1
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Wang H, Wang L, Liao J, Han BP. The complete mitochondrial genome of Chlorogomphus shanicus Wilson, 2002 (Anisoptera: Chlorogomphidae), an endemic species in South China. Mitochondrial DNA B Resour 2023; 8:1192-1195. [PMID: 37937100 PMCID: PMC10627042 DOI: 10.1080/23802359.2023.2276970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 10/24/2023] [Indexed: 11/09/2023] Open
Abstract
In this study, the complete mitochondrial genome of Chlorogomphus shanicus Wilson, 2002 was reported, and the maximum-likelihood (ML) phylogenetic tree was constructed using 13 protein-coding genes (PCGs). The total length of the mitogenome of C. shanicus was 15,497 bp. Twelve PCGs started with ATN codons, except cox1 began with TTG codon. Most transfer RNA genes (tRNAs) were predicted to fold in a typical cloverleaf structure, except the trnS1 (gct), which lacked a dihydrouridine arm that had been simplified to a loop. The phylogenetic tree showed that Anisoptera was split into two clades, and revealed that C. shanicus was closely related to Cordulegaster boltonii (Donovan, 1807) which is endemic to Europe.
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Affiliation(s)
- Haojie Wang
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Lu Wang
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Jian Liao
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Bo-Ping Han
- Department of Ecology and Institute of Hydrobiology, Jinan University, Guangzhou, China
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2
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The Quality of Sequence Data Affects Biodiversity and Conservation Perspectives in the Neotropical Damselfly Megaloprepus caerulatus. DIVERSITY 2022. [DOI: 10.3390/d14121056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Ideally, the footprint of the evolutionary history of a species is drawn from integrative studies including quantitative and qualitative taxonomy, biogeography, ecology, and molecular genetics. In today’s research, species delimitations and identification of conservation units is often accompanied by a set of—at minimum—two sequence markers appropriate for the systematic level under investigation. Two such studies re-evaluated the species status in the world’s largest Odonata, the Neotropical damselfly Megaloprepus caerulatus. The species status of the genus Megaloprepus has long been debated. Despite applying a highly similar set of sequence markers, the two studies reached different conclusions concerning species status and population genetic relationships. In this study, we took the unique opportunity to compare the two datasets and analyzed the reasons for those incongruences. The two DNA sequence markers used (16S rDNA and CO1) were re-aligned using a strict conservative approach and the analyses used in both studies were repeated. Going step by step back to the first line of data handling, we show that a high number of unresolved characters in the sequence alignments as well as internal gaps are responsible for the different outcomes in terms of species delimitations and population genetic relationships. Overall, this study shows that high quality raw sequence data are an indispensable requirement, not only in odonate research.
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3
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Jiang B, Li J, Zhang Y, Sun Y, He S, Yu G, Lv G, Mikolajewski DJ. Complete mitochondrial genomes of two damselfly species in coenagrionidae and phylogenetic implications. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2445-2448. [PMID: 34368442 PMCID: PMC8317919 DOI: 10.1080/23802359.2021.1955635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Agriocnemis femina (Brauer, 1868) and Ischnura senegalensis (Rambur, 1842) are two damselflies inhabiting paddy lands. As an intermediate predator, they play an important role in controlling certain crop pest and mosquitoes. In this study, we sequenced complete mitogenomes of these two species. The total length of mitogenomes is 15,936 bp in A. femina and 15,762 bp in I. senegalensis. Both of mitogenomes consist of 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and one control region. The close relationship between I. senegalensis and I. elegans was further proved by phylogenetic analysis. Our phylogenetic analysis indicated a clear two lineages in Coenagrionidae (Core and ridge-faced Coenagrionidae). Ridge-faced Coenagrionidae consisted of Megaloprepus caerulatus and Ceriagrion fallax. In core Coenagrionidae, Ischnura and Enallagma are most closely related; they formed one clade with Agriocnemis and then grouped together with Paracerion. Our study provides new genetic information for further study in phylogenetic analysis of Coenagrionidae.
