basic knowledge of the 37 Bulinus species remains incomplete, especially with respect to genome information, even including mitogenome sequences. We determined complete mitogenome sequences for Bulinus truncatus, B. nasutus, and B. ugandae, and three representatives of B. globosus from eastern, central, and western Kenya. A difference of the location of tRNA-Asp was found between mitogenomes from the three species of the Bulinus africanus group and B. truncatus. Phylogenetic analysis using partial cox1 sequences suggests that B. globosus is a complex comprised of multiple species. We also highlight the status of B. ugandae as a distinct species with unusual interactions with the S. haematobium group parasites deserving of additional investigation. We provide sequence data for potential development of genetic markers for specific or intraspecific Bulinus studies, help elucidate the relationships among Bulinus species, and suggest ways in which mitogenomes may help understand the complex interactions between Schistosoma and Bulinus snails and their relatives.
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Malkócs T, Viricel A, Becquet V, Evin L, Dubillot E, Pante E. Complex mitogenomic rearrangements within the Pectinidae (Mollusca: Bivalvia). BMC Ecol Evol 2022; 22:29. [PMID: 35272625 PMCID: PMC8915466 DOI: 10.1186/s12862-022-01976-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/18/2021] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Scallops (Bivalvia: Pectinidae) present extraordinary variance in both mitochondrial genome size, structure and content, even when compared to the extreme diversity documented within Mollusca and Bivalvia. In pectinids, mitogenome rearrangements involve protein coding and rRNA genes along with tRNAs, and different genome organization patterns can be observed even at the level of Tribes. Existing pectinid phylogenies fail to resolve some relationships in the family, Chlamydinae being an especially problematic group. RESULTS In our study, we sequenced, annotated and characterized the mitochondrial genome of a member of Chlamydinae, Mimachlamys varia-a species of commercial interest and an effective bioindicator-revealing yet another novel gene arrangement in the Pectinidae. The phylogeny based on all mitochondrial protein coding and rRNA genes suggests the paraphyly of the Mimachlamys genus, further commending the taxonomic revision of the classification within the Chlamydinae subfamily. At the scale of the Pectinidae, we found that 15 sequence blocks are involved in mitogenome rearrangements, which behave as separate units. CONCLUSIONS Our study reveals incongruities between phylogenies based on mitochondrial protein-coding versus rRNA genes within the Pectinidae, suggesting that locus sampling affects phylogenetic inference at the scale of the family. We also conclude that the available taxon sampling does not allow for understanding of the mechanisms responsible for the high variability of mitogenome architecture observed in the Pectinidae, and that unraveling these processes will require denser taxon sampling.
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Affiliation(s)
- Tamás Malkócs
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 Rue Olympe de Gouges, 17042, La Rochelle Cedex 01, France. .,Pál Juhász-Nagy Doctoral School of Biology and Environmental Sciences, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary. .,Institute of Biology and Ecology, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary. .,Institute of Aquatic Ecology, Centre for Ecological Research, 4026, Debrecen, Hungary.
| | - Amélia Viricel
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 Rue Olympe de Gouges, 17042, La Rochelle Cedex 01, France
| | - Vanessa Becquet
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 Rue Olympe de Gouges, 17042, La Rochelle Cedex 01, France
| | - Louise Evin
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 Rue Olympe de Gouges, 17042, La Rochelle Cedex 01, France
| | - Emmanuel Dubillot
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 Rue Olympe de Gouges, 17042, La Rochelle Cedex 01, France
| | - Eric Pante
- Littoral Environnement et Sociétés (LIENSs), UMR 7266, CNRS-Université de La Rochelle, 2 Rue Olympe de Gouges, 17042, La Rochelle Cedex 01, France
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Breton S, Stewart DT, Brémaud J, Havird JC, Smith CH, Hoeh WR. Did doubly uniparental inheritance (DUI) of mtDNA originate as a cytoplasmic male sterility (CMS) system? Bioessays 2022; 44:e2100283. [PMID: 35170770 PMCID: PMC9083018 DOI: 10.1002/bies.202100283] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 01/10/2023]
Abstract
Animal and plant species exhibit an astonishing diversity of sexual systems, including environmental and genetic determinants of sex, with the latter including genetic material in the mitochondrial genome. In several hermaphroditic plants for example, sex is determined by an interaction between mitochondrial cytoplasmic male sterility (CMS) genes and nuclear restorer genes. Specifically, CMS involves aberrant mitochondrial genes that prevent pollen development and specific nuclear genes that restore it, leading to a mixture of female (male-sterile) and hermaphroditic individuals in the population (gynodioecy). Such a mitochondrial-nuclear sex determination system is thought to be rare outside plants. Here, we present one possible case of CMS in animals. We hypothesize that the only exception to the strict maternal mtDNA inheritance in animals, the doubly uniparental inheritance (DUI) system in bivalves, might have originated as a mitochondrial-nuclear sex-determination system. We document and explore similarities that exist between DUI and CMS, and we propose various ways to test our hypothesis.
