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Yan ZT, Tang XY, Yang D, Fan ZH, Luo ST, Chen B. Phylogenetic and Comparative Genomics Study of Papilionidae Based on Mitochondrial Genomes. Genes (Basel) 2024; 15:964. [PMID: 39062743 PMCID: PMC11275471 DOI: 10.3390/genes15070964] [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: 06/12/2024] [Revised: 07/19/2024] [Accepted: 07/20/2024] [Indexed: 07/28/2024] Open
Abstract
Most species of Papilionidae are large and beautiful ornamental butterflies. They are recognized as model organisms in ecology, evolutionary biology, genetics, and conservation biology but present numerous unresolved phylogenetic problems. Complete mitochondrial genomes (mitogenomes) have been widely used in phylogenetic studies of butterflies, but mitogenome knowledge within the family Papilionidae is limited, and its phylogeny is far from resolved. In this study, we first report the mitogenome of Byasa confusa from the subfamily Papilioninae of Papilionidae. The mitogenome of B. confusa is 15,135 bp in length and contains 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and an AT-rich control region (CR), closely mirroring the genomic structure observed in related butterfly species. Comparative analysis of 77 Papilionidae mitogenomes shows gene composition and order to be identical to that of an ancestral insect, and the AT bias, Ka/Ks, and relative synonymous codon usage (RSCU) are all consistent with that of other reported butterfly mitogenomes. We conducted phylogenetic analyses using maximum-likelihood (ML) and Bayesian-inference (BI) methods, with 77 Papilionidae species as ingroups and two species of Nymphalidae and Lycaenidae as outgroups. The phylogenetic analysis indicated that B. confusa were clustered within Byasa. The phylogenetic trees show the monophyly of the subfamily Papilioninae and the tribes Leptocircini, Papilionini, and Troidini. The data supported the following relationships in tribe level on Papilioninae: (((Troidini + Papilionini) + Teinopalpini) + Leptocircini). The divergence time analysis suggests that Papilionidae originated in the late Creataceous. Overall, utilizing the largest number of Papilionidae mitogenomes sequenced to date, with the current first exploration in a phylogenetic analysis on Papilionidae (including four subfamilies), this study comprehensively reveals the mitogenome characteristics and mitogenome-based phylogeny, providing information for further studies on the mitogenome, phylogeny, evolution, and taxonomic revision of the Papilionidae family.
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Affiliation(s)
- Zhen-Tian Yan
- Chongqing Key Laboratory of Vector Control and Utilization, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Xiao-Ya Tang
- Chongqing Key Laboratory of Vector Control and Utilization, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Dong Yang
- Chongqing Key Laboratory of Vector Control and Utilization, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Zhen-Huai Fan
- Chongqing Key Laboratory of Vector Control and Utilization, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Si-Te Luo
- School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Bin Chen
- Chongqing Key Laboratory of Vector Control and Utilization, Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
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Wu YF, Yang WH, Jin A, Dong Y, Wang JJ, Zhu LX. Complete mitochondrial genome data and phylogenetic analysis of Papilio macilentus Janson, 1877 (Lepidoptera: Papilionoidea: Papilionidae). Mitochondrial DNA B Resour 2024; 9:631-635. [PMID: 38751733 PMCID: PMC11095290 DOI: 10.1080/23802359.2024.2351536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/30/2024] [Indexed: 05/18/2024] Open
Abstract
In the present study, the complete mitochondrial genome (mitogenome) of the Papilio macilentus (Lepidoptera: Papilionoidea: Papilionidae) was sequenced by next-generation sequencing method. The mitochondrial genome is a circular DNA molecule of 15,264 bp in size with 80.7% AT content, including 37 genes (13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes), and a long non-coding region (Control region). All protein-coding genes are initiated by ATN codons, and terminated with TAA, TAG, or single T. All tRNAs can be folded into common clover leaf secondary structure, except trn-S1. Phylogenetic analyses based on 13 protein-coding genes and 2 rRNA genes using maximum likelihood and Bayesian inference confirmed that P. macilentus and Papilio memnon are clustered into a clade, and revealed the relationships between Papilionini, Troidini, Teinopaippini and Leptocircini.
