101
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Fang WY, Wang ZL, Li C, Yang XQ, Yu XP. The complete mitogenome of a jumping spider Carrhotus xanthogramma (Araneae: Salticidae) and comparative analysis in four salticid mitogenomes. Genetica 2016; 144:699-709. [DOI: 10.1007/s10709-016-9936-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/31/2016] [Indexed: 11/27/2022]
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102
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Mitochondrial Genomes of Kinorhyncha: trnM Duplication and New Gene Orders within Animals. PLoS One 2016; 11:e0165072. [PMID: 27755612 PMCID: PMC5068742 DOI: 10.1371/journal.pone.0165072] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/05/2016] [Indexed: 11/19/2022] Open
Abstract
Many features of mitochondrial genomes of animals, such as patterns of gene arrangement, nucleotide content and substitution rate variation are extensively used in evolutionary and phylogenetic studies. Nearly 6,000 mitochondrial genomes of animals have already been sequenced, covering the majority of animal phyla. One of the groups that escaped mitogenome sequencing is phylum Kinorhyncha-an isolated taxon of microscopic worm-like ecdysozoans. The kinorhynchs are thought to be one of the early-branching lineages of Ecdysozoa, and their mitochondrial genomes may be important for resolving evolutionary relations between major animal taxa. Here we present the results of sequencing and analysis of mitochondrial genomes from two members of Kinorhyncha, Echinoderes svetlanae (Cyclorhagida) and Pycnophyes kielensis (Allomalorhagida). Their mitochondrial genomes are circular molecules approximately 15 Kbp in size. The kinorhynch mitochondrial gene sequences are highly divergent, which precludes accurate phylogenetic inference. The mitogenomes of both species encode a typical metazoan complement of 37 genes, which are all positioned on the major strand, but the gene order is distinct and unique among Ecdysozoa or animals as a whole. We predict four types of start codons for protein-coding genes in E. svetlanae and five in P. kielensis with a consensus DTD in single letter code. The mitochondrial genomes of E. svetlanae and P. kielensis encode duplicated methionine tRNA genes that display compensatory nucleotide substitutions. Two distant species of Kinorhyncha demonstrate similar patterns of gene arrangements in their mitogenomes. Both genomes have duplicated methionine tRNA genes; the duplication predates the divergence of two species. The kinorhynchs share a few features pertaining to gene order that align them with Priapulida. Gene order analysis reveals that gene arrangement specific of Priapulida may be ancestral for Scalidophora, Ecdysozoa, and even Protostomia.
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103
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Pentinsaari M, Salmela H, Mutanen M, Roslin T. Molecular evolution of a widely-adopted taxonomic marker (COI) across the animal tree of life. Sci Rep 2016; 6:35275. [PMID: 27734964 PMCID: PMC5062346 DOI: 10.1038/srep35275] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 09/15/2016] [Indexed: 11/28/2022] Open
Abstract
DNA barcodes are widely used for identification and discovery of species. While such use draws on information at the DNA level, the current amassment of ca. 4.7 million COI barcodes also offers a unique resource for exploring functional constraints on DNA evolution. Here, we explore amino acid variation in a crosscut of the entire animal kingdom. Patterns of DNA variation were linked to functional constraints at the level of the amino acid sequence in functionally important parts of the enzyme. Six amino acid sites show variation with possible effects on enzyme function. Overall, patterns of amino acid variation suggest convergent or parallel evolution at the protein level connected to the transition into a parasitic life style. Denser sampling of two diverse insect taxa revealed that the beetles (Coleoptera) show more amino acid variation than the butterflies and moths (Lepidoptera), indicating fundamental difference in patterns of molecular evolution in COI. Several amino acid sites were found to be under notably strong purifying selection in Lepidoptera as compared to Coleoptera. Overall, these findings demonstrate the utility of the global DNA barcode library to extend far beyond identification and taxonomy, and will hopefully be followed by a multitude of work.
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Affiliation(s)
- Mikko Pentinsaari
- Department of Genetics and Physiology, University of Oulu, P.O.Box 3000 (Pentti Kaiteran katu 1), FI-90014, Finland
| | - Heli Salmela
- Department of Biosciences, Centre of Excellence in Biological Interactions, University of Helsinki, Viikinkaari 1, FI-00014, Finland
| | - Marko Mutanen
- Department of Genetics and Physiology, University of Oulu, P.O.Box 3000 (Pentti Kaiteran katu 1), FI-90014, Finland
| | - Tomas Roslin
- Spatial Foodweb Ecology Group, Department of Agricultural Sciences, University of Helsinki, Latokartanonkaari 5, FI-00014, Finland
- Department of Ecology, Swedish University of Agricultural Sciences, Box 7044, 750 07 Uppsala, Sweden
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104
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Oliveira DS, Gomes TMFF, Loreto ELS. The rearranged mitochondrial genome of Leptopilina boulardi (Hymenoptera: Figitidae), a parasitoid wasp of Drosophila. Genet Mol Biol 2016; 39:611-615. [PMID: 27648767 PMCID: PMC5127158 DOI: 10.1590/1678-4685-gmb-2016-0062] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 08/02/2016] [Indexed: 11/22/2022] Open
Abstract
The partial mitochondrial genome sequence of Leptopilina boulardi (Hymenoptera: Figitidae) was characterized. Illumina sequencing was used yielding 35,999,679 reads, from which 102,482 were utilized in the assembly. The length of the sequenced region of this partial mitochondrial genome is 15,417 bp, consisting of 13 protein-coding, two rRNA, and 21tRNA genes (the trnaM failed to be sequenced) and a partial A+T-rich region. All protein-coding genes start with ATN codons. Eleven protein-coding genes presented TAA stop codons, whereas ND6 and COII that presented TA, and T nucleotides, respectively. The gene pattern revealed extensive rearrangements compared to the typical pattern generally observed in insects. These rearrangements involve two protein-coding and two ribosomal genes, along with the 16 tRNA genes. This gene order is different from the pattern described for Ibalia leucospoides (Ibaliidae, Cynipoidea), suggesting that this particular gene order can be variable among Cynipoidea superfamily members. A maximum likelihood phylogenetic analysis of the main groups of Apocrita was performed using amino acid sequence of 13 protein-coding genes, showing monophyly for the Cynipoidea superfamily within the Hymenoptera phylogeny.
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Affiliation(s)
- Daniel S Oliveira
- Curso Ciências Biológicas, Universidade Federal de Santa Maria (UFSM), Santa Maria, RS, Brazil
| | - Tiago M F F Gomes
- Curso Ciências Biológicas, Universidade Federal de Santa Maria (UFSM), Santa Maria, RS, Brazil
| | - Elgion L S Loreto
- Departamento de Bioquímica e Biologia Molecular (CCNE), Universidade Federal de Santa Maria (UFSM), Santa Maria, RS, Brazil
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105
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Al Arab M, Höner Zu Siederdissen C, Tout K, Sahyoun AH, Stadler PF, Bernt M. Accurate annotation of protein-coding genes in mitochondrial genomes. Mol Phylogenet Evol 2016; 106:209-216. [PMID: 27693569 DOI: 10.1016/j.ympev.2016.09.024] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 08/29/2016] [Accepted: 09/25/2016] [Indexed: 10/20/2022]
Abstract
Mitochondrial genome sequences are available in large number and new sequences become published nowadays with increasing pace. Fast, automatic, consistent, and high quality annotations are a prerequisite for downstream analyses. Therefore, we present an automated pipeline for fast de novo annotation of mitochondrial protein-coding genes. The annotation is based on enhanced phylogeny-aware hidden Markov models (HMMs). The pipeline builds taxon-specific enhanced multiple sequence alignments (MSA) of already annotated sequences and corresponding HMMs using an approximation of the phylogeny. The MSAs are enhanced by fixing unannotated frameshifts, purging of wrong sequences, and removal of non-conserved columns from both ends. A comparison with reference annotations highlights the high quality of the results. The frameshift correction method predicts a large number of frameshifts, many of which are unknown. A detailed analysis of the frameshifts in nad3 of the Archosauria-Testudines group has been conducted.
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Affiliation(s)
- Marwa Al Arab
- Bioinformatics Group, Department of Computer Science University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; Doctoral School of Science and Technology, AZM Center for Biotechnology Research, Lebanese University, Tripoli, Lebanon.
| | - Christian Höner Zu Siederdissen
- Bioinformatics Group, Department of Computer Science University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria.
| | - Kifah Tout
- Doctoral School of Science and Technology, AZM Center for Biotechnology Research, Lebanese University, Tripoli, Lebanon.
| | - Abdullah H Sahyoun
- Bioinformatics Group, Department of Computer Science University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; Doctoral School of Science and Technology, AZM Center for Biotechnology Research, Lebanese University, Tripoli, Lebanon; TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University Mainz gGmbH, Mainz, Germany.
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria; Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany; Fraunhofer Institut für Zelltherapie und Immunologie, Perlickstraße 1, D-04103 Leipzig, Germany; Center for Non-Coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark; Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, United States.
| | - Matthias Bernt
- Bioinformatics Group, Department of Computer Science University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany; Parallel Computing and Complex Systems Group, Department of Computer Science, University of Leipzig, Augustusplatz 10, D-04103 Leipzig, Germany.
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106
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Lavrov DV, Pett W. Animal Mitochondrial DNA as We Do Not Know It: mt-Genome Organization and Evolution in Nonbilaterian Lineages. Genome Biol Evol 2016; 8:2896-2913. [PMID: 27557826 PMCID: PMC5633667 DOI: 10.1093/gbe/evw195] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2016] [Indexed: 12/11/2022] Open
Abstract
Animal mitochondrial DNA (mtDNA) is commonly described as a small, circular molecule that is conserved in size, gene content, and organization. Data collected in the last decade have challenged this view by revealing considerable diversity in animal mitochondrial genome organization. Much of this diversity has been found in nonbilaterian animals (phyla Cnidaria, Ctenophora, Placozoa, and Porifera), which, from a phylogenetic perspective, form the main branches of the animal tree along with Bilateria. Within these groups, mt-genomes are characterized by varying numbers of both linear and circular chromosomes, extra genes (e.g. atp9, polB, tatC), large variation in the number of encoded mitochondrial transfer RNAs (tRNAs) (0-25), at least seven different genetic codes, presence/absence of introns, tRNA and mRNA editing, fragmented ribosomal RNA genes, translational frameshifting, highly variable substitution rates, and a large range of genome sizes. This newly discovered diversity allows a better understanding of the evolutionary plasticity and conservation of animal mtDNA and provides insights into the molecular and evolutionary mechanisms shaping mitochondrial genomes.
