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Complete mitochondrial genome of Hygrobates turcicus Pešić, Esen & Dabert, 2017 (Acari, Hydrachnidia, Hygrobatoidea). Sci Rep 2022; 12:22063. [PMID: 36543798 PMCID: PMC9772306 DOI: 10.1038/s41598-022-26188-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
The aim of the study was sequencing of the mitogenome of Hygrobates turcicus Pešić, Esen & Dabert, 2017 to expand knowledge of the polymorphism and cryptic or pseudocryptic diversity within Hydrachnidia. The samples originated from Bulgaria, Vidima River near Debnewo, 42°56'41.4''N, 24°48'44.6''E, depth 0.4 m, stones on the bottom, water flow 0.71 m/s, temperature 10 °C, pH 8.53, oxygen 110%, conductivity 279 µS/cm, hardness 121 CaO mg/l; 11 males, 27 females, 2 deutonymphs 12.x.2019 leg. Zawal, Michoński & Bańkowska; one male and one female dissected and slides mounted. The study was carried out using the following methods: DNA extraction, sequencing, assembly and annotation, comparison with other populations of H. turcicus, and multigene phylogeny. As a result of the study, it was determined that the mitogenome is 15,006 bp long and encodes for 13 proteins, 2 rRNAs, and 22 tRNAs. The genome is colinear with those of H. longiporus and H. taniguchii, the difference in size originating from a non-coding region located between protein-coding genes ND4L and ND3. Five genes have alternative start-codon, and four display premature termination. The multigene phylogeny obtained using all mitochondrial protein-coding genes unambiguously associates H. turcicus with the cluster formed by H. longiporus and H. taniguchii.
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Thia JA, Young ND, Korhnen PK, Yang Q, Gasser RB, Umina PA, Hoffmann AA. The mitogenome of Halotydeus destructor (Tucker) and its relationships with other trombidiform mites as inferred from nucleotide sequences and gene arrangements. Ecol Evol 2021; 11:14162-14174. [PMID: 34707848 PMCID: PMC8525180 DOI: 10.1002/ece3.8133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/25/2021] [Accepted: 09/01/2021] [Indexed: 01/02/2023] Open
Abstract
The redlegged earth mite, Halotydeus destructor (Tucker, 1925: Trombidiformes, Eupodoidea, Penthaleidae), is an invasive mite species. In Australia, this mite has become a pest of winter pastures and grain crops. We report the complete mitogenome for H. destructor, the first to represent the family Penthaleidae, superfamily Eupodoidea. The mitogenome of H. destructor is 14,691 bp in size, and has a GC content of 27.87%, 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. We explored evolutionary relationships of H. destructor with other members of the Trombidiformes using phylogenetic analyses of nucleotide sequences and the order of protein-coding and rRNA genes. We found strong, consistent support for the superfamily Tydeoidea being the sister taxon to the superfamily Eupodoidea based on nucleotide sequences and gene arrangements. Moreover, the gene arrangements of Eupodoidea and Tydeoidea are not only identical to each other but also identical to that of the hypothesized arthropod ancestor, showing a high level of conservatism in the mitogenomic structure of these mite superfamilies. Our study illustrates the utility of gene arrangements for providing complementary information to nucleotide sequences with respect to inferring the evolutionary relationships of species within the order Trombidiformes. The mitogenome of H. destructor provides a valuable resource for further population genetic studies of this important agricultural pest. Given the co-occurrence of closely related, morphologically similar Penthaleidae mites with H. destructor in the field, a complete mitogenome provides new opportunities to develop metabarcoding tools to study mite diversity in agro-ecosystems. Moreover, the H. destructor mitogenome fills an important taxonomic gap that will facilitate further study of trombidiform mite evolution.
