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Zhang W, Gan T, Xu T, Wang P, Tai J, Ma F. Characterization of the complete mitochondrial genome of Spirobolus grahami (Diplopoda: Spirobolidae) with phylogenetic analysis. Sci Rep 2024; 14:7541. [PMID: 38555348 PMCID: PMC10981682 DOI: 10.1038/s41598-024-57421-3] [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: 07/28/2023] [Accepted: 03/18/2024] [Indexed: 04/02/2024] Open
Abstract
Diplopoda is one of the most diverse and important groups of soil arthropods, but little research has been done on their phylogenetic relationship and evolution. Here, we sequenced and annotated the complete mitochondrial genomes of Spirobolus grahami. The total mitogenome of S. grahami was typical circular, double-stranded molecules, with 14,875 bp in length, including 13 protein-coding genes, 22 tRNAs, two rRNAs, and one control region. Base composition analysis suggested that the mitochondrial sequences were biased toward A and T, with A + T content of 58.68%. The mitogenomes of S. grahami exhibited negative AT and positive GC skews. Most of the 13 PCGs had ATN as the start codon, except COX1 start with CGA, and most PCGs ended with the T stop codon. The dN/dS values for most PCGs were lower than 1, suggesting that purifying selection was likely the main driver of mitochondrial PCG evolution. Phylogenetic analyses based on 13 PCGs using BI and ML methods support the classification of genus Spirobolus and Tropostreptus. Glomeridesmus spelaeus is distantly related to the other Diplopoda species.
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Affiliation(s)
- Wenwen Zhang
- Research Center for Biodiversity Conservation and Biosafety/State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains/Biodiversity Comprehensive Observation Station for Wuyi Mountains/State Environmental Protection Key Laboratory on Biosafety, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing, 210042, China
| | - Tianyi Gan
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Tangjun Xu
- College of Life Science, Nanjing Forestry University, Nanjing, 210037, China
| | - Peng Wang
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jingzhe Tai
- College of Life Science, Nanjing Forestry University, Nanjing, 210037, China
| | - Fangzhou Ma
- Research Center for Biodiversity Conservation and Biosafety/State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains/Biodiversity Comprehensive Observation Station for Wuyi Mountains/State Environmental Protection Key Laboratory on Biosafety, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of China, Nanjing, 210042, China.
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Zhang G, Xu T, Chen Y, Xu W, Wang Y, Li Y, Zhu F, Liu H, Ruan H. Complete Mitochondrial Genomes of Nedyopus patrioticus: New Insights into the Color Polymorphism of Millipedes. Curr Issues Mol Biol 2024; 46:2514-2527. [PMID: 38534775 DOI: 10.3390/cimb46030159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/04/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024] Open
Abstract
There has been debate about whether individuals with different color phenotypes should have different taxonomic status. In order to determine whether the different color phenotypes of Nedyopus patrioticus require separate taxonomic status or are simply synonyms, here, the complete mitochondrial genomes (mitogenomes) of two different colored N. patrioticus, i.e., red N. patrioticus and white N. patrioticus, are presented. The two mitogenomes were 15,781 bp and 15,798 bp in length, respectively. Each mitogenome contained 13 PCGs, 19 tRNAs, 2 rRNAs, and 1 CR, with a lack of trnI, trnL2, and trnV compared to other Polydesmida species. All genes were located on a single strand in two mitogenomes. Mitochondrial DNA analyses revealed that red N. patrioticus and white N. patrioticus did not show clear evolutionary differences. Furthermore, no significant divergence was discovered by means of base composition analysis. As a result, we suggest that white N. patrioticus might be regarded as a synonym for red N. patrioticus. The current findings confirmed the existence of color polymorphism in N. patrioticus, which provides exciting possibilities for future research. It is necessary to apply a combination of molecular and morphological methods in the taxonomy of millipedes.