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Affiliation(s)
- Dennis V Lavrov
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University
| | - Walker Pett
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University Laboratoire de Biométrie et Biologie Évolutive, Université Lyon 1, Villeurbanne, France
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107
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Li Q, Wei SJ, Tang P, Wu Q, Shi M, Sharkey MJ, Chen XX. Multiple Lines of Evidence from Mitochondrial Genomes Resolve Phylogenetic Relationships of Parasitic Wasps in Braconidae. Genome Biol Evol 2016; 8:2651-62. [PMID: 27503293 PMCID: PMC5630901 DOI: 10.1093/gbe/evw184] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2016] [Indexed: 11/30/2022] Open
Abstract
The rapid increase in the number of mitochondrial genomes in public databases provides opportunities for insect phylogenetic studies; but it also provides challenges because of gene rearrangements and variable substitution rates among both lineages and sites. Typically, phylogenetic studies use mitochondrial sequence data but exclude other features of the mitochondrial genome from analyses. Here, we undertook large-scale sequencing of mitochondrial genomes from a worldwide collection of specimens belonging to Braconidae, one of the largest families of Metazoa. The strand-asymmetry of base composition in the mitochondrial genomes of braconids is reversed, providing evidence for monophyly of the Braconidae. We have reconstructed a backbone phylogeny of the major lineages of Braconidae from gene order of the mitochondrial genomes. Standard phylogenetic analyses of DNA sequences provided strong support for both Cyclostomes and Noncyclostomes. Four subfamily complexes, that is, helconoid, euphoroid, sigalphoid, and microgastroid, within the Noncyclostomes were reconstructed robustly, the first three of which formed a monophyletic group sister to the last one. Aphidiinae was recovered as a lineage sister to other groups of Cyclostomes, while the Ichneutinae was recovered as paraphyletic. Separate analyses of the subdivided groups showed congruent relationships, employing different matrices and methods, for the internal nodes of the Cyclostomes and the microgastroid complex of subfamilies. This research, using multiple lines of evidence from mitochondrial genomes, illustrates multiple uses of mitochondrial genomes for phylogenetic inference in Braconidae.
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Affiliation(s)
- Qian Li
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Shu-Jun Wei
- Beijing Academy of Agriculture and Forestry Sciences, Institute of Plant and Environmental Protection, Beijing, China
| | - Pu Tang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Qiong Wu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Min Shi
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | | | - Xue-Xin Chen
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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108
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Plazzi F, Puccio G, Passamonti M. Comparative Large-Scale Mitogenomics Evidences Clade-Specific Evolutionary Trends in Mitochondrial DNAs of Bivalvia. Genome Biol Evol 2016; 8:2544-64. [PMID: 27503296 PMCID: PMC5010914 DOI: 10.1093/gbe/evw187] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2016] [Indexed: 12/28/2022] Open
Abstract
Despite the figure of complete bivalve mitochondrial genomes keeps growing, an assessment of the general features of these genomes in a phylogenetic framework is still lacking, despite the fact that bivalve mitochondrial genomes are unusual under different aspects. In this work, we constructed a dataset of one hundred mitochondrial genomes of bivalves to perform the first systematic comparative mitogenomic analysis, developing a phylogenetic background to scaffold the evolutionary history of the class' mitochondrial genomes. Highly conserved domains were identified in all protein coding genes; however, four genes (namely, atp6, nad2, nad4L, and nad6) were found to be very divergent for many respects, notwithstanding the overall purifying selection working on those genomes. Moreover, the atp8 gene was newly annotated in 20 mitochondrial genomes, where it was previously declared as lacking or only signaled. Supernumerary mitochondrial proteins were compared, but it was possible to find homologies only among strictly related species. The rearrangement rate on the molecule is too high to be used as a phylogenetic marker, but here we demonstrate for the first time in mollusks that there is correlation between rearrangement rates and evolutionary rates. We also developed a new index (HERMES) to estimate the amount of mitochondrial evolution. Many genomic features are phylogenetically congruent and this allowed us to highlight three main phases in bivalve history: the origin, the branching of palaeoheterodonts, and the second radiation leading to the present-day biodiversity.
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Affiliation(s)
- Federico Plazzi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3 - 40126 Bologna, Italy
| | - Guglielmo Puccio
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3 - 40126 Bologna, Italy
| | - Marco Passamonti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3 - 40126 Bologna, Italy
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109
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Breeschoten T, Doorenweerd C, Tarasov S, Vogler AP. Phylogenetics and biogeography of the dung beetle genus Onthophagus inferred from mitochondrial genomes. Mol Phylogenet Evol 2016; 105:86-95. [PMID: 27568212 DOI: 10.1016/j.ympev.2016.08.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 08/19/2016] [Accepted: 08/23/2016] [Indexed: 11/26/2022]
Abstract
Phylogenetic relationships of dung beetles in the tribe Onthophagini, including the species-rich, cosmopolitan genus Onthophagus, were inferred using whole mitochondrial genomes. Data were generated by shotgun sequencing of mixed genomic DNA from >100 individuals on 50% of an Illumina MiSeq flow cell. Genome assembly of the mixed reads produced contigs of 74 (nearly) complete mitogenomes. The final dataset included representatives of Onthophagus from all biogeographic regions, closely related genera of Onthophagini, and the related tribes Onitini and Oniticellini. The analysis defined four major clades of Onthophagini, which was paraphyletic for Oniticellini, with Onitini as sister group to all others. Several (sub)genera considered as members of Onthophagus in the older literature formed separate deep lineages. All New World species of Onthophagus formed a monophyletic group, and the Australian taxa are confined to a single or two closely related clades, one of which forms the sister group of the New World species. Dating the tree by constraining the basal splits with existing calibrations of Scarabaeoidea suggests an origin of Onthophagini sensu lato in the Eocene and a rapid spread from an African ancestral stock into the Oriental region, and secondarily to Australia and the Americas at about 20-24 Mya. The successful assembly of mitogenomes and the well-supported tree obtained from these sequences demonstrates the power of shotgun sequencing from total genomic DNA of species pools as an efficient tool in genus-level phylogenetics.
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Affiliation(s)
- Thijmen Breeschoten
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom; Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands; Institute Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands.
| | - Camiel Doorenweerd
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, The Netherlands; Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Sergei Tarasov
- National Institute for Mathematical and Biological Synthesis, University of Tennessee, 1122 Volunteer Blvd, Ste. 106, Knoxville, TN 37996, USA
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom; Department of Life Sciences, Silwood Park Campus, Imperial College London, Buckhurst Road, Ascot SL5 7PY, United Kingdom
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110
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Song N, Zhang H, Li H, Cai W. All 37 Mitochondrial Genes of Aphid Aphis craccivora Obtained from Transcriptome Sequencing: Implications for the Evolution of Aphids. PLoS One 2016; 11:e0157857. [PMID: 27314587 PMCID: PMC4912114 DOI: 10.1371/journal.pone.0157857] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 06/06/2016] [Indexed: 11/19/2022] Open
Abstract
The availability of mitochondrial genome data for Aphididae, one of the economically important insect pest families, in public databases is limited. The advent of next generation sequencing technology provides the potential to generate mitochondrial genome data for many species timely and cost-effectively. In this report, we used transcriptome sequencing technology to determine all the 37 mitochondrial genes of the cowpea aphid, Aphis craccivora. This method avoids the necessity of finding suitable primers for long PCRs or primer-walking amplicons, and is proved to be effective in obtaining the whole set of mitochondrial gene data for insects with difficulty in sequencing mitochondrial genome by PCR-based strategies. Phylogenetic analyses of aphid mitochondrial genome data show clustering based on tribe level, and strongly support the monophyly of the family Aphididae. Within the monophyletic Aphidini, three samples from Aphis grouped together. In another major clade of Aphididae, Pterocomma pilosum was recovered as a potential sister-group of Cavariella salicicola, as part of Macrosiphini.
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Affiliation(s)
- Nan Song
- College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Hao Zhang
- Henan Vocational and Technological College of Communication, Zhengzhou, China
| | - Hu Li
- Department of Entomology, China Agricultural University, Beijing, China
| | - Wanzhi Cai
- Department of Entomology, China Agricultural University, Beijing, China
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111
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Gouy R, Baurain D, Philippe H. Rooting the tree of life: the phylogenetic jury is still out. Philos Trans R Soc Lond B Biol Sci 2016; 370:20140329. [PMID: 26323760 DOI: 10.1098/rstb.2014.0329] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This article aims to shed light on difficulties in rooting the tree of life (ToL) and to explore the (sociological) reasons underlying the limited interest in accurately addressing this fundamental issue. First, we briefly review the difficulties plaguing phylogenetic inference and the ways to improve the modelling of the substitution process, which is highly heterogeneous, both across sites and over time. We further observe that enriched taxon samplings, better gene samplings and clever data removal strategies have led to numerous revisions of the ToL, and that these improved shallow phylogenies nearly always relocate simple organisms higher in the ToL provided that long-branch attraction artefacts are kept at bay. Then, we note that, despite the flood of genomic data available since 2000, there has been a surprisingly low interest in inferring the root of the ToL. Furthermore, the rare studies dealing with this question were almost always based on methods dating from the 1990s that have been shown to be inaccurate for much more shallow issues! This leads us to argue that the current consensus about a bacterial root for the ToL can be traced back to the prejudice of Aristotle's Great Chain of Beings, in which simple organisms are ancestors of more complex life forms. Finally, we demonstrate that even the best models cannot yet handle the complexity of the evolutionary process encountered both at shallow depth, when the outgroup is too distant, and at the level of the inter-domain relationships. Altogether, we conclude that the commonly accepted bacterial root is still unproven and that the root of the ToL should be revisited using phylogenomic supermatrices to ensure that new evidence for eukaryogenesis, such as the recently described Lokiarcheota, is interpreted in a sound phylogenetic framework.
