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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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2
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Nascimento‐Schulze JC, Bean TP, Peñaloza C, Paris JR, Whiting JR, Simon A, Fraser BA, Houston RD, Bierne N, Ellis RP. SNP discovery and genetic structure in blue mussel species using low coverage sequencing and a medium density 60 K SNP-array. Evol Appl 2023; 16:1044-1060. [PMID: 37216031 PMCID: PMC10197230 DOI: 10.1111/eva.13552] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/15/2023] [Accepted: 04/12/2023] [Indexed: 05/24/2023] Open
Abstract
Blue mussels from the genus Mytilus are an abundant component of the benthic community, found in the high latitude habitats. These foundation species are relevant to the aquaculture industry, with over 2 million tonnes produced globally each year. Mussels withstand a wide range of environmental conditions and species from the Mytilus edulis complex readily hybridize in regions where their distributions overlap. Significant effort has been made to investigate the consequences of environmental stress on mussel physiology, reproductive isolation, and local adaptation. Yet our understanding on the genomic mechanisms underlying such processes remains limited. In this study, we developed a multi species medium-density 60 K SNP-array including four species of the Mytilus genus. SNPs included in the platform were called from 138 mussels from 23 globally distributed mussel populations, sequenced using a whole-genome low coverage approach. The array contains polymorphic SNPs which capture the genetic diversity present in mussel populations thriving across a gradient of environmental conditions (~59 K SNPs) and a set of published and validated SNPs informative for species identification and for diagnosis of transmissible cancer (610 SNPs). The array will allow the consistent genotyping of individuals, facilitating the investigation of ecological and evolutionary processes in these taxa. The applications of this array extend to shellfish aquaculture, contributing to the optimization of this industry via genomic selection of blue mussels, parentage assignment, inbreeding assessment and traceability. Further applications such as genome wide association studies (GWAS) for key production traits and those related to environmental resilience are especially relevant to safeguard aquaculture production under climate change.
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Affiliation(s)
- Jennifer C. Nascimento‐Schulze
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
- Centre for Environment, Fisheries and Aquaculture ScienceWeymouth LaboratoryWeymouthUK
| | - Tim P. Bean
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Carolina Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Josephine R. Paris
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
| | - James R. Whiting
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
| | - Alexis Simon
- ISEMUniversity of Montpellier, CNRS, IRDMontpellierFrance
| | - Bonnie A. Fraser
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
| | | | - Nicolas Bierne
- ISEMUniversity of Montpellier, CNRS, IRDMontpellierFrance
| | - Robert P. Ellis
- Biosciences, Faculty of Health and Life SciencesUniversity of ExeterExeterUK
- Centre for Sustainable Aquaculture FuturesUniversity of ExeterExeterUK
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3
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Mitogenomic Codon Usage Patterns of Superfamily Certhioidea (Aves, Passeriformes): Insights into Asymmetrical Bias and Phylogenetic Implications. Animals (Basel) 2022; 13:ani13010096. [PMID: 36611705 PMCID: PMC9817927 DOI: 10.3390/ani13010096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/22/2022] [Accepted: 12/25/2022] [Indexed: 12/28/2022] Open
Abstract
The superfamily Certhioidea currently comprises five families. Due to the rapid diversification, the phylogeny of Certhioidea is still controversial. The advent of next generation sequencing provides a unique opportunity for a mitogenome-wide study. Here, we first provided six new complete mitogenomes of Certhioidea (Certhia americana, C. familiaris, Salpornis spilonota, Cantorchilus leucotis, Pheugopedius coraya, and Pheugopedius genibarbis). We further paid attention to the genomic characteristics, codon usages, evolutionary rates, and phylogeny of the Certhioidea mitogenomes. All mitogenomes we analyzed displayed typical ancestral avian gene order with 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, and one control region (CR). Our study indicated the strand-biased compositional asymmetry might shape codon usage preferences in mitochondrial genes. In addition, natural selection might be the main factor in shaping the codon usages of genes. Additionally, evolutionary rate analyses indicated all mitochondrial genes were under purifying selection. Moreover, MT-ATP8 and MT-CO1 were the most rapidly evolving gene and conserved genes, respectively. According to our mitophylogenetic analyses, the monophylies of Troglodytidae and Sittidae were strongly supported. Importantly, we suggest that Salpornis should be separated from Certhiidae and put into Salpornithidae to maintain the monophyly of Certhiidae. Our findings are useful for further evolutionary studies within Certhioidea.
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Full Mitochondrial Genomes Reveal Species Differences between the Venerid Clams Ruditapes philippinarum and R. variegatus. Genes (Basel) 2022; 13:genes13112157. [DOI: 10.3390/genes13112157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/10/2022] [Accepted: 11/12/2022] [Indexed: 11/22/2022] Open
Abstract
In natural sea areas along the coast of China, venerid clams Ruditapes philippinarum and R. variegatus exhibit similar adult shell forms and are especially difficult to distinguish as spat and juveniles. This study used comparative mitochondrial genome analysis to reveal differences between these species. The results showed that: (1) the mitochondrial genomes of R. philippinarum and R. variegatus share a large number of similar gene clusters arranged in consistent order, yet they also display noncommon genes, with both gene rearrangements and random losses found; (2) the 13 protein-coding genes in R. philippinarum as well as two-fold and four-fold degenerate sites in R. variegatus have an evident AT bias; (3) the Ka/Ks ratio of the mitochondrial ATP8 gene was significantly higher in R. philippinarum than in R. variegatus, and an analysis of selection pressure revealed that the mitochondrial NADH dehydrogenase subunit 2 gene and NADH dehydrogenase subunit 6 gene of R. variegatus were under great selective pressure during its evolution; and finally, (4) the two species clustered into one branch on a phylogenetic tree, further affirming their phylogenetic closeness. Based on these results, we speculate that the species differences between R. variegatus and R. philippinarum are largely attributable to adaptive evolution to the environment. The present findings provide a reference for the development of germplasm identification.
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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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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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He J, Yao Y, Dong Z, Ruan Y, Chang Z, Zhao R, Wang W, Li X. Complete mitochondrial genome of Pectocera sp. (Elateridae: Dendrometrinae: Oxynopterini) and its phylogenetic implications. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2022; 111:e21957. [PMID: 35933719 DOI: 10.1002/arch.21957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/19/2022] [Accepted: 07/21/2022] [Indexed: 06/15/2023]
Abstract
The Elateridae family (click beetles) represents a highly diverse lineage that possesses a specialized clicking mechanism to startle predators. At present, however, phylogenetic relationships, especially among recognized subfamilies, remain contentious. Mitochondrial genomes (mitogenomes) can help resolve previously intractable phylogenetic relationships using morphological or limited molecular data. Here, we report the complete mitogenome of Pectocera sp. (Elateridae: Dendrometrinae: Oxynopterini), which was 15,962 bp in length and showed a typical gene number and order as most beetle mitogenomes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 noncoding control region (AT-rich region). Comparative genomic analyses showed a high degree of feature similarity among Pectocera sp. and other click beetles. Evolutionary analysis of all PCGs based on the nonsynonymous/synonymous substitution rate ratio (ω) indicated that cox1 and atp8 exhibited the lowest and highest evolutionary rates, respectively, and that the evolutionary rates of all PCGs, except for cox3, nad2, and nad3, were lower than the average ω of click beetles. Phylogenetic analyses based on concatenated and coalescent approaches indicated that Pectocera sp. was sister to Campsosternus auratus in the same tribe (Oxynopterini) with high support. This study offers insight into the mitogenomic basis of Pectocera sp. and provides an important data resource for exploring the taxonomy, phylogeny, and evolution of click beetles.
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Affiliation(s)
- Jinwu He
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yuhao Yao
- College of Life Sciences, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Zhiwei Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yongying Ruan
- Plant Protection Research Center, Shenzhen Polytechnic, Shenzhen, China
| | - Zhou Chang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ruoping Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Wen Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xueyan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
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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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Lubośny M, Śmietanka B, Arculeo M, Burzyński A. No evidence of DUI in the Mediterranean alien species Brachidontes pharaonis (P. Fisher, 1870) despite mitochondrial heteroplasmy. Sci Rep 2022; 12:8569. [PMID: 35595866 PMCID: PMC9122905 DOI: 10.1038/s41598-022-12606-6] [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: 12/09/2021] [Accepted: 05/13/2022] [Indexed: 01/05/2023] Open
Abstract
Two genetically different mitochondrial haplogroups of Brachidontes pharaonis (p-distance 6.8%) have been identified in the Mediterranean Sea. This hinted at a possible presence of doubly uniparental inheritance in this species. To ascertain this possibility, we sequenced two complete mitogenomes of Brachidontes pharaonis mussels and performed a qPCR analysis to measure the relative mitogenome copy numbers of both mtDNAs. Despite the presence of two very similar regions composed entirely of repetitive sequences in the two haplogroups, no recombination between mitogenomes was detected. In heteroplasmic individuals, both mitogenomes were present in the generative tissues of both sexes, which argues against the presence of doubly uniparental inheritance in this species.