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Affiliation(s)
- Gaoji Zhang
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Tangjun Xu
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Yukun Chen
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Wei Xu
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Yinuo Wang
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Yuanyuan Li
- College of Ecology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Fuyuan Zhu
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Hongyi Liu
- College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
- College of Ecology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Honghua Ruan
- College of Ecology and the Environment, Nanjing Forestry University, Nanjing 210037, China
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Zhang G, Gao M, Chen Y, Wang Y, Gan T, Zhu F, Liu H. The First Complete Mitochondrial Genome of the Genus Litostrophus: Insights into the Rearrangement and Evolution of Mitochondrial Genomes in Diplopoda. Genes (Basel) 2024; 15:254. [PMID: 38397243 PMCID: PMC10888367 DOI: 10.3390/genes15020254] [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: 01/02/2024] [Revised: 02/13/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024] Open
Abstract
This study presents the complete mitochondrial genome (mitogenome) of Litostrophus scaber, which is the first mitogenome of the genus Litostrophus. The mitogenome is a circular molecule with a length of 15,081 bp. The proportion of adenine and thymine (A + T) was 69.25%. The gene ND4L used TGA as the initiation codon, while the other PCGs utilized ATN (A, T, G, C) as the initiation codons. More than half of the PCGs used T as an incomplete termination codon. The transcription direction of the L. scaber mitogenome matched Spirobolus bungii, in contrast to most millipedes. Novel rearrangements were found in the L. scaber mitogenome: trnQ -trnC and trnL1- trnP underwent short-distance translocations and the gene block rrnS-rrnL-ND1 moved to a position between ND4 and ND5, resulting in the formation of a novel gene order. The phylogenetic analysis showed that L. scaber is most closely related to S. bungii, followed by Narceus magnum. These findings enhance our understanding of the rearrangement and evolution of Diplopoda mitogenomes.
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Affiliation(s)
- Gaoji Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (G.Z.); (M.G.); (Y.C.); (Y.W.); (F.Z.)
| | - Ming Gao
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (G.Z.); (M.G.); (Y.C.); (Y.W.); (F.Z.)
| | - Yukun Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (G.Z.); (M.G.); (Y.C.); (Y.W.); (F.Z.)
| | - Yinuo Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (G.Z.); (M.G.); (Y.C.); (Y.W.); (F.Z.)
| | - Tianyi Gan
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, China;
| | - Fuyuan Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (G.Z.); (M.G.); (Y.C.); (Y.W.); (F.Z.)
| | - Hongyi Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China; (G.Z.); (M.G.); (Y.C.); (Y.W.); (F.Z.)
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A Rearrangement of the Mitochondrial Genes of Centipedes (Arthropoda, Myriapoda) with a Phylogenetic Analysis. Genes (Basel) 2022; 13:genes13101787. [DOI: 10.3390/genes13101787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/16/2022] Open
Abstract
Due to the limitations of taxon sampling and differences in results from the available data, the phylogenetic relationships of the Myriapoda remain contentious. Therefore, we try to reconstruct and analyze the phylogenetic relationships within the Myriapoda by examining mitochondrial genomes (the mitogenome). In this study, typical circular mitogenomes of Mecistocephalus marmoratus and Scolopendra subspinipes were sequenced by Sanger sequencing; they were 15,279 bp and 14,637 bp in length, respectively, and a control region and 37 typical mitochondrial genes were annotated in the sequences. The results showed that all 13 PCGs started with ATN codons and ended with TAR codons or a single T; what is interesting is that the gene orders of M. marmoratus have been extensively rearranged compared with most Myriapoda. Thus, we propose a simple duplication/loss model to explain the extensively rearranged genes of M. marmoratus, hoping to provide insights into mitogenome rearrangement events in Myriapoda. In addition, our mitogenomic phylogenetic analyses showed that the main myriapod groups are monophyletic and supported the combination of the Pauropoda and Diplopoda to form the Dignatha. Within the Chilopoda, we suggest that Scutigeromorpha is a sister group to the Lithobiomorpha, Geophilomorpha, and Scolopendromorpha. We also identified a close relationship between the Lithobiomorpha and Geophilomorpha. The results also indicate that the mitogenome can be used as an effective mechanism to understand the phylogenetic relationships within Myriapoda.