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Affiliation(s)
- Richard Gouy
- Eukaryotic Phylogenomics, Department of Life Sciences and PhytoSYSTEMS, University of Liège, Liège 4000, Belgium Centre for Biodiversity Theory and Modelling, USR CNRS 2936, Station d'Ecologie Expérimentale du CNRS, Moulis 09200, France
| | - Denis Baurain
- Eukaryotic Phylogenomics, Department of Life Sciences and PhytoSYSTEMS, University of Liège, Liège 4000, Belgium
| | - Hervé Philippe
- Centre for Biodiversity Theory and Modelling, USR CNRS 2936, Station d'Ecologie Expérimentale du CNRS, Moulis 09200, France Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, Montréal, Quebec, Canada H3C 3J7
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112
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Song F, Li H, Jiang P, Zhou X, Liu J, Sun C, Vogler AP, Cai W. Capturing the Phylogeny of Holometabola with Mitochondrial Genome Data and Bayesian Site-Heterogeneous Mixture Models. Genome Biol Evol 2016; 8:1411-26. [PMID: 27189999 PMCID: PMC4898802 DOI: 10.1093/gbe/evw086] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2016] [Indexed: 12/15/2022] Open
Abstract
After decades of debate, a mostly satisfactory resolution of relationships among the 11 recognized holometabolan orders of insects has been reached based on nuclear genes, resolving one of the most substantial branches of the tree-of-life, but the relationships are still not well established with mitochondrial genome data. The main reasons have been the absence of sufficient data in several orders and lack of appropriate phylogenetic methods that avoid the systematic errors from compositional and mutational biases in insect mitochondrial genomes. In this study, we assembled the richest taxon sampling of Holometabola to date (199 species in 11 orders), and analyzed both nucleotide and amino acid data sets using several methods. We find the standard Bayesian inference and maximum-likelihood analyses were strongly affected by systematic biases, but the site-heterogeneous mixture model implemented in PhyloBayes avoided the false grouping of unrelated taxa exhibiting similar base composition and accelerated evolutionary rate. The inclusion of rRNA genes and removal of fast-evolving sites with the observed variability sorting method for identifying sites deviating from the mean rates improved the phylogenetic inferences under a site-heterogeneous model, correctly recovering most deep branches of the Holometabola phylogeny. We suggest that the use of mitochondrial genome data for resolving deep phylogenetic relationships requires an assessment of the potential impact of substitutional saturation and compositional biases through data deletion strategies and by using site-heterogeneous mixture models. Our study suggests a practical approach for how to use densely sampled mitochondrial genome data in phylogenetic analyses.
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Affiliation(s)
- Fan Song
- Department of Entomology, China Agricultural University, Beijing, China
| | - Hu Li
- Department of Entomology, China Agricultural University, Beijing, China
| | - Pei Jiang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Xuguo Zhou
- Department of Entomology, University of Kentucky, Lexington
| | - Jinpeng Liu
- Markey Cancer Center, University of Kentucky, Lexington
| | - Changhai Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Alfried P Vogler
- Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, United Kingdom Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Wanzhi Cai
- Department of Entomology, China Agricultural University, Beijing, China
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113
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Oceguera-Figueroa A, Manzano-Marín A, Kvist S, Moya A, Siddall ME, Latorre A. Comparative Mitogenomics of Leeches (Annelida: Clitellata): Genome Conservation and Placobdella-Specific trnD Gene Duplication. PLoS One 2016; 11:e0155441. [PMID: 27176910 PMCID: PMC4866719 DOI: 10.1371/journal.pone.0155441] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 04/28/2016] [Indexed: 02/07/2023] Open
Abstract
Mitochondrial DNA sequences, often in combination with nuclear markers and morphological data, are frequently used to unravel the phylogenetic relationships, population dynamics and biogeographic histories of a plethora of organisms. The information provided by examining complete mitochondrial genomes also enables investigation of other evolutionary events such as gene rearrangements, gene duplication and gene loss. Despite efforts to generate information to represent most of the currently recognized groups, some taxa are underrepresented in mitochondrial genomic databases. One such group is leeches (Annelida: Hirudinea: Clitellata). Herein, we expand our knowledge concerning leech mitochondrial makeup including gene arrangement, gene duplication and the evolution of mitochondrial genomes by adding newly sequenced mitochondrial genomes for three bloodfeeding species: Haementeria officinalis, Placobdella lamothei and Placobdella parasitica. With the inclusion of three new mitochondrial genomes of leeches, a better understanding of evolution for this organelle within the group is emerging. We found that gene order and genomic arrangement in the three new mitochondrial genomes is identical to previously sequenced members of Clitellata. Interestingly, within Placobdella, we recovered a genus-specific duplication of the trnD gene located between cox2 and atp8. We performed phylogenetic analyses using 12 protein-coding genes and expanded our taxon sampling by including GenBank sequences for 39 taxa; the analyses confirm the monophyletic status of Clitellata, yet disagree in several respects with other phylogenetic hypotheses based on morphology and analyses of non-mitochondrial data.
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Affiliation(s)
- Alejandro Oceguera-Figueroa
- Laboratorio de Helmintología, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Coyoacán, 04510, Mexico City, Mexico
- Research Collaborator, Department of Invertebrate Zoology, Smithsonian Institution. National Museum of Natural History, Washington D. C., United States of America
| | - Alejandro Manzano-Marín
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Catedrático José Beltrán 2, 46008, Paterna, Valencia, Spain
| | - Sebastian Kvist
- Department of Natural History, Royal Ontario Museum, 100 Queen’s Park, Toronto, ON, M5S 2C6, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, M5S 3B2, Canada
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Catedrático José Beltrán 2, 46008, Paterna, Valencia, Spain
- Área de Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Avenida de Catalunya 21, 46020, Valencia, Spain
| | - Mark E. Siddall
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, United States of America
| | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Catedrático José Beltrán 2, 46008, Paterna, Valencia, Spain
- Área de Genómica y Salud de la Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunidad Valenciana (FISABIO), Avenida de Catalunya 21, 46020, Valencia, Spain
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Gaitán-Espitia JD, Solano-Iguaran JJ, Tejada-Martinez D, Quintero-Galvis JF. Mitogenomics of electric rays: evolutionary considerations within Torpediniformes (Batoidea; Chondrichthyes). Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12417] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Juan Diego Gaitán-Espitia
- Instituto de Ciencias Ambientales y Evolutivas; Universidad Austral de Chile; Casilla 567 Valdivia Chile
- CSIRO Oceans & Atmosphere; GPO Box 1538 Hobart 7001 TAS Australia
| | - Jaiber J. Solano-Iguaran
- Instituto de Ciencias Ambientales y Evolutivas; Universidad Austral de Chile; Casilla 567 Valdivia Chile
- Programa de Magister en Ciencias mención Genética; Facultad de Ciencias; Universidad Austral de Chile; Valdivia Chile
| | - Daniela Tejada-Martinez
- Instituto de Ciencias Ambientales y Evolutivas; Universidad Austral de Chile; Casilla 567 Valdivia Chile
- Programa de Doctorado en Ciencias mención Ecología y Evolución; Facultad de Ciencias; Universidad Austral de Chile; Valdivia Chile
| | - Julian F. Quintero-Galvis
- Instituto de Ciencias Ambientales y Evolutivas; Universidad Austral de Chile; Casilla 567 Valdivia Chile
- Programa de Magister en Ciencias mención Genética; Facultad de Ciencias; Universidad Austral de Chile; Valdivia Chile
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115
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Wang K, Li X, Ding S, Wang N, Mao M, Wang M, Yang D. The complete mitochondrial genome of the Atylotus miser (Diptera: Tabanomorpha: Tabanidae), with mitochondrial genome phylogeny of lower Brachycera (Orthorrhapha). Gene 2016; 586:184-96. [PMID: 27063560 DOI: 10.1016/j.gene.2016.04.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/22/2016] [Accepted: 04/05/2016] [Indexed: 11/25/2022]
Abstract
Brachycera is a clade with over 80,000 described species and originated from the Mesozoic, and its larvae employ comprehensive feeding strategies. The phylogeny of the lower Brachycera has been studied intensively over the past decades. In order to supplement the lack of genetic data in this important group, we sequenced the complete mitochondrial (mt) genome of Atylotus miser as well as the nearly complete mt genomes of another 11 orthorrhaphous flies. The mt genome of A. miser is 15,858bp, which is typical of Diptera, with 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a 993bp control region. The rest of the orthorrhaphous mt genomes in our study have the similar structure with A. miser. Additionally, we conducted a phylogenetic analysis of 20 mt genomes using Maximum-likelihood and Bayesian methods in order to reconstruct the evolutionary relationship of Orthorrhapha. The results show that all infraorders of Brachycera are monophyletic, and a relationship of Tabanomorpha+((Xylophagomorpha+Stratiomyomorpha)+Muscomorpha) has been proposed. Within Xylophagomorpha, Nemestrinoidae forms the sister group of Xylophagidae.
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Affiliation(s)
- Kai Wang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Xuankun Li
- Department of Entomology, China Agricultural University, Beijing, China
| | - Shuangmei Ding
- Department of Entomology, China Agricultural University, Beijing, China
| | - Ning Wang
- Department of Entomology, China Agricultural University, Beijing, China; Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot, China
| | - Meng Mao
- School of Biological Sciences, University of Wollongong, Wollongong, Australia
| | - Mengqing Wang
- Department of Entomology, China Agricultural University, Beijing, China; Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing, China.