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Affiliation(s)
- Sophie Breton
- Département des sciences biologiques, Université de Montréal, Montréal, Québec, Canada
| | - Donald T Stewart
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada
| | - Julie Brémaud
- Département des sciences biologiques, Université de Montréal, Montréal, Québec, Canada
| | - Justin C Havird
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Chase H Smith
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Walter R Hoeh
- Department of Biological Sciences, Kent State University, Kent, Ohio, USA
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Liu S, Liu Y, He J, Lin Z, Xue Q. The complete mitochondrial genome of Crassostrea hongkongensis from East China Sea indicates species' range may extend northward. Mol Biol Rep 2022; 49:1631-1635. [PMID: 35025030 DOI: 10.1007/s11033-021-07016-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 11/24/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Crassostrea hongkongensis is an important mariculture shellfish with a relatively narrow distribution range. Recently, larger wild oysters were identified as C. hongkongensis from Sanmen bay in East China Sea. No natural distribution had been reported for this species here, and its origin remains unknown. METHODS AND RESULTS We assembled the complete 18,617 bp circular mitochondrial genome of C. hongkongensis from Sanmen bay by next generation sequencing. It included 12 protein-coding genes, 23 tRNAs, and two rRNAs. The A/T content of the mitogenome was higher than its G/C content. Similar values and features were previously found for five other specimens of C. hongkongensis, and were comparable to those of other congeneric species. A phylogenetic analysis based on the 12 protein-coding genes and complete mitochondrial sequence indicated that the six specimens of C. hongkongensis formed a monophyletic group and shared a sister group relationship with C. ariakensis, C. nippona, C. sikamea, C. angulata, C. gigas, and C. iredalei, whereas specimens from the Sanmen bay area clustered later with the five other C. hongkongensis individuals, sharing a sub-clade. The newly sequenced mitogenome had more singleton sites than previously published C. hongkongensis mitogenomes. CONCLUSIONS Crassostrea hongkongensis may be a native species, and the species' range extends further to the north than previously known. Our data may therefore contribute to a better understanding of the species diversity and conservation of Crassostrea oysters.
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Affiliation(s)
- Sheng Liu
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, 315100, China.,Zhejiang Key Laboratory of Aquatic Germplasm Resource, Zhejiang Wanli University, Ningbo, 315100, China
| | - Youli Liu
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, 315100, China.,Zhejiang Key Laboratory of Aquatic Germplasm Resource, Zhejiang Wanli University, Ningbo, 315100, China
| | - Jing He
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, 315100, China.,Zhejiang Key Laboratory of Aquatic Germplasm Resource, Zhejiang Wanli University, Ningbo, 315100, China
| | - Zhihua Lin
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, 315100, China.,Zhejiang Key Laboratory of Aquatic Germplasm Resource, Zhejiang Wanli University, Ningbo, 315100, China
| | - Qinggang Xue
- Ninghai Institute of Mariculture Breeding and Seed Industry, Zhejiang Wanli University, Ningbo, 315100, China. .,Zhejiang Key Laboratory of Aquatic Germplasm Resource, Zhejiang Wanli University, Ningbo, 315100, China.
