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Cardoso DC, Baldez BCL, Pereira AH, Kalapothakis E, Rosse IC, Cristiano MP. De novo assembly of the complete mitochondrial genome of Mycetophylax simplex Emery, 1888 through organelle targeting revels no substantial expansion of gene spacers, but rather some slightly shorter genes. Mol Genet Genomics 2024; 299:16. [PMID: 38411741 DOI: 10.1007/s00438-024-02099-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 12/10/2023] [Indexed: 02/28/2024]
Abstract
Mitochondria play a key role in cell biology and have their own genome, residing in a highly oxidative environment that induces faster changes than the nuclear genome. Because of this, mitochondrial markers have been exploited to reconstruct phylogenetic and phylogeographic relationships in studies of adaptation and molecular evolution. In this study, we determined the complete mitogenome of the fungus-farming ant Mycetophylax simplex (Hymenoptera, Formicidae) and conducted a comparative analysis among 29 myrmicine ant mitogenomes. Mycetophylax simplex is an endemic ant that inhabits sand dunes along the southern Atlantic coast. Specifically, the species occur in the ecosystem known as "restinga", within the Atlantic Forest biome. Due to habitat degradation, land use and decline of restinga habitats, the species is considered locally extinct in extremely urban beaches and is listed as vulnerable on the Brazilian Red List (ICMBio). We employed a mitochondrion-targeting approach to obtain the complete mitogenome through high-throughput DNA sequencing technology. This method allowed us to determine the mitogenome with high performance, coverage and low cost. The circular mitogenome has a length of 16,367 base pairs enclosing 37 genes (13 protein-coding genes, 22 tRNAs and 2 rRNAs) along with one control region (CR). All the protein-coding genes begin with a typical ATN codon and end with the canonical stop codons. All tRNAs formed the fully paired acceptor stems and fold into the typical cloverleaf-shaped secondary structures. The gene order is consistent with the shared Myrmicinae structure, and the A + T content of the majority strand is 81.51%. Long intergenic spacers were not found but some gene are slightly shorter. The phylogenetic relationships based on concatenated nucleotide and amino acid sequences of the 13 protein-coding genes, using Maximum Likelihood and Bayesian Inference methods, indicated that mitogenome sequences were useful in resolving higher-level relationship within Formicidae.
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Affiliation(s)
- Danon Clemes Cardoso
- Genetics and Evolution of Ants Research Group - GEF, Universidade Federal de Ouro Preto, Ouro Preto, Mina Gerais, 35400-000, Brazil.
| | - Brenda Carla Lima Baldez
- Programa de Pós-Graduação em Ecologia de Biomas Tropicais, Universidade Federal de Ouro Preto, Ouro Preto, Mina Gerais, 35400-000, Brazil
| | - Adriana Heloísa Pereira
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-010, Brazil
| | - Evanguedes Kalapothakis
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-010, Brazil
| | - Izinara Cruz Rosse
- Departamento de Farmácia, Escola de Farmácia, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, 35400-000, Brazil
| | - Maykon Passos Cristiano
- Genetics and Evolution of Ants Research Group - GEF, Universidade Federal de Ouro Preto, Ouro Preto, Mina Gerais, 35400-000, Brazil
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Araujo NDS, Ogihara F, Martins PM, Arias MC. Insights from Melipona bicolor hybrid genome assembly: a stingless bee genome with chromosome-level scaffold. BMC Genomics 2024; 25:171. [PMID: 38350872 PMCID: PMC10863234 DOI: 10.1186/s12864-024-10075-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/01/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND The highly eusocial stingless bees are crucial pollinators of native and agricultural ecosystems. Nevertheless, genomic studies within this bee tribe remain scarce. We present the genome assembly of the stingless bee Melipona bicolor. This bee is a remarkable exception to the typical single-queen colony structure, since in this species, multiple queens may coexist and share reproductive duties, resulting in genetically diverse colonies with weak kinship connections. As the only known genuinely polygynous bee, M. bicolor's genome provides a valuable resource for investigating sociality beyond kin selection. RESULTS The genome was assembled employing a hybrid approach combining short and long reads, resulting in 241 contigs spanning 259 Mb (N50 of 6.2 Mb and 97.5% complete BUSCOs). Comparative analyses shed light on some evolutionary aspects of stingless bee genomics, including multiple chromosomal rearrangements in Melipona. Additionally, we explored the evolution of venom genes in M. bicolor and other stingless bees, revealing that, apart from two genes, the conserved repertoire of venom components remains under purifying selection in this clade. CONCLUSION This study advances our understanding of stingless bee genomics, contributing to the conservation efforts of these vital pollinators and offering insights into the evolutionary mechanisms driving their unique adaptations.