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Affiliation(s)
- Marek Lubośny
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland.
| | - Beata Śmietanka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Marco Arculeo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy
| | - Artur Burzyński
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
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Gao X, Zhang H, Cui J, Yan X, Zhang X, Luo M, Tang C, Ren L, Liu S. Interactions between mitochondrial and nuclear genomes and co-regulation of mitochondrial and nuclear gene expression in reciprocal intergeneric hybrids between Carassius auratus red var. × Cyprinus carpio L. REPRODUCTION AND BREEDING 2021. [DOI: 10.1016/j.repbre.2021.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Zhang S, Sekerka L, Liao C, Long C, Xu J, Dai X, Guo Q. The First Eight Mitogenomes of Leaf-Mining Dactylispa Beetles (Coleoptera: Chrysomelidae: Cassidinae) Shed New Light on Subgenus Relationships. INSECTS 2021; 12:insects12111005. [PMID: 34821805 PMCID: PMC8624545 DOI: 10.3390/insects12111005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/28/2021] [Accepted: 11/04/2021] [Indexed: 11/16/2022]
Abstract
The taxonomic classification of Dactylispa, a large genus of leaf-mining beetles, is problematic because it is currently based on morphology alone. Here, the first eight mitochondrial genomes of Dactylispa species, which were used to construct the first molecular phylogenies of this genus, are reported. The lengths of the eight mitogenomes range from 17,189 bp to 20,363 bp. All of the mitochondrial genomes include 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and 1 A + T-rich region. According to the nonsynonymous/synonymous mutation ratio (Ka/Ks) of all PCGs, the highest and the lowest evolutionary rates were found for atp8 and cox1, respectively, which is a common phenomenon among animals. According to relative synonymous codon usage, UUA(L) has the highest frequency. With two Gonophorini species as the outgroup, mitogenome-based phylogenetic trees of the eight Dactylispa species were constructed using maximum likelihood (ML) and Bayesian inference (BI) methods based on the PCGs, tRNAs, and rRNAs. Two DNA-based phylogenomic inferences and one protein-based phylogenomic inference support the delimitation of the subgenera Dactylispa s. str. and Platypriella as proposed in the system of Chen et al. (1986). However, the subgenus Triplispa is not recovered as monophyletic. The placement of Triplispa species requires further verification and testing with more species. We also found that both adult body shape and host plant relationship might explain the subgeneric relationships among Dactylispa beetles to a certain degree.
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Affiliation(s)
- Shengdi Zhang
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (S.Z.); (C.L.); (C.L.); (J.X.)
- National Navel-Orange Engineering Research Center, Ganzhou 341000, China
| | - Lukáš Sekerka
- Department of Entomology, National Museum, Natural History Museum, 1740 Cirkusová, Czech Republic;
| | - Chengqing Liao
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (S.Z.); (C.L.); (C.L.); (J.X.)
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China
| | - Chengpeng Long
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (S.Z.); (C.L.); (C.L.); (J.X.)
- National Navel-Orange Engineering Research Center, Ganzhou 341000, China
| | - Jiasheng Xu
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (S.Z.); (C.L.); (C.L.); (J.X.)
- National Navel-Orange Engineering Research Center, Ganzhou 341000, China
| | - Xiaohua Dai
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (S.Z.); (C.L.); (C.L.); (J.X.)
- National Navel-Orange Engineering Research Center, Ganzhou 341000, China
- Correspondence: (X.D.); (Q.G.)
| | - Qingyun Guo
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (S.Z.); (C.L.); (C.L.); (J.X.)
- National Navel-Orange Engineering Research Center, Ganzhou 341000, China
- Correspondence: (X.D.); (Q.G.)
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12
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Zieritz A, Froufe E, Bolotov I, Gonçalves DV, Aldridge DC, Bogan AE, Gan HM, Gomes-Dos-Santos A, Sousa R, Teixeira A, Varandas S, Zanatta D, Lopes-Lima M. Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- and M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia). Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa153] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AbstractThe Unionidae represent an excellent model taxon for unravelling the drivers of freshwater diversity, but, phylogeographic studies on Southeast Asian taxa are hampered by lack of a comprehensive phylogeny and mutation rates for this fauna. We present complete female- (F) and male-type (M) mitogenomes of four genera of the Southeast Asian clade Contradentini+Rectidentini. We calculate substitution rates for the mitogenome, the 13 protein-coding genes, the two ribosomal units and three commonly used fragments (co1, nd1 and 16S) of both F- and M-mtDNA, based on a fossil-calibrated, mitogenomic phylogeny of the Unionidae. Phylogenetic analyses, including an M+F concatenated dataset, consistently recovers a monophyletic Gonideinae. Subfamily-level topology is congruent with that of a previous nuclear genomic study and with patterns in mitochondrial gene order, suggesting Unionidae F-type 2 as a synapomorphy of the Gonideinae. Our phylogeny indicates that the clades Contradentini+Rectidentini and Lamprotulini+Pseudodontini+Gonideini split in the early Cretaceous (~125 Mya), and that the crown group of Contradentini+Rectidentini originated in the late Cretaceous (~79 Mya). Most gonideine tribes originated during the early Palaeogene. Substitution rates were comparable to those previously published for F-type co1 and 16S for certain Unionidae and Margaritiferidae species (pairs).
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Affiliation(s)
- Alexandra Zieritz
- School of Geography, Sir Clive Granger Building, University of Nottingham, University Park, Nottingham, UK
| | - Elsa Froufe
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, Matosinhos, Portugal
| | - Ivan Bolotov
- Federal Center for Integrated Arctic Research, Russian Academy of Sciences, Severnaya Dvina Emb. 23, Arkhangelsk, Russian Federation
- Northern Arctic Federal University, Northern Dvina Emb. 17, Arkhangelsk, Russian Federation
- Saint-Petersburg State University, Universitetskaya Emb. 7/9, Saint Petersburg, Russian Federation
| | - Duarte V Gonçalves
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, Matosinhos, Portugal
| | - David C Aldridge
- Aquatic Ecology Group, The David Attenborough Building, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Arthur E Bogan
- Research Laboratory, North Carolina State Museum of Natural Sciences, Raleigh, NC, USA
| | - Han Ming Gan
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong,, VIC, Australia
| | - André Gomes-Dos-Santos
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, Matosinhos, Portugal
- Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, Porto, Portugal
| | - Ronaldo Sousa
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campos de Gualtar, Braga, Portugal
| | - Amilcar Teixeira
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Santa Apolónia, Bragança, Portugal
| | - Simone Varandas
- CITAB-UTAD – Centre for Research and Technology of Agro-Environment and Biological Sciences, University of Trás-os-Montes and Alto Douro, Apartado 1013, Vila Real, Portugal
| | - David Zanatta
- Biology Department, Institute for Great Lakes Research, Central Michigan University, Biosciences, Mount Pleasant, MI, USA
| | - Manuel Lopes-Lima
- CIIMAR/CIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, Matosinhos, Portugal
- CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, Vairão, Portugal
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13
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Lubośny M, Przyłucka A, Śmietanka B, Burzyński A. Semimytilus algosus: first known hermaphroditic mussel with doubly uniparental inheritance of mitochondrial DNA. Sci Rep 2020; 10:11256. [PMID: 32647112 PMCID: PMC7347871 DOI: 10.1038/s41598-020-67976-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 06/11/2020] [Indexed: 11/08/2022] Open
Abstract
Doubly uniparental inheritance (DUI) of mitochondrial DNA is a rare phenomenon occurring in some freshwater and marine bivalves and is usually characterized by the mitochondrial heteroplasmy of male individuals. Previous research on freshwater Unionida mussels showed that hermaphroditic species do not have DUI even if their closest gonochoristic counterparts do. No records showing DUI in a hermaphrodite have ever been reported. Here we show for the first time that the hermaphroditic mussel Semimytilus algosus (Mytilida), very likely has DUI, based on the complete sequences of both mitochondrial DNAs and the distribution of mtDNA types between male and female gonads. The two mitogenomes show considerable divergence (34.7%). The presumably paternal M type mitogenome dominated the male gonads of most studied mussels, while remaining at very low or undetectable levels in the female gonads of the same individuals. If indeed DUI can function in the context of simultaneous hermaphroditism, a change of paradigm regarding its involvement in sex determination is needed. It is apparently associated with gonadal differentiation rather than with sex determination in bivalves.