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Affiliation(s)
- Bin Jiang
- College of Life Science, Anhui Normal University, Wuhu, China
| | - Jia Li
- College of Life Science, Anhui Normal University, Wuhu, China
| | - Yongmei Zhang
- College of Life Science, Anhui Normal University, Wuhu, China
| | - Yang Sun
- College of Life Science, Anhui Normal University, Wuhu, China
| | - Shulin He
- Faculty of Forestry and Wood Sciences, Czech University of Life Science Prague, Prague, Czech Republich
| | - Guozhi Yu
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - Guosheng Lv
- College of Life Science, Anhui Normal University, Wuhu, China
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4
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David FJ, Herzog R, Bielke A, Bergjürgen N, Osigus HJ, Hadrys H. The first complete mitochondrial genome of the migratory dragonfly Pantala flavescens Fabricius, 1798 (Libellulidae: Odonata). MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:808-810. [PMID: 33796648 PMCID: PMC7971328 DOI: 10.1080/23802359.2021.1882914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Pantala flavescens is the world’s most abundant and widely distributed dragonfly and with its outstanding migratory capacity an important model system to study insect migration at the evolutionary base of winged insects. We here report on the first complete mitochondrial genome (mitogenome) of P. flavescens sampled from a population in Rufiji River, Tanzania. The mitogenome is 14,853 bp long with an AT-biased base composition (72.7% A + T) and encodes a typical set of 13 protein-coding genes (PCGs), 22 tRNAs, and two rRNAs. The control region (CR) (171 bp) is the shortest reported in any anisopteran odonate, so far. Phylogenetic analyses support the placement of P. flavescens within the Libellulidae.
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Affiliation(s)
- Felix Joke David
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Rebecca Herzog
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Arne Bielke
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Nicole Bergjürgen
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Hans-Jürgen Osigus
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Heike Hadrys
- Institute of Animal Ecology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
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5
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Cao L, Hou W, Hu C. The complete mitochondrial genome sequence of Acisoma panorpoides Rambur, 1842 (Odonate: Libellulidae). Mitochondrial DNA B Resour 2019; 4:3644-3645. [PMID: 33366123 PMCID: PMC7707415 DOI: 10.1080/23802359.2019.1678416] [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: 07/29/2019] [Accepted: 08/16/2019] [Indexed: 11/11/2022] Open
Abstract
The phylogenetic relationships of dragonflies have received great attention all the time. For a better understanding the phylogenies among odonate insects, the paper presented the complete mitochondrial genome of Acisoma panorpoides based on next generation sequencing data of total genomic DNA. The total length comprised 15,249 bp and the 37 genes (2 rRNA genes, 13 protein coding genes and 22 tRNA genes). Gene content and gene arrangement were identical to other odonate mitogenomes. Phylogenetic analyses using the whole sequences of the mitochondrial genome placed A. panorpoides as a sister species to Hydrobasileus croceus in Libellulidae.
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Affiliation(s)
- Lingzhen Cao
- College of Life Science, Jiangxi Normal University, Nanchang, China
| | - Wen Hou
- College of Life Science, Jiangxi Normal University, Nanchang, China
| | - Chaoxing Hu
- College of Agriculture, Guizhou University, Guiyang, China
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6
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Okuyama H, Kiyoshi T, Takahashi JI, Tsubaki Y. A comparison of complete mitochondrial DNA sequences of Mnais costalis Selys, 1869 (Odonata: Calopterygidae) from three different populations (one allopatric and two sympatric). Mitochondrial DNA B Resour 2019; 4:3104-3105. [PMID: 33365872 PMCID: PMC7707004 DOI: 10.1080/23802359.2019.1667888] [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: 04/22/2019] [Accepted: 08/16/2019] [Indexed: 10/29/2022] Open
Abstract
In Japan, two closely-related damselflies, Mnais costalis Selys, 1869 (Odonata: Calopterygidae) and M. pruinosa Selys-Longchamps (Odonata: Calopterygidae), 1853, coexist, and they exhibit geographic variations in wing color, body size, and habitat preference. In this study, we analyzed the complete mitochondrial genome of M. costalis from Saga Prefecture, Japan (sympatric populations that exhibit wing color polymorphism), and compared the genome with M. costalis that exhibit monomorphic orange wing color. The mitochondrial genome of M. costalis from Saga Prefecture was identified as a circular molecule of 15,488 bp, similar to that found in other M. costalis populations. It was predicted to contain 13 protein-coding (PCG), 22 tRNA, and two rRNA genes, along with one A + T-rich control region. Among the PCGs, ATP8 and ATP6, ATP6 and COIII, ND4 and ND4L, and ND6 and Cytb shared seven, one, seven, and one nucleotides, respectively. The initiation codon ATG was found in eight genes, ATC in four, and ATT in one, while the termination codons TAA, TAG, TA, and T were observed in seven, one, two, and three genes, respectively. All the tRNA genes possessed a cloverleaf secondary structure, except for tRNA-His that lacks the TΨC loop. The average AT content of mitochondrial genome was 66.06%. From a phylogenetic analysis, the loss of wing color polymorphism in monomorphic sympatric populations is likely to occur with the coexistence of two Mnais species.
