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Lee Y, Kim KB, Choi EH, Hwang UW. Complete mitochondrial genome of the worm snail Thylacodes adamsii (Littorinimorpha: Vermetidae) from South Korea. Mitochondrial DNA B Resour 2024; 9:753-757. [PMID: 38895513 PMCID: PMC11185085 DOI: 10.1080/23802359.2024.2368209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024] Open
Abstract
The worm snail Thylacodes adamsii (Mörch, 1859) (Littorinimorpha: Vermetidae) is a sessile gastropod that mainly inhabits rocky shores along the warm temperate to tropical ocean. Herein, the complete mitochondrial genome (mitogenome) of T. adamsii from South Korea was characterized. The genome is 14,913 bp in length and contains 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes. The genome organization and base composition of T. adamsii are similar to those of other vermetids. A phylogenetic tree was reconstructed using maximum likelihood based on the nucleotide sequences of the 13 PCGs; this tree supported the monophyly of Vermetidae. The complete mitogenome of T. adamsii can assist with molecular species identification and vermetid phylogenetic research in the future.
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Affiliation(s)
- Yumin Lee
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
| | - Ki Beom Kim
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
- Institute for Korean Herb-Bio Convergence Promotion, Kyungpook National University, Daegu, South Korea
| | - Eun Hwa Choi
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
- Phylomics Inc., Daegu, South Korea
| | - Ui Wook Hwang
- Department of Biology Education, Teachers College and Institute for Phylogenomics and Evolution, Kyungpook National University, Daegu, South Korea
- Institute for Korean Herb-Bio Convergence Promotion, Kyungpook National University, Daegu, South Korea
- Phylomics Inc., Daegu, South Korea
- Department of Biomedical Convergence Science and Technology, School of Industrial Technology Advances, Kyungpook National University, Daegu, South Korea
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Ghiselli F, Gomes-Dos-Santos A, Adema CM, Lopes-Lima M, Sharbrough J, Boore JL. Molluscan mitochondrial genomes break the rules. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200159. [PMID: 33813887 DOI: 10.1098/rstb.2020.0159] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The first animal mitochondrial genomes to be sequenced were of several vertebrates and model organisms, and the consistency of genomic features found has led to a 'textbook description'. However, a more broad phylogenetic sampling of complete animal mitochondrial genomes has found many cases where these features do not exist, and the phylum Mollusca is especially replete with these exceptions. The characterization of full mollusc mitogenomes required considerable effort involving challenging molecular biology, but has created an enormous catalogue of surprising deviations from that textbook description, including wide variation in size, radical genome rearrangements, gene duplications and losses, the introduction of novel genes, and a complex system of inheritance dubbed 'doubly uniparental inheritance'. Here, we review the extraordinary variation in architecture, molecular functioning and intergenerational transmission of molluscan mitochondrial genomes. Such features represent a great potential for the discovery of biological history, processes and functions that are novel for animal mitochondrial genomes. This provides a model system for studying the evolution and the manifold roles that mitochondria play in organismal physiology, and many ways that the study of mitochondrial genomes are useful for phylogeny and population biology. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
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Affiliation(s)
- Fabrizio Ghiselli
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy
| | - André Gomes-Dos-Santos
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, and Department of Biology, Faculty of Sciences, University of Porto, Portugal
| | - Coen M Adema
- Center for Evolutionary and Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, USA
| | - Manuel Lopes-Lima
- CIBIO/InBIO, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - Joel Sharbrough
- Department of Biology, Colorado State University, Fort Collins, USA
| | - Jeffrey L Boore
- Providence St Joseph Health and the Institute for Systems Biology, Seattle, USA
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Han X, He H, Shen H, Tang J, Dong W, Shi Y, Wu S, Zhang F, Liang G. Comparative mitochondrial genome analysis of Dendrolimus houi (Lepidoptera: Lasiocampidae) and phylogenetic relationship among Lasiocampidae species. PLoS One 2020; 15:e0232527. [PMID: 32407393 PMCID: PMC7224488 DOI: 10.1371/journal.pone.0232527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 04/16/2020] [Indexed: 11/18/2022] Open
Abstract
Dendrolimus houi is one of the most common caterpillars infesting Gymnosperm trees, and widely distributed in several countries in Southeast Asia, and exists soley or coexists with several congeners and some Lasiocampidae species in various forest habitats. However, natural hybrids occasionally occur among some closely related species in the same habitat, and host preference, extreme climate stress, and geographic isolation probably lead to their uncertain taxonomic consensus. The mitochondrial DNA (mtDNA) of D. houi was extracted and sequenced by using high-throughput technology, and the mitogenome composition and characteristics were compared and analyzed of these species, then the phylogenetic relationship was constructed using the maximum likelihood method (ML) and the Bayesian method (BI) based on their 13 protein-coding genes (PCGs) dataset, which were combined and made available to download which were combined and made available to download among global Lasiocampidae species data. Mitogenome of D. houi was 15,373 bp in length, with 37 genes, including 13 PCGs, 22 tRNA genes (tRNAs) and 2 rRNA genes (rRNAs). The positions and sequences of genes were consistent with those of most known Lasiocampidae species. The nucleotide composition was highly A+T biased, accounting for ~80% of the whole mitogenome. All start codons of PCGs belonged to typical start codons ATN except for COI which used CGA, and most stop codons ended with standard TAA or TAG, while COI, COII, ND4 ended with incomplete T. Only tRNASer (AGN) lacked DHU arm, while the remainder formed a typical "clover-shaped" secondary structure. For Lasiocampidae species, their complete mitochondrial genomes ranged from 15,281 to 15,570 bp in length, and all first genes started from trnM in the same direction. And base composition was biased toward A and T. Finally, both two methods (ML and BI) separately revealed that the same phylogenetic relationship of D. spp. as ((((D. punctatus + D. tabulaeformis) + D. spectabilis) + D. superans) + (D. kikuchii of Hunan population + D. houi) as in previous research, but results were different in that D. kikuchii from a Yunnan population was included, indicating that different geographical populations of insects have differentiated. And the phylogenetic relationship among Lasiocampidae species was ((((Dendrolimus) + Kunugia) + Euthrix) + Trabala). This provides a better theoretical basis for Lasiocampidae evolution and classification for future research directions.