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Nielsen M, Margaryan A, Nielsen TL, Enghoff H, Allentoft ME. Complete mitochondrial genomes from museum specimens clarify millipede evolution in the Eastern Arc Mountains. Zool J Linn Soc 2022. [DOI: 10.1093/zoolinnean/zlac058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
The Eastern Arc Mountains in Tanzania represent a hotspot for biological diversity of global importance. The level of endemism is high, and Eastern Arc biodiversity has been studied extensively in vertebrates and invertebrates, including millipedes. However, millipede evolution is vastly understudied at the molecular level. Therefore, we used next-generation ‘shotgun’ sequencing to obtain mitochondrial genome sequences of 26 museum specimens, representing six genera and 12 millipede species found across the Eastern Arc Mountains. Bayesian and maximum likelihood methods yielded consistent topologies with high node support, confirming a high level of congruence between molecular and morphological analyses. The only exception was a Tropostreptus sigmatospinus individual from Zanzibar, which was placed outside an otherwise monophyletic group consisting of mainland individuals of the same assumed species. For two species with a distribution across several mountain blocks (Tropostreptus sigmatospinus and Tropostreptus hamatus), each mountain population represents a distinct monophyletic lineage. In contrast, we also observe that distinct species exist sympatrically in the same montane forests, indicative of older speciation events that are not defined by current forest distribution. Our results are important for understanding speciation mechanisms in montane rain forests and highlight that ethanol-preserved invertebrates exhibit a tremendous potential for genomic analyses.
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Affiliation(s)
- Martin Nielsen
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen , Copenhagen , Denmark
- Arctic Station, Faculty of Science, University of Copenhagen , Disko Island , Greenland
| | - Ashot Margaryan
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen , Copenhagen , Denmark
| | - Tejs Lind Nielsen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen , Copenhagen , Denmark
| | - Henrik Enghoff
- Natural History Museum of Denmark, University of Copenhagen , Copenhagen , Denmark
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen , Copenhagen , Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University , Perth, WA , Australia
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The Complete Mitochondrial Genome of Spirobolus bungii (Diplopoda, Spirobolidae): The First Sequence for the Genus Spirobolus. Genes (Basel) 2022; 13:genes13091587. [PMID: 36140755 PMCID: PMC9498733 DOI: 10.3390/genes13091587] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/14/2022] [Accepted: 09/01/2022] [Indexed: 11/21/2022] Open
Abstract
Millipedes (Diplopoda) comprise one of the most important groups of large soil arthropods in terrestrial ecosystems; however, their phylogenetic relationships are poorly understood. Herein, the mitochondrial genome (mitogenome) of Spirobolus bungii was sequenced and annotated, which was 14,879 bp in size and included 37 typical mitochondrial genes (13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs)). Most of the 13 PCGs had ATN (AT/A/T/G) as the start codon except for COX1, which used CGA, and most PCGs ended with the T end codon. By comparing the gene arrangements of the mitogenomes among Diplopoda species, rearrangement occurred between and within orders. In contrast to Narceus annularus, the mitogenome genes of S. bungii had consistent orders but were transcribed in completely opposite directions, which was a novel finding in Spirobolidae. Moreover, the phylogenetic relationships within Diplopoda, which were based on the sequences of 13 PCGs, showed that S. bungii was clustered with N. annularus, followed by Abacion magmun. This indicated that there might be a close relationship between Callipodida and Spirobolida. These results could contribute to further studies on the genetics and evolutionary processes of S. bungii and other Diplopoda species.