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Affiliation(s)
| | - Fernando Ogihara
- Laboratory of Genetics and Evolution of Bees, Bioscience Institute, Universidade de São Paulo - USP, São Paulo, Brazil
| | - Pedro Mariano Martins
- Gene Expression and Evolution Laboratory, Bioscience Institute, Universidade de São Paulo - USP, São Paulo, Brazil
| | - Maria Cristina Arias
- Laboratory of Genetics and Evolution of Bees, Bioscience Institute, Universidade de São Paulo - USP, São Paulo, Brazil
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Maia UM, Santos Júnior JED, Molina M, Galaschi-Teixeira JS, Carvalho AT, Miranda LDS, Imperatriz-Fonseca VL, Oliveira G, Giannini TC. Evidence for morphological and genetic structuring of Plebeia flavocincta (Apidae: Meliponini) populations in Northeast Brazil. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1057624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Tropical dry forests are increasingly threatened by human activities. In Northeast Brazil, the Caatinga, an area of tropical dry forests surrounded by wetlands, is considered globally unique among these habitats. In this region, the stingless bee Plebeia flavocincta is found in a variety of environmental, ecological, and demographic conditions. We aimed to characterize P. flavocincta populations within its natural range through wing geometric morphometrics and mitochondrial DNA (mtDNA) analyses. The characterization of population variability can clarify whether the species is morphologically and genetically diverse and whether populations are morphologically and genetically structured. We analyzed 673 samples by wing morphometry and 75 by cytochrome-b assays. Our results revealed P. flavocincta is genetically and morphologically diverse and populations are morphologically and genetically structured. Despite the differentiation between the two most morphologically distant populations, we verified a large overlap of morphological variation between all populations. The genetic analysis showed that the haplotypes were geographically structured into six clusters, four of which were located in coastal areas, and the remaining two in the drier inland region. The characterization of P. flavocincta populations is an important step toward decision-making in programs for the protection, management, and sustainable use of this stingless bee in local breeding efforts.