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Affiliation(s)
- Yun-Fei Wu
- College of Biology and Food Engineering, Chuzhou University, Chuzhou, China
| | - Wei-Hao Yang
- College of Biology and Food Engineering, Chuzhou University, Chuzhou, China
| | - Ai Jin
- College of Biology and Food Engineering, Chuzhou University, Chuzhou, China
| | - Yan Dong
- College of Biology and Food Engineering, Chuzhou University, Chuzhou, China
| | - Jia-Jia Wang
- College of Biology and Food Engineering, Chuzhou University, Chuzhou, China
| | - Li-Xin Zhu
- College of Biology and Food Engineering, Chuzhou University, Chuzhou, China
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Miga M, Jahari PNS, Vei Siang C, Kamarudin KR, Shamsir MS, Tokiman L, Parimannan S, Rajandas H, Mohamed F, Salleh FM. The complete mitochondrial genome data of the Common Rose butterfly, Pachliopta aristolochiae (Lepidoptera, Papilionoidea, Papilionidae) from Malaysia. Data Brief 2022; 40:107740. [PMID: 35141362 PMCID: PMC8813591 DOI: 10.1016/j.dib.2021.107740] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/24/2022] Open
Abstract
Here, we present the complete mitochondrial genome of Pachliopta aristolochiae, a Common Rose butterfly from Malaysia. The sequence was generated using Illumina NovaSeq 6000 sequencing platform. The mitogenome is 15,235bp long, consisting of 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and two D-loop regions. The total base composition was (81.6%), with A (39.3%), T (42.3%), C (11.0%) and G (7.3%). The gene order of the three tRNAs was trnM-trnI-trnQ, which differs from the ancestral insect gene order trnI-trnQ-trnM. Phylogenetic tree analysis revealed that the sequenced Pachliopta aristolochiae in this data is closely related to Losaria neptunus (NC 037868), with highly supported ML and BI analysis. The data presented in this work can provide useful resources for other researchers to study deeper into the phylogenetic relationships of Lepidoptera and the diversification of the Pachliopta species. Also, as one of the bioindicator species, this data can be used to assess environmental changes in the terrestrial and aquatic ecosystem via enviromental DNA approahes. The mitogenome of Pachliopta aristolochiae is available in GenBank under the accession number MZ781228.
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Affiliation(s)
- Marylin Miga
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor 81310, Malaysia
| | - Puteri Nur Syahzanani Jahari
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor 81310, Malaysia
| | - Chan Vei Siang
- School of Computing, Faculty of Engineering, Universiti Teknologi Malaysia, Johor Bahru, Johor 81310, Malaysia
| | - Kamarul Rahim Kamarudin
- Centre of Research for Sustainable Uses of Natural Resources (SUNR), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Johor 84600, Malaysia
| | - Mohd Shahir Shamsir
- Centre of Research for Sustainable Uses of Natural Resources (SUNR), Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Johor 84600, Malaysia
| | - Lili Tokiman
- Johor National Parks Corporation, Kota Iskandar, Iskandar Puteri, Johor 79575, Malaysia
| | - Sivachandran Parimannan
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Bedong, Kedah 08100, Malaysia.,Deakin Genomics Centre, School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Waurn Ponds Campus, Victoria 3216, Australia
| | - Heera Rajandas
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Bedong, Kedah 08100, Malaysia.,Deakin Genomics Centre, School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Waurn Ponds Campus, Victoria 3216, Australia
| | - Farhan Mohamed
- School of Computing, Faculty of Engineering, Universiti Teknologi Malaysia, Johor Bahru, Johor 81310, Malaysia
| | - Faezah Mohd Salleh
- Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, Johor Bahru, Johor 81310, Malaysia.,Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Bedong, Kedah 08100, Malaysia
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Wu Z, Chao-Bin H, Lu W, Meng-Na J, Shan-Yi Z, Jiang-Tao Z, Ju-Ping Z. The validity of the subspecies, Teinopalpus aureus wuyiensis Lee, from complete mitochondrial genome. MITOCHONDRIAL DNA PART B-RESOURCES 2021; 6:2589-2591. [PMID: 34395887 PMCID: PMC8354169 DOI: 10.1080/23802359.2021.1960214] [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: 10/26/2022]
Abstract
The complete mitochondrial genome (mtgenome) was determined from the emerged-pupa shell (Noninvasive sampling) of T. aureus wuyiensis Lee. It was 15,234 base pairs in length and contained 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a control region. By taking Meandrusa sciron and Teinopalpus imperialis as outgroups, a maximum-likelihood phylogenetic tree was constructed among five geographical populations of Teinopalpus aureus based on 13 PCGs and two rRNA genes. Our results showed that the WYS, MHS and PS populations, locating at or closing to Wuyishan Mountain-range, were in one cluster; while the JLS (locating at Nanling Mountain-range) and DYS (locating at Dayaoshan Mountain closing to Nanling Mountain-range) populations belonged to another cluster. It supported well the subspecies of T. aureus wuyiensis, and suggested that the genetic relationship between T. a. guangxiensis and the nominal subspecies of T. a. aureus were closer enough to combine into one subspecies.