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Affiliation(s)
- Joshua A. Thia
- Bio 21 Institute, School of BioSciencesThe University of MelbourneMelbourneVictoriaAustralia
| | - Neil D. Young
- Department of Veterinary Biosciences, Melbourne Veterinary SchoolThe University of MelbourneMelbourneVictoriaAustralia
| | - Pasi K. Korhnen
- Department of Veterinary Biosciences, Melbourne Veterinary SchoolThe University of MelbourneMelbourneVictoriaAustralia
| | - Qiong Yang
- Bio 21 Institute, School of BioSciencesThe University of MelbourneMelbourneVictoriaAustralia
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary SchoolThe University of MelbourneMelbourneVictoriaAustralia
| | - Paul A. Umina
- Bio 21 Institute, School of BioSciencesThe University of MelbourneMelbourneVictoriaAustralia
- Cesar AustraliaBrunswickVictoriaAustralia
| | - Ary A. Hoffmann
- Bio 21 Institute, School of BioSciencesThe University of MelbourneMelbourneVictoriaAustralia
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Chapurina YE, Bolotov IN, Vidrine MF, Vikhrev IV, Lunn Z, Chan N, Win T, Bespalaya YV, Aksenova OV, Gofarov MY, Kondakov AV, Konopleva ES. Taxonomic richness and host range of tropical Asian mussel‐associated mite assemblages (Acari: Unionicolidae) with a description of a new subgenus and species of parasitic mite from freshwater pearl mussels (Unionida: Margaritiferidae). J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yulia E. Chapurina
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences Arkhangelsk Russia
- Northern Arctic Federal University Arkhangelsk Russia
| | - Ivan N. Bolotov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences Arkhangelsk Russia
- Northern Arctic Federal University Arkhangelsk Russia
| | | | - Ilya V. Vikhrev
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences Arkhangelsk Russia
- Northern Arctic Federal University Arkhangelsk Russia
| | - Zau Lunn
- Fauna & Flora International –Myanmar Programme Yangon Myanmar
- Biology Department University of New Brunswick Saint John NB Canada
| | - Nyein Chan
- Fauna & Flora International –Myanmar Programme Yangon Myanmar
| | - Than Win
- Department of Zoology Dawei University Dawei Myanmar
| | - Yulia V. Bespalaya
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences Arkhangelsk Russia
- Northern Arctic Federal University Arkhangelsk Russia
| | - Olga V. Aksenova
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences Arkhangelsk Russia
- Northern Arctic Federal University Arkhangelsk Russia
| | - Mikhail Y. Gofarov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences Arkhangelsk Russia
- Northern Arctic Federal University Arkhangelsk Russia
| | - Alexander V. Kondakov
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences Arkhangelsk Russia
- Northern Arctic Federal University Arkhangelsk Russia
| | - Ekaterina S. Konopleva
- N. Laverov Federal Center for Integrated Arctic Research of the Ural Branch of the Russian Academy of Sciences Arkhangelsk Russia
- Northern Arctic Federal University Arkhangelsk Russia
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Alarcón-Elbal PM, García-Jiménez R, Peláez ML, Horreo JL, Valdecasas AG. Molecular Correlation between Larval, Deutonymph and Adult Stages of the Water Mite Arrenurus (Micruracarus) Novus. Life (Basel) 2020; 10:life10070108. [PMID: 32659940 PMCID: PMC7400179 DOI: 10.3390/life10070108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/05/2020] [Accepted: 07/07/2020] [Indexed: 12/03/2022] Open
Abstract
The systematics of many groups of organisms has been based on the adult stage. Morphological transformations that occur during development from the embryonic to the adult stage make it difficult (or impossible) to identify a juvenile (larval) stage in some species. Hydrachnidia (Acari, Actinotrichida, which inhabit mainly continental waters) are characterized by three main active stages—larval, deutonymph and adult—with intermediate dormant stages. Deutonymphs and adults may be identified through diagnostic morphological characters. Larvae that have not been tracked directly from a gravid female are difficult to identify to the species level. In this work, we compared the morphology of five water mite larvae and obtained the molecular sequences of that found on a pupa of the common mosquito Culex (Culex) pipiens with the sequences of 51 adults diagnosed as Arrenurus species and identified the undescribed larvae as Arrenurus(Micruracarus) novus. Further corroborating this finding, adult A. novus was found thriving in the same mosquito habitat. We established the identity of adult and deutonymph A. novus by morphology and by correlating COI and cytB sequences of the water mites at the larval, deutonymph and adult (both male and female) life stages in a particular case of ‘reverse taxonomy’. In addition, we constructed the Arrenuridae phylogeny based on mitochondrial DNA, which supports the idea that three Arrenurus subgenera are ‘natural’: Arrenurus, Megaluracarus and Micruracarus, and the somewhat arbitrary distinction of the species assigned to the subgenus Truncaturus.
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Affiliation(s)
- Pedro María Alarcón-Elbal
- Instituto de Medicina Tropical & Salud Global (IMTSAG), Universidad Iberoamericana (UNIBE), 22333 Santo Domingo, Dominican Republic;
| | - Ricardo García-Jiménez
- Museo Nacional de Ciencias Naturales, CSIC. C/José Gutiérrez Abascal, 2, 28006 Madrid, Spain; (R.G.-J.); (M.L.P.); (A.G.V.)
| | - María Luisa Peláez
- Museo Nacional de Ciencias Naturales, CSIC. C/José Gutiérrez Abascal, 2, 28006 Madrid, Spain; (R.G.-J.); (M.L.P.); (A.G.V.)
| | - Jose Luis Horreo
- UMIB Research Unit of Biodiversity (UO, CSIC, PA), C/Gonzalo Gutiérrez de Quirós s/n, 33600 Mieres, Spain
- Correspondence: ; Tel.: +34-985-10-30-00 (ext. 5943)
| | - Antonio G. Valdecasas
- Museo Nacional de Ciencias Naturales, CSIC. C/José Gutiérrez Abascal, 2, 28006 Madrid, Spain; (R.G.-J.); (M.L.P.); (A.G.V.)