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Li R, Li M, Yan J, Bai M, Zhang H. Five Mitochondrial Genomes of the Genus Eysarcoris Hahn, 1834 with Phylogenetic Implications for the Pentatominae (Hemiptera: Pentatomidae). INSECTS 2021; 12:insects12070597. [PMID: 34209052 PMCID: PMC8306050 DOI: 10.3390/insects12070597] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/27/2021] [Accepted: 06/28/2021] [Indexed: 11/30/2022]
Abstract
Simple Summary Pentatominae is the largest subfamily in the Pentatomidae, and most of its species are considered important agricultural pests. The phylogenetic relationships of tribes within Pentatominae remain controversial despite the fact that many studies have been performed using various molecular markers. In this study, five mitogenomes of the genus Eysarcoris were sequenced and analyzed, and the phylogenetic relationships of tribes within Pentatominae were reconstructed. The gene arrangement of the five mitochondrial genomes were found to be conserved and identical to other heteropteran mitogenomes. Differences in start codon usage and tandem repeats within control regions were found between E. gibbosus and the other four Eysarcoris species. In addition, the phylogenetic analyses showed that E. gibbosus is the first diverging clade within Eysarcorini. The results support the proposal to transfer E. gibbosus to the Stagonomus, another genus of Eysarcorini. Our results clarified the phylogenetic relationships among tribes of Pentatominae and laid a foundation for the further studies of Pentatominae. Abstract Four complete mitogenomes of Eysarcoris rosaceus, E. montivagus, E. gibbosus, E. annamita and one near-complete mitochondrial genome of E. ventralis were sequenced and used to explore the phylogenetic relationships of tribes within the subfamily Pentatominae. The mitogenomes range from 15,422 to 16,043 base pairs (bp) in length and encode 37 genes, including 13 protein-coding genes (PCGs), two rRNA genes, 22 tRNA genes (21 in E. ventralis), and a control region. Similar to other heteropteran species, the AT contents of the sequenced species were higher than their GC contents. The most frequently used start/stop codon was ATN/TAA. GTG was only found in atp6 and atp8 of E. gibbosus. All transfer RNA genes (tRNAs) exhibit the typical cloverleaf secondary structure, except for the trnS1 and trnV, which lacks the stem of the DHU arm. The length and copy number of repeat units were conserved within Eysarcoris, with the exception of E. gibbosus. Phylogenetic analyses based on mitogenomes using both maximum likelihood (ML) and Bayesian inference (BI) methods strongly supported the relationship among tribes within Pentatominae and confirmed that Graphosoma should be an intermediate lineage of Pentatominae. The relationship between Eysarcoris and Carbula was strongly supported and combined with our previous geometric morphometrics and chromosomal studies, suggest the Eysarcoris should belong to the tribe Eyasrcorini. This work will help to enhance our understanding of mitochondrial genomic evolution and phylogenetic relationships in Pentatominae.
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Affiliation(s)
- Rongrong Li
- Laboratory of Insect Evolution, Taiyuan Normal University, Jinzhong 030619, China
| | - Min Li
- Laboratory of Insect Evolution, Taiyuan Normal University, Jinzhong 030619, China
| | - Jiang Yan
- Laboratory of Insect Evolution, Taiyuan Normal University, Jinzhong 030619, China
| | - Ming Bai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hufang Zhang
- Xinzhou Teachers University, Xinzhou 034000, China
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Ricardo PC, Françoso E, Arias MC. Fidelity of DNA polymerases in the detection of intraindividual variation of mitochondrial DNA. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 5:108-112. [PMID: 33366444 PMCID: PMC7720943 DOI: 10.1080/23802359.2019.1697188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Here we investigated the consequences of PCR amplification errors in the identification of intraindividual mtDNA variation. The bumblebee Bombus morio was chosen as model for the COI gene amplification tests with two DNA polymerases (Taq and Q5) presenting different error rates. The amplifications using Taq resulted in a significant increase of singleton haplotypes per individual in comparison to Q5. The sequence characteristics indicated that Taq resulted haplotypes are mostly due to amplification errors. Studies focusing on intraindividual variability should address special attention to the DNA polymerase fidelity to avoid overestimation of heteroplasmic haplotypes.