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Affiliation(s)
- Xiaohong Han
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Huan He
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Haiyan Shen
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Jinhan Tang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Wanying Dong
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yufei Shi
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Songqing Wu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Feiping Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Guanghong Liang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Province University, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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Gemmell MR, Trewick SA, Hills SFK, Morgan‐Richards M. Phylogenetic topology and timing of New Zealand olive shells are consistent with punctuated equilibrium. J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michael R. Gemmell
- Ecology Group School of Agriculture and Environment Massey University Palmerston North New Zealand
| | - Steven A. Trewick
- Ecology Group School of Agriculture and Environment Massey University Palmerston North New Zealand
| | - Simon F. K. Hills
- Ecology Group School of Agriculture and Environment Massey University Palmerston North New Zealand
| | - Mary Morgan‐Richards
- Ecology Group School of Agriculture and Environment Massey University Palmerston North New Zealand
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Wong TKF, Ranjard L, Lin Y, Rodrigo AG. HaploJuice : accurate haplotype assembly from a pool of sequences with known relative concentrations. BMC Bioinformatics 2018; 19:389. [PMID: 30348075 PMCID: PMC6198429 DOI: 10.1186/s12859-018-2424-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 10/09/2018] [Indexed: 11/10/2022] Open
Abstract
Background Pooling techniques, where multiple sub-samples are mixed in a single sample, are widely used to take full advantage of high-throughput DNA sequencing. Recently, Ranjard et al. (PLoS ONE 13:0195090, 2018) proposed a pooling strategy without the use of barcodes. Three sub-samples were mixed in different known proportions (i.e. 62.5%, 25% and 12.5%), and a method was developed to use these proportions to reconstruct the three haplotypes effectively. Results HaploJuice provides an alternative haplotype reconstruction algorithm for Ranjard et al.’s pooling strategy. HaploJuice significantly increases the accuracy by first identifying the empirical proportions of the three mixed sub-samples and then assembling the haplotypes using a dynamic programming approach. HaploJuice was evaluated against five different assembly algorithms, Hmmfreq (Ranjard et al., PLoS ONE 13:0195090, 2018), ShoRAH (Zagordi et al., BMC Bioinformatics 12:119, 2011), SAVAGE (Baaijens et al., Genome Res 27:835-848, 2017), PredictHaplo (Prabhakaran et al., IEEE/ACM Trans Comput Biol Bioinform 11:182-91, 2014) and QuRe (Prosperi and Salemi, Bioinformatics 28:132-3, 2012). Using simulated and real data sets, HaploJuice reconstructed the true sequences with the highest coverage and the lowest error rate. Conclusion HaploJuice provides high accuracy in haplotype reconstruction, making Ranjard et al.’s pooling strategy more efficient, feasible, and applicable, with the benefit of reducing the sequencing cost.
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Affiliation(s)
- Thomas K F Wong
- The Research School of Biology, The Australian National University, Acton ACT, 2601, Australia.