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Affiliation(s)
- Marek Lubośny
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland.
| | - Aleksandra Przyłucka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Beata Śmietanka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Artur Burzyński
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
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14
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Soroka M. Doubly uniparental inheritance of mitochondrial DNA in freshwater mussels: History and status of the European species. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12381] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Der Sarkissian C, Möller P, Hofman CA, Ilsøe P, Rick TC, Schiøtte T, Sørensen MV, Dalén L, Orlando L. Unveiling the Ecological Applications of Ancient DNA From Mollusk Shells. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00037] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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16
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Passamonti M, Plazzi F. Doubly Uniparental Inheritance and beyond: The contribution of the Manila clamRuditapes philippinarum. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12371] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Marco Passamonti
- Department of Biological, Geological, and Environmental Sciences University of Bologna Bologna Italy
| | - Federico Plazzi
- Department of Biological, Geological, and Environmental Sciences University of Bologna Bologna Italy
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17
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Xiao L, Zhang S, Long C, Guo Q, Xu J, Dai X, Wang J. Complete Mitogenome of a Leaf-Mining Buprestid Beetle, Trachys auricollis, and Its Phylogenetic Implications. Genes (Basel) 2019; 10:E992. [PMID: 31805706 PMCID: PMC6947639 DOI: 10.3390/genes10120992] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 11/26/2019] [Accepted: 11/28/2019] [Indexed: 11/16/2022] Open
Abstract
A complete mitogenome of Trachys auricollis is reported, and a mitogenome-based phylogenetic tree of Elateriformia with all protein-coding genes (PCGs), rRNAs, and tRNAs is presented for the first time. The complete mitochondrial genome of T. auricollis is 16,429 bp in size and contains 13 PCGs, two rRNA genes, 22 tRNA genes, and an A + T-rich region. The A + T content of the entire genome is approximately 71.1%, and the AT skew and GC skew are 0.10 and -0.20, respectively. According to the the nonsynonymous substitution rate to synonymous substitution rates (Ka/Ks) of all PCGs, the highest and lowest evolutionary rates were observed for atp8 and cox1, respectively, which is a common finding among animals. The start codons of all PCGs are the typical ATN. Ten PCGs have complete stop codons, but three have incomplete stop codons with T or TA. As calculated based on the relative synonymous codon usage (RSCU) values, UUA(L) is the codon with the highest frequency. Except for trnS1, all 22 tRNA genes exhibit typical cloverleaf structures. The A + T-rich region of T. auricollis is located between rrnS and the trnI-trnG-trnM gene cluster, with six 72-bp tandem repeats. Both maximum likelihood (ML) and Bayesian (BI) trees suggest that Buprestoidea is close to Byrrhoidea and that Buprestoidea and Byrrhoidea are sister groups of Elateroidea, but the position of Psephenidae is undetermined. The inclusion of tRNAs might help to resolve the phylogeny of Coleoptera.
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Affiliation(s)
- Lifang Xiao
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China;
| | - Shengdi Zhang
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
| | - Chengpeng Long
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
| | - Qingyun Guo
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
| | - Jiasheng Xu
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
| | - Xiaohua Dai
- Leafminer Group, School of Life Sciences, Gannan Normal University, Ganzhou 341000, China; (L.X.); (S.Z.); (C.L.); (Q.G.); (J.X.)
- National Navel-Orange Engineering Research Center, Ganzhou 341000, China
| | - Jianguo Wang
- College of Agriculture, Jiangxi Agricultural University, Nanchang 330045, China;
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18
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Zeh JA, Zawlodzki MA, Bonilla MM, Su-Keene EJ, Padua MV, Zeh DW. Sperm competitive advantage of a rare mitochondrial haplogroup linked to differential expression of mitochondrial oxidative phosphorylation genes. J Evol Biol 2019; 32:1320-1330. [PMID: 31495025 DOI: 10.1111/jeb.13536] [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: 06/11/2019] [Revised: 08/06/2019] [Accepted: 08/25/2019] [Indexed: 11/27/2022]
Abstract
Maternal inheritance of mitochondria creates a sex-specific selective sieve through which mitochondrial mutations harmful to males but not females accumulate and contribute to sexual differences in longevity and disease susceptibility. Because eggs and sperm are under disruptive selection, sperm are predicted to be particularly vulnerable to the genetic load generated by maternal inheritance, yet evidence for mitochondrial involvement in male fertility is limited and controversial. Here, we exploit the coexistence of two divergent mitochondrial haplogroups (A and B2) in a Neotropical arachnid to investigate the role of mitochondria in sperm competition. DNA profiling demonstrated that B2-carrying males sired more than three times as many offspring in sperm competition experiments than A males, and this B2 competitive advantage cannot be explained by female mitochondrial haplogroup or male nuclear genetic background. RNA-Seq of testicular tissues implicates differential expression of mitochondrial oxidative phosphorylation (OXPHOS) genes in the B2 competitive advantage, including a 22-fold upregulation of atp8 in B2 males. Previous comparative genomic analyses have revealed functionally significant amino acid substitutions in differentially expressed genes, indicating that the mitochondrial haplogroups differ not only in expression but also in DNA sequence and protein functioning. However, mitochondrial haplogroup had no effect on sperm number or sperm viability, and, when females were mated to a single male, neither male haplogroup, female haplogroup nor the interaction between male/female haplogroup significantly affected female reproductive success. Our findings therefore suggest that mitochondrial effects on male reproduction may often go undetected in noncompetitive contexts and may prove more important in nature than is currently appreciated.
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Affiliation(s)
- Jeanne A Zeh
- Department of Biology and Graduate Program in Ecology, Evolution and Conservation Biology, University of Nevada, Reno, NV, USA
| | - Maya A Zawlodzki
- Department of Biology and Graduate Program in Ecology, Evolution and Conservation Biology, University of Nevada, Reno, NV, USA
| | - Melvin M Bonilla
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL, USA
| | - Eleanor J Su-Keene
- Department of Educational Leadership and Research Methodology, Florida Atlantic University, Boca Raton, FL, USA
| | | | - David W Zeh
- Department of Biology and Graduate Program in Ecology, Evolution and Conservation Biology, University of Nevada, Reno, NV, USA
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19
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Chacón GM, Arias‐Pérez A, Freire R, Martínez L, Nóvoa S, Naveira H, Insua A. Evidence of doubly uniparental inheritance of the mitochondrial
DNA
in
Polititapes rhomboides
(Bivalvia, Veneridae): Evolutionary and population genetic analysis of F and M mitotypes. J ZOOL SYST EVOL RES 2019. [DOI: 10.1111/jzs.12267] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Ginna M. Chacón
- Departamento de Bioloxía‐Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA)Universidade da Coruña A Coruña Spain
| | - Alberto Arias‐Pérez
- Departamento de Bioloxía‐Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA)Universidade da Coruña A Coruña Spain
| | - Ruth Freire
- Departamento de Bioloxía‐Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA)Universidade da Coruña A Coruña Spain
| | - Luisa Martínez
- Departamento de Bioloxía‐Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA)Universidade da Coruña A Coruña Spain
| | - Susana Nóvoa
- Centro de Cultivos Marinos de Ribadeo‐CIMAXunta de Galicia Ribadeo (Lugo) Spain
| | - Horacio Naveira
- Departamento de Bioloxía‐Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA)Universidade da Coruña A Coruña Spain
| | - Ana Insua
- Departamento de Bioloxía‐Facultade de Ciencias and Centro de Investigacións Científicas Avanzadas (CICA)Universidade da Coruña A Coruña Spain
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20
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Śmietanka B, Lubośny M, Przyłucka A, Gérard K, Burzyński A. Mitogenomics of Perumytilus purpuratus (Bivalvia: Mytilidae) and its implications for doubly uniparental inheritance of mitochondria. PeerJ 2018; 6:e5593. [PMID: 30245933 PMCID: PMC6149501 DOI: 10.7717/peerj.5593] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 08/14/2018] [Indexed: 12/29/2022] Open
Abstract
Animal mitochondria are usually inherited through the maternal lineage. The exceptional system allowing fathers to transmit their mitochondria to the offspring exists in some bivalves. Its taxonomic spread is poorly understood and new mitogenomic data are needed to fill the gap. Here, we present for the first time the two divergent mitogenomes from Chilean mussel Perumytilus purpuratus. The existence of these sex-specific mitogenomes confirms that this species has the doubly uniparental inheritance (DUI) of mitochondria. The genetic distance between the two mitochondrial lineages in P. purpuratus is not only much bigger than in the Mytilus edulis species complex but also greater than the distance observed in Musculista senhousia, the only other DUI-positive member of the Mytilidae family for which both complete mitochondrial genomes were published to date. One additional, long ORF (open reading frame) is present exclusively in the maternal mitogenome of P. purpuratus. This ORF evolves under purifying selection, and will likely be a target for future DUI research.
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Affiliation(s)
- Beata Śmietanka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Marek Lubośny
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Aleksandra Przyłucka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Karin Gérard
- Centro de Investigacion Gaia-Antartica, Departamento de Recursos Naturales, Universidad de Magallanes, Punta Arenas, Chile.,Laboratorio de Ecosistemas Marinos Antárticos y Subantárticos, Universidad de Magallanes, Punta Arenas, Chile
| | - Artur Burzyński
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
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21
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Yurchenko AA, Katolikova N, Polev D, Shcherbakova I, Strelkov P. Transcriptome of the bivalve Limecola balthica L. from Western Pacific: A new resource for studies of European populations. Mar Genomics 2018; 40:58-63. [DOI: 10.1016/j.margen.2018.03.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 03/29/2018] [Accepted: 03/31/2018] [Indexed: 10/17/2022]
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22
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Lubośny M, Przyłucka A, Śmietanka B, Breton S, Burzyński A. Actively transcribed and expressed atp8 gene in Mytilus edulis mussels. PeerJ 2018; 6:e4897. [PMID: 29900071 PMCID: PMC5995098 DOI: 10.7717/peerj.4897] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 05/11/2018] [Indexed: 01/08/2023] Open
Abstract
Background Animal mitochondrial genomes typically encode 37 genes: 13 proteins, 22 tRNAs and two rRNAs. However, many species represent exceptions to that rule. Bivalvia along with Nematoda and Platyhelminthes are often suspected to fully or partially lack the ATP synthase subunit 8 (atp8) gene. This raises the question as to whether they are really lacking this gene or is this maybe an annotation problem? Among bivalves, Mytilus edulis has been inferred to lack an ATP8 gene since the characterization of its mitochondrial genome in 1992. Even though recent bioinformatic analyses suggested that atp8 is present in Mytilus spp., due to high divergence in predicted amino acid sequences, the existence of a functional atp8 gene in this group remains controversial. Results Here we demonstrate that M. edulis mitochondrial open reading frames suggested to be atp8 (in male and female mtDNAs) are actively translated proteins. We also provide evidence that both proteins are an integral part of the ATP synthase complex based on in-gel detection of ATP synthase activity and two-dimensional Blue-Native and SDS polyacrylamide electrophoresis. Conclusion Many organisms (e.g., Bivalvia along with Nematoda and Platyhelminthes) are considered to be lacking certain mitochondrial genes often only based on poor similarity between protein coding gene sequences in genetically closed species. In some situations, this may lead to the inference that the ATP8 gene is absent, when it is in fact present, but highly divergent. This shows how important complementary role protein-based approaches, such as those in the present study, can provide to bioinformatic, genomic studies (i.e., ability to confirm the presence of a gene).