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Ding J, Lan H, Xu W, Chen Y, Wu H, Jiang H, Wang J, Wu Y, Liu H. Two complete mitochondrial genomes in Scolopendra and a comparative analysis of tRNA rearrangements in centipedes. Mol Biol Rep 2022; 49:6173-6180. [PMID: 35411482 DOI: 10.1007/s11033-022-07409-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 03/21/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Centipedes are one of the oldest terrestrial arthropods belonging to the sub phylum Myriapoda. With the expansion of our understanding of the application of the two centipedes Scolopendra morsitans and Scolopendra hainanum, belonging to the order Scolopendromorpha, an exhaustive classification was required. Although consensus has been reached on the phylogeny of Chilopoda based on morphological traits, recent analyses based on molecular data exhibited differences in results. METHODS AND RESULTS The mitochondrial genome sequences of S. morsitans and S. hainanum were obtained by next-generation sequencing. S. morsitans contains 13 PCGs, two rRNAs, 11 tRNAs, and one CR. whereas S. hainanum contains 12 PCGs, of which ATP8 remains unpredicted, two rRNAs, 14 tRNAs, and one CR. An obvious tRNA rearrangement was found in the genus Scolopendra. S. morsitans exhibited a loss of trnW, trnC, trnI, trnK, trnD, trnA, trnN, trnQ, trnF, trnT, trnS, trnL, and trnV, and a repeat of trnR and trnL. S. hainanum exhibited a loss of trnQ, trnC, trnW, trnI, trnD, trnQ, trnP, and trnV. Phylogenetic analyses of centipedes based on 12 PCGs supported the sister relationship between the orders Geophilomorpha and Lithobiomorpha and a close relationship between Scolopendra dehaani and S. hainanum. CONCLUSIONS The new mitogenomes determined in this study provide new genomic resources for gene rearrangements and contribute to the understanding of the evolution of gene rearrangement in Chilopoda.
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Affiliation(s)
- Jiayu Ding
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, Jiangsu Province, People's Republic of China
| | - Hong Lan
- Department of Agriculture, Zhejiang Open University, Hangzhou, 310030, China
| | - Wei Xu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, Jiangsu Province, People's Republic of China
| | - Yining Chen
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, Jiangsu Province, People's Republic of China
| | - Han Wu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, Jiangsu Province, People's Republic of China
| | - Haoming Jiang
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, Jiangsu Province, People's Republic of China
| | - Jiachen Wang
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, Jiangsu Province, People's Republic of China
| | - Yongbo Wu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, Jiangsu Province, People's Republic of China
| | - Hongyi Liu
- The Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, No.159 Longpan Road, Nanjing, 210037, Jiangsu Province, People's Republic of China.
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Cui Y, Yang L, Ding Y, Sun Y, Wang J, Xi Y, Han M, Yang L, Han Z, Wang Y. Complete chloroplast genome characterization and phylogenetic analysis of Clematis mandshurica (Ranunculaceae). Mitochondrial DNA B Resour 2022; 7:822-824. [PMID: 35573590 PMCID: PMC9103393 DOI: 10.1080/23802359.2022.2073839] [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: 10/26/2021] [Accepted: 05/02/2022] [Indexed: 11/04/2022] Open
Abstract
The complete chloroplast genome sequence of Clematis mandshurica Ruprecht (1867), a specie of the Ranunculaceae family, and its phylogenetic relationships with other species have been reported in this study. The complete chloroplast genome of C. mandshurica is 159,563 bp in length, including a large single-copy (LSC) region of 79,360 bp, a small single-copy (SSC) region of 18,121 bp, and a pair of identical inverted repeat regions (IRs) of 31,041 bp. The genome encodes a total of 132 genes, including 90 protein-coding genes, 34 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The phylogenetic analysis reveals that C. mandshurica was found to be closest to Clematis taeguensis. The complete chloroplast genome of C. mandshurica contributes to a better understanding of phylogenetic relationships among Clematis species.