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Li WN, Xue XF. Mitochondrial genome reorganization provides insights into the relationship between oribatid mites and astigmatid mites (Acari: Sarcoptiformes: Oribatida). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz044] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Oribatida s.l. represents one of the most species-rich mite lineages, including two recognized groups: oribatid mites (Oribatida s.s., non-astigmatan oribatids) and astigmatid mites (Astigmata). However, the relationship between these two groups has been debated. Here, we sequenced the complete mitochondrial (mt) genome of one oribatid mite and one astigmatid mite, retrieved complete mt genomes of three oribatid mites, and compared them with two other oribatid mites and 12 astigmatid mites sequenced previously. We find that gene orders in the mt genomes of both oribatid mites and astigmatid mites are rearranged relative to the hypothetical ancestral arrangement of the arthropods. Based on the shared derived gene clusters in each mt genome group, rearranged mt genomes are roughly divided into two groups corresponding to each mite group (oribatid mites or astigmatid mites). Phylogenetic results show that Astigmata nested in Oribatida. The monophyly of Astigmata is recovered, while paraphyly of Oribatida s.s. is observed. Our results show that rearranged gene orders in the mt genomes characterize various lineages of oribatid mites and astigmatid mites, and have potential phylogenetic information for resolving the high-level (cohort or supercohort) phylogeny of Oribatida.
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Affiliation(s)
- Wei-Ning Li
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
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Mitochondrial genome evolution and tRNA truncation in Acariformes mites: new evidence from eriophyoid mites. Sci Rep 2016; 6:18920. [PMID: 26732998 PMCID: PMC4702108 DOI: 10.1038/srep18920] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 11/30/2015] [Indexed: 11/08/2022] Open
Abstract
The subclass Acari (mites and ticks) comprises two super-orders: Acariformes and Parasitiformes. Most species of the Parasitiformes known retained the ancestral pattern of mitochondrial (mt) gene arrangement of arthropods, and their mt tRNAs have the typical cloverleaf structure. All of the species of the Acariformes known, however, have rearranged mt genomes and truncated mt tRNAs. We sequenced the mt genomes of two species of Eriophyoidea: Phyllocoptes taishanensis and Epitrimerus sabinae. The mt genomes of P. taishanensis and E. sabinae are 13,475 bp and 13,531 bp, respectively, are circular and contain the 37 genes typical of animals; most mt tRNAs are highly truncated in both mites. On the other hand, these two eriophyoid mites have the least rearranged mt genomes seen in the Acariformes. Comparison between eriophyoid mites and other Aacariformes mites showed that: 1) the most recent common ancestor of Acariformes mites retained the ancestral pattern of mt gene arrangement of arthropods with slight modifications; 2) truncation of tRNAs for cysteine, phenylalanine and histidine occurred once in the most recent common ancestor of Acariformes mites whereas truncation of other tRNAs occurred multiple times; and 3) the placement of eriophyoid mites in the order Trombidiformes needs to be reviewed.
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Characterization of the complete mitochondrial genome of the storage mite pest Tyrophagus longior (Gervais) (Acari: Acaridae) and comparative mitogenomic analysis of four acarid mites. Gene 2015; 576:807-19. [PMID: 26584537 DOI: 10.1016/j.gene.2015.11.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 11/03/2015] [Accepted: 11/11/2015] [Indexed: 02/07/2023]
Abstract
Mites of the genus Tyrophagus are economically important polyphagous pest commonly living on stored products and also responsible for allergic reactions to humans. Complete mitochondrial genomes (mitogenomes) and the gene features therein are widely used as molecular markers in the study of population genetics, phylogenetics as well as molecular evolution. However, scarcity on the sequence data has greatly impeded the studies in these areas pertaining to the Acari (mites and ticks). Information on the Tyrophagus mitogenomes is quite critical for phylogenetic evaluation and molecular evolution of the mitogenomes within Acariformes. Herein, we reported the complete mitogenome of the allergenic acarid storage mite Tyrophagus longior (Astigmata: Acaridae), an important member of stored food pests, and compared with those of other three acarid mites. The complete mitogenome of T. longior was a circular molecule of 13,271 bp. Unexpectedly, only 19 transfer RNA genes (tRNAs) were present, lacking trnF, trnS1 and trnQ. Furthermore, it also contained 13 protein-coding genes (PCGs) and 2 genes for rRNA (rrnS and rrnL) commonly detected in metazoans. The four mitogenomes displayed similar characteristics with respect to the gene content, nucleotide comparison, and codon usages. Yet, the gene order of T. longior was different from that in other Acari. The J-strands of the four mitogenomes possessed high A+T content (67.4-70.0%), and exhibited positive GC-skews and negative AT-skews. Most inferred tRNAs of T. longior were extremely truncated, lacking either a D- or T-arm, as found in other acarid mites. In T. longior mitogenome the A+T-rich region was just 50 bp in length and can be folded as a stable stem-loop structure, whereas in the region some structures of microsatellite-like (AT)n and palindromic sequences was not present. Besides, reconstructing of the phylogenetic relationship based on concatenated amino acid sequences of 13 PCGs supported that monophyly of the family Acaridae and the order Astigmata, to which the former belongs. Our results were consistent with the traditional classifications.