| | - Louis Ranjard
- The Research School of Biology, The Australian National University, Acton ACT, 2601, Australia
| | - Yu Lin
- College of Engineering and Computer Science, The Australian National University, Acton ACT, 2601, Australia
| | - Allen G Rodrigo
- The Research School of Biology, The Australian National University, Acton ACT, 2601, Australia
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Uribe JE, Zardoya R, Puillandre N. Phylogenetic relationships of the conoidean snails (Gastropoda: Caenogastropoda) based on mitochondrial genomes. Mol Phylogenet Evol 2018; 127:898-906. [DOI: 10.1016/j.ympev.2018.06.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 06/20/2018] [Accepted: 06/22/2018] [Indexed: 01/02/2023]
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Ranjard L, Wong TKF, Rodrigo AG. Reassembling haplotypes in a mixture of pooled amplicons when the relative concentrations are known: A proof-of-concept study on the efficient design of next-generation sequencing strategies. PLoS One 2018; 13:e0195090. [PMID: 29621260 PMCID: PMC5886459 DOI: 10.1371/journal.pone.0195090] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 03/18/2018] [Indexed: 12/02/2022] Open
Abstract
Next-generation sequencing can be costly and labour intensive. Usually, the sequencing cost per sample is reduced by pooling amplified DNA = amplicons) derived from different individuals on the same sequencing lane. Barcodes unique to each amplicon permit short-read sequences to be assigned appropriately. However, the cost of the library preparation increases with the number of barcodes used. We propose an alternative to barcoding: by using different known proportions of individually-derived amplicons in a pooled sample, each is characterised a priori by an expected depth of coverage. We have developed a Hidden Markov Model that uses these expected proportions to reconstruct the input sequences. We apply this method to pools of mitochondrial DNA amplicons extracted from kangaroo meat, genus Macropus. Our experiments indicate that the sequence coverage can be efficiently used to index the short-reads and that we can reassemble the input haplotypes when secondary factors impacting the coverage are controlled. We therefore demonstrate that, by combining our approach with standard barcoding, the cost of the library preparation is reduced to a third.
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Affiliation(s)
- Louis Ranjard
- The Research School of Biology, The Australian National University, Australia
- * E-mail:
| | - Thomas K. F. Wong
- The Research School of Biology, The Australian National University, Australia
| | - Allen G. Rodrigo
- The Research School of Biology, The Australian National University, Australia
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Wang JG, Zhang D, Jakovlić I, Wang WM. Sequencing of the complete mitochondrial genomes of eight freshwater snail species exposes pervasive paraphyly within the Viviparidae family (Caenogastropoda). PLoS One 2017; 12:e0181699. [PMID: 28742843 PMCID: PMC5526530 DOI: 10.1371/journal.pone.0181699] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 07/04/2017] [Indexed: 11/21/2022] Open
Abstract
Phylogenetic relationships among snails (Caenogastropoda) are still unresolved, and many taxonomic categories remain non-monophyletic. Paraphyly has been reported within a large family of freshwater snails, Viviparidae, where the taxonomic status of several species remains questionable. As many endemic Chinese viviparid species have become endangered during the last few decades, this presents a major obstacle for conservation efforts. Mitochondrial genomes (mitogenomes) carry a large amount of data, so they can often provide a much higher resolution for phylogenetic analyses in comparison to the traditionally used molecular markers. To help resolve their phylogenetic relationships, the complete mitogenomes of eight Chinese viviparid snails, Viviparus chui, Cipangopaludina chinensis, C. ussuriensis, C. dianchiensis (endangered), Margarya melanioides (endangered), M. monodi (critically endangered), Bellamya quadrata and B. aeruginosa, were sequenced and compared to almost all of the available caenogastropod mitogenomes. Viviparidae possess the largest mitogenomes (16 392 to 18 544 bp), exhibit the highest A+T bias (72.5% on average), and some exhibit unique gene orders (a rearrangement of the standard MYCWQGE box), among the Caenogastropoda. Apart from the Vermetidae family and Cerithioidea superfamily, which possessed unique gene orders, the remaining studied caenogastropod mitogenomes exhibited highly conserved gene order, with minimal variations. Maximum likelihood and Bayesian inference analyses, used to reconstruct the phylogenetic relationships among 49 almost complete (all 37 genes) caenogastropod mitogenomes, produced almost identical tree topologies. Viviparidae were divided into three clades: a) Margarya and Cipangopaludina (except C. ussuriensis), b) Bellamya and C. ussuriensis, c) Viviparus chui. Our results present evidence that some Cipangopaludina species (dianchiensis and cathayensis) should be renamed into the senior genus Margarya. The phylogenetic resolution obtained in this study is insufficient to fully resolve the relationships within the 'b' clade, but if C. chinensis proves to be a valid representative of the genus, C. ussuriensis may have to be reassigned a different genus (possibly Bellamya, or even a new genus). Non-monophyly also remains pervasive among the higher (above the family-level) Caenogastropod taxonomic classes. Gene order distance matrix produced a different phylogenetic signal from the nucleotide sequences, which indicates a limited usability of this approach for inferring caenogastropod phylogenies. As phenotypic homoplasy appears to be widespread among some viviparid genera, in order to effectively protect the rapidly diminishing endemic Viviparid populations in China, further detailed molecular phylogenetic studies are urgently needed to resolve the taxonomic status of several species.