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Affiliation(s)
- Marek Lubośny
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Aleksandra Przyłucka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Beata Śmietanka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
| | - Sophie Breton
- Department of Biological Sciences, Université de Montréal, Montréal, Québec, Canada
| | - Artur Burzyński
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland
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23
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Śmietanka B, Burzyński A. Disruption of doubly uniparental inheritance of mitochondrial DNA associated with hybridization area of European Mytilus edulis and Mytilus trossulus in Norway. MARINE BIOLOGY 2017; 164:209. [PMID: 29056761 PMCID: PMC5630648 DOI: 10.1007/s00227-017-3235-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 09/11/2017] [Indexed: 06/07/2023]
Abstract
Doubly uniparental inheritance of mitochondria (DUI) is best known in the blue mussel Mytilus. Under this model, two types of mitochondrial DNA exist: female type (F), transmitted from females to offspring of both genders, and male type (M), transmitted exclusively from males to sons. The mitogenomes are usually highly divergent, but an occasional replacement of a typical M genome by a particular F genome has been postulated to explain reduction of this divergence. Disruption of the DUI model has been reported in hybridization areas. Here, we present a new case of DUI disruption in a hybrid M. trossulus/M. edulis population from the North Sea (Norway). No M haplotypes derived from M. trossulus were identified in this population. Typical M haplotypes derived from M. edulis (ME) were rare. Two F-type haplogroups were found: one derived from M. edulis (FE) and the second derived from M. trossulus (FT). Many haplotypes from the FT group were recombinants, with the male CR sequence coming from the M. trossulus genome (FT1 haplogroup) in contrast to M. edulis CR as in the Baltic. FT1 haplotypes were abundant in the studied population, including homoplasmic females. However, males significantly more often carried these haplotypes; therefore, male heteroplasmy involved the original FE and recombinant FT, indicating that the FT genome undergoes masculinization. Structural similarity of FT1 CR with previously reported, masculinized Baltic haplotypes, which were derived from FE/ME recombination, provides further evidence that CR M-F recombination is a prerequisite for masculinization, also in the context of native M. trossulus mtDNA.
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Affiliation(s)
- Beata Śmietanka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - Artur Burzyński
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
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24
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Fernández-Pérez J, Nantón A, Ruiz-Ruano FJ, Camacho JPM, Méndez J. First complete female mitochondrial genome in four bivalve species genus Donax and their phylogenetic relationships within the Veneroida order. PLoS One 2017; 12:e0184464. [PMID: 28886105 PMCID: PMC5590976 DOI: 10.1371/journal.pone.0184464] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/24/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Four species of the genus Donax (D. semistriatus, D. trunculus, D. variegatus and D. vittatus) are common on Iberian Peninsula coasts. Nevertheless, despite their economic importance and overexploitation, scarce genetic resources are available. In this work, we newly determined the complete mitochondrial genomes of these four representatives of the family Donacidae, with the aim of contributing to unveil phylogenetic relationships within the Veneroida order, and of developing genetic markers being useful in wedge clam identification and authentication, and aquaculture stock management. PRINCIPAL FINDINGS The complete female mitochondrial genomes of the four species vary in size from 17,044 to 17,365 bp, and encode 13 protein-coding genes (including the atp8 gene), 2 rRNAs and 22 tRNAs, all located on the same strand. A long non-coding region was identified in each of the four Donax species between cob and cox2 genes, presumably corresponding to the Control Region. The Bayesian and Maximum Likelihood phylogenetic analysis of the Veneroida order indicate that all four species of Donax form a single clade as a sister group of other bivalves within the Tellinoidea superfamily. However, although Tellinoidea is actually monophyletic, none of its families are monophyletic. CONCLUSIONS Sequencing of complete mitochondrial genomes provides highly valuable information to establish the phylogenetic relationships within the Veneroida order. Furthermore, we provide here significant genetic resources for further research and conservation of this commercially important fishing resource.
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Affiliation(s)
- Jenyfer Fernández-Pérez
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and CICA (Centro de Investigacións Científicas Avanzadas), Universidade da Coruña, Campus de A Zapateira, A Coruña, Spain
| | - Ana Nantón
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and CICA (Centro de Investigacións Científicas Avanzadas), Universidade da Coruña, Campus de A Zapateira, A Coruña, Spain
| | | | - Juan Pedro M. Camacho
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Josefina Méndez
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and CICA (Centro de Investigacións Científicas Avanzadas), Universidade da Coruña, Campus de A Zapateira, A Coruña, Spain
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25
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Śmietanka B, Burzyński A. Complete female mitochondrial genome of Mytilus chilensis. MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:101-102. [PMID: 33473730 PMCID: PMC7799939 DOI: 10.1080/23802359.2017.1289343] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The controversy surrounding the origin of antitropical distribution of Mytilus mussels and the taxonomic status of southern hemisphere populations remain unsolved, despite the efforts. One of the limiting factors remains the lack of the complete sequences of the representative mitochondrial genomes which would allow their proper comparison with the relatively well-represented northern hemisphere congeneric mussels. To fill this gap we sequenced the representative maternal (F) genome of a native Chilean mussel. The genome is 16,748bp long and structurally identical to the northern hemisphere M. edulis and M. galloprovincialis F genomes. However, the genetic distance from them (≈5%) is twice as high as the maximum distance between them (<2.5%). Thus, the notion that the name M. chilensis should be used for native Chilean Mytilus mussels, with the same rank as M. galloprovincialis and M. edulis is supported.
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Affiliation(s)
- Beata Śmietanka
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
| | - Artur Burzyński
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
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26
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Robicheau BM, Breton S, Stewart DT. Sequence motifs associated with paternal transmission of mitochondrial DNA in the horse mussel, Modiolus modiolus (Bivalvia: Mytilidae). Gene 2016; 605:32-42. [PMID: 28027966 DOI: 10.1016/j.gene.2016.12.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/10/2016] [Accepted: 12/23/2016] [Indexed: 12/01/2022]
Abstract
In the majority of metazoans paternal mitochondria represent evolutionary dead-ends. In many bivalves, however, this paradigm does not hold true; both maternal and paternal mitochondria are inherited. Herein, we characterize maternal and paternal mitochondrial control regions of the horse mussel, Modiolus modiolus (Bivalvia: Mytilidae). The maternal control region is 808bp long, while the paternal control region is longer at 2.3kb. We hypothesize that the size difference is due to a combination of repeated duplications within the control region of the paternal mtDNA genome, as well as an evolutionarily ancient recombination event between two sex-associated mtDNA genomes that led to the insertion of a second control region sequence in the genome that is now transmitted via males. In a comparison to other mytilid male control regions, we identified two evolutionarily Conserved Motifs, CMA and CMB, associated with paternal transmission of mitochondrial DNA. CMA is characterized by a conserved purine/pyrimidine pattern, while CMB exhibits a specific 13bp nucleotide string within a stem and loop structure. The identification of motifs CMA and CMB in M. modiolus extends our understanding of Sperm Transmission Elements (STEs) that have recently been identified as being associated with the paternal transmission of mitochondria in marine bivalves.
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Affiliation(s)
| | - Sophie Breton
- Departement de Science Biologiques, Université de Montréal, QC, Canada
| | - Donald T Stewart
- Departement de Science Biologiques, Université de Montréal, QC, Canada.
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27
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The complete maternal and paternal mitochondrial genomes of Unio crassus: Mitochondrial molecular clock and the overconfidence of molecular dating. Mol Phylogenet Evol 2016; 107:605-608. [PMID: 27956259 DOI: 10.1016/j.ympev.2016.12.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 12/05/2016] [Accepted: 12/07/2016] [Indexed: 11/21/2022]
Abstract
The availability of a rapidly growing number of complete mitochondrial genome sequences provokes high confidence dating approaches. However, even if the congruence between mitochondrial and nuclear markers is reasonable, the resulting topologies are frequently questionable. The unique opportunity to study the evolutionary history of two independent mitochondrial genomes in one phylogenetic context exists in the freshwater mussels family Unionidae. The two lineages function under doubly uniparental inheritance since well before the emergence of the family. Despite the relatively high number of available complete sequences of maternally inherited genomes, comparative analyses are limited by the small number of sequences of counterpart paternally inherited genomes. We have sequenced for the first time the representative set of five sequences (two maternal and three paternal) from the species Unio crassus. Comparative analysis of the phylogenies reconstructed using relevant mitogenomic data available in GenBank (13 species in total) reveal that single - genome inferences are congruent only if the relaxed clock is assumed.
