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Voronova NV, Levykina S, Warner D, Shulinski R, Bandarenka Y, Zhorov D. Characteristic and variability of five complete aphid mitochondrial genomes: Aphis fabae mordvilkoi, Aphis craccivora, Myzus persicae, Therioaphis tenera and Appendiseta robiniae (Hemiptera; Sternorrhyncha; Aphididae). Int J Biol Macromol 2020; 149:187-206. [PMID: 31917211 DOI: 10.1016/j.ijbiomac.2019.12.276] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 12/31/2019] [Accepted: 12/31/2019] [Indexed: 02/06/2023]
Abstract
The complete mitochondrial genomes of aphids Aphis fabae mordvilkoi, A. craccivora, Myzus persicae from Aphidinae as well as Therioaphis tenera and Appendiseta robiniae from Calaphidinae were sequenced and compared with the genomes of other aphid species. A. fabae mordvilkoi, Th. tenera and A. robiniae mitogenomes were sequenced and analyzed for the first time. The annotation of A. craccivora and M. persicae were corrected compared to what was previously published. According to our data there is no translocation of tRNA-Tyr gene in A. craccivora mitogenome and this aphid species has an ancestral type of mitochondrial gene order. A + T content in all 5 mitogenomes was higher than 80%. A + T content in the Th. tenera CR was 59.5% which is untypically low. CRs of all 5 studied mitogenomes had 2 conserved motifs at their ends and extended G + C rich region. A. craccivora, M. persicae and Th. tenera had large tandem repeats inside the CRs. Detailed molecular analysis of all 5 aphid mitochondrial genomes showed the importance of a deep understanding of the molecular organization of all the functional regions of the mitochondrial DNA, which helps to avoid mistakes during genome annotation.
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Affiliation(s)
- Nina V Voronova
- Zoology Department, Belarusian State University, Minsk, Belarus.
| | - Sofiya Levykina
- Zoology Department, Belarusian State University, Minsk, Belarus
| | - Derek Warner
- DNA Sequencing Core Facility, University of Utah, Salt Lake City, UT, United States of America
| | - Raman Shulinski
- Zoology Department, Belarusian State University, Minsk, Belarus
| | - Yury Bandarenka
- Zoology Department, Belarusian State University, Minsk, Belarus
| | - Dmitrii Zhorov
- Zoology Department, Belarusian State University, Minsk, Belarus
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Shen X, Song J, Meng X, Tian M, Yan B, Cheng H, Cai Y, Zhao J. The first representative of Coelomactra antiquata mitochondrial genome from Liaoning (China) and phylogenetic consideration. MITOCHONDRIAL DNA PART B-RESOURCES 2016; 1:525-527. [PMID: 33473543 PMCID: PMC7800962 DOI: 10.1080/23802359.2016.1197064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Coelomactra antiquata is a famous delicacy and a promising new candidate for aquaculture, which belongs to the family Mactridae (Mollusca: Veneroida). The complete mitochondrial genome of C. antiquata (Liao Ning province, in China, LN) was finished, which is the first representative from this province. The results showed that the total length of LN-mtDNA sequence is 16,797 bp and the content of A + T is 65.01%. It encodes 35 genes, including 12 protein-coding genes, 21 transfer RNA genes and two ribosomal RNA genes. All coding genes are encoded on the heavy strand. Compared with the typical gene content of animal mitochondrial genomes, atp8 and trnSer(UCN) genes are missing in the mitochondrial genome. The complete mitochondrial genome contains 26 non-coding regions (1598 bp), one major non-coding region consists of 1046 bp in which 4.9 tandem repeat sequences (99bp per sequence) was observed. The phylogenetic tree showed that Liaoning population was clustered into one clade with Shandong (Rizhao, Jiaonan and Jimo) and Guangxi (Beihai) populations, meanwhile all of them are far from the Fujian populations (Pingtan, Zhangzhou and Changle). So, Liaoning, Shandong and Guangxi populations have a close relationship. Actually, Fujian is located between Liaoning, Shandong and Guangxi. So, the result challenges the previously assumed relevance between geographic distance and genetic distance. The genetic distance of Liaoning C. antiquata and Fujian (Changle, Zhangzhou and Pingtan) C. antiquata (0.176–0.177) is greater than the genetic distance between Mytilus galloprovincialis and Mytilus trossulus (0.160). The genetic difference of Liaoning population and Fujian populations has reached species level.
