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Hua CJ, Huang Y, Li HQ, Feng JM, Qiao JL, Hu S, Liu W, Shu XJ. Characterization of the complete mitochondrial genome of Ergasilus anchoratus Markevich, 1946 (Ergasilidae) and phylogeny of Copepoda. Syst Parasitol 2024; 101:33. [PMID: 38647718 DOI: 10.1007/s11230-023-10140-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 12/11/2023] [Indexed: 04/25/2024]
Abstract
The mitochondrial (mt) genome can provide data for phylogenetic analyses and evolutionary biology. Herein, we sequenced and annotated the complete mt genome of Ergasilus anchoratus. This mt genome was 13852 bp long and comprised 13 protein-coding genes (PCGs), 22 tRNAs and 2 rRNAs. All PCGs used the standard ATN start codons and complete TAA/TAG termination codons. A majority of tRNA genes exhibited standard cloverleaf secondary structures, with the exception of one tRNA that lacked the TψC arm (trnC), and three tRNAs that lacked the DHU arm (trnR, trnS1 and trnS2). Phylogenetic analyses conducted using Bayesian inference (BI) and maximum likelihood (ML) methods both supported Ergasilidae as a monophyletic family forming a sister group to Lernaea cyprinacea and Paracyclopina nana. It also supported the monophyly of orders Calanoida, Cyclopoida, and Siphonostomatoida; and the monophyly of families Harpacticidae, Ergasilidae, Diaptomidae, and Calanidae. The gene orders of E. anchoratus and Sinergasilus undulatus were identical, which represents the first instance of two identical gene orders in copepods. More mt genomes are needed to better understand the phylogenetic relationships within Copepoda in the future.
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Affiliation(s)
- Cong-Jie Hua
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
- Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Yan Huang
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Hui-Quan Li
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Jin-Mei Feng
- Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Jia-Lu Qiao
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Song Hu
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Wei Liu
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China
| | - Xi-Ji Shu
- Hubei Key Laboratory of Cognitive and Affective Disorders, Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan, 430056, China.
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Ma Y, Zheng B, Li J, Meng W, Xu K, Ye Y. Characterization of the complete mitochondrial genome of Desmaulus extinctorium (Littorinimorpha, Calyptraeoidea, Calyptraeidae) and molecular phylogeny of Littorinimorpha. PLoS One 2024; 19:e0301389. [PMID: 38547307 PMCID: PMC10977763 DOI: 10.1371/journal.pone.0301389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 03/12/2024] [Indexed: 04/02/2024] Open
Abstract
For the purpose of determining the placement of Calyptraeidae within the Littorinimorpha, we hereby furnish a thorough analysis of the mitochondrial genome (mitogenome) sequence of Desmaulus extinctorium. This mitogenome spans 16,605 base pairs and encompasses the entire set of 37 genes, including 13 PCGs, 22 tRNAs and two rRNAs, with an evident AT bias. Notably, tRNASer1 and tRNASer2 lack dihydrouracil (DHU) arms, resulting in an inability to form a secondary structure. Similarly, tRNAAla lacks a TΨC arm, rendering it incapable of forming a secondary structure. In contrast, the remaining tRNAs demonstrate a characteristic secondary structure reminiscent of a cloverleaf. A comparison with ancestral gastropods reveals distinct differences in three gene clusters (or genes), encompassing 15 tRNAs and eight PCGs. Notably, inversions and translocations represent the major types of rearrangements observed in D. extinctorium. Phylogenetic analysis demonstrates robust support for a monophyletic grouping of all Littorinimorpha species, with D. extinctorium representing a distinct Calyptraeoidea clade. In summary, this investigation provides the first complete mitochondrial dataset for a species of the Calyptraeidae, thus providing novel insights into the phylogenetic relationships within the Littorinimorpha.
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Affiliation(s)
- Yanwen Ma
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Biqi Zheng
- Department of Natural Resources, Ningde Marine Center, Ningde, 352000, China
| | - Jiji Li
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Wei Meng
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of China, Zhoushan, 316021, China
| | - Kaida Xu
- Key Laboratory of Sustainable Utilization of Technology Research for Fisheries Resources of Zhejiang Province, Zhejiang Marine Fisheries Research Institute, Scientific Observing and Experimental Station of Fishery Resources for Key Fishing Grounds, Ministry of Agriculture and Rural Affairs of China, Zhoushan, 316021, China
| | - Yingying Ye
- National Engineering Research Center for Marine Aquaculture, Zhejiang Ocean University, Zhoushan, 316022, China
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Zhang Q, Lu YW, Liu XY, Li Y, Gao WN, Sun JT, Hong XY, Shao R, Xue XF. Phylogenomics resolves the higher-level phylogeny of herbivorous eriophyoid mites (Acariformes: Eriophyoidea). BMC Biol 2024; 22:70. [PMID: 38519936 PMCID: PMC10960459 DOI: 10.1186/s12915-024-01870-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 03/14/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND Eriophyoid mites (Eriophyoidea) are among the largest groups in the Acariformes; they are strictly phytophagous. The higher-level phylogeny of eriophyoid mites, however, remains unresolved due to the limited number of available morphological characters-some of them are homoplastic. Nevertheless, the eriophyoid mites sequenced to date showed highly variable mitochondrial (mt) gene orders, which could potentially be useful for resolving the higher-level phylogenetic relationships. RESULTS Here, we sequenced and compared the complete mt genomes of 153 eriophyoid mite species, which showed 54 patterns of rearranged mt gene orders relative to that of the hypothetical ancestor of arthropods. The shared derived mt gene clusters support the monophyly of eriophyoid mites (Eriophyoidea) as a whole and the monophylies of six clades within Eriophyoidea. These monophyletic groups and their relationships were largely supported in the phylogenetic trees inferred from mt genome sequences as well. Our molecular dating results showed that Eriophyoidea originated in the Triassic and diversified in the Cretaceous, coinciding with the diversification of angiosperms. CONCLUSIONS This study reveals multiple molecular synapomorphies (i.e. shared derived mt gene clusters) at different levels (i.e. family, subfamily or tribe level) from the complete mt genomes of 153 eriophyoid mite species. We demonstrated the use of derived mt gene clusters in unveiling the higher-level phylogeny of eriophyoid mites, and underlines the origin of these mites and their co-diversification with angiosperms.
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Affiliation(s)
- Qi Zhang
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yi-Wen Lu
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xin-Yu Liu
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Ye Li
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Wei-Nan Gao
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jing-Tao Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Renfu Shao
- Centre for Bioinnovation, School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia
| | - Xiao-Feng Xue
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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Zhou Z, Ding L, Liu Z, Fu L, Xu L, Feng L, Yu S, Li P, Zhou Y. The complete mitochondrial genome of Goniurosaurus varius (Squamata: Eublepharidae). Mitochondrial DNA B Resour 2023; 8:1215-1219. [PMID: 38239912 PMCID: PMC10796122 DOI: 10.1080/23802359.2023.2278817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 10/29/2023] [Indexed: 01/22/2024] Open
Abstract
The complete mitochondrial genome sequence of Goniurosaurus varius is 17778 bp in length (GenBank accession number OQ992199), containing 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes. The gene order and orientation are identical to those of other Eublepharidae species in the GenBank database. Seven protein-coding genes (COX2, COX3, ND1, ND2, ND3, ND4 and CYTB) exhibit incomplete stop codon 'T.' Phylogenetic analysis revealed the monophyly of Goniurosaurus and Eublepharidae and suggested that G. varius is closely related to the lineage composed of G. luii and G. liboensis. Distinct from other published Eublepharidae species, G. varius contains an extra non-coding region between tRNA-Thr and tRNA-Pro, which may be formed by gene rearrangements. The complete mitochondrial genome will be helpful for further studies on the population genetics of this species and phylogenetic analyses of Eublepharidae.