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116
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Crampton-Platt A, Yu DW, Zhou X, Vogler AP. Mitochondrial metagenomics: letting the genes out of the bottle. Gigascience 2016; 5:15. [PMID: 27006764 PMCID: PMC4802855 DOI: 10.1186/s13742-016-0120-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 03/06/2016] [Indexed: 01/14/2023] Open
Abstract
‘Mitochondrial metagenomics’ (MMG) is a methodology for shotgun sequencing of total DNA from specimen mixtures and subsequent bioinformatic extraction of mitochondrial sequences. The approach can be applied to phylogenetic analysis of taxonomically selected taxa, as an economical alternative to mitogenome sequencing from individual species, or to environmental samples of mixed specimens, such as from mass trapping of invertebrates. The routine generation of mitochondrial genome sequences has great potential both for systematics and community phylogenetics. Mapping of reads from low-coverage shotgun sequencing of environmental samples also makes it possible to obtain data on spatial and temporal turnover in whole-community phylogenetic and species composition, even in complex ecosystems where species-level taxonomy and biodiversity patterns are poorly known. In addition, read mapping can produce information on species biomass, and potentially allows quantification of within-species genetic variation. The success of MMG relies on the formation of numerous mitochondrial genome contigs, achievable with standard genome assemblers, but various challenges for the efficiency of assembly remain, particularly in the face of variable relative species abundance and intra-specific genetic variation. Nevertheless, several studies have demonstrated the power of mitogenomes from MMG for accurate phylogenetic placement, evolutionary analysis of species traits, biodiversity discovery and the establishment of species distribution patterns; it offers a promising avenue for unifying the ecological and evolutionary understanding of species diversity.
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Affiliation(s)
- Alex Crampton-Platt
- Department of Life Sciences, Natural History Museum, London, SW7 5BD UK ; Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT UK
| | - Douglas W Yu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming, Yunnan Province 650223 China ; School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ UK
| | - Xin Zhou
- China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong Province 518083 China
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, SW7 5BD UK ; Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, SL5 7PY UK
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117
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Zhang D, Yan L, Zhang M, Chu H, Cao J, Li K, Hu D, Pape T. Phylogenetic inference of calyptrates, with the first mitogenomes for Gasterophilinae (Diptera: Oestridae) and Paramacronychiinae (Diptera: Sarcophagidae). Int J Biol Sci 2016; 12:489-504. [PMID: 27019632 PMCID: PMC4807417 DOI: 10.7150/ijbs.12148] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 12/22/2015] [Indexed: 11/05/2022] Open
Abstract
The complete mitogenome of the horse stomach bot fly Gasterophilus pecorum (Fabricius) and a near-complete mitogenome of Wohlfahrt's wound myiasis fly Wohlfahrtia magnifica (Schiner) were sequenced. The mitogenomes contain the typical 37 mitogenes found in metazoans, organized in the same order and orientation as in other cyclorrhaphan Diptera. Phylogenetic analyses of mitogenomes from 38 calyptrate taxa with and without two non-calyptrate outgroups were performed using Bayesian Inference and Maximum Likelihood. Three sub-analyses were performed on the concatenated data: (1) not partitioned; (2) partitioned by gene; (3) 3rd codon positions of protein-coding genes omitted. We estimated the contribution of each of the mitochondrial genes for phylogenetic analysis, as well as the effect of some popular methodologies on calyptrate phylogeny reconstruction. In the favoured trees, the Oestroidea are nested within the muscoid grade. Relationships at the family level within Oestroidea are (remaining Calliphoridae (Sarcophagidae (Oestridae, Pollenia + Tachinidae))). Our mito-phylogenetic reconstruction of the Calyptratae presents the most extensive taxon coverage so far, and the risk of long-branch attraction is reduced by an appropriate selection of outgroups. We find that in the Calyptratae the ND2, ND5, ND1, COIII, and COI genes are more phylogenetically informative compared with other mitochondrial protein-coding genes. Our study provides evidence that data partitioning and the inclusion of conserved tRNA genes have little influence on calyptrate phylogeny reconstruction, and that the 3rd codon positions of protein-coding genes are not saturated and therefore should be included.
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Affiliation(s)
- Dong Zhang
- 1. School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Liping Yan
- 1. School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Ming Zhang
- 1. School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Hongjun Chu
- 3. Wildlife Conservation Office of Altay Prefecture, Altay, Xinjiang, China
| | - Jie Cao
- 4. Xinjiang Research Centre for Breeding Przewalski's Horse, Ürümqi, Xinjiang, China
| | - Kai Li
- 1. School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Defu Hu
- 1. School of Nature Conservation, Beijing Forestry University, Beijing, China
| | - Thomas Pape
- 2. Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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118
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Ševčíková T, Klimeš V, Zbránková V, Strnad H, Hroudová M, Vlček Č, Eliáš M. A Comparative Analysis of Mitochondrial Genomes in Eustigmatophyte Algae. Genome Biol Evol 2016; 8:705-22. [PMID: 26872774 PMCID: PMC4824035 DOI: 10.1093/gbe/evw027] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Eustigmatophyceae (Ochrophyta, Stramenopiles) is a small algal group with species of the genus Nannochloropsis being its best studied representatives. Nuclear and organellar genomes have been recently sequenced for several Nannochloropsis spp., but phylogenetically wider genomic studies are missing for eustigmatophytes. We sequenced mitochondrial genomes (mitogenomes) of three species representing most major eustigmatophyte lineages, Monodopsis sp. MarTras21, Vischeria sp. CAUP Q 202 and Trachydiscus minutus, and carried out their comparative analysis in the context of available data from Nannochloropsis and other stramenopiles, revealing a number of noticeable findings. First, mitogenomes of most eustigmatophytes are highly collinear and similar in the gene content, but extensive rearrangements and loss of three otherwise ubiquitous genes happened in the Vischeria lineage; this correlates with an accelerated evolution of mitochondrial gene sequences in this lineage. Second, eustigmatophytes appear to be the only ochrophyte group with the Atp1 protein encoded by the mitogenome. Third, eustigmatophyte mitogenomes uniquely share a truncated nad11 gene encoding only the C-terminal part of the Nad11 protein, while the N-terminal part is encoded by a separate gene in the nuclear genome. Fourth, UGA as a termination codon and the cognate release factor mRF2 were lost from mitochondria independently by the Nannochloropsis and T. minutus lineages. Finally, the rps3 gene in the mitogenome of Vischeria sp. is interrupted by the UAG codon, but the genome includes a gene for an unusual tRNA with an extended anticodon loop that we speculate may serve as a suppressor tRNA to properly decode the rps3 gene.
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Affiliation(s)
- Tereza Ševčíková
- Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Czech Republic
| | - Vladimír Klimeš
- Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Czech Republic
| | - Veronika Zbránková
- Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Czech Republic
| | - Hynek Strnad
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Miluše Hroudová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Čestmír Vlček
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Marek Eliáš
- Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Czech Republic
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119
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Schierwater B, Holland PWH, Miller DJ, Stadler PF, Wiegmann BM, Wörheide G, Wray GA, DeSalle R. Never Ending Analysis of a Century Old Evolutionary Debate: “Unringing” the Urmetazoon Bell. Front Ecol Evol 2016. [DOI: 10.3389/fevo.2016.00005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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120
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Zhang L, Sechi P, Yuan M, Jiang J, Dong Y, Qiu J. Fifteen new earthworm mitogenomes shed new light on phylogeny within the Pheretima complex. Sci Rep 2016; 6:20096. [PMID: 26833286 PMCID: PMC4735579 DOI: 10.1038/srep20096] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 12/17/2015] [Indexed: 01/26/2023] Open
Abstract
The Pheretima complex within the Megascolecidae family is a major earthworm group. Recently, the systematic status of the Pheretima complex based on morphology was challenged by molecular studies. In this study, we carry out the first comparative mitogenomic study in oligochaetes. The mitogenomes of 15 earthworm species were sequenced and compared with other 9 available earthworm mitogenomes, with the main aim to explore their phylogenetic relationships and test different analytical approaches on phylogeny reconstruction. The general earthworm mitogenomic features revealed to be conservative: all genes encoded on the same strand, all the protein coding loci shared the same initiation codon (ATG), and tRNA genes showed conserved structures. The Drawida japonica mitogenome displayed the highest A + T content, reversed AT/GC-skews and the highest genetic diversity. Genetic distances among protein coding genes displayed their maximum and minimum interspecific values in the ATP8 and CO1 genes, respectively. The 22 tRNAs showed variable substitution patterns between the considered earthworm mitogenomes. The inclusion of rRNAs positively increased phylogenetic support. Furthermore, we tested different trimming tools for alignment improvement. Our analyses rejected reciprocal monophyly among Amynthas and Metaphire and indicated that the two genera should be systematically classified into one.
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Affiliation(s)
- Liangliang Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Pierfrancesco Sechi
- Institute of Ecosystem Study (ISE), Italian National Research Council, Sassari, Italy
| | - Minglong Yuan
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Gansu, China
| | - Jibao Jiang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Dong
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiangping Qiu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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121
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122
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Aguado MT, Grande C, Gerth M, Bleidorn C, Noreña C. Characterization of the complete mitochondrial genomes from Polycladida (Platyhelminthes) using next-generation sequencing. Gene 2016; 575:199-205. [DOI: 10.1016/j.gene.2015.08.054] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/18/2015] [Accepted: 08/26/2015] [Indexed: 10/23/2022]
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123
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Evolution of mitochondrial gene order in Annelida. Mol Phylogenet Evol 2016; 94:196-206. [DOI: 10.1016/j.ympev.2015.08.008] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Revised: 07/30/2015] [Accepted: 08/05/2015] [Indexed: 01/08/2023]
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124
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Haszprunar G. Review of data for a morphological look on Xenacoelomorpha (Bilateria incertae sedis). ORG DIVERS EVOL 2015. [DOI: 10.1007/s13127-015-0249-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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125
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Timmermans MJTN, Barton C, Haran J, Ahrens D, Culverwell CL, Ollikainen A, Dodsworth S, Foster PG, Bocak L, Vogler AP. Family-Level Sampling of Mitochondrial Genomes in Coleoptera: Compositional Heterogeneity and Phylogenetics. Genome Biol Evol 2015; 8:161-75. [PMID: 26645679 PMCID: PMC4758238 DOI: 10.1093/gbe/evv241] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2015] [Indexed: 12/29/2022] Open
Abstract
Mitochondrial genomes are readily sequenced with recent technology and thus evolutionary lineages can be densely sampled. This permits better phylogenetic estimates and assessment of potential biases resulting from heterogeneity in nucleotide composition and rate of change. We gathered 245 mitochondrial sequences for the Coleoptera representing all 4 suborders, 15 superfamilies of Polyphaga, and altogether 97 families, including 159 newly sequenced full or partial mitogenomes. Compositional heterogeneity greatly affected 3rd codon positions, and to a lesser extent the 1st and 2nd positions, even after RY coding. Heterogeneity also affected the encoded protein sequence, in particular in the nad2, nad4, nad5, and nad6 genes. Credible tree topologies were obtained with the nhPhyML ("nonhomogeneous") algorithm implementing a model for branch-specific equilibrium frequencies. Likelihood searches using RAxML were improved by data partitioning by gene and codon position. Finally, the PhyloBayes software, which allows different substitution processes for amino acid replacement at various sites, produced a tree that best matched known higher level taxa and defined basal relationships in Coleoptera. After rooting with Neuropterida outgroups, suborder relationships were resolved as (Polyphaga (Myxophaga (Archostemata + Adephaga))). The infraorder relationships in Polyphaga were (Scirtiformia (Elateriformia ((Staphyliniformia + Scarabaeiformia) (Bostrichiformia (Cucujiformia))))). Polyphagan superfamilies were recovered as monophyla except Staphylinoidea (paraphyletic for Scarabaeiformia) and Cucujoidea, which can no longer be considered a valid taxon. The study shows that, although compositional heterogeneity is not universal, it cannot be eliminated for some mitochondrial genes, but dense taxon sampling and the use of appropriate Bayesian analyses can still produce robust phylogenetic trees.