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Affiliation(s)
- Xin Shen
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Institute of Marine Resources, Lianyungang, P.R. China.,College of Marine Science, Huaihai Institute of Technology, Lianyungang, P.R. China.,Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Huaihai Institute of Technology, Lianyungang, P.R. China
| | - Jun Song
- College of Marine Science, Huaihai Institute of Technology, Lianyungang, P.R. China
| | - Xueping Meng
- College of Marine Science, Huaihai Institute of Technology, Lianyungang, P.R. China
| | - Mei Tian
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Institute of Marine Resources, Lianyungang, P.R. China
| | - Binlun Yan
- Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Institute of Marine Resources, Lianyungang, P.R. China.,College of Marine Science, Huaihai Institute of Technology, Lianyungang, P.R. China
| | - Hanliang Cheng
- College of Marine Science, Huaihai Institute of Technology, Lianyungang, P.R. China
| | - Yuling Cai
- College of Marine Science, Huaihai Institute of Technology, Lianyungang, P.R. China
| | - Jun Zhao
- College of Marine Science, Huaihai Institute of Technology, Lianyungang, P.R. China
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Demari-Silva B, Foster PG, de Oliveira TMP, Bergo ES, Sanabani SS, Pessôa R, Sallum MAM. Mitochondrial genomes and comparative analyses of Culex camposi, Culex coronator, Culex usquatus and Culex usquatissimus (Diptera:Culicidae), members of the coronator group. BMC Genomics 2015; 16:831. [PMID: 26489754 PMCID: PMC4618934 DOI: 10.1186/s12864-015-1951-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 09/23/2015] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The Coronator Group currently encompasses six morphologically similar species (Culex camposi Dyar, Culex coronator Dyar and Knab, Culex covagarciai Forattini, Culex usquatus Dyar, Culex usquatissimus Dyar, and Culex ousqua Dyar). Culex coronator has been incriminated as a potential vector of West Nile Virus (WNV), Saint Louis Encephalitis Virus (SLEV), and Venezuelan Equine Encephalitis Virus (VEEV). The complete mitochondrial genome of Cx. coronator, Cx. usquatus, Cx.usquatissimus, and Cx. camposi was sequenced, annotated, and analyzed to provide genetic information about these species. RESULTS The mitochondrial genomes of Cx. coronator, Cx. usquatus, Cx.usquatissimus, and Cx. camposi varied from 15,573 base pairs in Cx. usquatus to 15,576 in Cx. coronator. They contained 37 genes (13 protein-encoding genes, 2 rRNA genes, and 22 tRNA genes) and the AT-rich control region. Comparative analyses of the 37 genes demonstrated the mitochondrial genomes to be composed of variable and conserved genes. Despite the small size, the ATP8, ATP6 plus NADH5 protein-encoding genes were polymorphic, whereas tRNAs and rRNAs were conserved. The control region contained some poly-T stretch. The Bayesian phylogenetic tree corroborated that both the Coronator Group and the Culex pipens complex are monophyletic taxa. CONCLUSIONS The mitochondrial genomes of Cx. coronator, Cx. usquatus, Cx. usquatissimus and Cx. camposi share the same gene composition and arrangement features that match to those reported for most Culicidae species. They are composed of the same 37 genes and the AT-rich control region, which contains poly-T stretches that may be involved in the functional role of the mitochondrial genome. Taken together, results of the dN/dS ratios, the sliding window analyses and the Bayesian phylogenetic analyses suggest that ATP6, ATP8 and NADH5 are promising genes to be employed in phylogenetic studies involving species of the Coronator Group, and probably other species groups of the subgenus Culex. Bayesian topology corroborated the morphological hypothesis of the Coronator Group as monophyletic lineage within the subgenus Culex.