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Affiliation(s)
- Paulo Cseri Ricardo
- Departamento de Genética e Biologia Evolutiva - Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Elaine Françoso
- Departamento de Genética e Biologia Evolutiva - Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Maria Cristina Arias
- Departamento de Genética e Biologia Evolutiva - Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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Françoso E, Zuntini AR, Ricardo PC, Silva JPN, Brito R, Oldroyd BP, Arias MC. Conserved numts mask a highly divergent mitochondrial- COI gene in a species complex of Australian stingless bees Tetragonula (Hymenoptera: Apidae). Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:806-817. [PMID: 31526165 DOI: 10.1080/24701394.2019.1665036] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Tetragonula carbonaria, Tetragonula davenporti, Tetragonula hockingsi and Tetragonula mellipes comprise a species complex of Australian stingless bee species known as the 'Carbonaria' group. The species are difficult to distinguish morphologically and the major species-defining characters relate to comb architecture and nest entrance ornamentation. The taxonomy of the group is further complicated by likely nuclear mitochondrial pseudogenes (numts) and inter-specific hybrids. Here we demonstrate the existence of COI numts and isolate and characterize the 'true' mt-COI gene in T. carbonaria and T. hockingsi. Numts were isolated from enriched-nuclear DNA extraction followed by PCR amplification and Sanger sequencing, and were recognized by the presence of deletions and/or premature stop codons in the translated sequences. The mt-COI sequences were obtained from NGS sequencing using purified mtDNA. In T. carbonaria, two numts (numt1 and numt2) were identified and a third (numt3) was identified in T. hockingsi. Numt2 and numt3 are similar (1.2% sequence divergence), indicating a recent common origin. The genetic distance between the mt-COI of the two Tetragonula species was higher than might be expected for closely related species, 16.5%, corroborating previous studies in which T. carbonaria and T. hockingsi were regarded as separate species. The three numts are more similar to the COI of other stingless bee species, including Australian Austroplebia australis and South American Melipona bicolor (81.7-83.9%) than to the mt-COI of their own species (70-71.4%). This is because the mt-COI of T. carbonaria and T. hockingsi differ greatly from other Meliponinae. Our findings explain some formerly puzzling aspects of Carbonaria biogeography, and misinterpreted amplifications.
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Affiliation(s)
- Elaine Françoso
- Instituto de Biociências, Universidade de São Paulo , Rua do Matão , Brazil
| | | | | | | | - Rute Brito
- Instituto de Biotecnologia, Universidade Federal de Uberlândia , Uberlândia , Brazil
| | - Benjamin P Oldroyd
- Behaviour and Genetics of Social Insects Lab, University of Sydney , Sydney , Australia
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Carmo AOD, Faccin S, Thyssen PJ, Dias D, Rebelo MT, Kalapothakis E. Complete mitochondrial genomes from four species of the genus Oxysarcodexia (Sarcophagidae) with forensic entomology interest. MITOCHONDRIAL DNA PART B-RESOURCES 2019. [DOI: 10.1080/23802359.2018.1545538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Anderson Oliveira do Carmo
- Laboratório de Biotecnologia e Marcadores Moleculares, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- CESAM – Centro de Estudos do Ambiente e do Mar, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Susanne Faccin
- Laboratório de Biotecnologia e Marcadores Moleculares, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Patrícia J. Thyssen
- Departmento de Biologia Animal, Universidade Estadual de Campinas, Barão Geraldo, Campinas, Brazil
| | - Deodália Dias
- CESAM – Centro de Estudos do Ambiente e do Mar, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Maria Teresa Rebelo
- CESAM – Centro de Estudos do Ambiente e do Mar, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Evanguedes Kalapothakis
- Laboratório de Biotecnologia e Marcadores Moleculares, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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Faccin S, Carmo AOD, Thyssen PJ, Dias D, Rebelo MT, Kalapothakis E. Complete mitochondrial genomes from three species of the genus Peckia (Sarcophagidae) with forensic entomology interest. MITOCHONDRIAL DNA PART B-RESOURCES 2019. [DOI: 10.1080/23802359.2018.1545537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Susanne Faccin
- Laboratory of Biotechnology and Molecular Markers, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Anderson Oliveira do Carmo
- Laboratory of Biotechnology and Molecular Markers, Federal University of Minas Gerais, Belo Horizonte, Brazil