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Affiliation(s)
- Yi Cui
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
- State Key Laboratory of JLP-MOST for Ecological Restoration and Ecosystem Management, Changchun, China
| | - Lihua Yang
- College of Life Science, Changchun Sci-Tech University, Changchun, China
| | - Yanzhe Ding
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
- State Key Laboratory of JLP-MOST for Ecological Restoration and Ecosystem Management, Changchun, China
| | - Yingxin Sun
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
- State Key Laboratory of JLP-MOST for Ecological Restoration and Ecosystem Management, Changchun, China
| | - Jiao Wang
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
- State Key Laboratory of JLP-MOST for Ecological Restoration and Ecosystem Management, Changchun, China
| | - Yunfei Xi
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
- State Key Laboratory of JLP-MOST for Ecological Restoration and Ecosystem Management, Changchun, China
| | - Mei Han
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
- State Key Laboratory of JLP-MOST for Ecological Restoration and Ecosystem Management, Changchun, China
| | - Limin Yang
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
- State Key Laboratory of JLP-MOST for Ecological Restoration and Ecosystem Management, Changchun, China
| | - Zhongming Han
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
- State Key Laboratory of JLP-MOST for Ecological Restoration and Ecosystem Management, Changchun, China
| | - Yunhe Wang
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, China
- State Key Laboratory of JLP-MOST for Ecological Restoration and Ecosystem Management, Changchun, China
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Zuo Q, Zhang Z, Shen Y. Novel mitochondrial gene rearrangements pattern in the millipede Polydesmus sp. GZCS-2019 and phylogenetic analysis of the Myriapoda. Ecol Evol 2022; 12:e8764. [PMID: 35356579 PMCID: PMC8948135 DOI: 10.1002/ece3.8764] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/29/2022] [Accepted: 03/10/2022] [Indexed: 11/29/2022] Open
Abstract
The subphylum Myriapoda included four extant classes (Chilopoda, Symphyla, Diplopoda, and Pauropoda). Due to the limitation of taxon sampling, the phylogenetic relationships within Myriapoda remained contentious, especially for Diplopoda. Herein, we determined the complete mitochondrial genome of Polydesmus sp. GZCS-2019 (Myriapoda: Polydesmida) and the mitochondrial genomes are circular molecules of 15,036 bp, with all genes encoded on + strand. The A+T content is 66.1%, making the chain asymmetric, and exhibits negative AT-skew (-0.236). Several genes rearrangements were detected and we propose a new rearrangement model: "TD (N\R) L + C" based on the genome-scale duplication + (non-random/random) loss + recombination. Phylogenetic analyses demonstrated that Chilopoda and Symphyla both were monophyletic group, whereas Pauropoda was embedded in Diplopoda to form the Dignatha. Divergence time showed the first split of Myriapoda occurred between the Chilopoda and other classes (Wenlock period of Silurian). We combine phylogenetic analysis, divergence time, and gene arrangement to yield valuable insights into the evolutionary history and classification relationship of Myriapoda and these results support a monophyletic Progoneata and the relationship (Chilopoda + (Symphyla + (Diplopoda + Pauropoda))) within myriapod. Our results help to better explain the gene rearrangement events of the invertebrate mitogenome and lay the foundation for further phylogenetic study of Myriapoda.
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Affiliation(s)
- Qing Zuo
- Key Laboratory of Eco‐Environments in Three Gorges Reservoir Region (Ministry of Education)School of Life SciencesSouthwest UniversityChongqingChina
| | - Zhisheng Zhang
- Key Laboratory of Eco‐Environments in Three Gorges Reservoir Region (Ministry of Education)School of Life SciencesSouthwest UniversityChongqingChina
| | - Yanjun Shen
- Chongqing Key Laboratory of Animal BiologySchool of Life SciencesChongqing Normal UniversityChongqingChina
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Joo S, Lee J, Lee DY, Xi H, Park J. The complete mitochondrial genome of the millipede Epanerchodus koreanus Verhoeff, 1937 collected in limestone cave of Korea (Polydesmidae: Polydesmida). Mitochondrial DNA B Resour 2020; 5:3845-3847. [PMID: 33426298 PMCID: PMC7759294 DOI: 10.1080/23802359.2020.1840933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/18/2020] [Indexed: 01/22/2023] Open
Abstract
We have determined the second mitochondrial genome of Epanerchodus koreanus Verhoeff, 1937 collected in limestone cave of Korea. The circular mitochondrial genome of E. koreanus is 15,581 bp long. It includes 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. Its gene order was different from the rest three Polydesmida mitochondrial genomes, resulted from relocation of tRNAs, rRNAs, and ND1. The base composition was AT-biased (75.1%). Phylogenetic trees displayed phylogenetic relationship, which is congruent to previous study, except Sphaerotheriidae sp. clustering with Helminthomorpha.
