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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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