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Burzyński A, Śmietanka B, Fernández-Pérez J, Lubośny M. The absence of canonical respiratory complex I subunits in male-type mitogenomes of three Donax species. Sci Rep 2024; 14:14465. [PMID: 38914611 PMCID: PMC11196677 DOI: 10.1038/s41598-024-63764-8] [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: 08/03/2023] [Accepted: 05/31/2024] [Indexed: 06/26/2024] Open
Abstract
Bivalves are an extraordinary class of animals in which species with a doubly uniparental inheritance (DUI) of mitochondrial DNA have been described. DUI is characterized as a mitochondrial homoplasmy of females and heteroplasmy of male individuals where F-type mitogenomes are passed to the progeny with mother egg cells and divergent M-type mitogenomes are inherited with fathers sperm cells. However, in most cases only male individuals retain divergent mitogenome inherited with spermatozoa. Additionally, in many of bivalves, unique mitochondrial features, like additional genes, gene duplication, gene extensions, mitochondrial introns, and recombination, were observed. In this study, we sequenced and assembled male-type mitogenomes of three Donax species. Comparative analysis of mitochondrial sequences revealed a lack of all seven NADH dehydrogenase subunits as well as the presence of three long additional open reading frames lacking identifiable homology to any of the existing genes.
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Affiliation(s)
- Artur Burzyński
- 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
| | - Jenyfer Fernández-Pérez
- Departamento de Bioloxía, Facultade de Ciencias and CICA (Centro de Investigacións Científicas Avanzadas), Universidade da Coruña, Campus de A Zapateira, A Coruña, Spain
| | - Marek Lubośny
- Department of Genetics and Marine Biotechnology, Institute of Oceanology Polish Academy of Sciences, Sopot, Poland.
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Ma Y, Zheng B, Li J, Meng W, Xu K, Ye Y. Characterization of the complete mitochondrial genome of Desmaulus extinctorium (Littorinimorpha, Calyptraeoidea, Calyptraeidae) and molecular phylogeny of Littorinimorpha. PLoS One 2024; 19:e0301389. [PMID: 38547307 PMCID: PMC10977763 DOI: 10.1371/journal.pone.0301389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/12/2024] [Indexed: 04/02/2024] Open
Abstract
For the purpose of determining the placement of Calyptraeidae within the Littorinimorpha, we hereby furnish a thorough analysis of the mitochondrial genome (mitogenome) sequence of Desmaulus extinctorium. This mitogenome spans 16,605 base pairs and encompasses the entire set of 37 genes, including 13 PCGs, 22 tRNAs and two rRNAs, with an evident AT bias. Notably, tRNASer1 and tRNASer2 lack dihydrouracil (DHU) arms, resulting in an inability to form a secondary structure. Similarly, tRNAAla lacks a TΨC arm, rendering it incapable of forming a secondary structure. In contrast, the remaining tRNAs demonstrate a characteristic secondary structure reminiscent of a cloverleaf. A comparison with ancestral gastropods reveals distinct differences in three gene clusters (or genes), encompassing 15 tRNAs and eight PCGs. Notably, inversions and translocations represent the major types of rearrangements observed in D. extinctorium. Phylogenetic analysis demonstrates robust support for a monophyletic grouping of all Littorinimorpha species, with D. extinctorium representing a distinct Calyptraeoidea clade. In summary, this investigation provides the first complete mitochondrial dataset for a species of the Calyptraeidae, thus providing novel insights into the phylogenetic relationships within the Littorinimorpha.