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Palopoli MF, Minot S, Pei D, Satterly A, Endrizzi J. Complete mitochondrial genomes of the human follicle mites Demodex brevis and D. folliculorum: novel gene arrangement, truncated tRNA genes, and ancient divergence between species. BMC Genomics 2014; 15:1124. [PMID: 25515815 PMCID: PMC4320518 DOI: 10.1186/1471-2164-15-1124] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 11/26/2014] [Indexed: 01/14/2023] Open
Abstract
Background Follicle mites of the genus Demodex are found on a wide diversity of mammals, including humans; surprisingly little is known, however, about the evolution of this association. Additional sequence information promises to facilitate studies of Demodex variation within and between host species. Here we report the complete mitochondrial genome sequences of two species of Demodex known to live on humans—Demodex brevis and D. folliculorum—which are the first such genomes available for any member of the genus. We analyzed these sequences to gain insight into the evolution of mitochondrial genomes within the Acariformes. We also used relaxed molecular clock analyses, based on alignments of mitochondrial proteins, to estimate the time of divergence between these two species. Results Both Demodex genomes shared a novel gene order that differs substantially from the ancestral chelicerate pattern, with transfer RNA (tRNA) genes apparently having moved much more often than other genes. Mitochondrial tRNA genes of both species were unusually short, with most of them unable to encode tRNAs that could fold into the canonical cloverleaf structure; indeed, several examples lacked both D- and T-arms. Finally, the high level of sequence divergence observed between these species suggests that these two lineages last shared a common ancestor no more recently than about 87 mya. Conclusions Among Acariformes, rearrangements involving tRNA genes tend to occur much more often than those involving other genes. The truncated tRNA genes observed in both Demodex species would seem to require the evolution of extensive tRNA editing capabilities and/or coevolved interacting factors. The molecular machinery necessary for these unusual tRNAs to function might provide an avenue for developing treatments of skin disorders caused by Demodex. The deep divergence time estimated between these two species sets a lower bound on the time that Demodex have been coevolving with their mammalian hosts, and supports the hypothesis that there was an early split within the genus Demodex into species that dwell in different skin microhabitats. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1124) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michael F Palopoli
- Department of Biology, Bowdoin College, Brunswick 6500, College Station ME 04011, USA.
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Liu M, Zhang Z, Peng Z. The mitochondrial genome of the water spiderArgyroneta aquatica(Araneae: Cybaeidae). ZOOL SCR 2014. [DOI: 10.1111/zsc.12090] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Mingxin Liu
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education); Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education); School of Life Science; Southwest University; Chongqing 400715 China
| | - Zhisheng Zhang
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education); Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education); School of Life Science; Southwest University; Chongqing 400715 China
| | - Zuogang Peng
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education); Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education); School of Life Science; Southwest University; Chongqing 400715 China
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Chen DS, Jin PY, Zhang KJ, Ding XL, Yang SX, Ju JF, Zhao JY, Hong XY. The complete mitochondrial genomes of six species of Tetranychus provide insights into the phylogeny and evolution of spider mites. PLoS One 2014; 9:e110625. [PMID: 25329165 PMCID: PMC4199730 DOI: 10.1371/journal.pone.0110625] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 09/15/2014] [Indexed: 11/18/2022] Open
Abstract
Many spider mites belonging to the genus Tetranychus are of agronomical importance. With limited morphological characters, Tetranychus mites are usually identified by a combination of morphological characteristics and molecular diagnostics. To clarify their molecular evolution and phylogeny, the mitochondrial genomes of the green and red forms of Tetranychus urticae as well as T. kanzawai, T. ludeni, T. malaysiensis, T. phaselus, T. pueraricola were sequenced and compared. The seven mitochondrial genomes are typical circular molecules of about 13,000 bp encoding and they are composed of the complete set of 37 genes that are usually found in metazoans. The order of the mitochondrial (mt) genes is the same as that in the mt genomes of Panonychus citri and P. ulmi, but very different from that in other Acari. The J-strands of the mitochondrial genomes have high (∼ 84%) A+T contents, negative GC-skews and positive AT-skews. The nucleotide sequence of the cox1 gene, which is commonly used as a taxon barcode and molecular marker, is more highly conserved than the nucleotide sequences of other mitochondrial genes in these seven species. Most tRNA genes in the seven genomes lose the D-arm and/or the T-arm. The functions of these tRNAs need to be evaluated. The mitochondrial genome of T. malaysiensis differs from the other six genomes in having a slightly smaller genome size, a slight difference in codon usage, and a variable loop in place of the T-arm of some tRNAs by a variable loop. A phylogenic analysis shows that T. malaysiensis first split from other Tetranychus species and that the clade of the family Tetranychoidea occupies a basal position in the Trombidiformes. The mt genomes of the green and red forms of T. urticae have limited divergence and short evolutionary distance.