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Affiliation(s)
- Ju-Guang Wang
- Key Lab of Freshwater Animal Breeding of the Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, PR China
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, PR China
| | - Dong Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Wuhan Institute of Biotechnology, Wuhan, PR China
| | - Wei-Min Wang
- Key Lab of Freshwater Animal Breeding of the Ministry of Agriculture, College of Fisheries, Huazhong Agricultural University, Wuhan, PR China
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Freshwater Aquaculture Collaborative Innovation Center of Hubei Province, Wuhan, PR China
- Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde, China
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Gibb GC, England R, Hartig G, McLenachan PAT, Taylor Smith BL, McComish BJ, Cooper A, Penny D. New Zealand Passerines Help Clarify the Diversification of Major Songbird Lineages during the Oligocene. Genome Biol Evol 2015; 7:2983-95. [PMID: 26475316 PMCID: PMC5635589 DOI: 10.1093/gbe/evv196] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Passerines are the largest avian order, and the 6,000 species comprise more than half of all extant bird species. This successful radiation probably had its origin in the Australasian region, but dating this origin has been difficult due to a scarce fossil record and poor biogeographic assumptions. Many of New Zealand’s endemic passerines fall within the deeper branches of the passerine radiation, and a well resolved phylogeny for the modern New Zealand element in the deeper branches of the oscine lineage will help us understand both oscine and passerine biogeography. To this end we present complete mitochondrial genomes representing all families of New Zealand passerines in a phylogenetic framework of over 100 passerine species. Dating analyses of this robust phylogeny suggest Passeriformes originated in the early Paleocene, with the major lineages of oscines “escaping” from Australasia about 30 Ma, and radiating throughout the world during the Oligocene. This independently derived conclusion is consistent with the passerine fossil record.
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Affiliation(s)
- Gillian C Gibb
- Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Ryan England
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand Present address: Forensic Business Group, Institute of Environmental Science and Research (ESR Ltd.), Mt Albert Science Centre, Auckland, New Zealand
| | - Gerrit Hartig
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand Present address: Starlims Germany GmbH An Abbott Company, Witten, Germany
| | | | - Briar L Taylor Smith
- Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Bennet J McComish
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand Present address: School of Physical Sciences, University of Tasmania, Hobart, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, South Australia, Australia
| | - David Penny
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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Irisarri I, Eernisse DJ, Zardoya R. Molecular phylogeny of Acanthochitonina (Mollusca: Polyplacophora: Chitonida): three new mitochondrial genomes, rearranged gene orders and systematics. J NAT HIST 2014. [DOI: 10.1080/00222933.2014.963721] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Dodt WG, McComish BJ, Nilsson MA, Gibb GC, Penny D, Phillips MJ. The complete mitochondrial genome of the eastern grey kangaroo (Macropus giganteus). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1366-7. [PMID: 25103427 DOI: 10.3109/19401736.2014.947583] [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] [Indexed: 11/13/2022]
Abstract
We present the complete mitochondrial genome (accession number: LK995454) of an iconic Australian species, the eastern grey kangaroo (Macropus giganteus). The mitogenomic organization is consistent with other marsupials, encoding 13 protein-coding genes, 22 tRNA genes, 2 ribosomal RNA genes, an origin of light strand replication and a control region or D-loop. No repetitive sequences were detected in the control region. The M. giganteus mitogenome exemplifies a combination of tRNA gene order and structural peculiarities that appear to be unique to marsupials. We present a maximum likelihood phylogeny based on complete mitochondrial protein and RNA coding sequences that confirms the phylogenetic position of the grey kangaroo among macropodids.
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Affiliation(s)
- William G Dodt
- a School of Earth, Environmental and Biological Sciences, Queensland University of Technology , Brisbane , Australia
| | - Bennet J McComish
- b School of Physical Sciences, University of Tasmania , Hobart , Australia
| | - Maria A Nilsson
- c Biodiversity and Climate Research Center, BiK-F, Senckenberg Museum , Frankfurt am Main , Germany
| | - Gillian C Gibb
- d Institute of Agriculture and Environment, Massey University , Palmerston North , New Zealand , and
| | - David Penny
- e Institute of Fundamental Sciences, Massey University , Palmerston North , New Zealand
| | - Matthew J Phillips
- a School of Earth, Environmental and Biological Sciences, Queensland University of Technology , Brisbane , Australia
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Arquez M, Colgan D, Castro LR. Sequence and comparison of mitochondrial genomes in the genus Nerita (Gastropoda: Neritimorpha: Neritidae) and phylogenetic considerations among gastropods. Mar Genomics 2014; 15:45-54. [PMID: 24798873 DOI: 10.1016/j.margen.2014.04.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Revised: 04/17/2014] [Accepted: 04/22/2014] [Indexed: 10/25/2022]
Abstract
In the present study, we determined the mitochondrial DNA (mtDNA) sequence of three Neritas, Nerita versicolor, Nerita tessellata, and Nerita fulgurans. We present an analysis of the features of their gene content and genome organization and compare these within the genus Nerita, and among the main gastropod groups. The new sequences were used in a phylogenetic analysis including all available gastropod mitochondrial genomes. Genomic lengths were quite conserved, being 15,866bp for N. versicolor, 15,741bp for N. tessellata and 15,343bp for N. fulgurans. Intergenic regions were generally short; genes are transcribed from both strands and have a nucleotide composition high in A and T. The high similarity in nucleotide content of the different sequences, gene composition, as well as an identical genomic organization among the Nerita species compared in this study, indicates a high degree of conservation within this diverse genus. Values of Ka/Ks of the 13 protein coding genes (PCGs) of Nerita species ranged from 0 to 0.18, and suggested different selection pressures in gene sequences. Bayesian phylogenetic analyses using concatenated DNA sequences of the 13 PCGs and the two rRNAs, and of amino acid sequences strongly supported Neritimorpha and Vetigastropoda as sister groups.