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Affiliation(s)
- Zhengyan Zhou
- College of Life Science and bioengineering, Shenyang University, Shenyang, China
| | - Lin Ding
- College of Life Science and bioengineering, Shenyang University, Shenyang, China
| | - Ziyi Liu
- College of Life Science and bioengineering, Shenyang University, Shenyang, China
| | - Longming Fu
- College of Life Science and bioengineering, Shenyang University, Shenyang, China
| | - Lanying Xu
- College of Life Science and bioengineering, Shenyang University, Shenyang, China
| | - Lin Feng
- College of Life Science and bioengineering, Shenyang University, Shenyang, China
| | - Sufan Yu
- College of Life Science and bioengineering, Shenyang University, Shenyang, China
| | - Pipeng Li
- Institute of Herpetology, Shenyang Normal University, Shenyang, China
| | - Yu Zhou
- College of Life Science, Shenyang Normal University, Shenyang, China
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Xu T, Bravo H, van der Meij SE. Phylomitogenomics elucidates the evolution of symbiosis in Thoracotremata (Decapoda: Cryptochiridae, Pinnotheridae, Varunidae). PeerJ 2023; 11:e16217. [PMID: 37868050 PMCID: PMC10586294 DOI: 10.7717/peerj.16217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 09/11/2023] [Indexed: 10/24/2023] Open
Abstract
Background Thoracotremata belong to the large group of "true" crabs (infraorder Brachyura), and they exhibit a wide range of physiological and morphological adaptations to living in terrestrial, freshwater and marine habitats. Moreover, the clade comprises various symbiotic taxa (Aphanodactylidae, Cryptochiridae, Pinnotheridae, some Varunidae) that are specialised in living with invertebrate hosts, but the evolutionary history of these symbiotic crabs is still partially unresolved. Methods Here we assembled and characterised the complete mitochondrial genomes (hereafter mitogenomes) of three gall crab species (Cryptochiridae): Kroppcarcinus siderastreicola, Opecarcinus hypostegus and Troglocarcinus corallicola. A phylogenetic tree of the Thoracotremata was reconstructed using 13 protein-coding genes and two ribosomal RNA genes retrieved from three new gall crab mitogenomes and a further 72 available thoracotreme mitogenomes. Furthermore, we applied a comparative analysis to characterise mitochondrial gene order arrangement, and performed a selection analysis to test for selective pressure of the protein-coding genes in symbiotic Cryptochiridae, Pinnotheridae, and Varunidae (Asthenognathus inaequipes and Tritodynamia horvathi). Results The results of the phylogenetic reconstruction confirm the monophyly of Cryptochiridae, which clustered separately from the Pinnotheridae. The latter clustered at the base of the tree with robust branch values. The symbiotic varunids A. inaequipes and T. horvathi clustered together in a clade with free-living Varunidae species, highlighting that symbiosis in the Thoracotremata evolved independently on multiple occasions. Different gene orders were detected in symbionts and free-living species when compared with the ancestral brachyuran gene order. Lastly, the selective pressure analysis detected two positively selected sites in the nad6 gene of Cryptochiridae, but the evidence for positive selection in Pinnotheridae and A. inaequipes and T. horvathi was weak. Adaptive evolution of mitochondrial protein-coding genes is perhaps related to the presumably higher energetic demands of a symbiotic lifestyle.
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Affiliation(s)
- Tao Xu
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Henrique Bravo
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Sancia E.T. van der Meij
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
- Marine Biodiversity Group, Naturalis Biodiversity Center, Leiden, Netherlands
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An J, Yin X, Chen R, Boyko CB, Liu X. Integrative taxonomy of the subfamily Orbioninae (Crustacea: Isopoda) based on mitochondrial and nuclear data with evidence that supports Epicaridea as a suborder. Mol Phylogenet Evol 2023; 180:107681. [PMID: 36572163 DOI: 10.1016/j.ympev.2022.107681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022]
Abstract
Epicaridea is a group of isopods with high morphological diversity, reduction and loss of characters, and strong sexual dimorphism due to their parasitic lifestyles but their systematics is not well understood. Despite the use of nuclear and mitochondrial genes to test the phylogeny of many invertebrate groups, few molecular data from epicarideans are known, especially from the subfamily Orbioninae. Species in this group are obligate penaeoid shrimp parasites and the lack molecular data has hampered studies on the phylogeny of Orbioninae. To rectify this, mitochondrial and nuclear genes of 9 orbionine species are sequenced here. Compared to the isopod ground pattern, the sequences of orbionines seem to be more plastic near the control region and major translocations are located between rrns and cob. A phylogenetic analysis based on three data sets showed strong support for a monophyletic Orbioninae and that Epicaridea should be accepted at the rank of a suborder within Isopoda. The monophyly of Parapenaeon and Orbione is in doubt based on morphological and molecular data. The genus Parapenaeon is revised and a new genus Aparapenaeon is erected for Parapenaeon japonica and three closely related species.
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Affiliation(s)
- Jianmei An
- School of Life Science, Shanxi Normal University, Linfen 041000, PR China.
| | - Xiaotian Yin
- School of Life Science, Shanxi Normal University, Linfen 041000, PR China
| | - Ruru Chen
- School of Life Science, Shanxi Normal University, Linfen 041000, PR China
| | - Christopher B Boyko
- Department of Biology, Hofstra University, Hempstead, NY 11549, USA; Division of Invertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - Xinming Liu
- Guangxi University of Chinese Medicine, Nanning 530200, PR China
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Cunha RL, Nicastro KR, Zardi GI, Madeira C, McQuaid CD, Cox CJ, Castilho R. Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genus. PeerJ 2022; 10:e13953. [PMID: 36187748 PMCID: PMC9521344 DOI: 10.7717/peerj.13953] [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: 03/03/2022] [Accepted: 08/05/2022] [Indexed: 01/19/2023] Open
Abstract
Background The order and orientation of genes encoded by animal mitogenomes are typically conserved, although there is increasing evidence of multiple rearrangements among mollusks. The mitogenome from a Brazilian brown mussel (hereafter named B1) classified as Perna perna Linnaeus, 1758 and assembled from Illumina short-length reads revealed an unusual gene order very different from other congeneric species. Previous mitogenomic analyses based on the Brazilian specimen and other Mytilidae suggested the polyphyly of the genus Perna. Methods To confirm the proposed gene rearrangements, we sequenced a second Brazilian P. perna specimen using the "primer-walking" method and performed the assembly using as reference Perna canaliculus. This time-consuming sequencing method is highly effective when assessing gene order because it relies on sequentially-determined, overlapping fragments. We also sequenced the mitogenomes of eastern and southwestern South African P. perna lineages to analyze the existence of putative intraspecific gene order changes as the two lineages show overlapping distributions but do not exhibit a sister relationship. Results The three P. perna mitogenomes sequenced in this study exhibit the same gene order as the reference. CREx, a software that heuristically determines rearrangement scenarios, identified numerous gene order changes between B1 and our P. perna mitogenomes, rejecting the previously proposed gene order for the species. Our results validate the monophyly of the genus Perna and indicate a misidentification of B1.
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Affiliation(s)
- Regina L. Cunha
- Centre of Marine Sciences, CCMAR, University of Algarve, Campus de Gambelas, Faro, Algarve, Portugal
| | - Katy R. Nicastro
- Centre of Marine Sciences, CCMAR, University of Algarve, Campus de Gambelas, Faro, Algarve, Portugal,CNRS, Univ. Littoral Côte d’Opale, UMR 8187 – LOG – Laboratoire d’Océanologie et de Géosciences, Université de Lille, Lille, France,Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
| | - Gerardo I. Zardi
- Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
| | - Celine Madeira
- Centre of Marine Sciences, CCMAR, University of Algarve, Campus de Gambelas, Faro, Algarve, Portugal
| | | | - Cymon J. Cox
- Centre of Marine Sciences, CCMAR, University of Algarve, Campus de Gambelas, Faro, Algarve, Portugal
| | - Rita Castilho
- Centre of Marine Sciences, CCMAR, University of Algarve, Campus de Gambelas, Faro, Algarve, Portugal
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Wu R, Guo R, Xi Q, Paulay G, An J. Phylogenetic position of Bopyroides hippolytes, with comments on the rearrangement of the mitochondrial genome in isopods (Isopoda: Epicaridea: Bopyridae). BMC Genomics 2022; 23:253. [PMID: 35366795 PMCID: PMC8976331 DOI: 10.1186/s12864-022-08513-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Accepted: 03/23/2022] [Indexed: 11/10/2022] Open
Abstract
Background Classification of parasitic bopyrids has traditionally been based on morphological characteristics, but phylogenetic relationships have remained elusive due to limited information provided by morphological data and tendency for loss of morphological features as a result of parasitic lifestyle. Subfamily Argeiinae was separated from Bopyrinae based on morphological evidence, although the assignment of all genera has not been phylogenetically evaluated. Bopyroides hippolytes has been traditionally classified in Bopyrinae, but divergent morphological characters make this assignment questionable. To investigate the relationship of bopyrines, we sequenced the complete mitochondrial genome of B. hippolytes and four mitochondrial genes of two other Bopyrinae. Results The phylogenetic trees based on separate and combined cox1and 18S sequence data recovered Bopyridae as robustly monophyletic, but Bopyrinae as polyphyletic. Bopyroides hippolytes was a close sister to Argeia pugettensis, type species to Argeiinae. Mitochondrial phylogenomics also suggested that B. hippolytes was close to Argeiinae. We also found a novel gene order in B. hippolytes compared to other isopods. Conclusions Bopyroides hippolytes should be excluded from the Bopyrinae and has a close affinity with Argeia pugettensis based on molecular and morphological data. The conserved syntenic blocks of mitochondrial gene order have distinctive characteristics at a subordinal level and may be helpful for understanding the higher taxonomic level relationships of Isopoda. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08513-9.