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Affiliation(s)
- Yanwen Ma
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Biqi Zheng
- Department of Natural Resources, Ningde Marine Center, Ningde, 352000, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Wei Meng
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of China, Zhoushan, 316021, China
| | - Kaida Xu
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of China, Zhoushan, 316021, China
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
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Insights into the Deep Phylogeny and Novel Divergence Time Estimation of Patellogastropoda from Complete Mitogenomes. Genes (Basel) 2022; 13:genes13071273. [PMID: 35886056 PMCID: PMC9322768 DOI: 10.3390/genes13071273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/13/2022] [Accepted: 07/16/2022] [Indexed: 11/21/2022] Open
Abstract
To further understand the origin and evolution of Patellogastropoda, we determined the mitochondrial genome sequence of Cellana toreuma, and compared its mitogenome characteristics with the other four limpets of Nacellidae. The ratio of Ka and Ks indicated that these Nacellidae species were suffering a purifying selection, with exception of the atp6 gene. The gene sequence is basically consistent among families, while there are great differences among Lottidae species. According to the mitogenome sequences of selected gastropod species, we reconstructed a new phylogenetic tree with two methods. The data complement the mitogenome database of limpets and is a favorable research tool for the phylogenetic analysis of Gastropoda. It is found that there is a long-branch attraction (LBA) artefact in the family Lottiidae of Patellogastropoda. Therefore, the Patellogastropoda was separated by Heterobranchia, and Lottiidae is located at the root of the whole phylogenetic tree. Furthermore, we constructed the divergence time tree according to the Bayesian method and discussed the internal historical dynamics, and divergence differences among the main lineages of 12 Patellogastropoda under an uncorrelated relaxed molecular clock. In turn, we made a more comprehensive discussion on the divergence time of limpets at the molecular level.
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Marques RC, da Silva AM, Simone LRL. Cladistic analysis of the transisthmian genus Eurytellina (Bivalvia: Tellinoidea) based on morphological and morphometric data. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00561-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Nie H, Kartavtsev YP. The complete mitochondrial genome of Mactra chinensis (Bivalvia: Macridae). Mitochondrial DNA B Resour 2021; 6:2812-2815. [PMID: 34514137 PMCID: PMC8425691 DOI: 10.1080/23802359.2021.1970635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 08/15/2021] [Indexed: 10/25/2022] Open
Abstract
The structure and composition of the mitogenome of a bivalve mollusk, denoted as Mactra sp. (MT780813), has been obtained. The genome has a variable organization: it includes 12 protein-coding genes, 28 tRNAs, and two rRNA genes. Its content is sufficiently different from that of nearest specimen, accessed from GenBank, supposedly belonging to the other gender. All genes are encoded on the "+"-strand. All protein-coding genes are initiated with ATG codon. Analysis confirms the close topological position of the GenBank Mactra chinensis (KJ754823) and our M. sp. specimen on gene tree. Above data suggesting female- vs. male-type mitogenomes or cryptic species presence.
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Affiliation(s)
- Hongtao Nie
- Laboratory of Engineering and Technology Research, Center of Shellfish Breeding in Liaoning Province, College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Yuri Ph. Kartavtsev
- Laboratory of Molecular Systematic, A.V. Zhirmunsky National Scientific Center of Marine Biology, Russian Academy of Sciences, Vladivostok, Russia
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Feng J, Guo Y, Yan C, Ye Y, Yan X, Li J, Xu K, Guo B, Lü Z. Novel gene rearrangement in the mitochondrial genome of Siliqua minima (Bivalvia, Adapedonta) and phylogenetic implications for Imparidentia. PLoS One 2021; 16:e0249446. [PMID: 33822813 PMCID: PMC8023497 DOI: 10.1371/journal.pone.0249446] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/18/2021] [Indexed: 11/19/2022] Open
Abstract
Siliqua minima (Gmelin, 1791) is an important economic shellfish species belonging to the family Pharidae. To date, the complete mitochondrial genome of only one species in this family (Sinonovacula constricta) has been sequenced. Research on the Pharidae family is very limited; to improve the evolution of this bivalve family, we sequenced the complete mitochondrial genome of S. minima by next-generation sequencing. The genome is 17,064 bp in length, consisting of 12 protein-coding genes (PCGs), 22 transfer RNA genes (tRNA), and two ribosomal RNA genes (rRNA). From the rearrangement analysis of bivalves, we found that the gene sequences of bivalves greatly variable among species, and with closer genetic relationship, the more consistent of the gene arrangement is higher among the species. Moreover, according to the gene arrangement of seven species from Adapedonta, we found that gene rearrangement among families is particularly obvious, while the gene order within families is relatively conservative. The phylogenetic analysis between species of the superorder Imparidentia using 12 conserved PCGs. The S. minima mitogenome was provided and will improve the phylogenetic resolution of Pharidae species.
