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Guo ZQ, Gao YJ, Chen YX, Zhan LM, Storey KB, Yu DN, Zhang JY. Comparative Mitogenome of Phylogenetic Relationships and Divergence Time Analysis within Potamanthidae (Insecta: Ephemeroptera). INSECTS 2024; 15:357. [PMID: 38786913 PMCID: PMC11122660 DOI: 10.3390/insects15050357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/11/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
Potamanthidae belongs to the superfamily Ephemeroidea but has no complete mt genome released in the NCBI (except for two unchecked and one partial mt genome). Since the sister clade to Potamanthidae has always been controversial, we sequenced seven mt genomes of Potamanthidae (two species from Rhoenanthus and five species from Potamanthus) in order to rebuild the phylogenetic relationships of Potamanthidae in this study. The divergence time of Potamanthidae was also investigated by utilizing five fossil calibration points because of the indeterminate origin time. In addition, because Rhoenanthus coreanus and Potamanthus luteus are always in low-temperature environments, we aimed to explore whether these two species were under positive selection at the mt genome level. Amongst the 13 PCGs, CGA was used as the start codon in COX1, whereas other genes conformed to initiating with an ATN start codon. From this analysis, UUA (L), AUU (I), and UUU (F) had the highest usage. Furthermore, the DHU arm was absent in the secondary structure of S1 in all species. By combining the 13 PCGs and 2 rRNAs, we reconstructed the phylogenetic relationship of Potamanthidae within Ephemeroptera. The monophyly of Potamanthidae and the monophyly of Rhoenanthus and Potamanthus were supported in the results. The phylogenetic relationship of Potamanthidae + (Ephemeridae + Polymitarcyidae) was also recovered with a high prior probability. The divergence times of Potamanthidae were traced to be 90.44 Mya (95% HPD, 62.80-121.74 Mya), and the divergence times of Rhoenanthus and Potamanthus originated at approximately 64.77 Mya (95% HPD, 43.82-88.68 Mya), thus belonging to the late Pliocene Epoch or early Miocene Epoch. In addition, the data indicated that R. coreanus was under negative selection and that ATP8 and ND2 in Potamanthidae had a high evolutionary rate.
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Affiliation(s)
- Zhi-Qiang Guo
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Ya-Jie Gao
- School of Bioengineering, Aksu Vocational Technical College, Aksu 843000, China
| | - Yu-Xin Chen
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Le-Mei Zhan
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Dan-Na Yu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Covnservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Jia-Yong Zhang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Covnservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
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Li K, Yu SW, Hu H, Feng YF, Storey KB, Ma Y, Zhang JY, Yu DN. The Phylogenetic Relationship of Lamiinae (Coleoptera: Cerambycidae) Using Mitochondrial Genomes. Genes (Basel) 2023; 15:13. [PMID: 38275595 PMCID: PMC10815127 DOI: 10.3390/genes15010013] [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: 11/05/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
Lamiinae is the largest subfamily of the Cerambycidae (longhorn beetles), with approximately 21,863 described species. Previous phylogenetic studies of Lamiinae showed that this subfamily was monophyletic, but the relationship between the tribes of Lamiinae is still controversial. Partial molecular data and species morphological characteristics are not sufficient to resolve species phylogenetic studies perfectly. At the same time, the full mitochondrial genome contains more comprehensive genetic data. Benefiting from the development of next-generation sequencing (NGS), mitochondrial genomes can be easily acquired and used as reliable molecular markers to investigate phylogenetic relationships within Cerambycidae. Using NGS technology, we obtained 11 mitochondrial genome sequences of Lamiinae species. Based on this newly generated mitochondrial genome dataset matrix, we reconstructed the phylogeny of Lamiinae. The Bayesian Inference and Maximum Likelihood analyses strongly support the monophyly of four tribes (Lamiini, Batocerini, Mesosini, and Saperdini), whereas the tribe Acanthocinini was identified as paraphyletic. Other mitochondrial structural features were also observed: the start codon in the nad1 gene of all 11 mitochondrial genomes is TTG; 17-22 bp intergenic spacers (IGS) with a 'TACTA' motif were found between trnS2 and nad1. Moreover, two long IGS were found in Mesosa myops and Batocera sp. Tandem repeats were found in the IGS of Batocera sp.