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Pearman WS, Wells SJ, Dale J, Silander OK, Freed NE. Long-read sequencing reveals atypical mitochondrial genome structure in a New Zealand marine isopod. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211550. [PMID: 35242350 PMCID: PMC8753154 DOI: 10.1098/rsos.211550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/29/2021] [Indexed: 05/03/2023]
Abstract
Most animal mitochondrial genomes are small, circular and structurally conserved. However, recent work indicates that diverse taxa possess unusual mitochondrial genomes. In Isopoda, species in multiple lineages have atypical and rearranged mitochondrial genomes. However, more species of this speciose taxon need to be evaluated to understand the evolutionary origins of atypical mitochondrial genomes in this group. In this study, we report the presence of an atypical mitochondrial structure in the New Zealand endemic marine isopod, Isocladus armatus. Data from long- and short-read DNA sequencing suggest that I. armatus has two mitochondrial chromosomes. The first chromosome consists of two mitochondrial genomes that have been inverted and fused together in a circular form, and the second chromosome consists of a single mitochondrial genome in a linearized form. This atypical mitochondrial structure has been detected in other isopod lineages, and our data from an additional divergent isopod lineage (Sphaeromatidae) lends support to the hypothesis that atypical structure evolved early in the evolution of Isopoda. Additionally, we find that an asymmetrical site previously observed across many species within Isopoda is absent in I. armatus, but confirm the presence of two asymmetrical sites recently reported in two other isopod species.
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Affiliation(s)
- William S. Pearman
- School of Natural and Computational Sciences, Massey University-Albany Campus, Auckland, Auckland New Zealand
| | - Sarah J. Wells
- School of Environmental and Animal Sciences, Unitec Institute of Technology, Auckland, New Zealand
| | - James Dale
- School of Natural and Computational Sciences, Massey University-Albany Campus, Auckland, Auckland New Zealand
| | - Olin K. Silander
- School of Natural and Computational Sciences, Massey University-Albany Campus, Auckland, Auckland New Zealand
| | - Nikki E. Freed
- School of Natural and Computational Sciences, Massey University-Albany Campus, Auckland, Auckland New Zealand
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Lafuente E, Lürig MD, Rövekamp M, Matthews B, Buser C, Vorburger C, Räsänen K. Building on 150 Years of Knowledge: The Freshwater Isopod Asellus aquaticus as an Integrative Eco-Evolutionary Model System. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.748212] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Interactions between organisms and their environments are central to how biological diversity arises and how natural populations and ecosystems respond to environmental change. These interactions involve processes by which phenotypes are affected by or respond to external conditions (e.g., via phenotypic plasticity or natural selection) as well as processes by which organisms reciprocally interact with the environment (e.g., via eco-evolutionary feedbacks). Organism-environment interactions can be highly dynamic and operate on different hierarchical levels, from genes and phenotypes to populations, communities, and ecosystems. Therefore, the study of organism-environment interactions requires integrative approaches and model systems that are suitable for studies across different hierarchical levels. Here, we introduce the freshwater isopod Asellus aquaticus, a keystone species and an emerging invertebrate model system, as a prime candidate to address fundamental questions in ecology and evolution, and the interfaces therein. We review relevant fields of research that have used A. aquaticus and draft a set of specific scientific questions that can be answered using this species. Specifically, we propose that studies on A. aquaticus can help understanding (i) the influence of host-microbiome interactions on organismal and ecosystem function, (ii) the relevance of biotic interactions in ecosystem processes, and (iii) how ecological conditions and evolutionary forces facilitate phenotypic diversification.
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Jakovlić I, Zou H, Zhao XM, Zhang J, Wang GT, Zhang D. Evolutionary History of Inversions in Directional Mutational Pressures in Crustacean Mitochondrial Genomes: Implications for Evolutionary Studies. Mol Phylogenet Evol 2021; 164:107288. [PMID: 34365015 DOI: 10.1016/j.ympev.2021.107288] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/31/2021] [Accepted: 08/03/2021] [Indexed: 01/29/2023]
Abstract
Inversions of the origin of replication (ORI) in mitochondrial genomes produce asymmetrical mutational pressures that can cause strong base composition skews. Due to skews often being overlooked, the total number of crustacean lineages that underwent ORI events remains unknown. We analysed skews, cumulative skew plots, conserved sequence motifs, and mitochondrial architecture of all 965 available crustacean mitogenomes (699 unique species). We found indications of an ORI in 159 (22.7%) species, and mapped these to 23 ORI events: 16 identified with confidence and 7 putative (13 newly proposed, and for 5 we improved the resolution). Two ORIs occurred at or above the order level: Isopoda and Copepoda. Shifts in skew plots are not a precise tool for identifying the replication mechanism. We discuss how ORIs can produce mutational bursts in mitogenomes and show how these can interfere with various types of evolutionary studies. Phylogenetic analyses were plagued by artefactual clustering, and ORI lineages exhibited longer branches, a higher number of synonymous substitutions, higher mutational saturation, and higher compositional heterogeneity. ORI events also affected codon usage and protein properties. We discuss how this may have caused erroneous interpretation of data in previous studies that did not account for skew patterns.
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Affiliation(s)
- Ivan Jakovlić
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, 730000 Lanzhou, China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xu-Mao Zhao
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, 730000 Lanzhou, China
| | - Jin Zhang
- Bio-Transduction Lab, Wuhan 430075, China
| | - Gui-Tang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zhang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology, Lanzhou University, 730000 Lanzhou, China.
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An J, Zheng W, Liang J, Xi Q, Chen R, Jia J, Lu X, Jakovlić I. Disrupted architecture and fast evolution of the mitochondrial genome of Argeia pugettensis (Isopoda): implications for speciation and fitness. BMC Genomics 2020; 21:607. [PMID: 32883208 PMCID: PMC7469299 DOI: 10.1186/s12864-020-07021-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/24/2020] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Argeia pugettensis is an isopod species that parasitizes other crustaceans. Its huge native geographic range spans the Pacific from China to California, but molecular data are available only for a handful of specimens from North-American populations. We sequenced and characterised the complete mitogenome of a specimen collected in the Yellow Sea. RESULTS It exhibited a barcode (cox1) similarity level of only 87-89% with North-American populations, which is unusually low for conspecifics. Its mitogenome is among the largest in isopods (≈16.5 Kbp), mostly due to a large duplicated palindromic genomic segment (2 Kbp) comprising three genes. However, it lost a segment comprising three genes, nad4L-trnP-nad6, and many genes exhibited highly divergent sequences in comparison to isopod orthologues, including numerous mutations, deletions and insertions. Phylogenetic and selection analyses corroborated that this is one of the handful of most rapidly evolving available isopod mitogenomes, and that it evolves under highly relaxed selection constraints (as opposed to positive selection). However, its nuclear 18S gene is highly conserved, which suggests that rapid evolution is limited to its mitochondrial genome. The cox1 sequence analysis indicates that elevated mitogenomic evolutionary rates are not shared by North-American conspecifics, which suggests a breakdown of cox1 barcoding in this species. CONCLUSIONS A highly architecturally disrupted mitogenome and decoupling of mitochondrial and nuclear rates would normally be expected to have strong negative impacts on the fitness of the organism, so the existence of this lineage is a puzzling evolutionary question. Additional studies are needed to assess the phylogenetic breadth of this disrupted mitochondrial architecture and its impact on fitness.
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Affiliation(s)
- Jianmei An
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China.
| | - Wanrui Zheng
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Jielong Liang
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Qianqian Xi
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Ruru Chen
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Junli Jia
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Xia Lu
- School of Life Science, Shanxi Normal University, Linfen, 041000, PR China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Wuhan, 430075, Hubei, PR China
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Zou H, Jakovlić I, Zhang D, Hua CJ, Chen R, Li WX, Li M, Wang GT. Architectural instability, inverted skews and mitochondrial phylogenomics of Isopoda: outgroup choice affects the long-branch attraction artefacts. ROYAL SOCIETY OPEN SCIENCE 2020; 7:191887. [PMID: 32257344 PMCID: PMC7062073 DOI: 10.1098/rsos.191887] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 01/14/2020] [Indexed: 05/13/2023]
Abstract
The majority strand of mitochondrial genomes of crustaceans usually exhibits negative GC skews. Most isopods exhibit an inversed strand asymmetry, believed to be a consequence of an inversion of the replication origin (ROI). Recently, we proposed that an additional ROI event in the common ancestor of Cymothoidae and Corallanidae families resulted in a double-inverted skew (negative GC), and that taxa with homoplastic skews cluster together in phylogenetic analyses (long-branch attraction, LBA). Herein, we further explore these hypotheses, for which we sequenced the mitogenome of Asotana magnifica (Cymothoidae), and tested whether our conclusions were biased by poor taxon sampling and inclusion of outgroups. (1) The new mitogenome also exhibits a double-inverted skew, which supports the hypothesis of an additional ROI event in the common ancestor of Cymothoidae and Corallanidae families. (2) It exhibits a unique gene order, which corroborates that isopods possess exceptionally destabilized mitogenomic architecture. (3) Improved taxonomic sampling failed to resolve skew-driven phylogenetic artefacts. (4) The use of a single outgroup exacerbated the LBA, whereas both the use of a large number of outgroups and complete exclusion of outgroups ameliorated it.