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Affiliation(s)
- Hisashi Okuyama
- Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Takuya Kiyoshi
- Department of Zoology, National Museum of Nature and Science, Tokyo, Japan
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7
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Kim I, Jeong SY, Kim MJ. Complete mitochondrial genome sequence of Bekko Tombo Libellula angelina Selys, 1883 (Odonata: Libellulidae). Mitochondrial DNA B Resour 2019; 4:2201-2203. [PMID: 33365474 PMCID: PMC7687636 DOI: 10.1080/23802359.2019.1624216] [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: 05/08/2019] [Accepted: 05/17/2019] [Indexed: 11/21/2022] Open
Abstract
The dragonfly Libellula angelina Selys, 1883 (Odonata: Libellulidae) has been listed as a critically endangered species by the International Union for Conservation of Nature (IUCN) and is also an endangered insect in South Korea. We sequenced the whole genome (15,233 bp) of L. angelina species, which included a set of typical genes and one major non-coding AT-rich region with an arrangement identical to that observed in most insect genomes. The A + T-rich region harbored one identical repeat composed of 65 bp and two tRNA-like structures (trnF and trnK-like sequences) with proper anticodon and clover-leaf structures. Phylogenetic reconstruction using the concatenated sequences of 13 protein-coding genes (PCGs) and two rRNAs of the representative odonate mitogenomes utilizing both Bayesian inference and maximum-likelihood methods revealed a strong support for the monophyletic Zygoptera and a moderate to high support for the monophyletic Anisoptera suborders. Unlike that in conventional phylogenetic analysis, a relatively strong sister relationship was revealed between the suborders of Anisozygoptera and Zygoptera.
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Affiliation(s)
- Iksoo Kim
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Su Yeon Jeong
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Min Jee Kim
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
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Guan DL, Qian ZQ, Ma LB, Bai Y, Xu SQ. Different mitogenomic codon usage patterns between damselflies and dragonflies and nine complete mitogenomes for odonates. Sci Rep 2019; 9:678. [PMID: 30679466 PMCID: PMC6345984 DOI: 10.1038/s41598-018-35760-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/09/2018] [Indexed: 01/08/2023] Open
Abstract
Damselflies and dragonflies, of the order Odonata, have distinct body plans and predatory abilities. Knowledge of their various evolutionary histories will allow for an understanding of the genetic and phenotypic evolution of insects. Mitogenomes are suitable materials to elucidate this, but the mitogenome of only a few odonates have been annotated. Herein, we report the complete mitogenome of nine odonates, including seven dragonflies and two damselflies, and a comprehensive analysis of the codon usage in 31 Odonata mitogenomes with the aim to estimate their evolutionary characteristics. Overall, a weak codon bias exists among odonate mitogenomes, although this favours AT-ending codons. Damselflies have a weaker codon usage bias than dragonflies, and 37 codons have significantly different usages. Both directional mutation and purifying selection shape damselfly and dragonfly mitogenomes. Although inevitable, directional mutation bias plays a minor role, whereas purifying selection pressure is the dominant evolutionary force. A higher selection pressure is observed in dragonflies than in damselflies, but it mainly acts on codon usage patterns rather than amino acid translation. Our findings suggest that dragonflies might have more efficient mitochondrial gene expression levels than damselflies, producing more proteins that support their locomotion and predatory abilities.
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Affiliation(s)
- De-Long Guan
- College of life science, Shaanxi Normal University, Xi'an, 710119, P. R. China
| | - Zeng-Qiang Qian
- College of life science, Shaanxi Normal University, Xi'an, 710119, P. R. China
| | - Li-Bin Ma
- College of life science, Shaanxi Normal University, Xi'an, 710119, P. R. China
| | - Yi Bai
- School of Life Science, Taizhou University, Taizhou, 317000, P.R. China
| | - Sheng-Quan Xu
- College of life science, Shaanxi Normal University, Xi'an, 710119, P. R. China.