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Affiliation(s)
- Martijn J T N Timmermans
- Department of Life Sciences, Natural History Museum, London, United Kingdom Department of Life Sciences, Imperial College London - Silwood Park Campus, Ascot, United Kingdom Department of Natural Sciences, Middlesex University, Hendon Campus, London, United Kingdom
| | - Christopher Barton
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Julien Haran
- Department of Life Sciences, Natural History Museum, London, United Kingdom Present address: INRA, UR633 Zoologie Forestière, Orléans, France
| | - Dirk Ahrens
- Department of Life Sciences, Natural History Museum, London, United Kingdom Zoologisches Forschungsmuseum Alexander Koenig Bonn, Bonn, Germany
| | - C Lorna Culverwell
- Department of Life Sciences, Natural History Museum, London, United Kingdom Present address: Haartman Institute, Haartmaninkatu 3, University of Helsinki, Helsinki, Finland
| | - Alison Ollikainen
- Department of Life Sciences, Natural History Museum, London, United Kingdom Present address: Department of Medical Genetics, Genome-Scale Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Steven Dodsworth
- Department of Life Sciences, Natural History Museum, London, United Kingdom Present address: Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Richmond, Surrey, United Kingdom
| | - Peter G Foster
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Ladislav Bocak
- Department of Life Sciences, Natural History Museum, London, United Kingdom Department of Zoology, Faculty of Science UP, Olomouc, Czech Republic
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, United Kingdom Department of Life Sciences, Imperial College London - Silwood Park Campus, Ascot, United Kingdom
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127
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The complete mitochondrial genome of the golden mussel Limnoperna fortunei and comparative mitogenomics of Mytilidae. Gene 2015; 577:202-8. [PMID: 26639990 DOI: 10.1016/j.gene.2015.11.043] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 11/24/2015] [Accepted: 11/25/2015] [Indexed: 01/08/2023]
Abstract
Here we describe the mitochondrial genome of the golden mussel Limnoperna fortunei, an Asian bivalve which has become one of the most aggressive invasive species in Japan and South America. The mitochondrial genome of L. fortunei does not present conserved gene arrangement when compared to the other Mytilidae species suggesting a high degree of gene recombination in the mitochondria of this clade. In addition, the golden mussel mitogenome encodes two copies of tRNA(Lys) and presents a putative pseudogene for the atp8 gene sequence that encodes a 27 amino acid peptide containing an in-frame stop codon. The presence of this pseudogene raises the question as to whether atp8 is encoded in some bivalve mitochondrial genomes or not. The phylogenetic analysis of all complete mitochondrial genomes available from Mytilidae mussels confirmed the close evolutionary relationships among bivalves from the genus Mytilys and placed L. fortunei coming from a more ancestral branch on the family. The supermatrix phylogeny described used the concatenation of all 12 genes from the mitochondria and disputed the monophyly of the genus Perna, as Perna perna was shown to be more closely related to Brachidontes exustus than to Perna viridis. The comparative analysis of mitogenome synteny also confirmed the polyphyly of the genus Perna. The complete and annotated mitogenome has been published in GenBank under the accession number KP756905.
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128
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Heikkilä M, Mutanen M, Wahlberg N, Sihvonen P, Kaila L. Elusive ditrysian phylogeny: an account of combining systematized morphology with molecular data (Lepidoptera). BMC Evol Biol 2015; 15:260. [PMID: 26589618 PMCID: PMC4654798 DOI: 10.1186/s12862-015-0520-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 10/26/2015] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Ditrysia comprise close to 99 % of all butterflies and moths. The evolutionary relationships among the ditrysian superfamilies have received considerable attention in phylogenetic studies based on DNA and transcriptomic data, but the deepest divergences remain for large parts unresolved or contradictory. To obtain complementary insight into the evolutionary history of the clade, and to test previous hypotheses on the subdivision of Ditrysia based on morphology, we examine the morphology of larvae, pupae and adult males and females of 318 taxa representing nearly all ditrysian superfamilies and families. We present the most comprehensive morphological dataset on Ditrysia to date, consisting of over 500 morphological characters. The data are analyzed alone and combined with sequence data (one mitochondrial and seven nuclear protein-coding gene regions, sequenced from 422 taxa). The full dataset consists of 473 exemplar species. Analyses are performed using maximum likelihood methods, and parsimony methods for the morphological dataset. We explore whether combining morphological data and DNA-data can stabilize taxa that are unstable in phylogenetic studies based on genetic data only. RESULTS Morphological characters are found phylogenetically informative in resolving apical nodes (superfamilies and families), but characters serving as evidence of relatedness of larger assemblages are few. Results include the recovery of a monophyletic Tineoidea, Sesioidea and Cossoidea, and a stable position for some unstable taxa (e.g. Epipyropidae, Cyclotornidae, Urodoidea + Schreckensteinioidea). Several such taxa, however, remain unstable even though morphological characters indicate a position in the tree (e.g. Immidae). Evidence supporting affinities between clades are suggested, e.g. a novel larval synapomorphy for Tineidae. We also propose the synonymy of Tineodidae with Alucitidae, syn. nov. CONCLUSIONS The large morphological dataset provides information on the diversity and distribution of morphological traits in Ditrysia, and can be used in future research on the evolution of these traits, in identification keys and in identification of fossil Lepidoptera. The "backbone" of the phylogeny for Ditrysia remains largely unresolved. As previously proposed as an explanation for the scarcity of molecular signal in resolving the deeper nodes, this may be due to the rapid radiation of Ditrysia in the Cretaceous.
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Affiliation(s)
- Maria Heikkilä
- Finnish Museum of Natural History, Zoology Unit, University of Helsinki, PO Box 17, Helsinki, 00014, Finland.
| | - Marko Mutanen
- Department of Genetics and Physiology, University of Oulu, PO Box 3000, Oulu, 90014, Finland.
| | - Niklas Wahlberg
- Laboratory of Genetics, Department of Biology, University of Turku, Turku, 20014, Finland.
- Department of Biology, Lund University, 223 62, Lund, Sweden.
| | - Pasi Sihvonen
- University of Helsinki, Research Affairs, PO Box 33, Helsinki, 00014, Finland.
| | - Lauri Kaila
- Finnish Museum of Natural History, Zoology Unit, University of Helsinki, PO Box 17, Helsinki, 00014, Finland.
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129
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Halanych KM. The ctenophore lineage is older than sponges? That cannot be right! Or can it? ACTA ACUST UNITED AC 2015; 218:592-7. [PMID: 25696822 DOI: 10.1242/jeb.111872] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recent phylogenetic analyses resulting from collection of whole genome data suggest that ctenophores, or comb jellies, are sister to all other animals. Even before publication, this result prompted discussion among researchers. Here, I counter common criticisms raised about this result and show that assumptions placing sponges as the basal-most extant animal lineage are based on limited evidence and questionable premises. For example, the idea that sponges are simple and the reported similarity of sponge choanocytes to Choanflagellata do not provide useful characters for determining the positions of sponges within the animal tree. Intertwined with discussion of basal metazoan phylogeny is consideration of the evolution of neuronal systems. Recent data show that neural systems of ctenophores are vastly different from those of other animals and use different sets of cellular and genetic mechanisms. Thus, neural systems appear to have at least two independent origins regardless of whether ctenophores or sponges are the earliest branching extant animal lineage.
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Affiliation(s)
- Kenneth M Halanych
- Department of Biological Sciences, 101 Life Sciences Building, Auburn University, Auburn, AL 36849, USA Friday Harbor Laboratories, 620 University Road, University of Washington, Friday Harbor, WA 98250, USA
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130
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Wang K, Ding S, Yang D. The complete mitochondrial genome of a stonefly species, Kamimuria chungnanshana Wu, 1948 (Plecoptera: Perlidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3810-1. [DOI: 10.3109/19401736.2015.1082088] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Kai Wang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Shuangmei Ding
- Department of Entomology, China Agricultural University, Beijing, China
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing, China
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131
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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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132
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Luo YJ, Satoh N, Endo K. Mitochondrial gene order variation in the brachiopod Lingula anatina and its implications for mitochondrial evolution in lophotrochozoans. Mar Genomics 2015; 24 Pt 1:31-40. [PMID: 26342990 DOI: 10.1016/j.margen.2015.08.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Revised: 08/07/2015] [Accepted: 08/25/2015] [Indexed: 11/18/2022]
Abstract
Vertebrate mitochondrial (mt) genomes display highly conserved gene order and relatively low evolutionary rates. However, these features are variable in marine invertebrates. Here we present the mt genome of the lingulid brachiopod, Lingula anatina, from Amami Island, Japan, as part of the nuclear genome project. We obtain ~2000-fold coverage of the 17.9-kb mt genome using Illumina sequencing, and we identify hypervariable regions within the same individual. Transcriptome analyses show that mt transcripts are polycistronic and expressed differentially. Unexpectedly, we find that the mt gene order of Amami Lingula is completely shuffled compared to that of a specimen from Yanagawa, suggesting that there may be cryptic species. Using breakpoint distance analyses with 101 metazoan mt genomes, we show that the evolutionary history of mt gene order among lophotrochozoans is unique. Analyses of non-synonymous substitution rates reveal that mt protein-coding genes of Lingula have experienced rapid evolution comparable to that expected for interspecific comparisons. Whole genome phylogenetic analyses suggest that mt genomes have limited value for inferring the phylogenetic positions of lophotrochozoans because of their high evolutionary rates in brachiopods and bivalves.