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Plazzi F, Puccio G, Passamonti M. Comparative Large-Scale Mitogenomics Evidences Clade-Specific Evolutionary Trends in Mitochondrial DNAs of Bivalvia. Genome Biol Evol 2016; 8:2544-64. [PMID: 27503296 PMCID: PMC5010914 DOI: 10.1093/gbe/evw187] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2016] [Indexed: 12/28/2022] Open
Abstract
Despite the figure of complete bivalve mitochondrial genomes keeps growing, an assessment of the general features of these genomes in a phylogenetic framework is still lacking, despite the fact that bivalve mitochondrial genomes are unusual under different aspects. In this work, we constructed a dataset of one hundred mitochondrial genomes of bivalves to perform the first systematic comparative mitogenomic analysis, developing a phylogenetic background to scaffold the evolutionary history of the class' mitochondrial genomes. Highly conserved domains were identified in all protein coding genes; however, four genes (namely, atp6, nad2, nad4L, and nad6) were found to be very divergent for many respects, notwithstanding the overall purifying selection working on those genomes. Moreover, the atp8 gene was newly annotated in 20 mitochondrial genomes, where it was previously declared as lacking or only signaled. Supernumerary mitochondrial proteins were compared, but it was possible to find homologies only among strictly related species. The rearrangement rate on the molecule is too high to be used as a phylogenetic marker, but here we demonstrate for the first time in mollusks that there is correlation between rearrangement rates and evolutionary rates. We also developed a new index (HERMES) to estimate the amount of mitochondrial evolution. Many genomic features are phylogenetically congruent and this allowed us to highlight three main phases in bivalve history: the origin, the branching of palaeoheterodonts, and the second radiation leading to the present-day biodiversity.
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Affiliation(s)
- Federico Plazzi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3 - 40126 Bologna, Italy
| | - Guglielmo Puccio
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3 - 40126 Bologna, Italy
| | - Marco Passamonti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3 - 40126 Bologna, Italy
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Amaro R, Bouza C, Pardo BG, Castro J, San Miguel E, Villalba A, Lois S, Outeiro A, Ondina P. Identification of novel gender-associated mitochondrial haplotypes in Margaritifera margaritifera(Linnaeus, 1758). Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Rafaela Amaro
- Department of Genetics; Faculty of Veterinary Science; University of Santiago de Compostela; 27002 Lugo Spain
| | - Carmen Bouza
- Department of Genetics; Faculty of Veterinary Science; University of Santiago de Compostela; 27002 Lugo Spain
| | - Belén G. Pardo
- Department of Genetics; Faculty of Veterinary Science; University of Santiago de Compostela; 27002 Lugo Spain
| | - Jaime Castro
- Department of Genetics; Faculty of Veterinary Science; University of Santiago de Compostela; 27002 Lugo Spain
| | - Eduardo San Miguel
- Department of Genetics; Faculty of Veterinary Science; University of Santiago de Compostela; 27002 Lugo Spain
| | - Antonio Villalba
- Centro de Investigacións Mariñas de Corón (CIMA); Consellería do Medio Rural e do Mar da Xunta de Galicia; Aptdo. 13 36620 Vilanova de Arousa Spain
| | - Sabela Lois
- Department of Zoology; Faculty of Veterinary Science; University of Santiago de Compostela; 27002 Lugo Spain
| | - Adolfo Outeiro
- Department of Zoology; Faculty of Veterinary Science; University of Santiago de Compostela; 27002 Lugo Spain
| | - Paz Ondina
- Department of Zoology; Faculty of Veterinary Science; University of Santiago de Compostela; 27002 Lugo Spain
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Mitchell A, Guerra D, Stewart D, Breton S. In silico analyses of mitochondrial ORFans in freshwater mussels (Bivalvia: Unionoida) provide a framework for future studies of their origin and function. BMC Genomics 2016; 17:597. [PMID: 27507266 PMCID: PMC4979158 DOI: 10.1186/s12864-016-2986-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 08/02/2016] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Many species of bivalves exhibit a unique system of mtDNA transmission named Doubly Uniparental Inheritance (DUI). Under this system, species have two distinct, sex-linked mitochondrial genomes: the M-type mtDNA, which is transmitted by males to male offspring and found in spermatozoa, and the F-type mtDNA, which is transmitted by females to all offspring, and found in all tissues of females and in somatic tissues of males. Bivalves with DUI also have sex-specific mitochondrial ORFan genes, (M-orf in the M mtDNA, F-orf in the F mtDNA), which are open reading frames having no detectable homology and no known function. DUI ORFan proteins have previously been characterized in silico in a taxonomically broad array of bivalves including four mytiloid, one veneroid and one unionoid species. However, the large evolutionary distance among these taxa prevented a meaningful comparison of ORFan properties among these divergent lineages. The present in silico study focuses on a suite of more closely-related Unionoid freshwater mussel species to provide more reliably interpretable information on patterns of conservation and properties of DUI ORFans. Unionoid species typically have separate sexes, but hermaphroditism also occurs, and hermaphroditic species lack the M-type mtDNA and possess a highly mutated version of the F-orf in their maternally transmitted mtDNA (named H-orf in these taxa). In this study, H-orfs and their respective proteins are analysed for the first time. RESULTS Despite a rapid rate of evolution, strong structural and functional similarities were found for M-ORF proteins compared among species, and among the F-ORF and H-ORF proteins across the studied species. In silico analyses suggest that M-ORFs have a role in transport and cellular processes such as signalling, cell cycle and division, and cytoskeleton organisation, and that F-ORFs may be involved in cellular traffic and transport, and in immune response. H-ORFs appear to be structural glycoproteins, which may be involved in signalling, transport and transcription. Our results also support either a viral or a mitochondrial origin for the ORFans. CONCLUSIONS Our findings reveal striking structural and functional similarities among proteins encoded by mitochondrial ORFans in freshwater mussels, and strongly support a role for these genes in the DUI mechanism. Our analyses also support the possibility of DUI systems with elements of different sources/origins and different mechanisms of action in the distantly-related DUI taxa. Parallel situations to the novel mitochondrially-encoded functions of freshwater mussel ORFans present in some other eukaryotes are also discussed.
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Affiliation(s)
- Alyssa Mitchell
- Department of Biological Sciences, Université de Montréal, CP 6128, Succursale Centre-Ville, Montréal, QC H3C 3J7 Canada
| | - Davide Guerra
- Department of Biological Sciences, Université de Montréal, CP 6128, Succursale Centre-Ville, Montréal, QC H3C 3J7 Canada
| | - Donald Stewart
- Department of Biology, Acadia University, Wolfville, NS B4P 2R6 Canada
| | - Sophie Breton
- Department of Biological Sciences, Université de Montréal, CP 6128, Succursale Centre-Ville, Montréal, QC H3C 3J7 Canada
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Gaitán-Espitia JD, Quintero-Galvis JF, Mesas A, D’Elía G. Mitogenomics of southern hemisphere blue mussels (Bivalvia: Pteriomorphia): Insights into the evolutionary characteristics of the Mytilus edulis complex. Sci Rep 2016; 6:26853. [PMID: 27241855 PMCID: PMC4886515 DOI: 10.1038/srep26853] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 04/26/2016] [Indexed: 11/09/2022] Open
Abstract
Marine blue mussels (Mytilus spp.) are widespread species that exhibit an antitropical distribution with five species occurring in the Northern Hemisphere (M. trossulus, M. edulis, M. galloprovincialis, M. californianus and M. coruscus) and three in the Southern Hemisphere (M. galloprovincialis, M. chilensis and M. platensis). Species limits in this group remain controversial, in particular for those forms that live in South America. Here we investigated structural characteristics of marine mussels mitogenomes, based on published F mtDNA sequences of Northern Hemisphere species and two newly sequenced South American genomes, one from the Atlantic M. platensis and another from the Pacific M. chilensis. These mitogenomes exhibited similar architecture to those of other genomes of Mytilus, including the presence of the Atp8 gene, which is missing in most of the other bivalves. Our evolutionary analysis of mitochondrial genes indicates that purifying selection is the predominant force shaping the evolution of the coding genes. Results of our phylogenetic analyses supported the monophyly of Pteriomorphia and fully resolved the phylogenetic relationships among its five orders. Finally, the low genetic divergence of specimens assigned to M. chilensis and M. platensis suggests that these South American marine mussels represent conspecific variants rather than distinct species.