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9
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Lan DY, Shen SQ, Cai YY, Wang J, Zhang JY, Storey KB, Yu DN. The characteristics and phylogenetic relationship of two complete mitochondrial genomes of Matrona basilaris (Odonata: Zygoptera: Calopterygidae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2019.1610104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Affiliation(s)
- Deng-Yong Lan
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Shi-Qi Shen
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Yin-Yin Cai
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Jun Wang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Jia-Yong Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | | | - Dan-Na Yu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang Province, China
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10
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Wang LJ, Lin MY, Shiao SF, Sung CH. The complete mitochondrial genome of Psolodesmus mandarinus McLachlan, 1870 (Odonata: Calopterygidae). Mitochondrial DNA B Resour 2019. [DOI: 10.1080/23802359.2018.1544045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Affiliation(s)
- Liang-Jong Wang
- Division of Forest Protection, Taiwan Forestry Research Institute, Taipei, Taiwan
| | - Min-Ying Lin
- Department of Plant Medicine, National Chiayi University, Chiayi City, Taiwan
| | - Shiuh-Feng Shiao
- Department of Entomology, National Taiwan University, Taipei, Taiwan
| | - Chia-Hsuan Sung
- Planning and Information Division, Fisheries Research Institute, Keelung, Taiwan
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11
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Cai YY, Gao YJ, Zhang LP, Yu DN, Storey KB, Zhang JY. The mitochondrial genome of Caenis sp. (Ephemeroptera: Caenidae) and the phylogeny of Ephemeroptera in Pterygota. Mitochondrial DNA B Resour 2018; 3:577-579. [PMID: 33474248 PMCID: PMC7799546 DOI: 10.1080/23802359.2018.1467239] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 04/16/2018] [Indexed: 11/30/2022] Open
Abstract
The phylogenetic relationship between Ephemeroptera (mayflies) and Odonata (dragonflies and damselflies) remains hotly debated in the insect evolution community. We sequenced the complete mitochondrial genome of Caenis sp. (Ephemeroptera: Caenidae) to discuss the phylogenetic relationship of Palaeoptera. The mitochondrial genome of Caenis sp. is a circular molecule of 15,254 bp in length containing 37 genes (13 protein-coding genes, 22 tRNAs, and 2 rRNAs), which showed the typical insect mitochondrial gene arrangement. In BI and ML phylogenetic trees using 71 species of 12 orders, our results support the Ephemeroptera as the basal group of winged insects.
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Affiliation(s)
- Yin-Yin Cai
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Ya-Jie Gao
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Le-Ping Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | - Dan-Na Yu
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang Province, China
| | | | - Jia-Yong Zhang
- College of Chemistry and Life Science, Zhejiang Normal University, Jinhua, Zhejiang Province, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua, Zhejiang Province, China
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12
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Kim MJ, Jeong SY, Wang AR, An J, Kim I. Complete mitochondrial genome sequence of Macromia daimoji Okumura, 1949 (Odonata: Macromiidae). Mitochondrial DNA B Resour 2018; 3:365-367. [PMID: 33474171 PMCID: PMC7800519 DOI: 10.1080/23802359.2018.1450683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 03/06/2018] [Indexed: 11/20/2022] Open
Abstract
The dragonfly Macromia daimoji Okumura, 1949 (Odonata: Macromiidae) has been listed as an Endangered insect in South Korea. We sequenced the complete 15,198 bp mitochondrial genome (mitogenome) of this organism, which is the first mitogenome sequence reported from the family Macromiidae. The genome includes a typical set of genes [13 protein-coding genes (PCGs), 2 rRNA genes, and 22 tRNA genes) and one non-coding region with an arrangement identical to that observed in most insect genomes. Phylogenetic analyses using concatenated sequences of the 13 PCGs and 2 rRNA genes using the Bayesian inference (BI) method placed Macromiidae, represented by M. daimoji, as a sister group to Libellulidae with the highest nodal support [Bayesian posterior probabilities (BPP) = 1]. Unlike conventional phylogenetic analysis, the suborders Anisozygoptera and Zygoptera formed a strong sister group (BPP =1), justifying the use of different molecular markers for phylogenetic analysis.