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Affiliation(s)
- Yi-Jyun Luo
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan.
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Kazuyoshi Endo
- Department of Earth and Planetary Science, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
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133
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Zhang L, Jiang J, Dong Y, Qiu J. Complete mitochondrial genome of four pheretimoid earthworms (Clitellata: Oligochaeta) and their phylogenetic reconstruction. Gene 2015; 574:308-16. [PMID: 26291739 DOI: 10.1016/j.gene.2015.08.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 07/12/2015] [Accepted: 08/10/2015] [Indexed: 10/23/2022]
Abstract
Among oligochaetes, the Pheretima complex within the Megascolecidae is a major earthworm group. Recently, however, the systematics of the Pheretima complex based on morphology are challenged by molecular studies. Since little comparative analysis of earthworm complete mitochondrial genomes has been reported yet, we sequenced mitogenomes of four pheretimoid earthworm species to explore their phylogenetic relationships. The general earthworm genomic features are also found in four earthworms: all genes transcribed from the same strand, the same initiation codon ATG for each PCGs, and conserved structures of RNA genes. Interestingly we find an extra potential tRNA-leucine (CUN) in Amynthas longisiphonus. The earthworm mitochondrial ATP8 exhibits the highest evolutionary rate, while the gene CO1 evolves slowest. Phylogenetic analysis based on protein-coding genes (PCGs) strongly supports the monophyly of the Clitellata, Hirudinea, Oligochaeta, Megascolecidae and Pheretima complex. Our analysis, however, reveals non-monophyly within the genara Amynthas and Metaphire. Thus the generic divisions based on morphology in the Pheretima complex should be reconsidered.
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Affiliation(s)
- Liangliang Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
| | - Jibao Jiang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Dong
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiangping Qiu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
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134
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Shen H, Braband A, Scholtz G. The complete mitogenomes of lobsters and crayfish (Crustacea: Decapoda: Astacidea) reveal surprising differences in closely related taxa and convergences to Priapulida. J ZOOL SYST EVOL RES 2015. [DOI: 10.1111/jzs.12106] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Hong Shen
- Institut für Biologie/Vergleichende Zoologie; Humboldt-Universität zu Berlin; Berlin Germany
| | - Anke Braband
- Institut für Biologie/Vergleichende Zoologie; Humboldt-Universität zu Berlin; Berlin Germany
| | - Gerhard Scholtz
- Institut für Biologie/Vergleichende Zoologie; Humboldt-Universität zu Berlin; Berlin Germany
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135
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Aguado MT, Glasby CJ, Schroeder PC, Weigert A, Bleidorn C. The making of a branching annelid: an analysis of complete mitochondrial genome and ribosomal data of Ramisyllis multicaudata. Sci Rep 2015; 5:12072. [PMID: 26183383 PMCID: PMC4505326 DOI: 10.1038/srep12072] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 06/12/2015] [Indexed: 12/13/2022] Open
Abstract
Ramisyllis multicaudata is a member of Syllidae (Annelida, Errantia, Phyllodocida) with a remarkable branching body plan. Using a next-generation sequencing approach, the complete mitochondrial genomes of R. multicaudata and Trypanobia sp. are sequenced and analysed, representing the first ones from Syllidae. The gene order in these two syllids does not follow the order proposed as the putative ground pattern in Errantia. The phylogenetic relationships of R. multicaudata are discerned using a phylogenetic approach with the nuclear 18S and the mitochondrial 16S and cox1 genes. Ramisyllis multicaudata is the sister group of a clade containing Trypanobia species. Both genera, Ramisyllis and Trypanobia, together with Parahaplosyllis, Trypanosyllis, Eurysyllis, and Xenosyllis are located in a long branched clade. The long branches are explained by an accelerated mutational rate in the 18S rRNA gene. Using a phylogenetic backbone, we propose a scenario in which the postembryonic addition of segments that occurs in most syllids, their huge diversity of reproductive modes, and their ability to regenerate lost parts, in combination, have provided an evolutionary basis to develop a new branching body pattern as realised in Ramisyllis.
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Affiliation(s)
- M. Teresa Aguado
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Christopher J. Glasby
- Museum and Art Gallery of the Northern Territory, GPO Box 4646, Darwin, N.T., Australia
| | - Paul C. Schroeder
- School of Biological Sciences, Washington State University, Pullman, Washington 99163-4236, USA
| | - Anne Weigert
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstraße 33, D-04103 Leipzig, Germany
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Christoph Bleidorn
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Talstraße 33, D-04103 Leipzig, Germany
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136
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Cabrera-Brandt MA, Gaitán-Espitia JD. Phylogenetic analysis of the complete mitogenome sequence of the raspberry weevil, Aegorhinus superciliosus (Coleoptera: Curculionidae), supports monophyly of the tribe Aterpini. Gene 2015; 571:205-11. [PMID: 26117169 DOI: 10.1016/j.gene.2015.06.059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 05/29/2015] [Accepted: 06/22/2015] [Indexed: 11/29/2022]
Abstract
The superfamily Curculionoidea is one of the most diverse groups of insects in the world, including many species which are crop pests. Within this group, the native raspberry weevil, Aegorhinus superciliosus (Guérin, 1830), is an important pest in blueberry and raspberry fields in southern South America. Using a 454 sequencing approach, we sequenced and annotated the mitogenome of A. superciliosus, it, providing the first such information for any species in the tribe Aterpini, subfamily Cyclominae. The assembled mitogenome is a circular DNA molecule 15,121bp in length containing all 37 genes normally found in metazoans. Mitogenome organization and transcriptional orientation in A. superciliosus showed the same pattern that characterizes the suborder Polyphaga. Bayesian and Maximum Likelihood phylogenetic analyses supported the monophyly of the tribe Aterpini and the subfamily Cyclominae, recovering this clade in a sister group relationship with Entiminae and Hyperinae. The monophyly of these three subfamilies defines a critical transition to an ectophagous lifestyle in the larvae, from an ancestrally endophagous larval lifestyle in all other lineages. The sequenced mitogenome of A. superciliosus can provide basic data for future studies investigating population history, molecular systematics, stress ecophysiology and phylogeography.
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Affiliation(s)
- Marco A Cabrera-Brandt
- Departamento de Producción Agrícola, Facultad de Ciencias Agrarias, Universidad de Talca, Casilla 747, Talca, Chile; Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile.
| | - Juan D Gaitán-Espitia
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile; CSIRO Oceans and Atmosphere, GPO Box 1538, Hobart 7001, TAS, Australia
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137
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Crampton-Platt A, Timmermans MJTN, Gimmel ML, Kutty SN, Cockerill TD, Vun Khen C, Vogler AP. Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample. Mol Biol Evol 2015; 32:2302-16. [PMID: 25957318 PMCID: PMC4540967 DOI: 10.1093/molbev/msv111] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In spite of the growth of molecular ecology, systematics and next-generation sequencing, the discovery and analysis of diversity is not currently integrated with building the tree-of-life. Tropical arthropod ecologists are well placed to accelerate this process if all specimens obtained through mass-trapping, many of which will be new species, could be incorporated routinely into phylogeny reconstruction. Here we test a shotgun sequencing approach, whereby mitochondrial genomes are assembled from complex ecological mixtures through mitochondrial metagenomics, and demonstrate how the approach overcomes many of the taxonomic impediments to the study of biodiversity. DNA from approximately 500 beetle specimens, originating from a single rainforest canopy fogging sample from Borneo, was pooled and shotgun sequenced, followed by de novo assembly of complete and partial mitogenomes for 175 species. The phylogenetic tree obtained from this local sample was highly similar to that from existing mitogenomes selected for global coverage of major lineages of Coleoptera. When all sequences were combined only minor topological changes were induced against this reference set, indicating an increasingly stable estimate of coleopteran phylogeny, while the ecological sample expanded the tip-level representation of several lineages. Robust trees generated from ecological samples now enable an evolutionary framework for ecology. Meanwhile, the inclusion of uncharacterized samples in the tree-of-life rapidly expands taxon and biogeographic representation of lineages without morphological identification. Mitogenomes from shotgun sequencing of unsorted environmental samples and their associated metadata, placed robustly into the phylogenetic tree, constitute novel DNA “superbarcodes” for testing hypotheses regarding global patterns of diversity.