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Affiliation(s)
- Jiantong Feng
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Yahong Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Chengrui Yan
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Xiaojun Yan
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
| | - Kaida Xu
- Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, MOA, Key Laboratory of Sustainable Utilization of Technology Research, Marine Fisheries Research Institute of Zhejiang, Zhoushan, China
| | - Baoying Guo
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
| | - Zhenming Lü
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, China
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, Zhoushan, China
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Lamelas L, Aleix-Mata G, Rovatsos M, Marchal JA, Palomeque T, Lorite P, Sánchez A. Complete Mitochondrial Genome of Three Species of the Genus Microtus (Arvicolinae, Rodentia). Animals (Basel) 2020; 10:E2130. [PMID: 33207831 PMCID: PMC7696944 DOI: 10.3390/ani10112130] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/09/2020] [Accepted: 11/14/2020] [Indexed: 11/17/2022] Open
Abstract
The 65 species of the genus Microtus have unusual sex-related genetic features and a high rate of karyotype variation. However, only nine complete mitogenomes for these species are currently available. We describe the complete mitogenome sequences of three Microtus, which vary in length from 16,295 bp to 16,331 bp, contain 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes and a control region. The length of the 13 PCGs and the coded proteins is the same in all three species, and the start and stop codons are conserved. The non-coding regions include the L-strand origin of replication, with the same sequence of 35 bp, and the control region, which varies between 896 bp and 930 bp in length. The control region includes three domains (Domains I, II and III) with extended termination-associated sequences (ETAS-1 and ETAS-2) in Domain I. Domain II and Domain III include five (CSB-B, C, D, E and F) and three (CSB-1, CSB-2, and CSB-3) conserved sequence blocks, respectively. Phylogenetic reconstructions using the mitochondrial genomes of all the available Microtus species and one representative species from another genus of the Arvicolinae subfamily reproduced the established phylogenetic relationships for all the Arvicolinae genera that were analyzed.
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Affiliation(s)
- Luz Lamelas
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain; (L.L.); (G.A.-M.); (J.A.M.); (T.P.); (P.L.)
| | - Gaël Aleix-Mata
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain; (L.L.); (G.A.-M.); (J.A.M.); (T.P.); (P.L.)
| | - Michail Rovatsos
- Department of Ecology, Faculty of Science, Charles University, 12844 Prague, Czech Republic;
| | - Juan Alberto Marchal
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain; (L.L.); (G.A.-M.); (J.A.M.); (T.P.); (P.L.)
| | - Teresa Palomeque
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain; (L.L.); (G.A.-M.); (J.A.M.); (T.P.); (P.L.)
| | - Pedro Lorite
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain; (L.L.); (G.A.-M.); (J.A.M.); (T.P.); (P.L.)
| | - Antonio Sánchez
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n, 23071 Jaén, Spain; (L.L.); (G.A.-M.); (J.A.M.); (T.P.); (P.L.)
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Wang Y, Yang Y, Liu H, Kong L, Yu H, Liu S, Li Q. Phylogeny of Veneridae (Bivalvia) based on mitochondrial genomes. ZOOL SCR 2020. [DOI: 10.1111/zsc.12454] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu Wang
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
| | - Yi Yang
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
| | - Hongyue Liu
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education Ocean University of China Qingdao China
- Laboratory for Marine Fisheries Science and Food Production Processes Qingdao National Laboratory for Marine Science and Technology Qingdao China
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Mitogenomic architecture of the multivalent endemic black clam (Villorita cyprinoides) and its phylogenetic implications. Sci Rep 2020; 10:15438. [PMID: 32963308 PMCID: PMC7508841 DOI: 10.1038/s41598-020-72194-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 08/03/2020] [Indexed: 11/24/2022] Open
Abstract
The Indian black clam Villorita cyprinoides (Family: Cyrenidae), an extractive commercially exploited species with aquaculture importance contributing more than 70% of clam fishery in India, is endemic to the Indian peninsula. Currently, there is very sparse information, especially on the molecular data of Villorita. The present study aims to provide a comprehensive knowledge of mitogenome architecture and assess the phylogenetic status of Cyrenidae. This has resulted in reporting the first complete mitogenome of V. cyprinoides using next-generation sequencing technology. The A+T circular mitogenome was 15,880 bp long, exhibiting 13 protein-coding genes (PCGs) including ATP8 (absent in several bivalves), 22 transfer RNA, and two ribosomal RNA genes residing in the heavy strand in a clockwise orientation and a gene order akin to Corbicula fluminea. The molecular phylogeny inferred from a concatenated multi-gene sequence [14 mitochondrial (12 PCGs, rrnS and rrnL) and two nuclear genes (Histone H3, 18S rRNA)] from 47 representative species of superorder Imparidentia, clustered V. cyprinoides and Cyrenid clams to a single clade supporting the monophyly of Cyrenidae. The subsequent mitochondrial gene order analysis substantiates the close relationship of V. cyprinoides and C. fluminea, analogous to phylogenetic output. The multilocus tree topology calibrated with verified fossil data deciphered the origin and diversification of Cyrenid clams during late Triassic-early Jurassic. The data derived from this study shall contribute remarkably for further insights on cryptic species identification, molecular characterization of bivalve mitogenomes and mitochondrial evolutionary history of genus Villorita. Moreover, complete mitogenome can aid in potential marker development for assessing the genetic health of black clam populations.