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Affiliation(s)
- Juan Diego Gaitán-Espitia
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567 Valdivia, Chile
- CSIRO Oceans and Atmosphere, GPO Box 1538, Hobart 7001, TAS, Australia
| | - Julian F. Quintero-Galvis
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567 Valdivia, Chile
- Programa de Doctorado en Ciencias mención Ecología y Evolución, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Andres Mesas
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567 Valdivia, Chile
- Programa de Doctorado en Ciencias mención Ecología y Evolución, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Guillermo D’Elía
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567 Valdivia, Chile
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Bettinazzi S, Plazzi F, Passamonti M. The Complete Female- and Male-Transmitted Mitochondrial Genome of Meretrix lamarckii. PLoS One 2016; 11:e0153631. [PMID: 27083010 PMCID: PMC4833323 DOI: 10.1371/journal.pone.0153631] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 04/02/2016] [Indexed: 11/17/2022] Open
Abstract
Bivalve mitochondrial genomes show many uncommon features, like additional genes, high rates of gene rearrangement, high A-T content. Moreover, Doubly Uniparental Inheritance (DUI) is a distinctive inheritance mechanism allowing some bivalves to maintain and transmit two separate sex-linked mitochondrial genomes. Many bivalve mitochondrial features, such as gene extensions or additional ORFs, have been proposed to be related to DUI but, up to now, this topic is far from being understood. Several species are known to show this unusual organelle inheritance but, being widespread only among Unionidae and Mytilidae, DUI distribution is unclear. We sequenced and characterized the complete female- (F) and male-transmitted (M) mitochondrial genomes of Meretrix lamarckii, which, in fact, is the second species of the family Veneridae where DUI has been demonstrated so far. The two mitochondrial genomes are comparable in length and show roughly the same gene content and order, except for three additional tRNAs found in the M one. The two sex-linked genomes show an average nucleotide divergence of 16%. A 100-aminoacid insertion in M. lamarckii M-cox2 gene was found; moreover, additional ORFs have been found in both F and M Long Unassigned Regions of M. lamarckii. Even if no direct involvement in DUI process has been demonstrated so far, the finding of cox2 insertions and supernumerary ORFs in M. lamarckii both strengthens this hypothesis and widens the taxonomical distribution of such unusual features. Finally, the analysis of inter-sex genetic variability shows that DUI species form two separate clusters, namely Unionidae and Mytilidae+Veneridae; this dichotomy is probably due to different DUI regimes acting on separate taxa.
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Affiliation(s)
- Stefano Bettinazzi
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, BO, Italy
| | - Federico Plazzi
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, BO, Italy
| | - Marco Passamonti
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, BO, Italy
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Marín A, Fujimoto T, Arai K. The mitochondrial genomes of Pecten albicans and Pecten maximus (Bivalvia: Pectinidae) reveal a novel gene arrangement with low genetic differentiation. BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2015.06.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Saunier A, Garcia P, Becquet V, Marsaud N, Escudié F, Pante E. Mitochondrial genomes of the Baltic clam Macoma balthica (Bivalvia: Tellinidae): setting the stage for studying mito-nuclear incompatibilities. BMC Evol Biol 2014; 14:259. [PMID: 25527898 PMCID: PMC4302422 DOI: 10.1186/s12862-014-0259-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 12/05/2014] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Allopatric divergence across lineages can lead to post-zygotic reproductive isolation upon secondary contact and disrupt coevolution between mitochondrial and nuclear genomes, promoting emergence of genetic incompatibilities. A previous F ST scan on the transcriptome of the Baltic clam Macoma balthica highlighted several genes potentially involved in mito-nuclear incompatibilities (MNIs). As proteins involved in the mitochondrial oxidative phosphorylation (OXPHO) chain are prone to MNIs and can contribute to the maintenance of genetic barriers, the mitochondrial genomes of six Ma. balthica individuals spanning two secondary contact zones were sequenced using the Illumina MiSeq plateform. RESULTS The mitogenome has an approximate length of 16,806 bp and encodes 13 protein-coding genes, 2 rRNAs and 22 tRNAs, all located on the same strand. atp8, a gene long reported as rare in bivalves, was detected. It encodes 42 amino acids and is putatively expressed and functional. A large unassigned region was identified between rrnS and tRNA (Met) and could likely correspond to the Control Region. Replacement and synonymous mutations were mapped on the inferred secondary structure of all protein-coding genes of the OXPHO chain. The atp6 and atp8 genes were characterized by background levels of replacement mutations, relative to synonymous mutations. However, most nad genes (notably nad2 and nad5) were characterized by an elevated proportion of replacement mutations. CONCLUSIONS Six nearly complete mitochondrial genomes were successfully assembled and annotated, providing the necessary roadmap to study MNIs at OXPHO loci. Few replacement mutations were mapped on mitochondrial-encoded ATP synthase subunits, which is in contrast with previous data on nuclear-encoded subunits. Conversely, the high population divergence and the prevalence of non-synonymous mutations at nad genes are congruent with previous observations from the nuclear transcriptome. This further suggest that MNIs between subunits of Complex I of the OXPHO chain, coding for NADH dehydrogenase, may play a role in maintaining barriers to gene flow in Ma. balthica.
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Affiliation(s)
- Alice Saunier
- Littoral, Environnement et Sociétés, UMR 7266 CNRS, Université de La Rochelle, 2 rue Olympe de Gouges, La Rochelle, 17000, France.
| | - Pascale Garcia
- Littoral, Environnement et Sociétés, UMR 7266 CNRS, Université de La Rochelle, 2 rue Olympe de Gouges, La Rochelle, 17000, France.
| | - Vanessa Becquet
- Littoral, Environnement et Sociétés, UMR 7266 CNRS, Université de La Rochelle, 2 rue Olympe de Gouges, La Rochelle, 17000, France.
| | - Nathalie Marsaud
- GeT-PlaGe, Genotoul, INRA Auzeville, Castanet-Tolosan, 31326, France.
| | - Frédéric Escudié
- GeT-PlaGe, Genotoul, INRA Auzeville, Castanet-Tolosan, 31326, France.
| | - Eric Pante
- Littoral, Environnement et Sociétés, UMR 7266 CNRS, Université de La Rochelle, 2 rue Olympe de Gouges, La Rochelle, 17000, France.
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Zbawicka M, Wenne R, Burzyński A. Mitogenomics of recombinant mitochondrial genomes of Baltic Sea Mytilus mussels. Mol Genet Genomics 2014; 289:1275-87. [PMID: 25079914 PMCID: PMC4236608 DOI: 10.1007/s00438-014-0888-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 07/07/2014] [Indexed: 01/17/2023]
Abstract
Recombination in the control region (CR) of Mytilus mitochondrial DNA (mtDNA) was originally reported based on the relatively short, sequenced fragments of mitochondrial genomes. Recombination outside the CR has been reported recently with the suggestion that such processes are common in Mytilus. We have fully sequenced a set of 11 different mitochondrial haplotypes representing the high diversity of paternally inherited mitochondrial genomes of Baltic Sea Mytilus mussels, including the haplotype close to the native Mytilus trossulus mitochondrial genome, which was thought to have been entirely eliminated from this population. Phylogenetic and comparative analysis showed that the recombination is limited to the vicinity of the CR in all sequenced genomes. Coding sequence comparison indicated that all paternally inherited genomes showed increased accumulation of nonsynonymous substitutions, including the genomes which switched their transmission route very recently. The acquisition of certain CR sequences through recombination with highly divergent paternally inherited genomes seems to precede and favor the switch, but it is not a prerequisite for this process. Interspecies hybridization in the Baltic Sea during the recent 10,000 years created conditions for both structural and evolutionary mitochondrial instability which resulted in the observed variation and dynamics of mtDNA in Baltic Sea Mytilus mussels. In conclusion, the data shows that the effects of mitochondrial recombination are limited to the CR of few phylogenetic lineages.
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Affiliation(s)
- Małgorzata Zbawicka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712, Sopot, Poland,
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Soroka M, Burzyński A. Complete male mitochondrial genome of Anodonta anatina (Mollusca: Unionidae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1679-80. [PMID: 25317641 DOI: 10.3109/19401736.2014.958725] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Anodonta anatina is a freshwater mussel of the family Unionidae. These mussels have a unique mitochondria inheritance system named doubly uniparental inheritance (DUI). Under DUI males have two, potentially very divergent mitochondrial genomes: F-type inherited from mother and M-type inherited from father. F-type is present in soma whereas M-type is present in gonadal tissues and sperm. Here we report two M-type sequences of complete mitochondrial genomes from Anodonta anatina. They are 16,906 bp long and their sequences are similar (0.1% divergence). The genome organization is identical to the other Unionidean M-type genomes published to date. There are 38 genes, including the recently described M-type specific M ORF. The presence of tRNA-like repeat in one of the noncoding regions, suggests that the control region is located in this area. Nucleotide composition is quite extreme, with AT content (66.2%) higher than in any other of the six published Unionidean M genomes.
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Affiliation(s)
- Marianna Soroka
- a Department of Genetics , University of Szczecin , Szczecin , Poland
| | - Artur Burzyński
- b Institute of Oceanology, Polish Academy of Sciences , Sopot , Poland , and.,c Institute of Biology and Environmental Protection, Pommeranian University in Słupsk , Poland
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Śmietanka B, Wenne R, Burzyński A. Complete male mitochondrial genomes of European Mytilus edulis mussels. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1634-5. [PMID: 25208162 DOI: 10.3109/19401736.2014.958704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Doubly uniparental inheritance (DUI) results in the existence of two gender-specific, divergent mtDNA lineages within a single species. Under DUI, the female genome (F) is transmitted from mothers to the whole offspring, and the male genome (M) is transmitted exclusively from fathers to sons. This system was first described in a marine mussels Mytilus edulis inhabiting European coastal waters, over a decade ago. Despite that, the complete sequence of the M genome from the European M. edulis mussels remained unknown. Here we announce it for the first time. The announcement is based on the two haplotypes isolated from heteroplasmic males of European M. edulis sampled at two moderately distant locations: southern North Sea and western Baltic. The two M genomes are quite similar both in length (16,631 and 16,632 bp) and in sequence (98.3%). Furthermore, both newly sequenced genomes are closely related to the genomes described from Baltic M. trossulus.