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Affiliation(s)
- Min Jee Kim
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Su Yeon Jeong
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Ah Rha Wang
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Junghwa An
- Animal Resources Division, National Institute of Biological Resources, Incheon, Republic of Korea
| | - Iksoo Kim
- Department of Applied Biology, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
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Xu S, Guan Z, Huang Q, Xu L, Vierstraete A, Dumont HJ, Lin Q. The mitochondrial genome of Atrocalopteryx melli Ris, 1912 (Zygoptera: Calopterygidae) via Ion Torrent PGM NGS sequencing. Mitochondrial DNA B Resour 2018; 3:115-117. [PMID: 33474087 PMCID: PMC7800031 DOI: 10.1080/23802359.2017.1413307] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 12/01/2017] [Indexed: 11/03/2022] Open
Abstract
The mitochondrial genome of Atrocalopteryx melli was sequenced and assembled via Next-Generation Sequencing (NGS) and iteratively assembly process with a reference seed. This genome is 15,562 bp long and A + T biased (71%), with 37 genes arranged in common order of Odonata. All protein-coding genes are initiated by typical "ATN" codon, and 9 genes are terminated with a complete stop codon, except nad4, nad5, cox2, and cox3, which are terminated with an incomplete codon "T(aa)". The S5 intergenic spacer is absent in this genome, supporting that lacking of S5 as a specific character for damselflies. The A + T rich region of A. melli is 267 bp longer than that of A. atrata. This mitogenome provides new molecular information for understanding of A. melli and Atrocalopteryx.
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Affiliation(s)
- Shaolin Xu
- Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Zhaoying Guan
- School of Applied Biology, Shenzhen Institute of Technology, Shenzhen, China
| | - Qi Huang
- Institute of Hydrobiology, Jinan University, Guangzhou, China
| | - Lei Xu
- South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences; Guangdong Provincial Key Laboratory of Fishery Ecology and Environment; Key Laboratory of South China Sea Fishery Resources Development and Utilization, Ministry of Agriculture, Guangzhou, China
| | | | - Henri J. Dumont
- Institute of Hydrobiology, Jinan University, Guangzhou, China
- Department of Biology, University of Gent, Gent, Belgium
| | - Qiuqi Lin
- Institute of Hydrobiology, Jinan University, Guangzhou, China
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14
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Simon S, Sagasser S, Saccenti E, Brugler MR, Schranz ME, Hadrys H, Amato G, DeSalle R. Comparative transcriptomics reveal developmental turning points during embryogenesis of a hemimetabolous insect, the damselfly Ischnura elegans. Sci Rep 2017; 7:13547. [PMID: 29051502 PMCID: PMC5648782 DOI: 10.1038/s41598-017-13176-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 09/21/2017] [Indexed: 11/12/2022] Open
Abstract
Identifying transcriptional changes during embryogenesis is of crucial importance for unravelling evolutionary, molecular and cellular mechanisms that underpin patterning and morphogenesis. However, comparative studies focusing on early/embryonic stages during insect development are limited to a few taxa. Drosophila melanogaster is the paradigm for insect development, whereas comparative transcriptomic studies of embryonic stages of hemimetabolous insects are completely lacking. We reconstructed the first comparative transcriptome covering the daily embryonic developmental progression of the blue-tailed damselfly Ischnura elegans (Odonata), an ancient hemimetabolous representative. We identified a "core" set of 6,794 transcripts - shared by all embryonic stages - which are mainly involved in anatomical structure development and cellular nitrogen compound metabolic processes. We further used weighted gene co-expression network analysis to identify transcriptional changes during Odonata embryogenesis. Based on these analyses distinct clusters of transcriptional active sequences could be revealed, indicating that embryos at different development stages have their own transcriptomic profile according to the developmental events and leading to sequential reprogramming of metabolic and developmental genes. Interestingly, a major change in transcriptionally active sequences is correlated with katatrepsis (revolution) during mid-embryogenesis, a 180° rotation of the embryo within the egg and specific to hemimetabolous insects.