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Comparative mitogenomic analysis of the superfamily Tellinoidea (Mollusca: Bivalvia): Insights into the evolution of the gene rearrangements. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100739. [PMID: 32932163 DOI: 10.1016/j.cbd.2020.100739] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/19/2020] [Accepted: 08/27/2020] [Indexed: 11/23/2022]
Abstract
The superfamily Tellinoidea is widespread and contains approximately 180 living species, which is one of the most diverse and representative groups among the bivalves. In order to extend our knowledge on evolution of tellinoidean species, we newly determined five tellinoidean mitochondrial genomes (mitogenomes). The newly determined mitogenome vary in size from 16,333 to 16,986 bp. The results show that the genome size and genome organization are conserved in tellinoideans. However, gene arrangement and the location of the major non-coding region (NCR) show diversity. The atp8 gene presents in all the five new mitogenomes. Two trnK and trnP genes were detected in Gari togata mitogenome. Phylogenetic analysis supports the monophyly of Tellinoidea, however, it's family Psammobiidae is polyphyletic. CREx analysis suggests that the gene order of Nuttallia olivacea is assumed as the most primitive condition of Tellinoidea. We map the gene order onto the phylogeny and infers the possible gene rearrangement scenarios among tellinoidean mitogenomes. The mitochondrial gene rearrangement is a useful information that help reassessing the phylogeny of Tellinoidea. Phylogenetic relationship and gene arrangement analyses suggest that a careful review for the current taxonomy of the family Psammobiidae is required.
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Abstract
Ever since its discovery, the double-stranded DNA contained in the mitochondria of eukaryotes has fascinated researchers because of its bacterial endosymbiotic origin, crucial role in encoding subunits of the respiratory complexes, compact nature, and specific inheritance mechanisms. In the last few years, high-throughput sequencing techniques have accelerated the sequencing of mitochondrial genomes (mitogenomes) and uncovered the great diversity of organizations, gene contents, and modes of replication and transcription found in living eukaryotes. Some early divergent lineages of unicellular eukaryotes retain certain synteny and gene content resembling those observed in the genomes of alphaproteobacteria (the inferred closest living group of mitochondria), whereas others adapted to anaerobic environments have drastically reduced or even lost the mitogenome. In the three main multicellular lineages of eukaryotes, mitogenomes have pursued diverse evolutionary trajectories in which different types of molecules (circular versus linear and single versus multipartite), gene structures (with or without self-splicing introns), gene contents, gene orders, genetic codes, and transfer RNA editing mechanisms have been selected. Whereas animals have evolved a rather compact mitochondrial genome between 11 and 50 Kb in length with a highly conserved gene content in bilaterians, plants exhibit large mitochondrial genomes of 66 Kb to 11.3 Mb with large intergenic repetitions prone to recombination, and fungal mitogenomes have intermediate sizes of 12 to 236 Kb.
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Affiliation(s)
- Rafael Zardoya
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
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Liu J, Zeng Q, Wang H, Teng M, Guo X, Bao Z, Wang S. The complete mitochondrial genome and phylogenetic analysis of the dwarf surf clam Mulinia lateralis. Mitochondrial DNA B Resour 2019; 5:140-141. [PMID: 33366458 PMCID: PMC7748403 DOI: 10.1080/23802359.2019.1698352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 11/23/2019] [Indexed: 11/06/2022] Open
Abstract
Mulinia lateralis (Say, 1822) is a species of the bivalve family Mactridae and represents a promising model species for molluscan research. In this study, the complete mitochondrial genome (mitogenome) of M. lateralis was sequenced and assembled for the first time. The 21,668 bp mitogenome contained 13 protein-coding genes, 2 rRNAs, 22 tRNA genes, and an AT-rich region. The overall AT content (69.56%) was higher than GC content (30.44%). Phylogenetic analysis supported that M. lateralis belongs to the family Mactridae. The mitochondrial genome of M. lateralis provides a valuable resource for further understanding the phylogeny of the family Mactridae and for functional studies of molluscan mitochondrial genes.