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Affiliation(s)
- Da-Song Chen
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Peng-Yu Jin
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Kai-Jun Zhang
- Department of Entomology, College of Plant Protection, Southwest University, Chongqing, China
| | - Xiu-Lei Ding
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Si-Xia Yang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jia-Fei Ju
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jing-Yu Zhao
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Xiao-Yue Hong
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing, Jiangsu, China
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Sun ET, Li CP, Nie LW, Jiang YX. The complete mitochondrial genome of the brown leg mite, Aleuroglyphus ovatus (Acari: Sarcoptiformes): evaluation of largest non-coding region and unique tRNAs. EXPERIMENTAL & APPLIED ACAROLOGY 2014; 64:141-157. [PMID: 24777358 DOI: 10.1007/s10493-014-9816-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 04/08/2014] [Indexed: 06/03/2023]
Abstract
The circular mitochondrial genome (mitogenome) of Aleuroglyphus ovatus was sequenced. It was 14,328 bp long, and consisted of 37 coding genes including 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. This is the first description of the complete mitogenome of a species in the Acaridae (Acari: Sarcoptiformes). The mtDNA gene order for A. ovatus is identical to those of Dermatophagoides farinae and D. pteronyssinus, but distinctly different from the mtDNA of other Acari. Most inferred tRNA genes of A. ovatus are extremely truncated (48-62 bp), lack stem-loops on either the T- or D-arm (except the trnK), and are unable to fold into the canonical tRNA cloverleaf structure. The largest non-coding region (378 bp) contained several conserved sequences involved in the regulation of mitogenome replication, including one core sequence (ACAT) associated with termination of the J-strand replication and several hypothetical stem-loop structures. The microsatellite-like (AT)n sequence in the largest non-coding region was observed in two other Astigmata species, but it has not been found in other Acari.
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Affiliation(s)
- En-Tao Sun
- The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Life Science College, Anhui Normal University, Wuhu, 241000, People's Republic of China
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Baek SY, Choi EH, Jang KH, Ryu SH, Park SM, Suk HY, Chang CY, Hwang UW. Complete mitochondrial genomes of Carcinoscorpius rotundicauda and Tachypleus tridentatus (Xiphosura, Arthropoda) and implications for chelicerate phylogenetic studies. Int J Biol Sci 2014; 10:479-89. [PMID: 24795529 PMCID: PMC4007361 DOI: 10.7150/ijbs.8739] [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: 02/01/2014] [Accepted: 04/02/2014] [Indexed: 11/05/2022] Open
Abstract
Horseshoe crabs (order Xiphosura) are often referred to as an ancient order of marine chelicerates and have been considered as keystone taxa for the understanding of chelicerate evolution. However, the mitochondrial genome of this order is only available from a single species, Limulus polyphemus. In the present study, we analyzed the complete mitochondrial genomes from two Asian horseshoe crabs, Carcinoscorpius rotundicauda and Tachypleus tridentatus to offer novel data for the evolutionary relationship within Xiphosura and their position in the chelicerate phylogeny. The mitochondrial genomes of C. rotundicauda (15,033 bp) and T. tridentatus (15,006 bp) encode 13 protein-coding genes, two ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes. Overall sequences and genome structure of two Asian species were highly similar to that of Limulus polyphemus, though clear differences among three were found in the stem-loop structure of the putative control region. In the phylogenetic analysis with complete mitochondrial genomes of 43 chelicerate species, C. rotundicauda and T. tridentatus were recovered as a monophyly, while L. polyphemus solely formed an independent clade. Xiphosuran species were placed at the basal root of the tree, and major other chelicerate taxa were clustered in a single monophyly, clearly confirming that horseshoe crabs composed an ancestral taxon among chelicerates. By contrast, the phylogenetic tree without the information of Asian horseshoe crabs did not support monophyletic clustering of other chelicerates. In conclusion, our analyses may provide more robust and reliable perspective on the study of evolutionary history for chelicerates than earlier analyses with a single Atlantic species.
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Affiliation(s)
- Su Youn Baek
- 1. School of Life Sciences, Graduate School, Kyungpook National University, Daegu 702-701, South Korea
| | - Eun Hwa Choi
- 2. Department of Biology, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu 702-701, South Korea
| | - Kuem Hee Jang
- 2. Department of Biology, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu 702-701, South Korea
| | - Shi Hyun Ryu
- 2. Department of Biology, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu 702-701, South Korea
| | - Sang Myeon Park
- 3. Department of Science Education, Graduate School, Kyungpook National University, Daegu 702-701, South Korea
| | - Ho Young Suk
- 4. Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsangbuk-do 705-717, South Korea
| | - Cheon Young Chang
- 5. Department of Biology, College of Natural Science, Daegu University, Gyeongsan, Gyeongsangbuk-do 712-714, South Korea
| | - Ui Wook Hwang
- 2. Department of Biology, Teachers College & Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu 702-701, South Korea
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Briscoe AG, Goodacre S, Masta SE, Taylor MI, Arnedo MA, Penney D, Kenny J, Creer S. Can long-range PCR be used to amplify genetically divergent mitochondrial genomes for comparative phylogenetics? A case study within spiders (Arthropoda: Araneae). PLoS One 2013; 8:e62404. [PMID: 23667474 PMCID: PMC3648539 DOI: 10.1371/journal.pone.0062404] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 03/21/2013] [Indexed: 11/19/2022] Open
Abstract
The development of second generation sequencing technology has resulted in the rapid production of large volumes of sequence data for relatively little cost, thereby substantially increasing the quantity of data available for phylogenetic studies. Despite these technological advances, assembling longer sequences, such as that of entire mitochondrial genomes, has not been straightforward. Existing studies have been limited to using only incomplete or nominally intra-specific datasets resulting in a bottleneck between mitogenome amplification and downstream high-throughput sequencing. Here we assess the effectiveness of a wide range of targeted long-range PCR strategies, encapsulating single and dual fragment primer design approaches to provide full mitogenomic coverage within the Araneae (Spiders). Despite extensive rounds of optimisation, full mitochondrial genome PCR amplifications were stochastic in most taxa, although 454 Roche sequencing confirmed the successful amplification of 10 mitochondrial genomes out of the 33 trialled species. The low success rates of amplification using long-Range PCR highlights the difficulties in consistently obtaining genomic amplifications using currently available DNA polymerases optimised for large genomic amplifications and suggests that there may be opportunities for the use of alternative amplification methods.