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Affiliation(s)
- Moises Arquez
- Grupo de Investigación en Evolución, Sistemática y Ecología Molecular, Universidad del Magdalena, Santa Marta, Colombia.
| | - Donald Colgan
- The Australian Museum, 6 College Street, Sydney 2010, Australia.
| | - Lyda R Castro
- Grupo de Investigación en Evolución, Sistemática y Ecología Molecular, Universidad del Magdalena, Santa Marta, Colombia.
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Rubinstein ND, Feldstein T, Shenkar N, Botero-Castro F, Griggio F, Mastrototaro F, Delsuc F, Douzery EJ, Gissi C, Huchon D. Deep sequencing of mixed total DNA without barcodes allows efficient assembly of highly plastic ascidian mitochondrial genomes. Genome Biol Evol 2013; 5:1185-99. [PMID: 23709623 PMCID: PMC3698926 DOI: 10.1093/gbe/evt081] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Ascidians or sea squirts form a diverse group within chordates, which includes a few thousand members of marine sessile filter-feeding animals. Their mitochondrial genomes are characterized by particularly high evolutionary rates and rampant gene rearrangements. This extreme variability complicates standard polymerase chain reaction (PCR) based techniques for molecular characterization studies, and consequently only a few complete Ascidian mitochondrial genome sequences are available. Using the standard PCR and Sanger sequencing approach, we produced the mitochondrial genome of Ascidiella aspersa only after a great effort. In contrast, we produced five additional mitogenomes (Botrylloides aff. leachii, Halocynthia spinosa, Polycarpa mytiligera, Pyura gangelion, and Rhodosoma turcicum) with a novel strategy, consisting in sequencing the pooled total DNA samples of these five species using one Illumina HiSeq 2000 flow cell lane. Each mitogenome was efficiently assembled in a single contig using de novo transcriptome assembly, as de novo genome assembly generally performed poorly for this task. Each of the new six mitogenomes presents a different and novel gene order, showing that no syntenic block has been conserved at the ordinal level (in Stolidobranchia and in Phlebobranchia). Phylogenetic analyses support the paraphyly of both Ascidiacea and Phlebobranchia, with Thaliacea nested inside Phlebobranchia, although the deepest nodes of the Phlebobranchia-Thaliacea clade are not well resolved. The strategy described here thus provides a cost-effective approach to obtain complete mitogenomes characterized by a highly plastic gene order and a fast nucleotide/amino acid substitution rate.
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Affiliation(s)
- Nimrod D. Rubinstein
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
- Present address: Department of Molecular and Cellular Biology, Harvard University
| | - Tamar Feldstein
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
- The Steinhardt National Collections of Natural History Tel Aviv University, Ramat Aviv, Israel
| | - Noa Shenkar
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Fidel Botero-Castro
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR 5554 - CNRS, Université Montpellier II, Montpellier, France
| | | | | | - Frédéric Delsuc
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR 5554 - CNRS, Université Montpellier II, Montpellier, France
| | - Emmanuel J.P. Douzery
- Institut des Sciences de l'Evolution de Montpellier (ISEM), UMR 5554 - CNRS, Université Montpellier II, Montpellier, France
| | - Carmela Gissi
- Dip. di Bioscienze, Università degli Studi di Milano, Milano, Italy
- *Corresponding authors: E-mail: ;
| | - Dorothée Huchon
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
- *Corresponding authors: E-mail: ;
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15
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Corser CA, McLenachan PA, Pierson MJ, Harrison GLA, Penny D. The Q2 mitochondrial haplogroup in Oceania. PLoS One 2013; 7:e52022. [PMID: 23284859 PMCID: PMC3527380 DOI: 10.1371/journal.pone.0052022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 11/09/2012] [Indexed: 12/03/2022] Open
Abstract
Many details surrounding the origins of the peoples of Oceania remain to be resolved, and as a step towards this we report seven new complete mitochondrial genomes from the Q2a haplogroup, from Papua New Guinea, Fiji and Kiribati. This brings the total to eleven Q2 genomes now available. The Q haplogroup (that includes Q2) is an old and diverse lineage in Near Oceania, and is reasonably common; within our sample set of 430, 97 are of the Q haplogroup. However, only 8 are Q2, and we report 7 here. The tree with all complete Q genomes is proven to be minimal. The dating estimate for the origin of Q2 (around 35 Kya) reinforces the understanding that humans have been in Near Oceania for tens of thousands of years; nevertheless the Polynesian maternal haplogroups remain distinctive. A major focus now, with regard to Polynesian ancestry, is to address the differences and timing of the ‘Melanesian’ contribution to the maternal and paternal lineages as people moved further and further into Remote Oceania. Input from other fields such as anthropology, history and linguistics is required for a better understanding and interpretation of the genetic data.