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Affiliation(s)
- Jing Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
| | - Qifan Zeng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
| | - Hao Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
| | - Mingxuan Teng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, Port Norris, New Jersey, USA
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, Shandong, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
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Fernández-Pérez J, Nantón A, Méndez J. Sequence characterization of the 5S ribosomal DNA and the internal transcribed spacer (ITS) region in four European Donax species (Bivalvia: Donacidae). BMC Genet 2018; 19:97. [PMID: 30367592 PMCID: PMC6204057 DOI: 10.1186/s12863-018-0684-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 10/11/2018] [Indexed: 01/04/2023] Open
Abstract
Background The whole repeat unit of 5S rDNA and the internal transcribed spacer (ITS) of four European Donax species were analysed. After amplifying, cloning and sequencing several 5S and ITS units, their basic features and their variation were described. The phylogenetic usefulness of 5S and ITS sequences in the inference of evolutionary relationships among these wedge clams was also investigated. Results The length of the 5S repeat presented little variation among species, except D. trunculus that differed from the rest of the Donax species in 170–210 bp. The deduced coding region covered 120 bp, and showed recognizable internal control regions (ICRs) involved in the transcription. The length of non-transcribed spacer region (NTS) ranged from 157 bp to 165 bp in Donax trunculus and from 335 bp to 367 bp in the other three species. The conservation degree of transcriptional regulatory regions was analysed revealing a conserved TATA-like box in the upstream region. Regarding ITS sequences, the four Donax species showed slight size differences among clones due to the variation occurring in the ITS1 and ITS2, except Donax variegatus did not display size differences in the ITS2. The total length of the ITS sequence ranged between 814 and 1014 bp. Resulting phylogenetic trees display that the two ribosomal DNA regions provide well-resolved phylogenies where the four European Donax species form a single clade receiving high support in nodes. The topology obtained with 5S sequences was in agreement with Donax evolutionary relationships inferred from several sequences of different nature in previous studies. Conclusions This is not only a basic research work, where new data and new knowledge is provided about Donax species, but also have allowed the authentication of these wedge clams and offers future applications to provide other genetic resources. Electronic supplementary material The online version of this article (10.1186/s12863-018-0684-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jenyfer Fernández-Pérez
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, Campus de A Zapateira, 15071, A Coruña, Spain.
| | - Ana Nantón
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, Campus de A Zapateira, 15071, A Coruña, Spain
| | - Josefina Méndez
- Grupo Xenomar, Departamento de Bioloxía, Facultade de Ciencias and Centro de Investigaciones Científicas Avanzadas (CICA), Universidade da Coruña, Campus de A Zapateira, 15071, A Coruña, Spain
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Li Q, Liao M, Yang M, Xiong C, Jin X, Chen Z, Huang W. Characterization of the mitochondrial genomes of three species in the ectomycorrhizal genus Cantharellus and phylogeny of Agaricomycetes. Int J Biol Macromol 2018; 118:756-769. [DOI: 10.1016/j.ijbiomac.2018.06.129] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/23/2018] [Accepted: 06/26/2018] [Indexed: 12/15/2022]
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Zhang D, Zou H, Wu SG, Li M, Jakovlić I, Zhang J, Chen R, Li WX, Wang GT. Three new Diplozoidae mitogenomes expose unusual compositional biases within the Monogenea class: implications for phylogenetic studies. BMC Evol Biol 2018; 18:133. [PMID: 30176801 PMCID: PMC6122551 DOI: 10.1186/s12862-018-1249-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 08/20/2018] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND As the topologies produced by previous molecular and morphological studies were contradictory and unstable (polytomy), evolutionary relationships within the Diplozoidae family and the Monogenea class (controversial relationships among the Discocotylinea, Microcotylinea and Gastrocotylinea suborders) remain unresolved. Complete mitogenomes carry a relatively large amount of information, sufficient to provide