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Affiliation(s)
- Sabrina Simon
- Biosystematics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY, 10024, USA.
| | - Sven Sagasser
- Ludwig Institute for Cancer Research, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Stippeng 4, 6708 WE, Wageningen, The Netherlands
| | - Mercer R Brugler
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY, 10024, USA
- Biological Sciences Department, NYC College of Technology, City University of New York, 300 Jay Street, Brooklyn, New York, 11201, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Heike Hadrys
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY, 10024, USA
- ITZ, Ecology&Evolution, University of Veterinary Medicine Hanover, Buenteweg 17d, D-30559, Hannover, Germany
- Yale University, Department of Ecology & Evolutionary Biology, 165 Prospect Street, New Haven, CT, 06511, USA
| | - George Amato
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY, 10024, USA
| | - Rob DeSalle
- Sackler Institute for Comparative Genomics, American Museum of Natural History, Central Park West and 79th St., New York, NY, 10024, USA
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Zhang L, Wang XT, Wen CL, Wang MY, Yang XZ, Yuan ML. The complete mitochondrial genome of Enallagma cyathigerum (Odonata: Coenagrionidae) and phylogenetic analysis. Mitochondrial DNA B Resour 2017; 2:640-641. [PMID: 33473930 PMCID: PMC7800175 DOI: 10.1080/23802359.2017.1375879] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 09/01/2017] [Indexed: 11/17/2022] Open
Abstract
To better understand the diversity and evolution of Odonata, we sequenced and annotated the complete mitochondrial genome (mitogenome) of Enallagma cyathigerum. This mitogenome was 16,661 bp in size and encoded the typical 37 genes, i.e. 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and two ribosomal RNA genes. The nucleotide composition of the E. cyathigerum mitogenome was significantly biased toward A and T, with an A + T content of 74.2%. Eleven PCGs started with a typical ATN codon, whereas the remaining two PCGs (nad1 and nad3) used TTG as the initial codon. All the 22 tRNAs had a typical secondary cloverleaf structure. The Bayesian phylogenetic analysis based on the concatenated nucleotide sequences of 13 PCGs strongly supported the sister relationship of E. cyathigerum and two Ischnura species from the same family Coenagrionidae. The phylogenetic tree strongly supported the monophyly of each of the two suborders (Zygoptera and Anisoptera) and recovered a phylogeny of Zygoptera + (Anisoptera + Anisozygoptera).
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Affiliation(s)
- Li Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Xiao-Tong Wang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Chun-Li Wen
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Meng-Yao Wang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Xing-Zhuo Yang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, People's Republic of China
| | - Ming-Long Yuan
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, People's Republic of China
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Osigus HJ, Eitel M, Schierwater B. Deep RNA sequencing reveals the smallest known mitochondrial micro exon in animals: The placozoan cox1 single base pair exon. PLoS One 2017; 12:e0177959. [PMID: 28542197 PMCID: PMC5436844 DOI: 10.1371/journal.pone.0177959] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 05/05/2017] [Indexed: 11/18/2022] Open
Abstract
The phylum Placozoa holds a key position for our understanding of the evolution of mitochondrial genomes in Metazoa. Placozoans possess large mitochondrial genomes which harbor several remarkable characteristics such as a fragmented cox1 gene and trans-splicing cox1 introns. A previous study also suggested the existence of cox1 mRNA editing in Trichoplax adhaerens, yet the only formally described species in the phylum Placozoa. We have analyzed RNA-seq data of the undescribed sister species, Placozoa sp. H2 ("Panama" clone), with special focus on the mitochondrial mRNA. While we did not find support for a previously postulated cox1 mRNA editing mechanism, we surprisingly found two independent transcripts representing intermediate cox1 mRNA splicing stages. Both transcripts consist of partial cox1 exon as well as overlapping intron fragments. The data suggest that the cox1 gene harbors a single base pair (cytosine) micro exon. Furthermore, conserved group I intron structures flank this unique micro exon also in other placozoans. We discuss the evolutionary origin of this micro exon in the context of a self-splicing intron gain in the cox1 gene of the last common ancestor of extant placozoans.