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Affiliation(s)
- Chris A. Corser
- Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand
| | | | - Melanie J. Pierson
- Department of Anthropology, University of Auckland, Auckland, New Zealand
| | - G. L. Abby Harrison
- Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand
- Peter Medawar Building for Pathogen Research, Oxford University, Oxford, United Kingdom
| | - David Penny
- Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand
- * E-mail:
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16
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Brauer A, Kurz A, Stockwell T, Baden-Tillson H, Heidler J, Wittig I, Kauferstein S, Mebs D, Stöcklin R, Remm M. The mitochondrial genome of the venomous cone snail Conus consors. PLoS One 2012; 7:e51528. [PMID: 23236512 PMCID: PMC3517553 DOI: 10.1371/journal.pone.0051528] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 11/05/2012] [Indexed: 11/18/2022] Open
Abstract
Cone snails are venomous predatory marine neogastropods that belong to the species-rich superfamily of the Conoidea. So far, the mitochondrial genomes of two cone snail species (Conus textile and Conus borgesi) have been described, and these feed on snails and worms, respectively. Here, we report the mitochondrial genome sequence of the fish-hunting cone snail Conus consors and describe a novel putative control region (CR) which seems to be absent in the mitochondrial DNA (mtDNA) of other cone snail species. This possible CR spans about 700 base pairs (bp) and is located between the genes encoding the transfer RNA for phenylalanine (tRNA-Phe, trnF) and cytochrome c oxidase subunit III (cox3). The novel putative CR contains several sequence motifs that suggest a role in mitochondrial replication and transcription.
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17
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D'Onorio de Meo P, D'Antonio M, Griggio F, Lupi R, Borsani M, Pavesi G, Castrignanò T, Pesole G, Gissi C. MitoZoa 2.0: a database resource and search tools for comparative and evolutionary analyses of mitochondrial genomes in Metazoa. Nucleic Acids Res 2011; 40:D1168-72. [PMID: 22123747 PMCID: PMC3245153 DOI: 10.1093/nar/gkr1144] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The MITOchondrial genome database of metaZOAns (MitoZoa) is a public resource for comparative analyses of metazoan mitochondrial genomes (mtDNA) at both the sequence and genomic organizational levels. The main characteristics of the MitoZoa database are the careful revision of mtDNA entry annotations and the possibility of retrieving gene order and non-coding region (NCR) data in appropriate formats. The MitoZoa retrieval system enables basic and complex queries at various taxonomic levels using different search menus. MitoZoa 2.0 has been enhanced in several aspects, including: a re-annotation pipeline to check the correctness of protein-coding gene predictions; a standardized annotation of introns and of precursor ORFs whose functionality is post-transcriptionally recovered by RNA editing or programmed translational frameshifting; updates of taxon-related fields and a BLAST sequence similarity search tool. Database novelties and the definition of standard mtDNA annotation rules, together with the user-friendly retrieval system and the BLAST service, make MitoZoa a valuable resource for comparative and evolutionary analyses as well as a reference database to assist in the annotation of novel mtDNA sequences. MitoZoa is freely accessible at http://www.caspur.it/mitozoa.
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Affiliation(s)
- Paolo D'Onorio de Meo
- CASPUR, Consorzio interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca, Rome, Italy
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18
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Pareek CS, Smoczynski R, Tretyn A. Sequencing technologies and genome sequencing. J Appl Genet 2011; 52:413-35. [PMID: 21698376 PMCID: PMC3189340 DOI: 10.1007/s13353-011-0057-x] [Citation(s) in RCA: 370] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Revised: 05/27/2011] [Accepted: 05/31/2011] [Indexed: 12/21/2022]
Abstract
The high-throughput - next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human and animals genomics researches, which can produce over 100 times more data compared to the most sophisticated capillary sequencers based on the Sanger method. With the ongoing developments of high throughput sequencing machines and advancement of modern bioinformatics tools at unprecedented pace, the target goal of sequencing individual genomes of living organism at a cost of $1,000 each is seemed to be realistically feasible in the near future. In the relatively short time frame since 2005, the HT-NGS technologies are revolutionizing the human and animal genome researches by analysis of chromatin immunoprecipitation coupled to DNA microarray (ChIP-chip) or sequencing (ChIP-seq), RNA sequencing (RNA-seq), whole genome genotyping, genome wide structural variation, de novo assembling and re-assembling of genome, mutation detection and carrier screening, detection of inherited disorders and complex human diseases, DNA library preparation, paired ends and genomic captures, sequencing of mitochondrial genome and personal genomics. In this review, we addressed the important features of HT-NGS like, first generation DNA sequencers, birth of HT-NGS, second generation HT-NGS platforms, third generation HT-NGS platforms: including single molecule Heliscope™, SMRT™ and RNAP sequencers, Nanopore, Archon Genomics X PRIZE foundation, comparison of second and third HT-NGS platforms, applications, advances and future perspectives of sequencing technologies on human and animal genome research.