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Affiliation(s)
- Andrew G. Briscoe
- Environment Centre Wales Building, Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, College of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Sara Goodacre
- Institute of Genetics, Queens Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Susan E. Masta
- Department of Biology, Portland State University, Portland, Oregon, United States of America
| | - Martin I. Taylor
- Environment Centre Wales Building, Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, College of Natural Sciences, Bangor University, Bangor, United Kingdom
| | - Miquel A. Arnedo
- Departament Biologia Animal, Universitat de Barcelona, Barcelona, Spain
| | - David Penney
- Faculty of Life Sciences, The University of Manchester, Manchester, United Kingdom
| | - John Kenny
- Centre for Genomic Research, School of Biological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Simon Creer
- Environment Centre Wales Building, Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, College of Natural Sciences, Bangor University, Bangor, United Kingdom
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14
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Ovchinnikov S, Masta SE. Pseudoscorpion mitochondria show rearranged genes and genome-wide reductions of RNA gene sizes and inferred structures, yet typical nucleotide composition bias. BMC Evol Biol 2012; 12:31. [PMID: 22409411 PMCID: PMC3325882 DOI: 10.1186/1471-2148-12-31] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 03/12/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pseudoscorpions are chelicerates and have historically been viewed as being most closely related to solifuges, harvestmen, and scorpions. No mitochondrial genomes of pseudoscorpions have been published, but the mitochondrial genomes of some lineages of Chelicerata possess unusual features, including short rRNA genes and tRNA genes that lack sequence to encode arms of the canonical cloverleaf-shaped tRNA. Additionally, some chelicerates possess an atypical guanine-thymine nucleotide bias on the major coding strand of their mitochondrial genomes. RESULTS We sequenced the mitochondrial genomes of two divergent taxa from the chelicerate order Pseudoscorpiones. We find that these genomes possess unusually short tRNA genes that do not encode cloverleaf-shaped tRNA structures. Indeed, in one genome, all 22 tRNA genes lack sequence to encode canonical cloverleaf structures. We also find that the large ribosomal RNA genes are substantially shorter than those of most arthropods. We inferred secondary structures of the LSU rRNAs from both pseudoscorpions, and find that they have lost multiple helices. Based on comparisons with the crystal structure of the bacterial ribosome, two of these helices were likely contact points with tRNA T-arms or D-arms as they pass through the ribosome during protein synthesis.The mitochondrial gene arrangements of both pseudoscorpions differ from the ancestral chelicerate gene arrangement. One genome is rearranged with respect to the location of protein-coding genes, the small rRNA gene, and at least 8 tRNA genes. The other genome contains 6 tRNA genes in novel locations. Most chelicerates with rearranged mitochondrial genes show a genome-wide reversal of the CA nucleotide bias typical for arthropods on their major coding strand, and instead possess a GT bias. Yet despite their extensive rearrangement, these pseudoscorpion mitochondrial genomes possess a CA bias on the major coding strand. Phylogenetic analyses of all 13 mitochondrial protein-coding gene sequences consistently yield trees that place pseudoscorpions as sister to acariform mites. CONCLUSION The well-supported phylogenetic placement of pseudoscorpions as sister to Acariformes differs from some previous analyses based on morphology. However, these two lineages share multiple molecular evolutionary traits, including substantial mitochondrial genome rearrangements, extensive nucleotide substitution, and loss of helices in their inferred tRNA and rRNA structures.