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Affiliation(s)
- Beata Śmietanka
- a Institute of Oceanology, Polish Academy of Sciences , Sopot , Poland
| | - Roman Wenne
- a Institute of Oceanology, Polish Academy of Sciences , Sopot , Poland
| | - Artur Burzyński
- a Institute of Oceanology, Polish Academy of Sciences , Sopot , Poland
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Śmietanka B, Burzyński A, Hummel H, Wenne R. Glacial history of the European marine mussels Mytilus, inferred from distribution of mitochondrial DNA lineages. Heredity (Edinb) 2014; 113:250-8. [PMID: 24619178 PMCID: PMC4815643 DOI: 10.1038/hdy.2014.23] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 12/20/2013] [Accepted: 01/31/2014] [Indexed: 11/09/2022] Open
Abstract
Mussels of the genus Mytilus have been used to assess the circumglacial phylogeography of the intertidal zone. These mussels are representative components of the intertidal zone and have rapidly evolving mitochondrial DNA, suitable for high resolution phylogeographic analyses. In Europe, the three Mytilus species currently share mitochondrial haplotypes, owing to the cases of extensive genetic introgression. Genetic diversity of Mytilus edulis, Mytilus trossulus and Mytilus galloprovincialis was studied using a 900-bp long part of the most variable fragment of the control region from one of their two mitochondrial genomes. To this end, 985 specimens were sampled along the European coasts, at sites ranging from the Black Sea to the White Sea. The relevant DNA fragments were amplified, sequenced and analyzed. Contrary to the earlier findings, our coalescence and nested cladistics results show that only a single M. edulis glacial refugium existed in the Atlantic. Despite that, the species survived the glaciation retaining much of its diversity. Unsurprisingly, M. galloprovincialis survived in the Mediterranean Sea. In a relatively short time period, around the climatic optimum at 10 ky ago, the species underwent rapid expansion coupled with population differentiation. Following the expansion, further contemporary gene flow between populations was limited.
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Affiliation(s)
- B Śmietanka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Powstańców Warszawy 55, Sopot, Poland
| | - A Burzyński
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Powstańców Warszawy 55, Sopot, Poland
| | - H Hummel
- Netherlands Institute of Ecology, Centre for Estuarine and Marine Ecology, AC Yerseke, The Netherlands
| | - R Wenne
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Powstańców Warszawy 55, Sopot, Poland
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Zheng J, Chen Y, Deng F, Huang R, Petersen F, Ibrahim S, Yu X. mtDNA sequence, phylogeny and evolution of laboratory mice. Mitochondrion 2014; 17:126-31. [PMID: 25038446 DOI: 10.1016/j.mito.2014.07.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 07/08/2014] [Accepted: 07/09/2014] [Indexed: 11/29/2022]
Abstract
Laboratory mice are important tools for biomedical research. Aiming to investigate the phylogeny and evolution of laboratory mice, we investigated the mtDNA sequences of classic inbred strains, classic outbred stocks and wild-derived inbred strains. Our results showed that the most classic outbred stocks and classic inbred strains are descended from a single mtDNA ancestor. The phylogenic analysis supports the topology of M. m. castaneus/M. m. domesticus as sister subspecies, and the divergence time between the two sister subspecies and M. m. musculus was 493,000 (435,000-557,000) years ago. Furthermore, the mtDNA polymorphisms accumulated in the last 100years in the laboratory mice are under a relaxed purifying selection.
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Affiliation(s)
- Junfeng Zheng
- The Medical College of Xiamen University, Xiamen University, 361005 Xiamen, China
| | - Yan Chen
- The Medical College of Xiamen University, Xiamen University, 361005 Xiamen, China
| | - Fengyuan Deng
- The Medical College of Xiamen University, Xiamen University, 361005 Xiamen, China
| | - Renliang Huang
- The Medical College of Xiamen University, Xiamen University, 361005 Xiamen, China
| | - Frank Petersen
- Priority Area Asthma and Allergy, Research Center Borstel, 23845 Borstel, Germany, Airway Research Center North (ARCN), UGMLC, Member of the German Center for Lung Research (DZL)
| | - Saleh Ibrahim
- Department of Dermatology, University of Lübeck, 23538 Lübeck, Germany
| | - Xinhua Yu
- The Medical College of Xiamen University, Xiamen University, 361005 Xiamen, China; Priority Area Asthma and Allergy, Research Center Borstel, 23845 Borstel, Germany, Airway Research Center North (ARCN), UGMLC, Member of the German Center for Lung Research (DZL).
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40
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Śmietanka B, Filipowicz M, Burzyński A. Recombinant mitochondrial genome with standard transmission route from Mediterranean mussel Mytilus galloprovincialis. Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:585-586. [PMID: 24724974 DOI: 10.3109/19401736.2014.908356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Several bivalve species, including marine mussels Mytilus are atypical in having two gender-specific and highly divergent mtDNA genomes. This peculiar genetic system allows not only the recombination to occur but also facilitates its detection. Previous reports associated the existence of mosaic recombinant haplotypes with the switch of their transmission route. Here we report nearly complete sequence of a mitochondrial genome isolated from a homoplasmic female individual of Mediterranean Mytilus galloprovincialis. The genome has clear phylogenetic affinity with and organization identical to the M. galloprovincialis female haplotypes, in the coding part. However, the genome is very large, approximately 20,600 bp long, exclusively due to a long and complex control region. It contains an array of repeats, some of which are degenerated. A large part of the control region is derived from the paternal genome. This finding shows that not all haplotypes with recombinant control regions must be paternally inherited in Mytilus.
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Affiliation(s)
- Beata Śmietanka
- a Institute of Oceanology, Polish Academy of Sciences , Sopot , Poland and
| | - Monika Filipowicz
- a Institute of Oceanology, Polish Academy of Sciences , Sopot , Poland and
| | - Artur Burzyński
- a Institute of Oceanology, Polish Academy of Sciences , Sopot , Poland and
- b Institute of Biology and Environmental Protection, Pommeranian University in Słupsk , Poland
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Sańko TJ, Burzyński A. Co-expressed mitochondrial genomes: recently masculinized, recombinant mitochondrial genome is co-expressed with the female-transmitted mtDNA genome in a male Mytilus trossulus mussel from the Baltic Sea. BMC Genet 2014; 15:28. [PMID: 24575766 PMCID: PMC3941564 DOI: 10.1186/1471-2156-15-28] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 02/13/2014] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Few exceptions have been described from strict maternal inheritance of mitochondrial DNA in animals, including sea mussels (Mytilidae), clams (Donacidae, Veneridae and Solenidae) and freshwater mussels (Unionoidae) order. In these bivalves mitochondria and their DNA are transferred through two separate routes. The females inherit only the maternal mitochondrial DNA whereas the males inherit maternal as well as paternal mitochondrial DNA, which is usually present only in gonads and sperm. The mechanism controlling this phenomenon is unclear but leads to the existence of two separate mitochondrial DNA lineages in a single species. The lineages are usually well differentiated: up to 20-50% divergence in nucleotide sequence. Occasionally, a maternal mitochondrial DNA can invade the paternal transmission route, eventually replacing the diverged M-type and lowering the divergence. Such role reversal (masculinization) event has happened recently in the Mytilus population of the Baltic Sea which consists of M. edulis × M. trossulus hybrids, but the functional status of the resulting mitochondrial genome was unknown. RESULTS In this paper we sequenced transcripts from one specimen that was identified as male carrying both the female mitochondrial genome and a recently masculinized mitochondrial genome. Additionally, the analysis of the control region has showed that the recently masculinized, recombinant genome, not only has an M-type control region and all coding regions derived from the F-type, but also is transcriptionally active along side the maternally inherited F-type genome. In the comparative analysis, the two genomes exhibit different substitution patterns, typical for the M vs. F genome comparisons. The genetic distances and ratios of non-synonymous substitutions also suggest that one of the genomes is transitioning from the maternal to the paternal inheritance mode, consistent with its recent masculinization. CONCLUSION We have shown, for the first time, that the recently masculinized mitochondrial genome is active and that it accumulates excess of non-synonymous substitutions across its coding sequence. This suggests, that, under certain cytonuclear incompatibility conditions, masculinization may serve to restore the endangered functionality of the paternally inherited genome. This is also another example of a mitochondrial genome in which the recombination in the control region predated its transition from paternal to maternal transmission route.
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Affiliation(s)
- Tomasz J Sańko
- Genetics and Marine Biotechnology Department, Institute of Oceanology of Polish Academy of Sciences, Powstańców Warszawy 55, Sopot 81-712, Poland.