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Affiliation(s)
- Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, People's Republic of China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Wuhan 430075, People's Republic of China
| | - Dong Zhang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Cong-Jie Hua
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, People's Republic of China
- Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan 430056, People's Republic of China
| | - Rong Chen
- Bio-Transduction Lab, Wuhan 430075, People's Republic of China
| | - Wen-Xiang Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Ming Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
| | - Gui-Tang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, People's Republic of China
- University of Chinese Academy of Sciences, Beijing 100049, People's Republic of China
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Zhang D, Li WX, Zou H, Wu SG, Li M, Jakovlić I, Zhang J, Chen R, Wang G. Homoplasy or plesiomorphy? Reconstruction of the evolutionary history of mitochondrial gene order rearrangements in the subphylum Neodermata. Int J Parasitol 2019; 49:819-829. [PMID: 31401064 DOI: 10.1016/j.ijpara.2019.05.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 05/15/2019] [Accepted: 05/22/2019] [Indexed: 12/31/2022]
Abstract
Recent mitogenomic studies have exposed a gene order (GO) shared by two classes, four orders and 31 species ('common GO') within the flatworm subphylum Neodermata. There are two possible hypotheses for this phenomenon: convergent evolution (homoplasy) or shared ancestry (plesiomorphy). To test those, we conducted a meta-analysis on all available mitogenomes to infer the evolutionary history of GO in Neodermata. To improve the resolution, we added a newly sequenced mitogenome that exhibited the common GO, Euryhaliotrema johni (Ancyrocephalinae), to the dataset. Phylogenetic analyses conducted on two datasets (nucleotides of all 36 genes and amino acid sequences of 12 protein coding genes) and four algorithms (MrBayes, RAxML, IQ-TREE and PhyloBayes) produced topology instability towards the tips, so ancestral GO reconstructions were conducted using TreeREx and MLGO programs using all eight obtained topologies, plus three unique topologies from previous studies. The results consistently supported the second hypothesis, resolving the common GO as a plesiomorphic ancestral GO for Neodermata, Cestoda, Monopisthocotylea, Cestoda + Trematoda and Cestoda + Trematoda + Monopisthocotylea. This allowed us to trace the evolutionary GO scenarios from each common ancestor to its descendants amongst the Monogenea and Cestoda classes, and propose that the common GO was most likely retained throughout all of the common ancestors, leading to the extant species possessing the common GO. Neodermatan phylogeny inferred from GOs was largely incongruent with all 11 topologies described above, but it did support the mitogenomic dataset in resolving Polyopisthocotylea as the earliest neodermatan branch. Although highly derived GOs might be of some use in resolving isolated taxonomic and phylogenetic uncertainties, we conclude that, due to the discontinuous nature of their evolution, they tend to produce artefactual phylogenetic relationships, which makes them unsuitable for phylogenetic reconstruction in Neodermata. Wider and denser sampling of neodermatan mitogenomic sequences will be needed to infer the evolutionary pathways leading to the observed diversity of GOs with confidence.
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Affiliation(s)
- Dong Zhang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China; University of Chinese Academy of Sciences, Beijing, PR China
| | - Wen X Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Shan G Wu
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | - Ming Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China
| | | | - Jin Zhang
- Bio-Transduction Lab, Wuhan 430075, PR China
| | - Rong Chen
- Bio-Transduction Lab, Wuhan 430075, PR China
| | - Guitang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, PR China.
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15
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Zhang D, Zou H, Hua CJ, Li WX, Mahboob S, Al-Ghanim KA, Al-Misned F, Jakovlić I, Wang GT. Mitochondrial Architecture Rearrangements Produce Asymmetrical Nonadaptive Mutational Pressures That Subvert the Phylogenetic Reconstruction in Isopoda. Genome Biol Evol 2019; 11:1797-1812. [PMID: 31192351 PMCID: PMC6601869 DOI: 10.1093/gbe/evz121] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2019] [Indexed: 01/04/2023] Open
Abstract
The phylogeny of Isopoda, a speciose order of crustaceans, remains unresolved, with different data sets (morphological, nuclear, mitochondrial) often producing starkly incongruent phylogenetic hypotheses. We hypothesized that extreme diversity in their life histories might be causing compositional heterogeneity/heterotachy in their mitochondrial genomes, and compromising the phylogenetic reconstruction. We tested the effects of different data sets (mitochondrial, nuclear, nucleotides, amino acids, concatenated genes, individual genes, gene orders), phylogenetic algorithms (assuming data homogeneity, heterogeneity, and heterotachy), and partitioning; and found that almost all of them produced unique topologies. As we also found that mitogenomes of Asellota and two Cymothoida families (Cymothoidae and Corallanidae) possess inversed base (GC) skew patterns in comparison to other isopods, we concluded that inverted skews cause long-branch attraction phylogenetic artifacts between these taxa. These asymmetrical skews are most likely driven by multiple independent inversions of origin of replication (i.e., nonadaptive mutational pressures). Although the PhyloBayes CAT-GTR algorithm managed to attenuate some of these artifacts (and outperform partitioning), mitochondrial data have limited applicability for reconstructing the phylogeny of Isopoda. Regardless of this, our analyses allowed us to propose solutions to some unresolved phylogenetic debates, and support Asellota are the most likely candidate for the basal isopod branch. As our findings show that architectural rearrangements might produce major compositional biases even on relatively short evolutionary timescales, the implications are that proving the suitability of data via composition skew analyses should be a prerequisite for every study that aims to use mitochondrial data for phylogenetic reconstruction, even among closely related taxa.
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Affiliation(s)
- Dong Zhang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- University of Chinese Academy of Sciences, Beijing, P.R. China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
| | - Cong-Jie Hua
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
| | - Wen-Xiang Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
| | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Zoology, GC University, Faisalabad, Pakistan
| | | | - Fahad Al-Misned
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Gui-Tang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P.R. China
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16
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Hua CJ, Li WX, Zhang D, Zou H, Li M, Jakovlić I, Wu SG, Wang GT. Basal position of two new complete mitochondrial genomes of parasitic Cymothoida (Crustacea: Isopoda) challenges the monophyly of the suborder and phylogeny of the entire order. Parasit Vectors 2018; 11:628. [PMID: 30526651 PMCID: PMC6287365 DOI: 10.1186/s13071-018-3162-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 10/22/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Isopoda is a highly diverse order of crustaceans with more than 10,300 species, many of which are parasitic. Taxonomy and phylogeny within the order, especially those of the suborder Cymothoida Wägele, 1989, are still debated. Mitochondrial (mt) genomes are a useful tool for phylogenetic studies, but their availability for isopods is very limited. To explore these phylogenetic controversies on the mt genomic level and study the mt genome evolution in Isopoda, we sequenced mt genomes of two parasitic isopods, Tachaea chinensis Thielemann, 1910 and Ichthyoxenos japonensis Richardson, 1913, belonging to the suborder Cymothoida, and conducted comparative and phylogenetic mt genomic analyses across Isopoda. RESULTS The complete mt genomes of T. chinensis and I. japonensis were 14,616 bp and 15,440 bp in size, respectively, with the A+T content higher than in other isopods (72.7 and 72.8%, respectively). Both genomes code for 13 protein-coding genes, 21 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and possess a control region (CR). Both are missing a gene from the complete tRNA set: T. chinensis lacks trnS1 and I. japonensis lacks trnI. Both possess unique gene orders among isopods. Within the CR of I. japonensis (284 bp), we identified a repetitive region with four tandem repeats. Phylogenetic analysis based on concatenated nucleotide sequences of 13 protein-coding genes showed that the two parasitic cymothoids clustered together and formed a basal clade within Isopoda. However, another parasitic cymothoid, Gyge ovalis Shiino, 1939, formed a sister group with the suborder Limnoriidea Brandt & Poore in Poore, 2002, whereas two free-living cymothoid species were located in the derived part of the phylogram: Bathynomus sp. formed a sister group with the suborder Sphaeromatidea Wägele, 1989, and Eurydice pulchra Leach, 1815 with a clade including Bathynomus sp., Sphaeromatidea and Valvifera G. O. Sars, 1883. CONCLUSIONS Our results did not recover the suborders Cymothoida and Oniscidea Latreille, 1802 as monophyletic, with parasitic and free-living cymothoidans forming separate clades. Furthermore, two parasitic cymothoidans formed the sister-clade to all other isopods, separated from Epicaridea Latreille, 1825, which challenges currently prevalent isopod phylogeny. Additional mt genomes of parasitic and free-living isopods might confer a sufficient phylogenetic resolution to enable us to resolve their relationships, and ultimately allow us to better understand the evolutionary history of the entire isopod order.