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Affiliation(s)
- Alex Crampton-Platt
- Department of Life Sciences, Natural History Museum, London, United Kingdom Department of Genetics, Evolution and Environment, Faculty of Life Sciences, University College London, London, United Kingdom
| | - Martijn J T N Timmermans
- Department of Life Sciences, Natural History Museum, London, United Kingdom Division of Biology, Imperial College London, Silwood Park Campus, Ascot, United Kingdom
| | - Matthew L Gimmel
- Department of Biology, Faculty of Education, Palacký University, Olomouc, Czech Republic
| | | | - Timothy D Cockerill
- Department of Life Sciences, Natural History Museum, London, United Kingdom Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Chey Vun Khen
- Entomology Section, Forest Research Centre, Forestry Department, Sandakan, Sabah, Malaysia
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, United Kingdom Division of Biology, Imperial College London, Silwood Park Campus, Ascot, United Kingdom
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138
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Golombek A, Tobergte S, Struck TH. Elucidating the phylogenetic position of Gnathostomulida and first mitochondrial genomes of Gnathostomulida, Gastrotricha and Polycladida (Platyhelminthes). Mol Phylogenet Evol 2015; 86:49-63. [DOI: 10.1016/j.ympev.2015.02.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 01/18/2015] [Accepted: 02/17/2015] [Indexed: 01/06/2023]
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139
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García LE, Sánchez-Puerta MV. Comparative and evolutionary analyses of Meloidogyne spp. Based on mitochondrial genome sequences. PLoS One 2015; 10:e0121142. [PMID: 25799071 PMCID: PMC4370701 DOI: 10.1371/journal.pone.0121142] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 02/12/2015] [Indexed: 01/11/2023] Open
Abstract
Molecular taxonomy and evolution of nematodes have been recently the focus of several studies. Mitochondrial sequences were proposed as an alternative for precise identification of Meloidogyne species, to study intraspecific variability and to follow maternal lineages. We characterized the mitochondrial genomes (mtDNAs) of the root knot nematodes M. floridensis, M. hapla and M. incognita. These were AT rich (81–83%) and highly compact, encoding 12 proteins, 2 rRNAs, and 22 tRNAs. Comparisons with published mtDNAs of M. chitwoodi, M. incognita (another strain) and M. graminicola revealed that they share protein and rRNA gene order but differ in the order of tRNAs. The mtDNAs of M. floridensis and M. incognita were strikingly similar (97–100% identity for all coding regions). In contrast, M. floridensis, M. chitwoodi, M. hapla and M. graminicola showed 65–84% nucleotide identity for coding regions. Variable mitochondrial sequences are potentially useful for evolutionary and taxonomic studies. We developed a molecular taxonomic marker by sequencing a highly-variable ~2 kb mitochondrial region, nad5-cox1, from 36 populations of root-knot nematodes to elucidate relationships within the genus Meloidogyne. Isolates of five species formed monophyletic groups and showed little intraspecific variability. We also present a thorough analysis of the mitochondrial region cox2-rrnS. Phylogenies based on either mitochondrial region had good discrimination power but could not discriminate between M. arenaria, M. incognita and M. floridensis.
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Affiliation(s)
- Laura Evangelina García
- IBAM-CONICET and Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Chacras de Coria, Mendoza, Argentina
| | - M. Virginia Sánchez-Puerta
- IBAM-CONICET and Facultad de Ciencias Agrarias, Universidad Nacional de Cuyo, Chacras de Coria, Mendoza, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Mendoza, Mendoza, Argentina
- * E-mail:
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140
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Laumer CE, Hejnol A, Giribet G. Nuclear genomic signals of the 'microturbellarian' roots of platyhelminth evolutionary innovation. eLife 2015; 4:e05503. [PMID: 25764302 PMCID: PMC4398949 DOI: 10.7554/elife.05503] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 03/06/2015] [Indexed: 12/25/2022] Open
Abstract
Flatworms number among the most diverse invertebrate phyla and represent the most biomedically significant branch of the major bilaterian clade Spiralia, but to date, deep evolutionary relationships within this group have been studied using only a single locus (the rRNA operon), leaving the origins of many key clades unclear. In this study, using a survey of genomes and transcriptomes representing all free-living flatworm orders, we provide resolution of platyhelminth interrelationships based on hundreds of nuclear protein-coding genes, exploring phylogenetic signal through concatenation as well as recently developed consensus approaches. These analyses robustly support a modern hypothesis of flatworm phylogeny, one which emphasizes the primacy of the often-overlooked 'microturbellarian' groups in understanding the major evolutionary transitions within Platyhelminthes: perhaps most notably, we propose a novel scenario for the interrelationships between free-living and vertebrate-parasitic flatworms, providing new opportunities to shed light on the origins and biological consequences of parasitism in these iconic invertebrates.
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Affiliation(s)
- Christopher E Laumer
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
| | - Andreas Hejnol
- Sars International Centre for Marine Molecular Biology, University of Bergen, Bergen, Norway
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, United States
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141
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Li H, Shao R, Song N, Song F, Jiang P, Li Z, Cai W. Higher-level phylogeny of paraneopteran insects inferred from mitochondrial genome sequences. Sci Rep 2015; 5:8527. [PMID: 25704094 PMCID: PMC4336943 DOI: 10.1038/srep08527] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 01/22/2015] [Indexed: 11/09/2022] Open
Abstract
Mitochondrial (mt) genome data have been proven to be informative for animal phylogenetic studies but may also suffer from systematic errors, due to the effects of accelerated substitution rate and compositional heterogeneity. We analyzed the mt genomes of 25 insect species from the four paraneopteran orders, aiming to better understand how accelerated substitution rate and compositional heterogeneity affect the inferences of the higher-level phylogeny of this diverse group of hemimetabolous insects. We found substantial heterogeneity in base composition and contrasting rates in nucleotide substitution among these paraneopteran insects, which complicate the inference of higher-level phylogeny. The phylogenies inferred with concatenated sequences of mt genes using maximum likelihood and Bayesian methods and homogeneous models failed to recover Psocodea and Hemiptera as monophyletic groups but grouped, instead, the taxa that had accelerated substitution rates together, including Sternorrhyncha (a suborder of Hemiptera), Thysanoptera, Phthiraptera and Liposcelididae (a family of Psocoptera). Bayesian inference with nucleotide sequences and heterogeneous models (CAT and CAT + GTR), however, recovered Psocodea, Thysanoptera and Hemiptera each as a monophyletic group. Within Psocodea, Liposcelididae is more closely related to Phthiraptera than to other species of Psocoptera. Furthermore, Thysanoptera was recovered as the sister group to Hemiptera.
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Affiliation(s)
- Hu Li
- Department of Entomology, China Agricultural University, Beijing. 100193, China
- Department of Ornamental Horticulture, China Agricultural University, Beijing. 100193, China
| | - Renfu Shao
- GeneCology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Nan Song
- Department of Entomology, China Agricultural University, Beijing. 100193, China
- College of Plant Protection, Henan Agricultural University, Zhengzhou, Henan. 450002, China
| | - Fan Song
- Department of Entomology, China Agricultural University, Beijing. 100193, China
| | - Pei Jiang
- Department of Entomology, China Agricultural University, Beijing. 100193, China
| | - Zhihong Li
- Department of Entomology, China Agricultural University, Beijing. 100193, China
| | - Wanzhi Cai
- Department of Entomology, China Agricultural University, Beijing. 100193, China
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142
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Dunn CW, Giribet G, Edgecombe GD, Hejnol A. Animal Phylogeny and Its Evolutionary Implications. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2014. [DOI: 10.1146/annurev-ecolsys-120213-091627] [Citation(s) in RCA: 261] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Casey W. Dunn
- Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island 02912;
| | - Gonzalo Giribet
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138;
| | - Gregory D. Edgecombe
- Department of Earth Sciences, The Natural History Museum, London SW7 5BD, United Kingdom;
| | - Andreas Hejnol
- Sars International Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway;
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143
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Kumazawa Y, Miura S, Yamada C, Hashiguchi Y. Gene rearrangements in gekkonid mitochondrial genomes with shuffling, loss, and reassignment of tRNA genes. BMC Genomics 2014; 15:930. [PMID: 25344428 PMCID: PMC4223735 DOI: 10.1186/1471-2164-15-930] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Accepted: 10/13/2014] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Vertebrate mitochondrial genomes (mitogenomes) are 16-18 kbp double-stranded circular DNAs that encode a set of 37 genes. The arrangement of these genes and the major noncoding region is relatively conserved through evolution although gene rearrangements have been described for diverse lineages. The tandem duplication-random loss model has been invoked to explain the mechanisms of most mitochondrial gene rearrangements. Previously reported mitogenomic sequences for geckos rarely included gene rearrangements, which we explore in the present study. RESULTS We determined seven new mitogenomic sequences from Gekkonidae using a high-throughput sequencing method. The Tropiocolotes tripolitanus mitogenome involves a tandem duplication of the gene block: tRNAArg, NADH dehydrogenase subunit 4L, and NADH dehydrogenase subunit 4. One of the duplicate copies for each protein-coding gene may be pseudogenized. A duplicate copy of the tRNAArg gene appears to have been converted to a tRNAGln gene by a C to T base substitution at the second anticodon position, although this gene may not be fully functional in protein synthesis. The Stenodactylus petrii mitogenome includes several tandem duplications of tRNALeu genes, as well as a translocation of the tRNAAla gene and a putative origin of light-strand replication within a tRNA gene cluster. Finally, the Uroplatus fimbriatus and U. ebenaui mitogenomes feature the apparent loss of the tRNAGlu gene from its original position. Uroplatus fimbriatus appears to retain a translocated tRNAGlu gene adjacent to the 5' end of the major noncoding region. CONCLUSIONS The present study describes several new mitochondrial gene rearrangements from Gekkonidae. The loss and reassignment of tRNA genes is not very common in vertebrate mitogenomes and our findings raise new questions as to how missing tRNAs are supplied and if the reassigned tRNA gene is fully functional. These new examples of mitochondrial gene rearrangements in geckos should broaden our understanding of the evolution of mitochondrial gene arrangements.
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Affiliation(s)
- Yoshinori Kumazawa
- Department of Information and Biological Sciences and Research Center for Biological Diversity, Graduate School of Natural Sciences, Nagoya City University, 1 Yamanohata, Mizuho-cho, Mizuho-ku, Nagoya 467-8501, Japan.