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Affiliation(s)
- Hans-Jürgen Osigus
- ITZ, Ecology & Evolution, Stiftung Tierärztliche Hochschule Hannover, Hannover, Germany
| | - Michael Eitel
- ITZ, Ecology & Evolution, Stiftung Tierärztliche Hochschule Hannover, Hannover, Germany
| | - Bernd Schierwater
- ITZ, Ecology & Evolution, Stiftung Tierärztliche Hochschule Hannover, Hannover, Germany
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, New York, United States of America
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Herzog R, Osigus H, Feindt W, Schierwater B, Hadrys H. The complete mitochondrial genome of the emperor dragonfly Anax imperator LEACH, 1815 (Odonata : Aeshnidae) via NGS sequencing. Mitochondrial DNA B Resour 2016; 1:783-786. [PMID: 33473626 PMCID: PMC7799497 DOI: 10.1080/23802359.2016.1186523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 05/03/2016] [Indexed: 11/05/2022] Open
Abstract
Here we report the complete mitochondrial genome of the emperor dragonfly, Anax imperator (Odonata: Aeshnidae) as the first of its genus. Data were generated via next generation sequencing (NGS) and assembled using an iterative approach. The typical metazoan set of 37 genes (13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes) was detected in the same gene order as in other odonate mitogenomes. However, only three intergenic spacer regions are present in A. imperator lacking the distinct s5 spacer, which was regarded as informative feature of the odonate suborder Anisoptera (dragonflies) but absent in Zygoptera (damselflies). With 16,087 bp, it is the longest anisopteran mitogenome to date, mainly due to the long A + T-rich control region of 1291 bp.
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Affiliation(s)
- Rebecca Herzog
- Division of Ecology and Evolution, ITZ, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Hans − Jürgen Osigus
- Division of Ecology and Evolution, ITZ, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Wiebke Feindt
- Division of Ecology and Evolution, ITZ, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Bernd Schierwater
- Division of Ecology and Evolution, ITZ, University of Veterinary Medicine Hannover, Hannover, Germany
- EEB, Yale University, New Haven, CT, USA
| | - Heike Hadrys
- Division of Ecology and Evolution, ITZ, University of Veterinary Medicine Hannover, Hannover, Germany
- EEB, Yale University, New Haven, CT, USA
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18
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Feindt W, Herzog R, Osigus HJ, Schierwater B, Hadrys H. Short read sequencing assembly revealed the complete mitochondrial genome of Ischnura elegans Vander Linden, 1820 (Odonata: Zygoptera). Mitochondrial DNA B Resour 2016; 1:574-576. [PMID: 33473559 PMCID: PMC7800176 DOI: 10.1080/23802359.2016.1192510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 05/18/2016] [Indexed: 11/23/2022] Open
Abstract
Damselflies of the genus Ischnura emerge as organisms with high potential in ecological, evolutionary and developmental research at the base of flying insects. Ischnura elegans and Ischnura hastata are for example one of the few odonate species where a complete life cycle over generations can be reared under laboratory conditions. We here report the complete mitochondrial genome of Ischnura elegans as a valuable genomic resource for future eco-evo-devo studies at the base of flying insects. The genome has a total length of 15,962 bp and displays all typical features of Odonata (dragonflies and damselflies) mitochondrial genomes in gene content and order as well as A + T content. Start and stop codons of all protein-coding genes are consistent. Most interestingly, we found four intergenic spacer regions and a long A + T rich (control) region of 1196 bp, which is almost double the size of the close relative Ischnura pumilio. We assume that the adequate insert size and iterative mapping may be more efficient in assembling this duplicated and repetitive region.
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Affiliation(s)
- Wiebke Feindt
- ITZ – Forschungsstätte ‘Alter Bahnhof Schapen’ Braunschweig, University of Veterinary Medicine Hannover, Hannover/Braunschweig, Germany
| | - Rebecca Herzog
- ITZ – Forschungsstätte ‘Alter Bahnhof Schapen’ Braunschweig, University of Veterinary Medicine Hannover, Hannover/Braunschweig, Germany
| | - Hans-Jürgen Osigus
- ITZ – Forschungsstätte ‘Alter Bahnhof Schapen’ Braunschweig, University of Veterinary Medicine Hannover, Hannover/Braunschweig, Germany
| | - Bernd Schierwater
- ITZ – Forschungsstätte ‘Alter Bahnhof Schapen’ Braunschweig, University of Veterinary Medicine Hannover, Hannover/Braunschweig, Germany
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
| | - Heike Hadrys
- ITZ – Forschungsstätte ‘Alter Bahnhof Schapen’ Braunschweig, University of Veterinary Medicine Hannover, Hannover/Braunschweig, Germany
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
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