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Kyriakou E, Chatzoglou E, Zouros E, Rodakis GC. The rRNA and tRNA transcripts of maternally and paternally inherited mitochondrial DNAs of Mytilus galloprovincialis suggest presence of a "degradosome" in mussel mitochondria and necessitate the re-annotation of the l-rRNA/CR boundary. Gene 2014; 540:78-85. [PMID: 24561285 DOI: 10.1016/j.gene.2014.01.080] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 01/15/2014] [Accepted: 01/21/2014] [Indexed: 11/24/2022]
Abstract
Species of the genus Mytilus carry two mitochondrial genomes in obligatory coexistence; one transmitted though the eggs (the F type) and one through the sperm (the M type). We have studied the 3' and 5' ends of rRNA and tRNA transcripts using RT-PCR and RNA circularization techniques in both the F and M genomes of Mytilus galloprovincialis. We have found polyadenylated and non-adenylated transcripts for both ribosomal and transfer RNAs. In all these genes the 5' ends of the transcripts coincided with the first nucleotide of the annotated genes, but the 3' ends were heterogeneous. The l-rRNA 3' end is 47 or 48 nucleotides upstream from the one assigned by a previous annotation, which makes the adjacent first domain (variable domain one, VD1) of the main control region (CR) correspondingly longer. We have observed s-rRNA and l-rRNA transcripts with truncated 3' end and polyadenylated tRNA transcripts carrying the CCA trinucleotide. We have also detected polyadenylated RNA remnants carrying the sequences of the control region, which strongly suggests RNA degradation activity and thus presence of degradosomes in Mytilus mitochondria.
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Affiliation(s)
- Eleni Kyriakou
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15701 Athens, Greece
| | - Evanthia Chatzoglou
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15701 Athens, Greece
| | - Eleftherios Zouros
- Department of Biology, University of Crete, 71409 Heraklion, Crete, Greece
| | - George C Rodakis
- Department of Biochemistry and Molecular Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15701 Athens, Greece.
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Fišer Pečnikar Ž, Buzan EV. 20 years since the introduction of DNA barcoding: from theory to application. J Appl Genet 2013; 55:43-52. [PMID: 24203863 DOI: 10.1007/s13353-013-0180-y] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Revised: 10/14/2013] [Accepted: 10/15/2013] [Indexed: 01/29/2023]
Abstract
Traditionally, taxonomic identification has relied upon morphological characters. In the last two decades, molecular tools based on DNA sequences of short standardised gene fragments, termed DNA barcodes, have been developed for species discrimination. The most common DNA barcode used in animals is a fragment of the cytochrome c oxidase (COI) mitochondrial gene, while for plants, two chloroplast gene fragments from the RuBisCo large subunit (rbcL) and maturase K (matK) genes are widely used. Information gathered from DNA barcodes can be used beyond taxonomic studies and will have far-reaching implications across many fields of biology, including ecology (rapid biodiversity assessment and food chain analysis), conservation biology (monitoring of protected species), biosecurity (early identification of invasive pest species), medicine (identification of medically important pathogens and their vectors) and pharmacology (identification of active compounds). However, it is important that the limitations of DNA barcoding are understood and techniques continually adapted and improved as this young science matures.
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Affiliation(s)
- Živa Fišer Pečnikar
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, Glagoljaška 8, 6000, Koper, Slovenia,
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Gaitán-Espitia JD, Nespolo RF, Opazo JC. The complete mitochondrial genome of the land snail Cornu aspersum (Helicidae: Mollusca): intra-specific divergence of protein-coding genes and phylogenetic considerations within Euthyneura. PLoS One 2013; 8:e67299. [PMID: 23826260 PMCID: PMC3691120 DOI: 10.1371/journal.pone.0067299] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2013] [Accepted: 05/16/2013] [Indexed: 11/19/2022] Open
Abstract
The complete sequences of three mitochondrial genomes from the land snail Cornu aspersum were determined. The mitogenome has a length of 14050 bp, and it encodes 13 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes. It also includes nine small intergene spacers, and a large AT-rich intergenic spacer. The intra-specific divergence analysis revealed that COX1 has the lower genetic differentiation, while the most divergent genes were NADH1, NADH3 and NADH4. With the exception of Euhadra herklotsi, the structural comparisons showed the same gene order within the family Helicidae, and nearly identical gene organization to that found in order Pulmonata. Phylogenetic reconstruction recovered Basommatophora as polyphyletic group, whereas Eupulmonata and Pulmonata as paraphyletic groups. Bayesian and Maximum Likelihood analyses showed that C. aspersum is a close relative of Cepaea nemoralis, and with the other Helicidae species form a sister group of Albinaria caerulea, supporting the monophyly of the Stylommatophora clade.
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Affiliation(s)
- Juan Diego Gaitán-Espitia
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
- Programa de Doctorado en Ciencias mención Ecología y Evolución, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Roberto F. Nespolo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
| | - Juan C. Opazo
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Valdivia, Chile
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Chatzoglou E, Kyriakou E, Zouros E, Rodakis GC. The mRNAs of maternally and paternally inherited mtDNAs of the mussel Mytilus galloprovincialis: Start/end points and polycistronic transcripts. Gene 2013; 520:156-65. [DOI: 10.1016/j.gene.2013.02.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 02/07/2013] [Indexed: 10/27/2022]
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Śmietanka B, Zbawicka M, Sańko T, Wenne R, Burzyński A. Molecular population genetics of male and female mitochondrial genomes in subarctic Mytilus trossulus.. MARINE BIOLOGY 2013; 160:1709-1721. [PMID: 24391284 PMCID: PMC3873064 DOI: 10.1007/s00227-013-2223-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 03/16/2013] [Indexed: 06/03/2023]
Abstract
The doubly uniparental inheritance system allows for the use of two independent mitochondrial genomes for population history investigations. Under this system, two lineages of mitochondrial DNA (mtDNA) exist and males are typically heteroplasmic, having the additional, usually divergent, mitochondrial genome inherited from their male parent. This additional mtDNA typically evolves faster, potentially allowing for insight into more recent events in population history. Few studies did explore this possibility in marine mussels Mytilus showing its usefulness. Recent observations of the Mytilus trossulus mussels who have retained their native mtDNA in European waters posed the question of their origin. Are they part of a population present, but previously undetected, or is this a potentially human mediated, ongoing spread of an invasive species? To tackle this question, we amplified with species-specific primers and sequenced an approximately 1,200-bp-long fragment spanning COIII and ND2 genes from both mitochondrial genomes of mussels sampled at five locations worldwide, covering the whole M. trossulus range. The overall pattern of polymorphisms is compatible with the entirely postglacial history of the whole species, indicating a very deep bottleneck at last glacial maximum, with possible retention of the whole species in a single refugium, and the effective population size of no more than a few thousands. Both analyses of molecular variance and isolation with migration (IM) models point at the West Atlantic as the source of the European M. trossulus mussels, at least the ones who retained their native mtDNA. The hypothesis that this is an ongoing, human-mediated process was considered. To this end, comparison with the well-known case: the introduction of congeneric mussel, Mytilus galloprovincialis, from Mediterranean Sea to Asia was used. This introduction occurred within the last 100 years. The results inferred by the IM model suggest that the timing and structure of transatlantic migration of M. trossulus differs significantly from the M. galloprovincialis case: it is more than 1,000 years old and involves a much larger fraction of the ancestral population. Therefore, most likely, this invasion is not a human-mediated process.
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Affiliation(s)
- Beata Śmietanka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - Małgorzata Zbawicka
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - Tomasz Sańko
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - Roman Wenne
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - Artur Burzyński
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
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Wysocka A, Grabowski M, Sworobowicz L, Burzyński A, Kilikowska A, Kostoski G, Sell J. A tale of time and depth: intralacustrine radiation in endemicGammarusspecies flock from the ancient Lake Ohrid. Zool J Linn Soc 2013. [DOI: 10.1111/j.1096-3642.2012.00878.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anna Wysocka
- Department of Genetics; University of Gdańsk; Kładki 24; 80-822; Gdańsk; Poland
| | - Michał Grabowski
- Department of Invertebrate Zoology and Hydrobiology; University of Lodz; Banacha 12/16; 90-237; Łódź; Poland
| | - Lidia Sworobowicz
- Department of Genetics; University of Gdańsk; Kładki 24; 80-822; Gdańsk; Poland
| | | | - Adrianna Kilikowska
- Department of Genetics; University of Gdańsk; Kładki 24; 80-822; Gdańsk; Poland
| | - Goce Kostoski
- P.S.I. Hydrobiological Institute; Naum Ohridski; 50-6000; Ohrid; Macedonia
| | - Jerzy Sell
- Department of Genetics; University of Gdańsk; Kładki 24; 80-822; Gdańsk; Poland
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48
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Gosset CC, Bierne N. Differential introgression from a sister species explains high F
ST
outlier loci within a mussel species. J Evol Biol 2012. [DOI: 10.1111/jeb.12046] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- C. C. Gosset
- Université Montpellier 2; Montpellier Cedex France
- CNRS; Institut des Sciences de l'Evolution - ISEM UMR 5554; Station Méditerranéenne de l'Environnement Littoral; Sete France
| | - N. Bierne
- Université Montpellier 2; Montpellier Cedex France
- CNRS; Institut des Sciences de l'Evolution - ISEM UMR 5554; Station Méditerranéenne de l'Environnement Littoral; Sete France
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49
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Biparental Inheritance Through Uniparental Transmission: The Doubly Uniparental Inheritance (DUI) of Mitochondrial DNA. Evol Biol 2012. [DOI: 10.1007/s11692-012-9195-2] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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50
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Species status and population structure of mussels (Mollusca: Bivalvia: Mytilus spp.) in the Wadden Sea of Lower Saxony (Germany). ORG DIVERS EVOL 2012. [DOI: 10.1007/s13127-012-0075-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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