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Affiliation(s)
- Bruna Demari-Silva
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, Brazil.
| | - Peter G Foster
- Department of Life Sciences, Natural History Museum, Cromwell Road, London, England.
| | - Tatiane M P de Oliveira
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, Brazil.
| | - Eduardo S Bergo
- Superintendência de Controle de Endemias, Secretaria de Estado da Saúde de São Paulo, Araraquara, São Paulo, Brazil.
| | - Sabri S Sanabani
- Department of Pathology, LIM 03, Hospital das Clínicas (HC), School of Medicine, University of São Paulo, São Paulo, Brazil.
| | - Rodrigo Pessôa
- Department of Pathology, LIM 03, Hospital das Clínicas (HC), School of Medicine, University of São Paulo, São Paulo, Brazil.
| | - Maria Anice M Sallum
- Departamento de Epidemiologia, Faculdade de Saúde Pública, Universidade de São Paulo, São Paulo, Brazil.
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Shen X, Sun S, Zhao FQ, Zhang GT, Tian M, Tsang LM, Wang JF, Chu KH. Phylomitogenomic analyses strongly support the sister relationship of the Chaetognatha and Protostomia. ZOOL SCR 2015. [DOI: 10.1111/zsc.12140] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xin Shen
- Jiangsu Key Laboratory of Marine Biotechnology/Co-Innovation Center of Jiangsu Marine Bio-industry Technology; Huaihai Institute of Technology; Lianyungang 222005 China
- Beijing Institutes of Life Science; Chinese Academy of Sciences; Beijing 100101 China
- Simon F. S. Li Marine Science Laboratory; School of Life Sciences; The Chinese University of Hong Kong; Shatin Hong Kong China
| | - Song Sun
- KLMEES and JBMERS; Institute of Oceanology; Chinese Academy of Sciences; Qingdao 266071 China
| | - Fang Qing Zhao
- Beijing Institutes of Life Science; Chinese Academy of Sciences; Beijing 100101 China
| | - Guang Tao Zhang
- KLMEES and JBMERS; Institute of Oceanology; Chinese Academy of Sciences; Qingdao 266071 China
| | - Mei Tian
- Jiangsu Key Laboratory of Marine Biotechnology/Co-Innovation Center of Jiangsu Marine Bio-industry Technology; Huaihai Institute of Technology; Lianyungang 222005 China
| | - Ling Ming Tsang
- Institute of Marine Biology; National Taiwan Ocean University; Keelung 20224 Taiwan
| | - Jin Feng Wang
- Beijing Institutes of Life Science; Chinese Academy of Sciences; Beijing 100101 China
| | - Ka Hou Chu
- Simon F. S. Li Marine Science Laboratory; School of Life Sciences; The Chinese University of Hong Kong; Shatin Hong Kong China
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Irisarri I, Eernisse DJ, Zardoya R. Molecular phylogeny of Acanthochitonina (Mollusca: Polyplacophora: Chitonida): three new mitochondrial genomes, rearranged gene orders and systematics. J NAT HIST 2014. [DOI: 10.1080/00222933.2014.963721] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Pons J, Bauzà-Ribot MM, Jaume D, Juan C. Next-generation sequencing, phylogenetic signal and comparative mitogenomic analyses in Metacrangonyctidae (Amphipoda: Crustacea). BMC Genomics 2014; 15:566. [PMID: 24997985 PMCID: PMC4112215 DOI: 10.1186/1471-2164-15-566] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 06/26/2014] [Indexed: 11/16/2022] Open
Abstract
Background Comparative mitochondrial genomic analyses are rare among crustaceans below the family or genus level. The obliged subterranean crustacean amphipods of the family Metacrangonyctidae, found from the Hispaniola (Antilles) to the Middle East, including the Canary Islands and the peri-Mediterranean region, have an evolutionary history and peculiar biogeography that can respond to Tethyan vicariance. Indeed, recent phylogenetic analysis using all protein-coding mitochondrial sequences and one nuclear ribosomal gene have lent support to this hypothesis (Bauzà-Ribot et al. 2012). Results We present the analyses of mitochondrial genome sequences of 21 metacrangonyctids in the genera Metacrangonyx and Longipodacrangonyx, covering the entire geographical range of the family. Most mitogenomes were attained by