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Affiliation(s)
- Cong J. Hua
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Wen X. Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Dong Zhang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
| | - Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Ming Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Ivan Jakovlić
- Bio-Transduction Lab, Biolake, Wuhan, 430075 People’s Republic of China
| | - Shan G. Wu
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
| | - Gui T. Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072 People’s Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049 People’s Republic of China
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17
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Saclier N, François CM, Konecny-Dupré L, Lartillot N, Guéguen L, Duret L, Malard F, Douady CJ, Lefébure T. Life History Traits Impact the Nuclear Rate of Substitution but Not the Mitochondrial Rate in Isopods. Mol Biol Evol 2018; 35:2900-2912. [DOI: 10.1093/molbev/msy184] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Nathanaëlle Saclier
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne, France
| | - Clémentine M François
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne, France
| | - Lara Konecny-Dupré
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne, France
| | - Nicolas Lartillot
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Laurent Guéguen
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Laurent Duret
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Florian Malard
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne, France
| | - Christophe J Douady
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne, France
- Institut Universitaire de France, Paris, France
| | - Tristan Lefébure
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5023, ENTPE, Laboratoire d’Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne, France
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Zou H, Jakovlić I, Zhang D, Chen R, Mahboob S, Al-Ghanim KA, Al-Misned F, Li WX, Wang GT. The complete mitochondrial genome of Cymothoa indica has a highly rearranged gene order and clusters at the very base of the Isopoda clade. PLoS One 2018; 13:e0203089. [PMID: 30180209 PMCID: PMC6122833 DOI: 10.1371/journal.pone.0203089] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/14/2018] [Indexed: 11/18/2022] Open
Abstract
As a result of great diversity in life histories and a large number of described species, taxonomic and phylogenetic uncertainty permeates the entire crustacean order of Isopoda. Large molecular datasets capable of providing sufficiently high phylogenetic resolution, such as mitochondrial genomes (mitogenomes), are needed to infer their evolutionary history with confidence, but isopod mitogenomes remain remarkably poorly represented in public databases. We sequenced the complete mitogenome of Cymothoa indica, a species belonging to a family from which no mitochondrial genome was sequenced yet, Cymothoidae. The mitogenome (circular, 14484 bp, A+T = 63.8%) is highly compact, appears to be missing two tRNA genes (trnI and trnE), and exhibits a unique gene order with a large number of rearrangements. High compactness and the existence of palindromes indicate that the mechanism behind these rearrangements might be associated with linearization events in its evolutionary history, similar to those proposed for isopods from the Armadillidium genus (Oniscidea). Isopods might present an important model system to study the proposed discontinuity in the dynamics of mitochondrial genomic architecture evolution. Phylogenetic analyses (Bayesian Inference and Maximum Likelihood) conducted using nucleotide sequences of all mitochondrial genes resolved Oniscidea and Cymothoida suborders as paraphyletic. Cymothoa indica was resolved as a sister group (basal) to all remaining isopods, which challenges the accepted isopod phylogeny, where Cymothoida are the most derived, and Phreatoicidea the most basal isopod group. There is growing evidence that Cymothoida suborder might be split into two evolutionary distant clades, with parasitic species being the most basal split in the Isopoda clade, but a much larger amount of molecular resources carrying a high phylogenetic resolution will be needed to infer the remarkably complex evolutionary history of this group of animals with confidence.
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Affiliation(s)
- Hong Zou
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | | | - Dong Zhang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
- University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Rong Chen
- Bio-Transduction Lab, Biolake, Wuhan, P. R. China
| | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Zoology, GC University, Faisalabad, Pakistan
| | | | - Fahad Al-Misned
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Wen-Xiang Li
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
| | - Gui-Tang Wang
- Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, and State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, P. R. China
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19
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Yu J, An J, Li Y, Boyko CB. The first complete mitochondrial genome of a parasitic isopod supports Epicaridea Latreille, 1825 as a suborder and reveals the less conservative genome of isopods. Syst Parasitol 2018; 95:465-478. [PMID: 29644508 DOI: 10.1007/s11230-018-9792-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Accepted: 03/14/2018] [Indexed: 11/26/2022]
Abstract
The complete mitochondrial genome sequence of the holoparasitic isopod Gyge ovalis (Shiino, 1939) has been determined. The mitogenome is 14,268 bp in length and contains 34 genes: 13 protein-coding genes, two ribosomal RNA, 19 tRNA and a control region. Three tRNA genes (trnE, trnI and trnS1) are missing. Most of the tRNA genes show secondary structures which derive from the usual cloverleaf pattern except for trnC which is characterised by the loss of the DHU-arm. Compared to the isopod ground pattern and Eurydice pulchra Leach, 1815 (suborder Cymothoida Wägele, 1989), the genome of G. ovalis shows few differences, with changes only around the control region. However, the genome of G. ovalis is very different from that of non-cymothoidan isopods and reveals that the gene order evolution in isopods is less conservative compared to other crustaceans. Phylogenic trees were constructed using maxiumum likelihood and Bayesian inference analyses based on 13 protein-coding genes. The results do not support the placement of G. ovalis with E. pulchra and Bathynomus sp. in the same suborder; rather, G. ovalis appears to have a closer relationship to Ligia oceanica (Linnaeus, 1767), but this result suggests a need for more data and further analysis. Nevertheless, these results cast doubt that Epicaridea Latreille, 1825 can be placed as an infraorder within the suborder Cymothoida, and Epicaridea appears to also deserve subordinal rank. Further development of robust phylogenetic relationships across Isopoda Latreille, 1817 will require more genetic data from a greater diversity of taxa belonging to all isopod suborders.
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Affiliation(s)
- Jialu Yu
- School of Life Science, Shanxi Normal University, Linfen, 041000, People's Republic of China
| | - Jianmei An
- School of Life Science, Shanxi Normal University, Linfen, 041000, People's Republic of China.
| | - Yue Li
- School of Life Science, Shanxi Normal University, Linfen, 041000, People's Republic of China
| | - Christopher B Boyko
- Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
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20
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Untangling Heteroplasmy, Structure, and Evolution of an Atypical Mitochondrial Genome by PacBio Sequencing. Genetics 2017; 207:269-280. [PMID: 28679546 DOI: 10.1534/genetics.117.203380] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 07/01/2017] [Indexed: 01/12/2023] Open
Abstract
The highly compact mitochondrial (mt) genome of terrestrial isopods (Oniscidae) presents two unusual features. First, several loci can individually encode two tRNAs, thanks to single nucleotide polymorphisms at anticodon sites. Within-individual variation (heteroplasmy) at these loci is thought to have been maintained for millions of years because individuals that do not carry all tRNA genes die, resulting in strong balancing selection. Second, the oniscid mtDNA genome comes in two conformations: a ∼14 kb linear monomer and a ∼28 kb circular dimer comprising two monomer units fused in palindrome. We hypothesized that heteroplasmy actually results from two genome units of the same dimeric molecule carrying different tRNA genes at mirrored loci. This hypothesis, however, contradicts the earlier proposition that dimeric molecules result from the replication of linear monomers-a process that should yield totally identical genome units within a dimer. To solve this contradiction, we used the SMRT (PacBio) technology to sequence mirrored tRNA loci in single dimeric molecules. We show that dimers do present different tRNA genes at mirrored loci; thus covalent linkage, rather than balancing selection, maintains vital variation at anticodons. We also leveraged unique features of the SMRT technology to detect linear monomers closed by hairpins and carrying noncomplementary bases at anticodons. These molecules contain the necessary information to encode two tRNAs at the same locus, and suggest new mechanisms of transition between linear and circular mtDNA. Overall, our analyses clarify the evolution of an atypical mt genome where dimerization counterintuitively enabled further mtDNA compaction.