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Affiliation(s)
- Ke Li
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
| | - Sheng-Wu Yu
- Longquan Protection Center of Qianjiangyuan-Baishanzu National Park, Lishui 323700, China
| | - Hao Hu
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
| | - Yu-Feng Feng
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
| | - Kenneth B. Storey
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Yue Ma
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Jia-Yong Zhang
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Dan-Na Yu
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
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Liu J, Yu J, Yu X, Bi W, Yang H, Xue F, Zhang G, Zhang J, Yi D, Ma R, Zhou Y, Lan G, Gu J, Wu W, Li Z, Qi G. Complete Mitogenomes of Ticks Ixodes acutitarsus and Ixodes ovatus Parasitizing Giant Panda: Deep Insights into the Comparative Mitogenomic and Phylogenetic Relationship of Ixodidae Species. Genes (Basel) 2022; 13:2049. [PMID: 36360286 PMCID: PMC9691169 DOI: 10.3390/genes13112049] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/24/2022] [Accepted: 11/03/2022] [Indexed: 04/11/2024] Open
Abstract
Ticks rank second in the world as vectors of disease. Tick infestation is one of the factors threatening the health and survival of giant pandas. Here, we describe the mitogenomes of Ixodes acutitarsus and Ixodes ovatus parasitizing giant pandas, and perform comparative and phylogenetic genomic analyses on the newly sequenced and other available mitogenomes of hard ticks. All six newly determined mitogenomes contain a typical gene component and share an ancient Arthropoda gene arrangement pattern. Our study suggests that I. ovatus is a species complex with high genetic divergence, indicating that different clades of I. ovatus represent distinct species. Comparative mitogenomic analyses show that the average A + T content of Ixodidae mitogenomes is 78.08%, their GC-skews are strongly negative, while AT-skews fluctuate around 0. A large number of microsatellites are detected in Ixodidae mitogenomes, and the main microsatellite motifs are mononucleotide A and trinucleotide AAT. We summarize five gene arrangement types, and identify the trnY-COX1-trnS1-COX2-trnK-ATP8-ATP6-COX3-trnG fragment is the most conserved region, whereas the region near the control region is the rearrangement hotspot in Ixodidae mitogenomes. The phylogenetic trees based on 15 genes provide a very convincing relationship (Ixodes + (Robertsicus + ((Bothriocroton + Haemaphysalis) + (Amblyomma + (Dermacentor + (Rhipicentor + (Hyalomma + Rhipicephalus))))))) with very strong supports. Remarkably, Archaeocroton sphenodonti is embedded in the Haemaphysalis clade with strong supports, resulting in paraphyly of the Haemaphysalis genus, so in-depth morphological and molecular studies are essential to determine the taxonomic status of A. sphenodonti and its closely related species. Our results provide new insights into the molecular phylogeny and evolution of hard ticks, as well as basic data for population genetics assessment and efficient surveillance and control for the giant panda-infesting ticks.
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Affiliation(s)
- Jiabin Liu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Jiaojiao Yu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Xiang Yu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Wenlei Bi
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Hong Yang
- Management Center of Daxiangling Nature Reserve in Yingjing County, Ya’an 625200, China
| | - Fei Xue
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Gexiang Zhang
- College of Computer Science and Cyber Security, Chengdu University of Technology, Chengdu 610059, China
| | - Jindong Zhang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China
| | - Dejiao Yi
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Rui Ma
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Yanshan Zhou
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Guanwei Lan
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China
| | - Jiang Gu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Wei Wu
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Zusheng Li
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu 610081, China
| | - Guilan Qi
- Chengdu Academy of Agriculture and Forestry Sciences, Chengdu 611130, China
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