- CESAM - Centre for Environmental and Marine Studies, Lisbon, Portugal
| | - Patrícia J. Thyssen
- Department of Animal Biology, IB, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Deodália Dias
- CESAM - Centre for Environmental and Marine Studies, Lisbon, Portugal
- Department of Animal Biology, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Maria Teresa Rebelo
- CESAM - Centre for Environmental and Marine Studies, Lisbon, Portugal
- Department of Animal Biology, Faculty of Sciences, University of Lisbon, Lisbon, Portugal
| | - Evanguedes Kalapothakis
- Laboratory of Biotechnology and Molecular Markers, Federal University of Minas Gerais, Belo Horizonte, Brazil
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Queiroz ALL, Pereira AH, Lucio N, Kalapothakis Y, Miranda KG, Kalapothakis E. Complete mitochondrial genome of Saltator similis (Aves, Passeriformes). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1618210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Ana Luiza Lemos Queiroz
- Laboratory of Biotechnology and Molecular Markers, Biological Sciences Institute, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Adriana Heloísa Pereira
- Laboratory of Biotechnology and Molecular Markers, Biological Sciences Institute, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Nazaré Lucio
- Laboratory of Biotechnology and Molecular Markers, Biological Sciences Institute, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Yan Kalapothakis
- Laboratory of Biotechnology and Molecular Markers, Biological Sciences Institute, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Kelton Gonçalves Miranda
- Laboratory of Biotechnology and Molecular Markers, Biological Sciences Institute, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Evanguedes Kalapothakis
- Laboratory of Biotechnology and Molecular Markers, Biological Sciences Institute, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
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Anderson Oliveira C, Faccin S, Thyssen PJ, Dias D, Kalapothakis E, Rebelo MT. Complete mitochondrial genomes of three species of fresh flies of forensic entomology interest from the genus Sarcophaga (Sarcophagidae) from Portugal and Brazil. MITOCHONDRIAL DNA PART B-RESOURCES 2018. [DOI: 10.1080/23802359.2018.1545539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Carmo Anderson Oliveira
- Laboratório de Biotecnologia e Marcadores Moleculares, Universidade Federal de Minas Gerais, UFMG, Brazil
- Departmento de Biologia Animal, Universidade Estadual de Campinas, UNICAMP, Brazil
| | - Susanne Faccin
- Laboratório de Biotecnologia e Marcadores Moleculares, Universidade Federal de Minas Gerais, UFMG, Brazil
| | - Patrícia J. Thyssen
- CESAM – Centro de Estudos do Ambiente e do Mar Faculdade de Ciências da Universidade de Lisboa, Portugal
| | - Deodália Dias
- Departmento de Biologia Animal, Universidade Estadual de Campinas, UNICAMP, Brazil
- Departamento de Biologia Animal Faculdade de Ciências da Universidade de Lisboa, Portugal
| | - Evanguedes Kalapothakis
- Laboratório de Biotecnologia e Marcadores Moleculares, Universidade Federal de Minas Gerais, UFMG, Brazil
| | - Maria Teresa Rebelo
- Departmento de Biologia Animal, Universidade Estadual de Campinas, UNICAMP, Brazil
- Departamento de Biologia Animal Faculdade de Ciências da Universidade de Lisboa, Portugal
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Gajić B, Stevanović J, Radulović Ž, Kulišić Z, Vejnović B, Glavinić U, Stanimirović Z. Haplotype identification and detection of mitochondrial DNA heteroplasmy in Varroa destructor mites using ARMS and PCR-RFLP methods. EXPERIMENTAL & APPLIED ACAROLOGY 2016; 70:287-297. [PMID: 27631761 DOI: 10.1007/s10493-016-0086-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 08/08/2016] [Indexed: 06/06/2023]
Abstract
In the present study, amplification refractory mutation system (ARMS) and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methods were used for identification of recently described Serbia 1 (S1) and Peshter 1 (P1) mitochondrial haplotypes of Varroa destructor. Based on single nucleotide polymorphisms (SNPs) within cytochrome oxidase 1 (cox1) and cytochrome b (cytb) gene sequences, a total of 64 adult V. destructor females were analyzed from locations where the S1 and P1 haplotypes had been detected previously. Results of haplotype identification obtained by ARMS and PCR-RFLP methods were completely consistent with the sequencing data. Furthermore, in some analyzed samples the occurrence of site heteroplasmy at haplotype-defining sites was detected, as it was confirmed by double peaks in the sequence chromatograms. Neither mites with simultaneous nucleotide variability, nor those with combined SNP and heteroplasmy in cox1 and cytb were found. Given that this is the first occurrence of site heteroplasmy in V. destructor, the origin of this phenomenon and possible specific traits of heteroplasmic mites have yet to be determined.