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Affiliation(s)
- Chandra Shekhar Pareek
- Laboratory of Functional Genomics, Institute of General and Molecular Biology, Nicolaus Copernicus University, Torun, Poland.
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19
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HILLS SIMONFK, TREWICK STEVENA, MORGAN-RICHARDS MARY. Phylogenetic information of genes, illustrated with mitochondrial data from a genus of gastropod molluscs. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01756.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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20
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Xin Y, Ren J, Liu X. Mitogenome of the small abalone Haliotis diversicolor Reeve and phylogenetic analysis within Gastropoda. Mar Genomics 2011; 4:253-62. [PMID: 22118637 DOI: 10.1016/j.margen.2011.06.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Revised: 06/18/2011] [Accepted: 06/22/2011] [Indexed: 10/17/2022]
Abstract
The complete mitochondrial coding regions of three small abalones Haliotis diversicolor Reeve, two collected from Vietnam and one from southern China, were successfully sequenced. The molecular feature of the mitochondrial genome is identical with the general description of the family Haliotidae mtDNAs that have been sequenced so far. The sequenced nucleotides are 16,186-16,266bp in length. The mitogenome encodes 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Between adjacent genes trnH and nad5 there is an overlapping region. Comparison of the ratios of Ka and Ks among four species of Haliotis (H. diversicolor, H. discus hannai, H. rubra and H. tuberculata tuberculata) reveals that values of Ka/Ks in some NADH dehydrogenase and ATPase genes such as nad2, nad6 and atp8 are higher than those in other mitochondrial genes. Genome-wide gene arrangement among four species of Haliotis has been compared. Although all gene arrangement is the same in H. diversicolor, H. discus hannai and H. rubra, the location of trnS₂ and trnF in H. tuberculata tuberculata are inter-exchanged. Both gene arrangement and phylogenetic analysis support that the family Haliotidae is at a relatively primordial phylogenetic position in Gastropoda. Through alignment between Vietnam and southern China individuals, 111 SNPs are detected, most SNPs are synonymous mutations, and 7, 94 and 10 SNPs are observed at NCR, protein-coding region and RNA region, respectively. The result of SNP analysis also demonstrates that the difference is mainly in some NADH dehydrogenase genes between the Vietnam and southern China individuals.
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Affiliation(s)
- Yi Xin
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
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21
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Robins JH, McLenachan PA, Phillips MJ, McComish BJ, Matisoo-Smith E, Ross HA. Evolutionary relationships and divergence times among the native rats of Australia. BMC Evol Biol 2010; 10:375. [PMID: 21126350 PMCID: PMC3014932 DOI: 10.1186/1471-2148-10-375] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Accepted: 12/02/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genus Rattus is highly speciose and has a complex taxonomy that is not fully resolved. As shown previously there are two major groups within the genus, an Asian and an Australo-Papuan group. This study focuses on the Australo-Papuan group and particularly on the Australian rats. There are uncertainties regarding the number of species within the group and the relationships among them. We analysed 16 mitochondrial genomes, including seven novel genomes from six species, to help elucidate the evolutionary history of the Australian rats. We also demonstrate, from a larger dataset, the usefulness of short regions of the mitochondrial genome in identifying these rats at the species level. RESULTS Analyses of 16 mitochondrial genomes representing species sampled from Australo-Papuan and Asian clades of Rattus indicate divergence of these two groups ~2.7 million years ago (Mya). Subsequent diversification of at least 4 lineages within the Australo-Papuan clade was rapid and occurred over the period from ~ 0.9-1.7 Mya, a finding that explains the difficulty in resolving some relationships within this clade. Phylogenetic analyses of our 126 taxon, but shorter sequence (1952 nucleotides long), Rattus database generally give well supported species clades. CONCLUSIONS Our whole mitochondrial genome analyses are concordant with a taxonomic division that places the native Australian rats into the Rattus fuscipes species group. We suggest the following order of divergence of the Australian species. R. fuscipes is the oldest lineage among the Australian rats and is not part of a New Guinean radiation. R. lutreolus is also within this Australian clade and shallower than R. tunneyi while the R. sordidus group is the shallowest lineage in the clade. The divergences within the R. sordidus and R. leucopus lineages occurring about half a million years ago support the hypotheses of more recent interchanges of rats between Australia and New Guinea. While problematic for inference of deeper divergences, we report that the analysis of shorter mitochondrial sequences is very useful for species identification in rats.