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Tsang LM, Shen X, Cheang CC, Chu KH, Chan BKK. Gene rearrangement and sequence analysis of mitogenomes suggest polyphyly of Archaeobalanid and Balanid barnacles (Cirripedia: Balanomorpha). ZOOL SCR 2017. [DOI: 10.1111/zsc.12246] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Ling Ming Tsang
- Institute of Marine Biology; National Taiwan Ocean University; Keelung 20224 Taiwan
| | - Xin Shen
- Simon F. S. Li Marine Science Laboratory; School of Life Sciences; The Chinese University of Hong Kong; Shatin NT Hong Kong China
- Jiangsu Key Laboratory of Marine Biotechnology/College of Marine Science; Huaihai Institute of Technology; Lianyungang 222005 China
| | - Chi Chiu Cheang
- Department of Science and Environmental Studies; The Education University of Hong Kong; Taipo Hong Kong China
| | - Ka Hou Chu
- Simon F. S. Li Marine Science Laboratory; School of Life Sciences; The Chinese University of Hong Kong; Shatin NT Hong Kong China
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Grandjean F, Tan MH, Gan HM, Lee YP, Kawai T, Distefano RJ, Blaha M, Roles AJ, Austin CM. Rapid recovery of nuclear and mitochondrial genes by genome skimming from Northern Hemisphere freshwater crayfish. ZOOL SCR 2017. [DOI: 10.1111/zsc.12247] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Frederic Grandjean
- UMR CNRS 7267 Equipe Ecologie Evolution Symbiose; Laboratoire Ecologie et Biologie des Interactions; 5 rue Albert Turpin Poitiers Cedex France
| | - Mun Hua Tan
- School of Science; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- Genomics Facility; Tropical Medicine and Biology Platform; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- School of Life and Environmental Sciences; Deakin University; Geelong Victoria 3126 Australia
| | - Han Ming Gan
- School of Science; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- Genomics Facility; Tropical Medicine and Biology Platform; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- School of Life and Environmental Sciences; Deakin University; Geelong Victoria 3126 Australia
| | - Yin Peng Lee
- School of Science; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- Genomics Facility; Tropical Medicine and Biology Platform; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
| | - Tadashi Kawai
- Fisheries Research Department; Wakkanai Fisheries Research Institute; 4-5-15 Suehiro Wakkanai-shi 097-0001 Hokkaido Japan
| | - Robert J. Distefano
- Missouri Department of Conservation; East Gans Road Columbia Missouri 65201 USA
| | - Martin Blaha
- Faculty of Fisheries and Protection of Waters; South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses; University of South Bohemia in České Budějovice; Zátiší 728/II Vodňany Czech Republic
| | - Angela J. Roles
- Biology Department; Oberlin College, Oberlin; Ohio 44074 USA
| | - Christopher M. Austin
- School of Science; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- Genomics Facility; Tropical Medicine and Biology Platform; Monash University Malaysia; Jalan Lagoon Selatan Bandar Sunway 47500 Petaling Jaya Selangor Malaysia
- School of Life and Environmental Sciences; Deakin University; Geelong Victoria 3126 Australia
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Shen Y, Kou Q, Zhong Z, Li X, He L, He S, Gan X. The first complete mitogenome of the South China deep-sea giant isopod Bathynomus sp. (Crustacea: Isopoda: Cirolanidae) allows insights into the early mitogenomic evolution of isopods. Ecol Evol 2017; 7:1869-1881. [PMID: 28331594 PMCID: PMC5355201 DOI: 10.1002/ece3.2737] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 11/07/2016] [Accepted: 12/21/2016] [Indexed: 12/02/2022] Open
Abstract
In this study, the complete mitochondrial (mt) genome sequence of the South China deep‐sea giant isopod Bathynomus sp. was determined, and this study is the first to explore in detail the mt genome of a deep‐sea member of the order Isopoda. This species belongs to the genus Bathynomus, the members of which are saprophagous residents of the deep‐sea benthic environment; based on their large size, Bathynomus is included in the “supergiant group” of isopods. The mt genome of Bathynomus sp. is 14,965 bp in length and consists of 13 protein‐coding genes, two ribosomal RNA genes, only 18 transfer RNA genes, and a noncoding control region 362 bp in length, which is the smallest control region discovered in Isopoda to date. Although the overall genome organization is typical for metazoans, the mt genome of Bathynomus sp. shows a number of derived characters, such as an inversion of 10 genes when compared to the pancrustacean ground pattern. Rearrangements in some genes (e.g., cob, trnT, nad5, and trnF) are shared by nearly all isopod mt genomes analyzed thus far, and when compared to the putative isopod ground pattern, five rearrangements were found in Bathynomus sp. Two tRNAs exhibit modified secondary structures: The TΨC arm is absent from trnQ, and trnC lacks the DHU. Within the class Malacostraca, trnC arm loss is only found in other isopods. Phylogenetic analysis revealed that Bathynomus sp. (Cymothoida) and Sphaeroma serratum (Sphaeromatidea) form a single clade, although it is unclear whether Cymothoida is monophyletic or paraphyletic. Moreover, the evolutionary rate of Bathynomus sp. (dN/dS [nonsynonymous mutational rate/synonymous mutational rate] = 0.0705) is the slowest measured to date among Cymothoida, which may be associated with its relatively constant deep‐sea environment. Overall, our results may provide useful information for understanding the evolution of deep‐sea Isopoda species.
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Affiliation(s)
- Yanjun Shen
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of Hydrobiology Chinese Academy of Sciences Wuhan Hubei China; University of Chinese Academy of Sciences Beijing China
| | - Qi Kou
- Institute of Oceanology Chinese Academy of Sciences Qingdao China
| | - Zaixuan Zhong
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of Hydrobiology Chinese Academy of Sciences Wuhan Hubei China; University of Chinese Academy of Sciences Beijing China
| | - Xinzheng Li
- Institute of Oceanology Chinese Academy of Sciences Qingdao China
| | - Lisheng He
- Institute of Deep-sea Science and Engineering Chinese Academy of Sciences Sanya China
| | - Shunping He
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of Hydrobiology Chinese Academy of Sciences Wuhan Hubei China
| | - Xiaoni Gan
- The Key Laboratory of Aquatic Biodiversity and Conservation of Chinese Academy of Sciences Institute of Hydrobiology Chinese Academy of Sciences Wuhan Hubei China
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Panova M, Nygren A, Jonsson PR, Leidenberger S. A molecular phylogeny of the north-east Atlantic species of the genusIdotea(Isopoda) with focus on the Baltic Sea. ZOOL SCR 2016. [DOI: 10.1111/zsc.12200] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marina Panova
- Department of Marine Sciences - Tjärnö; University of Gothenburg; SE-452 96 Strömstad Sweden
| | - Arne Nygren
- The Maritime Museum & Aquarium; Karl Johansgatan 1-3 SE-414 59 Göteborg Sweden
| | - Per R. Jonsson
- Department of Marine Sciences - Tjärnö; University of Gothenburg; SE-452 96 Strömstad Sweden
| | - Sonja Leidenberger
- Swedish Species Information Centre/ArtDatabanken; Swedish University of Agricultural Sciences; Bäcklösavägen 10 SE-750 07 Uppsala Sweden
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Lin MF, Kitahara MV, Luo H, Tracey D, Geller J, Fukami H, Miller DJ, Chen CA. Mitochondrial genome rearrangements in the scleractinia/corallimorpharia complex: implications for coral phylogeny. Genome Biol Evol 2016; 6:1086-95. [PMID: 24769753 PMCID: PMC4040992 DOI: 10.1093/gbe/evu084] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Corallimorpharia is a small Order of skeleton-less animals that is closely related to the reef-building corals (Scleractinia) and of fundamental interest in the context of understanding the potential impacts of climate change in the future on coral reefs. The relationship between the nominal Orders Corallimorpharia and Scleractinia is controversial—the former is either the closest outgroup to the Scleractinia or alternatively is derived from corals via skeleton loss. This latter scenario, the “naked coral” hypothesis, is strongly supported by analyses based on mitochondrial (mt) protein sequences, whereas the former is equally strongly supported by analyses of mt nucleotide sequences. The “naked coral” hypothesis seeks to link skeleton loss in the putative ancestor of corallimorpharians with a period of elevated oceanic CO2 during the Cretaceous, leading to the idea that these skeleton-less animals may be harbingers for the fate of coral reefs under global climate change. In an attempt to better understand their evolutionary relationships, we examined mt genome organization in a representative range (12 species, representing 3 of the 4 extant families) of corallimorpharians and compared these patterns with other Hexacorallia. The most surprising finding was that mt genome organization in Corallimorphus profundus, a deep-water species that is the most scleractinian-like of all corallimorpharians on the basis of morphology, was much more similar to the common scleractinian pattern than to those of other corallimorpharians. This finding is consistent with the idea that C. profundus represents a key position in the coral <-> corallimorpharian transition.