a much higher phylogenetic resolution than traditionally used morphological traits and/or single molecular markers. However, their implementation is hampered by the scarcity of available monogenean mitogenomes. Therefore, we sequenced and characterized mitogenomes belonging to three Diplozoidae family species, and conducted comparative genomic and phylogenomic analyses for the entire Monogenea class. RESULTS Taxonomic identification was inconclusive, so two of the species were identified merely to the genus level. The complete mitogenomes of Sindiplozoon sp. and Eudiplozoon sp. are 14,334 bp and 15,239 bp in size, respectively. Paradiplozoon opsariichthydis (15,385 bp) is incomplete: an approximately 2000 bp-long gap within a non-coding region could not be sequenced. Each genome contains the standard 36 genes (atp8 is missing). G + T content and the degree of GC- and AT-skews of these three mitogenome (and their individual elements) were higher than in other monogeneans. nad2, atp6 and nad6 were the most variable PCGs, whereas cox1, nad1 and cytb were the most conserved. Mitochondrial phylogenomics analysis, conducted using concatenated amino acid sequences of all PCGs, indicates that evolutionary relationships of the three genera are: (Eudiplozoon, (Paradiplozoon, Sindiplozoon)); and of the three suborders: (Discocotylinea, (Microcotylinea, Gastrocotylinea)). These intergeneric relationships were also supported by the skewness and principal component analyses. CONCLUSIONS Our results show that nad2, atp6 and nad6 (fast-evolving) would be better candidates than cox1 (slow-evolving) for species identification and population genetics studies in Diplozoidae. Nucleotide bias and codon and amino acid usage patterns of the three diplozoid mitogenomes are more similar to cestodes and trematodes than to other monogenean flatworms. This unusual mutational bias was reflected in disproportionately long branches in the phylogram. Our study offsets the scarcity of molecular data for the subclass Polyopisthocotylea to some extent, and might provide important new insights into the evolutionary history of the three genera and three suborders.
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Affiliation(s)
- Dong Zhang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Shan G. Wu
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Ming Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Biolake, Wuhan, 430075 People’s Republic of China
| | - Jin Zhang
- Bio-Transduction Lab, Biolake, Wuhan, 430075 People’s Republic of China
| | - Rong Chen
- Bio-Transduction Lab, Biolake, Wuhan, 430075 People’s Republic of China
| | - Wen X. Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Gui T. Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
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Gutiérrez J, Lamelas L, Aleix-Mata G, Arroyo M, Marchal JA, Palomeque T, Lorite P, Sánchez A. Complete mitochondrial genome of the Iberian Mole Talpa occidentalis (Talpidae, Insectivora) and comparison with Talpa europaea. Genetica 2018; 146:415-423. [PMID: 30145730 DOI: 10.1007/s10709-018-0033-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 08/01/2018] [Indexed: 12/23/2022]
Abstract
The complete mitogenome of Talpa occidentalis, the Iberian mole, was sequenced using a combination of the Illumina and Sanger methods. The 16,962 bp genome obtained contains 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and a control region. Thirty-seven identical repetitions of a 10-nucleotide (CACACGTACG) repeat element were identified in the non-coding control region (D-loop). The number, order, and orientation of the mitochondrial genes are the same as in T. europaea, the only mitogenome published so far for this genus. These two mitogenomes differ only at the repeat element included in the control region. The phylogeny obtained for the Talpidae species using the protein-coding genes of these mitogenomes agrees with the current classification of this family.
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Affiliation(s)
- Juana Gutiérrez
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - Luz Lamelas
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - Gaël Aleix-Mata
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - María Arroyo
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - Juan Alberto Marchal
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - Teresa Palomeque
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - Pedro Lorite
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain
| | - Antonio Sánchez
- Departamento de Biología Experimental, Área de Genética, Universidad de Jaén, Paraje de las Lagunillas s/n., 23071, Jaén, Spain.