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Affiliation(s)
- Sungbae Joo
- Division of Ecological Information, National Institute of Ecology, Seocheon, Republic of Korea
| | - Jungmo Lee
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Da-Young Lee
- Division of Ecological Information, National Institute of Ecology, Seocheon, Republic of Korea
| | - Hong Xi
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Jongsun Park
- InfoBoss Inc., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
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Hu C, Wang S, Huang B, Liu H, Xu L, Zhigang Hu, Liu Y. The complete mitochondrial genome sequence of Scolopendra mutilans L. Koch, 1878 (Scolopendromorpha, Scolopendridae), with a comparative analysis of other centipede genomes. Zookeys 2020; 925:73-88. [PMID: 32390741 PMCID: PMC7197263 DOI: 10.3897/zookeys.925.47820] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/20/2020] [Indexed: 02/07/2023] Open
Abstract
Scolopendramutilans L. Koch, 1878 is an important Chinese animal with thousands of years of medicinal history. However, the genomic information of this species is limited, which hinders its further application. Here, the complete mitochondrial genome (mitogenome) of S.mutilans was sequenced and assembled by next-generation sequencing. The genome is 15,011 bp in length, consisting of 13 protein-coding genes (PCGs), 14 tRNA genes, and two rRNA genes. Most PCGs start with the ATN initiation codon, and all PCGs have the conventional stop codons TAA and TAG. The S.mutilans mitogenome revealed nine simple sequence repeats (SSRs), and an obviously lower GC content compared with other seven centipede mitogenomes previously sequenced. After analysis of homologous regions between the eight centipede mitogenomes, the S.mutilans mitogenome further showed clear genomic rearrangements. The phylogenetic analysis of eight centipedes using 13 conserved PCG genes was finally performed. The phylogenetic reconstructions showed Scutigeromorpha as a separate group, and Scolopendromorpha in a sister-group relationship with Lithobiomorpha and Geophilomorpha. Collectively, the S.mutilans mitogenome provided new genomic resources, which will improve its medicinal research and applications in the future.
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Affiliation(s)
| | | | | | | | | | - Zhigang Hu
- College of Pharmacy.,Hubei University of Chinese Medicine, No. 1 Huangjiahu West Road, Hongshan District, Wuhan, China
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Yang C, Li XJ, Yuan H, Shen J, Yang MX. Complete mitochondrial genome of Sellanucheza jaegeri Golovatch, 2013 by next generation sequencing (Polydesmida: Paradoxosomatidae) and phylogenetic analysis in Diplopoda. Mitochondrial DNA B Resour 2018; 3:603-604. [PMID: 33474258 PMCID: PMC7799721 DOI: 10.1080/23802359.2018.1473729] [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] [Indexed: 11/06/2022] Open
Abstract
The mitogenome of Sellanucheza jaegeri was 15,623 bp long, revealed the same gene order to that of typical Polydesmida. Both the tRNASer(AGN) and tRNASer(UCN) lacked the DHU arms. No tandem repeat was found in two control regions. Phylogenetic analysis indicated that Sphaerotheriida was so antiquity that divided out earlier than others. We supported that Polydesmida had a relatively systematic affinity between Julida and Playtdesmida, and suggested that the interordinal phylogenetic relationships within Diplopoda should be further investigated.
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Affiliation(s)
- Chao Yang
- Shaanxi Institute of Zoology, Xi’an, China
- School of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Xue-Juan Li
- School of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Hao Yuan
- School of Life Sciences, Shaanxi Normal University, Xi’an, China
| | - Jian Shen
- Shaanxi Institute of Zoology, Xi’an, China
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