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Affiliation(s)
- Judith H Robins
- Department of Anthropology and School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
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22
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Timmermans MJTN, Dodsworth S, Culverwell CL, Bocak L, Ahrens D, Littlewood DTJ, Pons J, Vogler AP. Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics. Nucleic Acids Res 2010; 38:e197. [PMID: 20876691 PMCID: PMC2995086 DOI: 10.1093/nar/gkq807] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 08/09/2010] [Accepted: 08/29/2010] [Indexed: 02/03/2023] Open
Abstract
Mitochondrial genome sequences are important markers for phylogenetics but taxon sampling remains sporadic because of the great effort and cost required to acquire full-length sequences. Here, we demonstrate a simple, cost-effective way to sequence the full complement of protein coding mitochondrial genes from pooled samples using the 454/Roche platform. Multiplexing was achieved without the need for expensive indexing tags ('barcodes'). The method was trialled with a set of long-range polymerase chain reaction (PCR) fragments from 30 species of Coleoptera (beetles) sequenced in a 1/16th sector of a sequencing plate. Long contigs were produced from the pooled sequences with sequencing depths ranging from ∼10 to 100× per contig. Species identity of individual contigs was established via three 'bait' sequences matching disparate parts of the mitochondrial genome obtained by conventional PCR and Sanger sequencing. This proved that assembly of contigs from the sequencing pool was correct. Our study produced sequences for 21 nearly complete and seven partial sets of protein coding mitochondrial genes. Combined with existing sequences for 25 taxa, an improved estimate of basal relationships in Coleoptera was obtained. The procedure could be employed routinely for mitochondrial genome sequencing at the species level, to provide improved species 'barcodes' that currently use the cox1 gene only.
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Affiliation(s)
- M. J. T. N. Timmermans
- Department of Entomology, Natural History Museum, Cromwell Road, London SW7 5BD, Division of Biology, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK, Department of Zoology, Science Faculty, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Department of Zoology, Natural History Museum, Cromwell Road, London SW7 5BD, UK and IMEDEA (CSIC-UIB), Miquel Marqués, 21 Esporlas, 07190 Illes Balears, Spain
| | - S. Dodsworth
- Department of Entomology, Natural History Museum, Cromwell Road, London SW7 5BD, Division of Biology, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK, Department of Zoology, Science Faculty, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Department of Zoology, Natural History Museum, Cromwell Road, London SW7 5BD, UK and IMEDEA (CSIC-UIB), Miquel Marqués, 21 Esporlas, 07190 Illes Balears, Spain
| | - C. L. Culverwell
- Department of Entomology, Natural History Museum, Cromwell Road, London SW7 5BD, Division of Biology, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK, Department of Zoology, Science Faculty, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Department of Zoology, Natural History Museum, Cromwell Road, London SW7 5BD, UK and IMEDEA (CSIC-UIB), Miquel Marqués, 21 Esporlas, 07190 Illes Balears, Spain
| | - L. Bocak
- Department of Entomology, Natural History Museum, Cromwell Road, London SW7 5BD, Division of Biology, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK, Department of Zoology, Science Faculty, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Department of Zoology, Natural History Museum, Cromwell Road, London SW7 5BD, UK and IMEDEA (CSIC-UIB), Miquel Marqués, 21 Esporlas, 07190 Illes Balears, Spain
| | - D. Ahrens
- Department of Entomology, Natural History Museum, Cromwell Road, London SW7 5BD, Division of Biology, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK, Department of Zoology, Science Faculty, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Department of Zoology, Natural History Museum, Cromwell Road, London SW7 5BD, UK and IMEDEA (CSIC-UIB), Miquel Marqués, 21 Esporlas, 07190 Illes Balears, Spain
| | - D. T. J. Littlewood
- Department of Entomology, Natural History Museum, Cromwell Road, London SW7 5BD, Division of Biology, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK, Department of Zoology, Science Faculty, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Department of Zoology, Natural History Museum, Cromwell Road, London SW7 5BD, UK and IMEDEA (CSIC-UIB), Miquel Marqués, 21 Esporlas, 07190 Illes Balears, Spain
| | - J. Pons
- Department of Entomology, Natural History Museum, Cromwell Road, London SW7 5BD, Division of Biology, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK, Department of Zoology, Science Faculty, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Department of Zoology, Natural History Museum, Cromwell Road, London SW7 5BD, UK and IMEDEA (CSIC-UIB), Miquel Marqués, 21 Esporlas, 07190 Illes Balears, Spain
| | - A. P. Vogler
- Department of Entomology, Natural History Museum, Cromwell Road, London SW7 5BD, Division of Biology, Imperial College London, Silwood Park Campus, Ascot SL5 7PY, UK, Department of Zoology, Science Faculty, Palacky University, tr. Svobody 26, 771 46 Olomouc, Czech Republic, Department of Zoology, Natural History Museum, Cromwell Road, London SW7 5BD, UK and IMEDEA (CSIC-UIB), Miquel Marqués, 21 Esporlas, 07190 Illes Balears, Spain
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