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Affiliation(s)
- Zou Wu
- Key laboratory of National Forestry and Grass and Administration on Forest Ecosystem Protection and Restoration of Poyang Lake Watershed, College of Forestry, Jiangxi Agricultural University, Nanchang, PR China.,Jiulianshan Forest Ecosystem Observation Station, Longnan, PR China
| | - Huang Chao-Bin
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, College of Life Science, Guangxi Normal University, Guilin, PR China
| | - Wang Lu
- Key laboratory of National Forestry and Grass and Administration on Forest Ecosystem Protection and Restoration of Poyang Lake Watershed, College of Forestry, Jiangxi Agricultural University, Nanchang, PR China.,Jiulianshan Forest Ecosystem Observation Station, Longnan, PR China
| | - Jiang Meng-Na
- Key laboratory of National Forestry and Grass and Administration on Forest Ecosystem Protection and Restoration of Poyang Lake Watershed, College of Forestry, Jiangxi Agricultural University, Nanchang, PR China.,Jiulianshan Forest Ecosystem Observation Station, Longnan, PR China
| | - Zhou Shan-Yi
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, College of Life Science, Guangxi Normal University, Guilin, PR China
| | - Zhang Jiang-Tao
- Key laboratory of National Forestry and Grass and Administration on Forest Ecosystem Protection and Restoration of Poyang Lake Watershed, College of Forestry, Jiangxi Agricultural University, Nanchang, PR China.,Jiulianshan Forest Ecosystem Observation Station, Longnan, PR China
| | - Zeng Ju-Ping
- Key laboratory of National Forestry and Grass and Administration on Forest Ecosystem Protection and Restoration of Poyang Lake Watershed, College of Forestry, Jiangxi Agricultural University, Nanchang, PR China.,Jiulianshan Forest Ecosystem Observation Station, Longnan, PR China.,Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, College of Life Science, Guangxi Normal University, Guilin, PR China
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Organization and phylogenetic relationships of the mitochondrial genomes of Speiredonia retorta and other lepidopteran insects. Sci Rep 2021; 11:2957. [PMID: 33536496 PMCID: PMC7859238 DOI: 10.1038/s41598-021-82561-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/21/2021] [Indexed: 11/08/2022] Open
Abstract
In this study, we analyzed the complete mitochondrial genome (mitogenome) of Speiredonia retorta, which is a pest and a member of the Lepidoptera order. In total, the S. retorta mitogenome was found to contain 15,652 base pairs encoding 13 protein-coding genes (PCGs), 22 tRNAs, 2 rRNAs, as well as an adenine (A) + thymine (T)-rich region. These findings were consistent with the mitogenome composition of other lepidopterans, as we identified all 13 PCGs beginning at ATN codons. We also found that 11 PCGs terminated with canonical stop codons, whereas cox2 and nad4 exhibited incomplete termination codons. By analyzing the mitogenome of S. retorta using Bayesian inference (BI) and maximum likelihood (ML) models, we were able to further confirm that this species is a member of the Erebidae family.
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