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Affiliation(s)
- Bojan Gajić
- Department of Parasitology, Faculty of Veterinary Medicine, University of Belgrade, Bul. oslobodjenja 18, Belgrade, 11000, Serbia.
| | - Jevrosima Stevanović
- Department of Biology, Faculty of Veterinary Medicine, University of Belgrade, Bul. oslobodjenja 18, Belgrade, 11000, Serbia
| | - Željko Radulović
- Laboratory for Medical Entomology, Department for Parasitology, Center of Exellence for Toxoplasmosis and Medical Entomology, Institute for Medical Research, University of Belgrade, Dr. Subotića 4, POB 102, Belgrade, 11129, Serbia
| | - Zoran Kulišić
- Department of Parasitology, Faculty of Veterinary Medicine, University of Belgrade, Bul. oslobodjenja 18, Belgrade, 11000, Serbia
| | - Branislav Vejnović
- Department of Biology, Faculty of Veterinary Medicine, University of Belgrade, Bul. oslobodjenja 18, Belgrade, 11000, Serbia
| | - Uroš Glavinić
- Department of Biology, Faculty of Veterinary Medicine, University of Belgrade, Bul. oslobodjenja 18, Belgrade, 11000, Serbia
| | - Zoran Stanimirović
- Department of Biology, Faculty of Veterinary Medicine, University of Belgrade, Bul. oslobodjenja 18, Belgrade, 11000, Serbia
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Chimeric mitochondrial peptides from contiguous regular and swinger RNA. Comput Struct Biotechnol J 2016; 14:283-97. [PMID: 27453772 PMCID: PMC4942731 DOI: 10.1016/j.csbj.2016.06.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 06/19/2016] [Accepted: 06/23/2016] [Indexed: 12/20/2022] Open
Abstract
Previous mass spectrometry analyses described human mitochondrial peptides entirely translated from swinger RNAs, RNAs where polymerization systematically exchanged nucleotides. Exchanges follow one among 23 bijective transformation rules, nine symmetric exchanges (X ↔ Y, e.g. A ↔ C) and fourteen asymmetric exchanges (X → Y → Z → X, e.g. A → C → G → A), multiplying by 24 DNA's protein coding potential. Abrupt switches from regular to swinger polymerization produce chimeric RNAs. Here, human mitochondrial proteomic analyses assuming abrupt switches between regular and swinger transcriptions, detect chimeric peptides, encoded by part regular, part swinger RNA. Contiguous regular- and swinger-encoded residues within single peptides are stronger evidence for translation of swinger RNA than previously detected, entirely swinger-encoded peptides: regular parts are positive controls matched with contiguous swinger parts, increasing confidence in results. Chimeric peptides are 200 × rarer than swinger peptides (3/100,000 versus 6/1000). Among 186 peptides with > 8 residues for each regular and swinger parts, regular parts of eleven chimeric peptides correspond to six among the thirteen recognized, mitochondrial protein-coding genes. Chimeric peptides matching partly regular proteins are rarer and less expressed than chimeric peptides matching non-coding sequences, suggesting targeted degradation of misfolded proteins. Present results strengthen hypotheses that the short mitogenome encodes far more proteins than hitherto assumed. Entirely swinger-encoded proteins could exist. Chimeric peptides are translated from contiguous regular and swinger RNA They are 200x rarer than mitochondrial swinger peptides Chimeric peptides integrated in regular mitochondrial proteins are downregulated Contiguous regular parts are matched positive controls for swinger parts The last point validates results beyond other statistical tests for robustness
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