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Schrödl M, Stöger I. A review on deep molluscan phylogeny: old markers, integrative approaches, persistent problems. J NAT HIST 2014. [DOI: 10.1080/00222933.2014.963184] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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145
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Osca D, Irisarri I, Todt C, Grande C, Zardoya R. The complete mitochondrial genome of Scutopus ventrolineatus (Mollusca: Chaetodermomorpha) supports the Aculifera hypothesis. BMC Evol Biol 2014; 14:197. [PMID: 25288450 PMCID: PMC4189740 DOI: 10.1186/s12862-014-0197-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 09/01/2014] [Indexed: 11/16/2022] Open
Abstract
Background With more than 100000 living species, mollusks are the second most diverse metazoan phylum. The current taxonomic classification of mollusks recognizes eight classes (Neomeniomorpha, Chaetodermomorpha, Polyplacophora, Monoplacophora, Cephalopoda, Gastropoda, Bivalvia, and Scaphopoda) that exhibit very distinct body plans. In the past, phylogenetic relationships among mollusk classes have been contentious due to the lack of indisputable morphological synapomorphies. Fortunately, recent phylogenetic analyses based on multi-gene data sets are rendering promising results. In this regard, mitochondrial genomes have been widely used to reconstruct deep phylogenies. For mollusks, complete mitochondrial genomes are mostly available for gastropods, bivalves, and cephalopods, whereas other less-diverse lineages have few or none reported. Results The complete DNA sequence (14662 bp) of the mitochondrial genome of the chaetodermomorph Scutopus ventrolineatus Salvini-Plawen, 1968 was determined. Compared with other mollusks, the relative position of protein-coding genes in the mitochondrial genome of S. ventrolineatus is very similar to those reported for Polyplacophora, Cephalopoda and early-diverging lineages of Bivalvia and Gastropoda (Vetigastropoda and Neritimorpha; but not Patellogastropoda). The reconstructed phylogenetic tree based on combined mitochondrial and nuclear sequence data recovered monophyletic Aplacophora, Aculifera, and Conchifera. Within the latter, Cephalopoda was the sister group of Gastropoda and Bivalvia + Scaphopoda. Conclusions Phylogenetic analyses of mitochondrial sequences showed strong among-lineage rate heterogeneity that produced long-branch attraction biases. Removal of long branches (namely those of bivalves and patellogastropods) ameliorated but not fully resolved the problem. Best results in terms of statistical support were achieved when mitochondrial and nuclear sequence data were concatenated. Electronic supplementary material The online version of this article (doi:10.1186/s12862-014-0197-9) contains supplementary material, which is available to authorized users.
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146
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Gillett CPDT, Crampton-Platt A, Timmermans MJTN, Jordal BH, Emerson BC, Vogler AP. Bulk de novo mitogenome assembly from pooled total DNA elucidates the phylogeny of weevils (Coleoptera: Curculionoidea). Mol Biol Evol 2014; 31:2223-37. [PMID: 24803639 PMCID: PMC4104315 DOI: 10.1093/molbev/msu154] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Complete mitochondrial genomes have been shown to be reliable markers for phylogeny reconstruction among diverse animal groups. However, the relative difficulty and high cost associated with obtaining de novo full mitogenomes have frequently led to conspicuously low taxon sampling in ensuing studies. Here, we report the successful use of an economical and accessible method for assembling complete or near-complete mitogenomes through shot-gun next-generation sequencing of a single library made from pooled total DNA extracts of numerous target species. To avoid the use of separate indexed libraries for each specimen, and an associated increase in cost, we incorporate standard polymerase chain reaction-based "bait" sequences to identify the assembled mitogenomes. The method was applied to study the higher level phylogenetic relationships in the weevils (Coleoptera: Curculionoidea), producing 92 newly assembled mitogenomes obtained in a single Illumina MiSeq run. The analysis supported a separate origin of wood-boring behavior by the subfamilies Scolytinae, Platypodinae, and Cossoninae. This finding contradicts morphological hypotheses proposing a close relationship between the first two of these but is congruent with previous molecular studies, reinforcing the utility of mitogenomes in phylogeny reconstruction. Our methodology provides a technically simple procedure for generating densely sampled trees from whole mitogenomes and is widely applicable to groups of animals for which bait sequences are the only required prior genome knowledge.
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Affiliation(s)
- Conrad P D T Gillett
- Department of Life Sciences, Natural History Museum, London, United KingdomSchool of Biological Sciences, Centre for Ecology, Evolution and Conservation, University of East Anglia, Norwich, United Kingdom
| | - Alex Crampton-Platt
- Department of Life Sciences, Natural History Museum, London, United KingdomDepartment of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Martijn J T N Timmermans
- Department of Life Sciences, Natural History Museum, London, United KingdomDepartment of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, United Kingdom
| | - Bjarte H Jordal
- The Natural History Museum, University Museum of Bergen, Bergen, Norway
| | - Brent C Emerson
- School of Biological Sciences, Centre for Ecology, Evolution and Conservation, University of East Anglia, Norwich, United KingdomIsland Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología, La Laguna, Tenerife, Canary Islands, Spain
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, United KingdomDepartment of Life Sciences, Silwood Park Campus, Imperial College London, Ascot, Berkshire, United Kingdom
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147
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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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148
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GC skew and mitochondrial origins of replication. Mitochondrion 2014; 17:56-66. [DOI: 10.1016/j.mito.2014.05.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 05/09/2014] [Accepted: 05/28/2014] [Indexed: 11/18/2022]
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149
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Struck TH, Wey-Fabrizius AR, Golombek A, Hering L, Weigert A, Bleidorn C, Klebow S, Iakovenko N, Hausdorf B, Petersen M, Kück P, Herlyn H, Hankeln T. Platyzoan paraphyly based on phylogenomic data supports a noncoelomate ancestry of spiralia. Mol Biol Evol 2014; 31:1833-49. [PMID: 24748651 DOI: 10.1093/molbev/msu143] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Based on molecular data three major clades have been recognized within Bilateria: Deuterostomia, Ecdysozoa, and Spiralia. Within Spiralia, small-sized and simply organized animals such as flatworms, gastrotrichs, and gnathostomulids have recently been grouped together as Platyzoa. However, the representation of putative platyzoans was low in the respective molecular phylogenetic studies, in terms of both, taxon number and sequence data. Furthermore, increased substitution rates in platyzoan taxa raised the possibility that monophyletic Platyzoa represents an artifact due to long-branch attraction. In order to overcome such problems, we employed a phylogenomic approach, thereby substantially increasing 1) the number of sampled species within Platyzoa and 2) species-specific sequence coverage in data sets of up to 82,162 amino acid positions. Using established and new measures (long-branch score), we disentangled phylogenetic signal from misleading effects such as long-branch attraction. In doing so, our phylogenomic analyses did not recover a monophyletic origin of platyzoan taxa that, instead, appeared paraphyletic with respect to the other spiralians. Platyhelminthes and Gastrotricha formed a monophylum, which we name Rouphozoa. To the exclusion of Gnathifera, Rouphozoa and all other spiralians represent a monophyletic group, which we name Platytrochozoa. Platyzoan paraphyly suggests that the last common ancestor of Spiralia was a simple-bodied organism lacking coelomic cavities, segmentation, and complex brain structures, and that more complex animals such as annelids evolved from such a simply organized ancestor. This conclusion contradicts alternative evolutionary scenarios proposing an annelid-like ancestor of Bilateria and Spiralia and several independent events of secondary reduction.
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Affiliation(s)
- Torsten H Struck
- Zoological Research Museum Alexander Koenig, Bonn, GermanyUniversity of Osnabrück, FB05 Biology/Chemistry, AG Zoology, Osnabrück, Germany
| | - Alexandra R Wey-Fabrizius
- Institute of Molecular Genetics, Biosafety Research and Consulting, Johannes Gutenberg University, Mainz, Germany
| | - Anja Golombek
- Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Lars Hering
- Animal Evolution and Development, Institute of Biology II, University of Leipzig, Leipzig, Germany
| | - Anne Weigert
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Leipzig, Germany
| | - Christoph Bleidorn
- Molecular Evolution and Systematics of Animals, Institute of Biology, University of Leipzig, Leipzig, Germany
| | - Sabrina Klebow
- Institute of Molecular Genetics, Biosafety Research and Consulting, Johannes Gutenberg University, Mainz, Germany
| | - Nataliia Iakovenko
- Department of Biology and Ecology, Ostravian University in Ostrava, Ostrava, Czech RepublicDepartment of Invertebrate Fauna and Systematics, Schmalhausen Institute of Zoology NAS of Ukraine, Kyiv, Ukraine
| | | | - Malte Petersen
- Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Patrick Kück
- Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Holger Herlyn
- Institute of Anthropology, Johannes Gutenberg University, Mainz, Germany
| | - Thomas Hankeln
- Institute of Molecular Genetics, Biosafety Research and Consulting, Johannes Gutenberg University, Mainz, Germany
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150
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Coates BS. Assembly and annotation of full mitochondrial genomes for the corn rootworm species, Diabrotica virgifera virgifera and Diabrotica barberi (Insecta: Coleoptera: Chrysomelidae), using Next Generation Sequence data. Gene 2014; 542:190-7. [PMID: 24657060 DOI: 10.1016/j.gene.2014.03.035] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 03/13/2014] [Accepted: 03/18/2014] [Indexed: 01/08/2023]
Abstract
Complete mitochondrial genomes for two corn rootworm species, Diabrotica virgifera virgifera (16,747 bp) and Diabrotica barberi (16,632; Insecta: Coleoptera: Chrysomelidae), were assembled from Illumina HiSeq2000 read data. Annotation indicated that the order and orientation of 13 protein coding genes (PCGs), and 22 tRNA and 2 rRNA sequences were in typical of insect mitochondrial genomes. Non-standard nad4 and cox3 stop codons were composed of single T nucleotides and likely completed by adenylation, and atypical TTT start codons was predicted for both D. v. virgifera and D. barberinad1 genes. The D. v. virgifera and D. barberi haplotypes showed 819 variable nucleotide positions within PCG regions (7.36% divergence), which suggest that speciation may have occurred ~3.68 million years ago assuming a linear rate of short-term substitution. Phylogenetic analyses of Coleopteran MtD genome show clustering based on family level, and may have the capacity to resolve the evolutionary history within this Order of insects.
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Affiliation(s)
- Brad S Coates
- United States Department of Agriculture, Agricultural Research Service, Corn Insects & Crop Genetics Research Unit, Iowa State University, Ames, IA, 50011, USA; Iowa State University Department of Entomology, Ames, IA, 50011, USA.
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