next-generation sequencing techniques using long-PCR fragments sequenced by Roche FLX/454 or GS Junior pyro-sequencing, obtaining a coverage depth per nucleotide of up to 281×. All mitogenomes were AT-rich and included the usual 37 genes of the metazoan mitochondrial genome, but showed a unique derived gene order not matched in any other amphipod mitogenome. We compare and discuss features such as strand bias, phylogenetic informativeness, non-synonymous/synonymous substitution rates and other mitogenomic characteristics, including ribosomal and transfer RNAs annotation and structure. Conclusions Next-generation sequencing of pooled long-PCR amplicons can help to rapidly generate mitogenomic information of a high number of related species to be used in phylogenetic and genomic evolutionary studies. The mitogenomes of the Metacrangonyctidae have the usual characteristics of the metazoan mitogenomes (circular molecules of 15,000-16,000 bp, coding for 13 protein genes, 22 tRNAs and two ribosomal genes) and show a conserved gene order with several rearrangements with respect to the presumed Pancrustacean ground pattern. Strand nucleotide bias appears to be reversed with respect to the condition displayed in the majority of crustacean mitogenomes since metacrangonyctids show a GC-skew at the (+) and (-) strands; this feature has been reported also in the few mitogenomes of Isopoda (Peracarida) known thus far. The features of the rRNAs, tRNAs and sequence motifs of the control region of the Metacrangonyctidae are similar to those of the few crustaceans studied at present. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-566) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joan Pons
- IMEDEA (CSIC-UIB), Mediterranean Institute for Advanced Studies, c/Miquel Marquès 21, 07190 Esporles, Spain.
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Stampar SN, Maronna MM, Kitahara MV, Reimer JD, Morandini AC. Fast-evolving mitochondrial DNA in Ceriantharia: a reflection of hexacorallia paraphyly? PLoS One 2014; 9:e86612. [PMID: 24475157 PMCID: PMC3903554 DOI: 10.1371/journal.pone.0086612] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 12/12/2013] [Indexed: 11/19/2022] Open
Abstract
The low evolutionary rate of mitochondrial genes in Anthozoa has challenged their utility for phylogenetic and systematic purposes, especially for DNA barcoding. However, the evolutionary rate of Ceriantharia, one of the most enigmatic "orders" within Anthozoa, has never been specifically examined. In this study, the divergence of mitochondrial DNA of Ceriantharia was compared to members of other Anthozoa and Medusozoa groups. In addition, nuclear markers were used to check the relative phylogenetic position of Ceriantharia in relation to other Cnidaria members. The results demonstrated a pattern of divergence of mitochondrial DNA completely different from those estimated for other anthozoans, and phylogenetic analyses indicate that Ceriantharia is not included within hexacorallians in most performed analyses. Thus, we propose that the Ceriantharia should be addressed as a separate clade.
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Affiliation(s)
- Sérgio N. Stampar
- Universidade Estadual Paulista “Júlio de Mesquita Filho”, Laboratório de Biologia Aquática - LABIA, Faculdade de Ciências e Letras de Assis, Departamento de Ciências Biológicas, Assis, São Paulo, Brazil
- Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, São Paulo, São Paulo, Brazil
| | - Maximiliano M. Maronna
- Universidade de São Paulo, Instituto de Biociências, Departamento de Genética e Biologia Evolutiva, São Paulo, São Paulo, Brazil
| | - Marcelo V. Kitahara
- Universidade de São Paulo, Centro de Biologia Marinha, São Sebastião, São Paulo, Brazil
| | - James D. Reimer
- Molecular Invertebrate Systematics and Ecology Laboratory, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - André C. Morandini
- Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, São Paulo, São Paulo, Brazil
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