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Affiliation(s)
- Sergey Ovchinnikov
- Department of Biology, Portland State University, P.O. Box 751, Portland, OR 97207, USA
| | - Susan E Masta
- Department of Biology, Portland State University, P.O. Box 751, Portland, OR 97207, USA
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15
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Arabi J, Judson MLI, Deharveng L, Lourenço WR, Cruaud C, Hassanin A. Nucleotide composition of CO1 sequences in Chelicerata (Arthropoda): detecting new mitogenomic rearrangements. J Mol Evol 2012; 74:81-95. [PMID: 22362465 DOI: 10.1007/s00239-012-9490-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 02/02/2012] [Indexed: 11/26/2022]
Abstract
Here we study the evolution of nucleotide composition in third codon-positions of CO1 sequences of Chelicerata, using a phylogenetic framework, based on 180 taxa and three markers (CO1, 18S, and 28S rRNA; 5,218 nt). The analyses of nucleotide composition were also extended to all CO1 sequences of Chelicerata found in GenBank (1,701 taxa). The results show that most species of Chelicerata have a positive strand bias in CO1, i.e., in favor of C nucleotides, including all Amblypygi, Palpigradi, Ricinulei, Solifugae, Uropygi, and Xiphosura. However, several taxa show a negative strand bias, i.e., in favor of G nucleotides: all Scorpiones, Opisthothelae spiders and several taxa within Acari, Opiliones, Pseudoscorpiones, and Pycnogonida. Several reversals of strand-specific bias can be attributed to either a rearrangement of the control region or an inversion of a fragment containing the CO1 gene. Key taxa for which sequencing of complete mitochondrial genomes will be necessary to determine the origin and nature of mtDNA rearrangements involved in the reversals are identified. Acari, Opiliones, Pseudoscorpiones, and Pycnogonida were found to show a strong variability in nucleotide composition. In addition, both mitochondrial and nuclear genomes have been affected by higher substitution rates in Acari and Pseudoscorpiones. The results therefore indicate that these two orders are more liable to fix mutations of all types, including base substitutions, indels, and genomic rearrangements.
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Affiliation(s)
- Juliette Arabi
- Département Systématique et Evolution, UMR 7205, Origine, Structure et Evolution de la Biodiversité, Muséum national d'Histoire naturelle, 57, Rue Cuvier, 75005, Paris, France
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16
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Giegé R, Jühling F, Pütz J, Stadler P, Sauter C, Florentz C. Structure of transfer RNAs: similarity and variability. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 3:37-61. [DOI: 10.1002/wrna.103] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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17
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Edwards DD, Jackson LE, Johnson AJ, Ernsting BR. Mitochondrial genome sequence of Unionicola parkeri (Acari: Trombidiformes: Unionicolidae): molecular synapomorphies between closely-related Unionicola gill mites. EXPERIMENTAL & APPLIED ACAROLOGY 2011; 54:105-117. [PMID: 21350973 DOI: 10.1007/s10493-011-9433-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Accepted: 02/08/2011] [Indexed: 05/30/2023]
Abstract
The mitochondrial genome of Unionicola parkeri is a 14,734 bp circular DNA molecule. The sequence and annotation revealed a unique gene order, related to but distinct from the gene order in the closely related species U. foili. Mitochondrial tRNA sequences annotated in this genome predict non-canonical secondary structures for these molecules. The continuing patterns of unique gene orders and unusual tRNA structures in the Trombidiformes in general and Unionicola in particular support the use of phylogenetic approaches that use these types of molecular features as shared, derived character states. Further progress in using these molecular character states to reconstruct phylogeny will depend on careful annotation, especially of tRNA genes.
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Affiliation(s)
- Dale D Edwards
- Department of Biology, University of Evansville, Evansville, IN 47722, USA
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Yuan ML, Wei DD, Wang BJ, Dou W, Wang JJ. The complete mitochondrial genome of the citrus red mite Panonychus citri (Acari: Tetranychidae): high genome rearrangement and extremely truncated tRNAs. BMC Genomics 2010; 11:597. [PMID: 20969792 PMCID: PMC3091742 DOI: 10.1186/1471-2164-11-597] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2010] [Accepted: 10/23/2010] [Indexed: 01/04/2023] Open
Abstract
Background The family Tetranychidae (Chelicerata: Acari) includes ~1200 species, many of which are of agronomic importance. To date, mitochondrial genomes of only two Tetranychidae species have been sequenced, and it has been found that these two mitochondrial genomes are characterized by many unusual features in genome organization and structure such as gene order and nucleotide frequency. The scarcity of available sequence data has greatly impeded evolutionary studies in Acari (mites and ticks). Information on Tetranychidae mitochondrial genomes is quite important for phylogenetic evaluation and population genetics, as well as the molecular evolution of functional genes such as acaricide-resistance genes. In this study, we sequenced the complete mitochondrial genome of Panonychus citri (Family Tetranychidae), a worldwide citrus pest, and provide a comparison to other Acari. Results The mitochondrial genome of P. citri is a typical circular molecule of 13,077 bp, and contains the complete set of 37 genes that are usually found in metazoans. This is the smallest mitochondrial genome within all sequenced Acari and other Chelicerata, primarily due to the significant size reduction of protein coding genes (PCGs), a large rRNA gene, and the A + T-rich region. The mitochondrial gene order for P. citri is the same as those for P. ulmi and Tetranychus urticae, but distinctly different from other Acari by a series of gene translocations and/or inversions. The majority of the P. citri mitochondrial genome has a high A + T content (85.28%), which is also reflected by AT-rich codons being used more frequently, but exhibits a positive GC-skew (0.03). The Acari mitochondrial nad1 exhibits a faster amino acid substitution rate than other genes, and the variation of nucleotide substitution patterns of PCGs is significantly correlated with the G + C content. Most tRNA genes of P. citri are extremely truncated and atypical (44-65, 54.1 ± 4.1 bp), lacking either the T- or D-arm, as found in P. ulmi, T. urticae, and other Acariform mites. Conclusions The P. citri mitochondrial gene order is markedly different from those of other chelicerates, but is conserved within the family Tetranychidae indicating that high rearrangements have occurred after Tetranychidae diverged from other Acari. Comparative analyses suggest that the genome size, gene order, gene content, codon usage, and base composition are strongly variable among Acari mitochondrial genomes. While extremely small and unusual tRNA genes seem to be common for Acariform mites, further experimental evidence is needed.