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Affiliation(s)
- Mei-Fang Lin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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Abstract
In contrast to the well mapped molecular orchestration of circadian timekeeping in terrestrial organisms, the mechanisms that direct tidal and lunar rhythms in marine species are entirely unknown. Using a combination of biochemical and molecular approaches we have identified a series of metabolic markers of the tidal clock of the intertidal isopod Eurydice pulchra. Specifically, we show that the overoxidation of peroxiredoxin (PRX), a conserved marker of circadian timekeeping in terrestrial eukaryotes [1], follows a circatidal (approximately 12.4 hours) pattern in E. pulchra, in register with the tidal pattern of swimming. In parallel, we show that mitochondrially encoded genes are expressed with a circatidal rhythm. Together, these findings demonstrate that PRX overoxidation rhythms are not intrinsically circadian; rather they appear to resonate with the dominant metabolic cycle of an organism, regardless of its frequency. Moreover, they provide the first molecular leads for dissecting the tidal clockwork.
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Hiruta SF, Hiruta SI. Description of a species of Fabaeformiscandona (Ostracoda, Crustacea) from Kushiro Marsh, Hokkaido, Japan, with the nearly complete mitochondrial genomic sequence. Biodivers Data J 2016:e7074. [PMID: 26751633 PMCID: PMC4698455 DOI: 10.3897/bdj.3.e7074] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 12/07/2015] [Indexed: 01/05/2023] Open
Abstract
Background So far, 16 species of non-marine ostracods have been reported from Kushiro Marsh, Kushiro Shitsugen National Park, eastern Hokkaido, Japan (Hiruta and Smith 2001, Smith and Hiruta 2004). Nine of these species are in Candonidae, the second-most diverse family of non-marine ostracods. This family contains ca. 550 species, or around 25% of the total number of non-marine ostracod species (Martens et al. 2008). New information We sampled ostracods in Kushiro Marsh on 27 December 2012 and identified an undescribed species in the family Candonidae, herein described as Fabaeformiscandonakushiroensis sp. nov. This species belongs to the F.acuminata species group and is characterized by the shapes of the elongate, dorsally directed medial and outer lobes on the distal end of each hemipenis. We also determined for this species the sequence of the nearly complete mitochondrial genome, the first record from the order Podocopa. The genome (ca. 17 kbp) contains two ribosomal RNA, 22 transfer RNA, and 13 protein-coding genes, as also found in other arthropods for which the mitochondrial genome has been sequenced. The gene arrangement is similar to the pancrustacean ground pattern, except that in the control region there is an approximately 2 kbp tandem repeat region composed of 220-bp motif sequences. We describe the genetic features of the mitochondrial genome, including nucleotide composition and the secondary structures of tRNAs and rRNAs, and compare them with the genome of Vargulahilgendorfii (Myodocopa, Ostracoda).
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Affiliation(s)
| | - Shin-Ichi Hiruta
- Department of Biology, Hokkaido University of Education, Kushiro Campus, Kushiro, Japan
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Doublet V, Ubrig E, Alioua A, Bouchon D, Marcadé I, Maréchal-Drouard L. Large gene overlaps and tRNA processing in the compact mitochondrial genome of the crustacean Armadillidium vulgare. RNA Biol 2015; 12:1159-68. [PMID: 26361137 DOI: 10.1080/15476286.2015.1090078] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
A faithful expression of the mitochondrial DNA is crucial for cell survival. Animal mitochondrial DNA (mtDNA) presents a highly compact gene organization. The typical 16.5 kbp animal mtDNA encodes 13 proteins, 2 rRNAs and 22 tRNAs. In the backyard pillbug Armadillidium vulgare, the rather small 13.9 kbp mtDNA encodes the same set of proteins and rRNAs as compared to animal kingdom mtDNA, but seems to harbor an incomplete set of tRNA genes. Here, we first confirm the expression of 13 tRNA genes in this mtDNA. Then we show the extensive repair of a truncated tRNA, the expression of tRNA involved in large gene overlaps and of tRNA genes partially or fully integrated within protein-coding genes in either direct or opposite orientation. Under selective pressure, overlaps between genes have been likely favored for strong genome size reduction. Our study underlines the existence of unknown biochemical mechanisms for the complete gene expression of A. vulgare mtDNA, and of co-evolutionary processes to keep overlapping genes functional in a compacted mitochondrial genome.
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Affiliation(s)
- Vincent Doublet
- a Equipe Ecologie Evolution Symbiose; Laboratoire Ecologie et Biologie des Interactions , UMR CNRS 7267, Poitiers , France
| | - Elodie Ubrig
- b Institut de biologie moléculaire des plantes; associated with the University of Strasbourg , Strasbourg , France
| | - Abdelmalek Alioua
- b Institut de biologie moléculaire des plantes; associated with the University of Strasbourg , Strasbourg , France
| | - Didier Bouchon
- a Equipe Ecologie Evolution Symbiose; Laboratoire Ecologie et Biologie des Interactions , UMR CNRS 7267, Poitiers , France
| | - Isabelle Marcadé
- a Equipe Ecologie Evolution Symbiose; Laboratoire Ecologie et Biologie des Interactions , UMR CNRS 7267, Poitiers , France
| | - Laurence Maréchal-Drouard
- b Institut de biologie moléculaire des plantes; associated with the University of Strasbourg , Strasbourg , France
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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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Multiple Conserved Heteroplasmic Sites in tRNA Genes in the Mitochondrial Genomes of Terrestrial Isopods (Oniscidea). G3-GENES GENOMES GENETICS 2015; 5:1317-22. [PMID: 25911226 PMCID: PMC4502366 DOI: 10.1534/g3.115.018283] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Mitochondrial genome structure and organization are relatively conserved among metazoans. However, in many isopods, especially the terrestrial isopods (Oniscidea), the mitochondrial genome consists of both ∼14-kb linear monomers and ∼28-kb circular dimers. This unusual organization is associated with an ancient and conserved constitutive heteroplasmic site. This heteroplasmy affects the anticodon of a tRNA gene, allowing this single locus to function as a “dual” tRNA gene for two different amino acids. Here, we further explore the evolution of these unusual mitochondrial genomes by assembling complete mitochondrial sequences for two additional Oniscidean species, Trachelipus rathkei and Cylisticus convexus. Strikingly, we find evidence of two additional heteroplasmic sites that also alter tRNA anticodons, creating additional dual tRNA genes, and that are conserved across both species. These results suggest that the unique linear/circular organization of isopods’ mitochondrial genomes may facilitate the evolution of stable mitochondrial heteroplasmies, and, conversely, once such heteroplasmies have evolved, they constrain the multimeric structure of the mitochondrial genome in these species. Finally, we outline some possible future research directions to identify the factors influencing mitochondrial genome evolution in this group.
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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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Gan HM, Schultz MB, Austin CM. Integrated shotgun sequencing and bioinformatics pipeline allows ultra-fast mitogenome recovery and confirms substantial gene rearrangements in Australian freshwater crayfishes. BMC Evol Biol 2014; 14:19. [PMID: 24484414 PMCID: PMC3915555 DOI: 10.1186/1471-2148-14-19] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 01/29/2014] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Although it is possible to recover the complete mitogenome directly from shotgun sequencing data, currently reported methods and pipelines are still relatively time consuming and costly. Using a sample of the Australian freshwater crayfish Engaeus lengana, we demonstrate that it is possible to achieve three-day turnaround time (four hours hands-on time) from tissue sample to NCBI-ready submission file through the integration of MiSeq sequencing platform, Nextera sample preparation protocol, MITObim assembly algorithm and MITOS annotation pipeline. RESULTS The complete mitochondrial genome of the parastacid freshwater crayfish, Engaeus lengana, was recovered by modest shotgun sequencing (1.2 giga bases) using the Illumina MiSeq benchtop sequencing platform. Genome assembly using the MITObim mitogenome assembler recovered the mitochondrial genome as a single contig with a 97-fold mean coverage (min. = 17; max. = 138). The mitogenome consists of 15,934 base pairs and contains the typical 37 mitochondrial genes and a non-coding AT-rich region. The genome arrangement is similar to the only other published parastacid mitogenome from the Australian genus Cherax. CONCLUSIONS We infer that the gene order arrangement found in Cherax destructor is common to Australian crayfish and may be a derived feature of the southern hemisphere family Parastacidae. Further, we report to our knowledge, the simplest and fastest protocol for the recovery and assembly of complete mitochondrial genomes using the MiSeq benchtop sequencer.
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Affiliation(s)
- Han Ming Gan
- School of Science, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, 46150 Petaling Jaya, Selangor, Malaysia.