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OUP accepted manuscript. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Hitchcock TJ, Gardner A. Sex-biased demography modulates male harm across the genome. Proc Biol Sci 2021; 288:20212237. [PMID: 34933602 PMCID: PMC8692969 DOI: 10.1098/rspb.2021.2237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/26/2021] [Indexed: 11/22/2022] Open
Abstract
Recent years have seen an explosion of theoretical and empirical interest in the role that kin selection plays in shaping patterns of sexual conflict, with a particular focus on male harming traits. However, this work has focused solely on autosomal genes, and as such it remains unclear how demography modulates the evolution of male harm loci occurring in other portions of the genome, such as sex chromosomes and cytoplasmic elements. To investigate this, we extend existing models of sexual conflict for application to these different modes of inheritance. We first analyse the general case, revealing how sex-specific relatedness, reproductive value and the intensity of local competition combine to determine the potential for male harm. We then analyse a series of demographically explicit models, to assess how dispersal, overlapping generations, reproductive skew and the mechanism of population regulation affect sexual conflict across the genome, and drive conflict between nuclear and cytoplasmic genes. We then explore the effects of sex biases in these demographic parameters, showing how they may drive further conflicts between autosomes and sex chromosomes. Finally, we outline how different crossing schemes may be used to identify signatures of these intragenomic conflicts.
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Affiliation(s)
| | - Andy Gardner
- School of Biology, University of St Andrews, St Andrews KY16 9TH, UK
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Mitochondrial Genomic Landscape: A Portrait of the Mitochondrial Genome 40 Years after the First Complete Sequence. Life (Basel) 2021; 11:life11070663. [PMID: 34357035 PMCID: PMC8303319 DOI: 10.3390/life11070663] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 12/11/2022] Open
Abstract
Notwithstanding the initial claims of general conservation, mitochondrial genomes are a largely heterogeneous set of organellar chromosomes which displays a bewildering diversity in terms of structure, architecture, gene content, and functionality. The mitochondrial genome is typically described as a single chromosome, yet many examples of multipartite genomes have been found (for example, among sponges and diplonemeans); the mitochondrial genome is typically depicted as circular, yet many linear genomes are known (for example, among jellyfish, alveolates, and apicomplexans); the chromosome is normally said to be “small”, yet there is a huge variation between the smallest and the largest known genomes (found, for example, in ctenophores and vascular plants, respectively); even the gene content is highly unconserved, ranging from the 13 oxidative phosphorylation-related enzymatic subunits encoded by animal mitochondria to the wider set of mitochondrial genes found in jakobids. In the present paper, we compile and describe a large database of 27,873 mitochondrial genomes currently available in GenBank, encompassing the whole eukaryotic domain. We discuss the major features of mitochondrial molecular diversity, with special reference to nucleotide composition and compositional biases; moreover, the database is made publicly available for future analyses on the MoZoo Lab GitHub page.
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48
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Davison A, Neiman M. Pearls of wisdom-a Theo Murphy issue on molluscan genomics. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200151. [PMID: 33813890 PMCID: PMC8059963 DOI: 10.1098/rstb.2020.0151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2021] [Indexed: 12/16/2022] Open
Affiliation(s)
- Angus Davison
- School of Life Sciences, University of Nottingham, Nottingham, Nottinghamshire NG7 2RD, UK
| | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, IA 52245, USA
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Ghiselli F, Iannello M, Piccinini G, Milani L. Bivalve molluscs as model systems for studying mitochondrial biology. Integr Comp Biol 2021; 61:1699-1714. [PMID: 33944910 DOI: 10.1093/icb/icab057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The class Bivalvia is a highly successful and ancient taxon including ∼25,000 living species. During their long evolutionary history bivalves adapted to a wide range of physicochemical conditions, habitats, biological interactions, and feeding habits. Bivalves can have strikingly different size, and despite their apparently simple body plan, they evolved very different shell shapes, and complex anatomic structures. One of the most striking features of this class of animals is their peculiar mitochondrial biology: some bivalves have facultatively anaerobic mitochondria that allow them to survive prolonged periods of anoxia/hypoxia. Moreover, more than 100 species have now been reported showing the only known evolutionarily stable exception to the strictly maternal inheritance of mitochondria in animals, named doubly uniparental inheritance. Mitochondrial activity is fundamental to eukaryotic life, and thanks to their diversity and uncommon features, bivalves represent a great model system to expand our knowledge about mitochondrial biology, so far limited to a few species. We highlight recent works studying mitochondrial biology in bivalves at either genomic or physiological level. A link between these two approaches is still missing, and we believe that an integrated approach and collaborative relationships are the only possible ways to be successful in such endeavour.
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Affiliation(s)
- Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Mariangela Iannello
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Giovanni Piccinini
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Liliana Milani
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
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