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Affiliation(s)
- Ming-Long Yuan
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China
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Dermauw W, Vanholme B, Tirry L, Van Leeuwen T. Mitochondrial genome analysis of the predatory mite Phytoseiulus persimilis and a revisit of the Metaseiulus occidentalis mitochondrial genome. Genome 2010; 53:285-301. [DOI: 10.1139/g10-004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this study we sequenced and analysed the complete mitochondrial (mt) genome of the Chilean predatory mite Phytoseiulus persimilis Athias-Henriot (Chelicerata: Acari: Mesostigmata: Phytoseiidae: Amblyseiinae). The 16 199 bp genome (79.8% AT) contains the standard set of 13 protein-coding and 24 RNA genes. Compared with the ancestral arthropod mtDNA pattern, the gene order is extremely reshuffled (35 genes changed position) and represents a novel arrangement within the arthropods. This is probably related to the presence of several large noncoding regions in the genome. In contrast with the mt genome of the closely related species Metaseiulus occidentalis (Phytoseiidae: Typhlodrominae) — which was reported to be unusually large (24 961 bp), to lack nad6 and nad3 protein-coding genes, and to contain 22 tRNAs without T-arms — the genome of P. persimilis has all the features of a standard metazoan mt genome. Consequently, we performed additional experiments on the M. occidentalis mt genome. Our preliminary restriction digests and Southern hybridization data revealed that this genome is smaller than previously reported. In addition, we cloned nad3 in M. occidentalis and positioned this gene between nad4L and 12S-rRNA on the mt genome. Finally, we report that at least 15 of the 22 tRNAs in the M. occidentalis mt genome can be folded into canonical cloverleaf structures similar to their counterparts in P. persimilis.
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Affiliation(s)
- Wannes Dermauw
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
- Department of Plant Biotechnology and Genetics, Faculty of Science, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Technologiepark 927, B-9052, Ghent, Belgium
| | - Bartel Vanholme
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
- Department of Plant Biotechnology and Genetics, Faculty of Science, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Technologiepark 927, B-9052, Ghent, Belgium
| | - Luc Tirry
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
- Department of Plant Biotechnology and Genetics, Faculty of Science, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Technologiepark 927, B-9052, Ghent, Belgium
| | - Thomas Van Leeuwen
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, B-9000, Ghent, Belgium
- Department of Plant Biotechnology and Genetics, Faculty of Science, Ghent University, Technologiepark 927, B-9052, Ghent, Belgium
- Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Technologiepark 927, B-9052, Ghent, Belgium
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Improved tRNA prediction in the American house dust mite reveals widespread occurrence of extremely short minimal tRNAs in acariform mites. BMC Genomics 2009; 10:598. [PMID: 20003349 PMCID: PMC2797822 DOI: 10.1186/1471-2164-10-598] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Accepted: 12/11/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Atypical tRNAs are functional minimal tRNAs, lacking either the D- or T-arm. They are significantly shorter than typical cloverleaf tRNAs. Widespread occurrence of atypical tRNAs was first demonstrated for secernentean nematodes and later in various arachnids. Evidence started to accumulate that tRNAs of certain acariform mites are even shorter than the minimal tRNAs of nematodes, raising the possibility that tRNAs lacking both D- and T-arms might exist in these organisms. The presence of cloverleaf tRNAs in acariform mites, particularly in the house dust mite genus Dermatophagoides, is still disputed. RESULTS Mitochondrial tRNAs of Dermatophagoides farinae are minimal, atypical tRNAs lacking either the T- or D-arm. The size (49-62, 54.4 +/- 2.86 nt) is significantly (p = 0.019) smaller than in Caenorhabditis elegans (53-63, 56.3 +/- 2.30 nt), a model minimal tRNA taxon. The shortest tRNA (49 nt) in Dermatophagoides is approaching the length of the shortest known tRNAs (45-49 nt) described in other acariform mites. The D-arm is absent in these tRNAs, and the inferred T-stem is small (2-3 bp) and thermodynamically unstable, suggesting that it may not exist in reality. The discriminator nucleotide is probably not encoded and is added postranscriptionally in many Dermatophagoides tRNAs. CONCLUSIONS Mitochondrial tRNAs of acariform mites are largely atypical, non-cloverleaf tRNAs. Among them, the shortest known tRNAs with no D-arm and a short and unstable T-arm can be inferred. While our study confirmed seven tRNAs in Dermatophagoides by limited EST data, further experimental evidence is needed to demonstrate extremely small and unusual tRNAs in acariform mites.
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