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Cytogenetics in Arctica islandica (Bivalvia, Arctidae): the Longest Lived Non-Colonial Metazoan. Genes (Basel) 2018; 9:genes9060299. [PMID: 29899300 PMCID: PMC6027238 DOI: 10.3390/genes9060299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 06/08/2018] [Accepted: 06/12/2018] [Indexed: 11/16/2022] Open
Abstract
Due to its extraordinary longevity and wide distribution, the ocean quahog Arctica islandica has become an important species model in both aging and environmental change research. Notwithstanding that, most genetic studies on ocean quahogs have been focused on fishery related, phylogeographic and phylogenetic aspects but nothing is known about their chromosomes. In this work, the chromosomes of the ocean quahog Arctica islandica were analysed by means of 4′,6-diamidino-2-phenylindole (DAPI)/propidium iodide (PI) staining and fluorescent in situ hybridization (FISH) with rDNA, histone gene and telomeric probes. Whilst both 5S rDNA and 45S rDNA were clustered at single subcentromeric locations on the long arms of chromosome pairs 2 and 12, respectively, histone gene clusters located on the short arms of chromosome pairs 7, 10 and 17. As happens with most bivalves, the location of the vertebrate type telomeric sequence clusters was restricted to chromosome ends. The knowledge of the karyotype can facilitate the anchoring of genomic sequences to specific chromosome pairs in this species.
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Lv C, Li Q, Kong L. Comparative analyses of the complete mitochondrial genomes of Dosinia clams and their phylogenetic position within Veneridae. PLoS One 2018; 13:e0196466. [PMID: 29718949 PMCID: PMC5931646 DOI: 10.1371/journal.pone.0196466] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 04/13/2018] [Indexed: 11/19/2022] Open
Abstract
Mitochondrial genomes have proved to be a powerful tool in resolving phylogenetic relationship. In order to understand the mitogenome characteristics and phylogenetic position of the genus Dosinia, we sequenced the complete mitochondrial genomes of Dosinia altior and Dosinia troscheli (Bivalvia: Veneridae), compared them with that of Dosinia japonica and established a phylogenetic tree for Veneridae. The mitogenomes of D. altior (17,536 bp) and D. troscheli (17,229 bp) are the two smallest in Veneridae, which include 13 protein-coding genes, 2 ribosomal RNA genes, 22 tRNA genes, and non-coding regions. The mitogenomes of the Dosinia species are similar in size, gene content, AT content, AT- and GC- skews, and gene arrangement. The phylogenetic relationships of family Veneridae were established based on 12 concatenated protein-coding genes using maximum likelihood and Bayesian analyses, which supported that Dosininae and Meretricinae have a closer relationship, with Tapetinae being the sister taxon. The information obtained in this study will contribute to further understanding of the molecular features of bivalve mitogenomes and the evolutionary history of the genus Dosinia.
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Affiliation(s)
- Changda Lv
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, China
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García-Souto D, Pérez-García C, Pasantes JJ. Are Pericentric Inversions Reorganizing Wedge Shell Genomes? Genes (Basel) 2017; 8:genes8120370. [PMID: 29215567 PMCID: PMC5748688 DOI: 10.3390/genes8120370] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 11/30/2017] [Accepted: 12/01/2017] [Indexed: 11/27/2022] Open
Abstract
Wedge shells belonging to the Donacidae family are the dominant bivalves in exposed beaches in almost all areas of the world. Typically, two or more sympatric species of wedge shells differentially occupy intertidal, sublittoral, and offshore coastal waters in any given locality. A molecular cytogenetic analysis of two sympatric and closely related wedge shell species, Donax trunculus and Donax vittatus, was performed. Results showed that the karyotypes of these two species were both strikingly different and closely alike; whilst metacentric and submetacentric chromosome pairs were the main components of the karyotype of D. trunculus, 10–11 of the 19 chromosome pairs were telocentric in D. vittatus, most likely as a result of different pericentric inversions. GC-rich heterochromatic bands were present in both species. Furthermore, they showed coincidental 45S ribosomal RNA (rRNA), 5S rRNA and H3 histone gene clusters at conserved chromosomal locations, although D. trunculus had an additional 45S rDNA cluster. Intraspecific pericentric inversions were also detected in both D. trunculus and D. vittatus. The close genetic similarity of these two species together with the high degree of conservation of the 45S rRNA, 5S rRNA and H3 histone gene clusters, and GC-rich heterochromatic bands indicate that pericentric inversions contribute to the karyotype divergence in wedge shells.
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Affiliation(s)
- Daniel García-Souto
- Dpto. Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310 Vigo, Spain.
| | | | - Juan J Pasantes
- Dpto. Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, E-36310 Vigo, Spain.
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