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Doublet V, Helleu Q, Raimond R, Souty-Grosset C, Marcadé I. Inverted repeats and genome architecture conversions of terrestrial isopods mitochondrial DNA. J Mol Evol 2013; 77:107-18. [PMID: 24068302 DOI: 10.1007/s00239-013-9587-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 09/18/2013] [Indexed: 10/26/2022]
Abstract
Mitochondrial DNA (mtDNA) is usually depicted as a circular molecule, however, there is increasing evidence that linearization of mtDNA evolved independently many times in organisms such as fungi, unicellular eukaryotes, and animals. Recent observations in various models with linear mtDNA revealed the presence of conserved inverted repeats (IR) at both ends that, when they become single-stranded, may be able to fold on themselves to create telomeric-hairpins involved in genome architecture conversions. The atypical mtDNA of terrestrial isopods (Crustacea: Oniscidea) composed of linear monomers and circular dimers is an interesting model to study genome architecture conversions. Here, we present the mtDNA control region sequences of two species of the genus Armadillidium: A. vulgare and A. pelagicum. All features of arthropods mtDNA control regions are present (origin of replication, poly-T stretch, GA and TA-rich blocks and one variable domain), plus a conserved IR. This IR can potentially fold into a hairpin structure and is present in two different orientations among the A. vulgare populations: either in one sense or in its reverse complement. This polymorphism, also observed in a single individual (heteroplasmy), might be a signature of genome architecture conversions from linear to circular monomeric mtDNA via successive opening and closing of the molecules.
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Affiliation(s)
- Vincent Doublet
- Equipe Ecologie Evolution Symbiose, Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université de Poitiers, 40 Avenue du Recteur Pineau, 86022, Poitiers Cedex, France,
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Bernt M, Bleidorn C, Braband A, Dambach J, Donath A, Fritzsch G, Golombek A, Hadrys H, Jühling F, Meusemann K, Middendorf M, Misof B, Perseke M, Podsiadlowski L, von Reumont B, Schierwater B, Schlegel M, Schrödl M, Simon S, Stadler PF, Stöger I, Struck TH. A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny. Mol Phylogenet Evol 2013; 69:352-64. [PMID: 23684911 DOI: 10.1016/j.ympev.2013.05.002] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 04/27/2013] [Accepted: 05/03/2013] [Indexed: 12/16/2022]
Abstract
About 2800 mitochondrial genomes of Metazoa are present in NCBI RefSeq today, two thirds belonging to vertebrates. Metazoan phylogeny was recently challenged by large scale EST approaches (phylogenomics), stabilizing classical nodes while simultaneously supporting new sister group hypotheses. The use of mitochondrial data in deep phylogeny analyses was often criticized because of high substitution rates on nucleotides, large differences in amino acid substitution rate between taxa, and biases in nucleotide frequencies. Nevertheless, mitochondrial genome data might still be promising as it allows for a larger taxon sampling, while presenting a smaller amount of sequence information. We present the most comprehensive analysis of bilaterian relationships based on mitochondrial genome data. The analyzed data set comprises more than 650 mitochondrial genomes that have been chosen to represent a profound sample of the phylogenetic as well as sequence diversity. The results are based on high quality amino acid alignments obtained from a complete reannotation of the mitogenomic sequences from NCBI RefSeq database. However, the results failed to give support for many otherwise undisputed high-ranking taxa, like Mollusca, Hexapoda, Arthropoda, and suffer from extreme long branches of Nematoda, Platyhelminthes, and some other taxa. In order to identify the sources of misleading phylogenetic signals, we discuss several problems associated with mitochondrial genome data sets, e.g. the nucleotide and amino acid landscapes and a strong correlation of gene rearrangements with long branches.
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Affiliation(s)
- Matthias Bernt
- Parallel Computing and Complex Systems Group, Department of Computer Science, University of Leipzig, Augustusplatz 10, D-04109 Leipzig, Germany.
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Leese F, Brand P, Rozenberg A, Mayer C, Agrawal S, Dambach J, Dietz L, Doemel JS, Goodall-Copstake WP, Held C, Jackson JA, Lampert KP, Linse K, Macher JN, Nolzen J, Raupach MJ, Rivera NT, Schubart CD, Striewski S, Tollrian R, Sands CJ. Exploring Pandora's box: potential and pitfalls of low coverage genome surveys for evolutionary biology. PLoS One 2012. [PMID: 23185309 PMCID: PMC3504011 DOI: 10.1371/journal.pone.0049202] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
High throughput sequencing technologies are revolutionizing genetic research. With this “rise of the machines”, genomic sequences can be obtained even for unknown genomes within a short time and for reasonable costs. This has enabled evolutionary biologists studying genetically unexplored species to identify molecular markers or genomic regions of interest (e.g. micro- and minisatellites, mitochondrial and nuclear genes) by sequencing only a fraction of the genome. However, when using such datasets from non-model species, it is possible that DNA from non-target contaminant species such as bacteria, viruses, fungi, or other eukaryotic organisms may complicate the interpretation of the results. In this study we analysed 14 genomic pyrosequencing libraries of aquatic non-model taxa from four major evolutionary lineages. We quantified the amount of suitable micro- and minisatellites, mitochondrial genomes, known nuclear genes and transposable elements and searched for contamination from various sources using bioinformatic approaches. Our results show that in all sequence libraries with estimated coverage of about 0.02–25%, many appropriate micro- and minisatellites, mitochondrial gene sequences and nuclear genes from different KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways could be identified and characterized. These can serve as markers for phylogenetic and population genetic analyses. A central finding of our study is that several genomic libraries suffered from different biases owing to non-target DNA or mobile elements. In particular, viruses, bacteria or eukaryote endosymbionts contributed significantly (up to 10%) to some of the libraries analysed. If not identified as such, genetic markers developed from high-throughput sequencing data for non-model organisms may bias evolutionary studies or fail completely in experimental tests. In conclusion, our study demonstrates the enormous potential of low-coverage genome survey sequences and suggests bioinformatic analysis workflows. The results also advise a more sophisticated filtering for problematic sequences and non-target genome sequences prior to developing markers.
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Affiliation(s)
- Florian Leese
- Ruhr University Bochum, Department of Animal Ecology, Evolution and Biodiversity, Bochum, Germany.
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Nelson LA, Lambkin CL, Batterham P, Wallman JF, Dowton M, Whiting MF, Yeates DK, Cameron SL. Beyond barcoding: a mitochondrial genomics approach to molecular phylogenetics and diagnostics of blowflies (Diptera: Calliphoridae). Gene 2012; 511:131-42. [PMID: 23043935 DOI: 10.1016/j.gene.2012.09.103] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 09/21/2012] [Accepted: 09/29/2012] [Indexed: 11/28/2022]
Abstract
Members of the Calliphoridae (blowflies) are significant for medical and veterinary management, due to the ability of some species to consume living flesh as larvae, and for forensic investigations due to the ability of others to develop in corpses. Due to the difficulty of accurately identifying larval blowflies to species there is a need for DNA-based diagnostics for this family, however the widely used DNA-barcoding marker, cox1, has been shown to fail for several groups within this family. Additionally, many phylogenetic relationships within the Calliphoridae are still unresolved, particularly deeper level relationships. Sequencing whole mt genomes has been demonstrated both as an effective method for identifying the most informative diagnostic markers and for resolving phylogenetic relationships. Twenty-seven complete, or nearly so, mt genomes were sequenced representing 13 species, seven genera and four calliphorid subfamilies and a member of the related family Tachinidae. PCR and sequencing primers developed for sequencing one calliphorid species could be reused to sequence related species within the same superfamily with success rates ranging from 61% to 100%, demonstrating the speed and efficiency with which an mt genome dataset can be assembled. Comparison of molecular divergences for each of the 13 protein-coding genes and 2 ribosomal RNA genes, at a range of taxonomic scales identified novel targets for developing as diagnostic markers which were 117-200% more variable than the markers which have been used previously in calliphorids. Phylogenetic analysis of whole mt genome sequences resulted in much stronger support for family and subfamily-level relationships. The Calliphoridae are polyphyletic, with the Polleninae more closely related to the Tachinidae, and the Sarcophagidae are the sister group of the remaining calliphorids. Within the Calliphoridae, there was strong support for the monophyly of the Chrysomyinae and Luciliinae and for the sister-grouping of Luciliinae with Calliphorinae. Relationships within Chrysomya were not well resolved. Whole mt genome data, supported the previously demonstrated paraphyly of Lucilia cuprina with respect to L. sericata and allowed us to conclude that it is due to hybrid introgression prior to the last common ancestor of modern sericata populations, rather than due to recent hybridisation, nuclear pseudogenes or incomplete lineage sorting.
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Affiliation(s)
- Leigh A Nelson
- Australian National Insect Collection, CSIRO Ecosystem Sciences, Canberra, ACT, 2601, Australia
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