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Zhang D, Jin WD, Xu HF, Li XB, Jiang YW, Li DQ, Lin XL. Characteristics and Comparative Analysis of Six Mitogenomes of Genus Kiefferulus Goetghebuer, 1922 (Diptera: Chironomidae). INSECTS 2024; 15:646. [PMID: 39336614 PMCID: PMC11432734 DOI: 10.3390/insects15090646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Revised: 08/25/2024] [Accepted: 08/26/2024] [Indexed: 09/30/2024]
Abstract
Chironomidae is a cosmopolitan and species-rich family of insects, with many species serving as useful indicators of aquatic ecosystem health. In this study, we newly sequenced six species of Kiefferulus Goetghebuer, 1922 (Chironomidae: Chironominae) by high-throughput sequencing technology. We analyzed characters of the mitochondrial genome, including the sequence length, nucleotide composition, and evolutionary rates of this genus. The size of the newly obtained sequences ranged from 15,588 to 15,767 bp, and all of them included 22 tRNAs, 13 PCGs, 2 rRNAs, and 1 CR. The CR showed the highest AT content relative to the PCGs, rRNAs, and tRNAs. Relative synonymous codon usage analysis showed that UUA, UUU, and AUU are the preferred codons. The ratio of nonsynonymous (Ka) to synonymous (Ks) substitution rates showed that all Ka/Ks of PCGs were lower than 1, with ATP8 having the highest evolution rate, while COX1 exhibited the lowest evolution rate. We reconstructed the phylogenetic relationship of the genus Kiefferulus based on eight species (six ingroups and two outgroups), using five matrices and employing Maximum likelihood and Bayesian inference approaches. Phylogenetic analysis of the Kiefferulus showed that six species within this genus were classified into a monophyletic clade.
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Affiliation(s)
- Dan Zhang
- Characteristic Laboratory of Forensic Science in Universities of Shandong Province, Shandong University of Political Science and Law, Jinan 250014, China
| | - Wei-Dong Jin
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Hai-Feng Xu
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
| | - Xue-Bo Li
- Characteristic Laboratory of Forensic Science in Universities of Shandong Province, Shandong University of Political Science and Law, Jinan 250014, China
| | - Yong-Wei Jiang
- College of Water Sciences, Beijing Normal University, Beijing 100875, China
| | - Dai-Qing Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xiao-Long Lin
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
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2
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Bello-González OC, Andersen T, Mercado-Silva N. A revised, annotated checklist of Mexican non-biting midges (Diptera, Chironomidae). Zookeys 2024; 1191:237-286. [PMID: 38389584 PMCID: PMC10882552 DOI: 10.3897/zookeys.1191.117223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/12/2024] [Indexed: 02/24/2024] Open
Abstract
An updated checklist of Mexican non-biting midges (Chironomidae) is presented. A total of 110 species of Chironomidae are known for Mexico: 52 species in 25 genera belong to the subfamily Chironominae, 30 species in 13 genera to Orthocladiinae, 21 species in nine genera to Tanypodinae, five species in two genera to Telmatogetoninae, and two species in one genus to Diamesinae. In addition, 41 genera without identified species are listed. The highest number of species (29) is recorded from the state of Campeche, while 19 species have been found in Veracruz and 15 in Nuevo León. Few or no records exist for states in Central and Northern Mexico, or those on the Pacific coast. The type localities for 34 species are in Mexico; of these, 27 species (25% of the total number of species recorded in the country) are endemic. Twenty-nine species recorded in Mexico have a Neotropical distribution, 15 a Nearctic distribution, and 39 species are distributed in both the Neotropical and Nearctic regions or more widely. It has been suggested that as many as 1000 species might occur in Mexico; so only a little more than 10% of the expected diversity has so far been recorded.
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Affiliation(s)
- Orestes C Bello-González
- Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, C.P. 62209, Cuernavaca, Morelos, Mexico
| | - Trond Andersen
- Department of Natural History, University Museum of Bergen, University of Bergen, P.O. Box 7800, NO-5020, Bergen, Norway
| | - Norman Mercado-Silva
- Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, C.P. 62209, Cuernavaca, Morelos, Mexico
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3
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Li SY, Chen MH, Sun L, Wang RH, Li CH, Gresens S, Li Z, Lin XL. New mitogenomes from the genus Cricotopus (Diptera: Chironomidae, Orthocladiinae): Characterization and phylogenetic implications. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 115:e22067. [PMID: 38014568 DOI: 10.1002/arch.22067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 11/29/2023]
Abstract
Cricotopus is a large and diverse genus of non-biting midges composed of several subgenera. Complete mitogenome sequences are available for very few Cricotopus species. The subgenus Pseudocricotopus unites species with unusual morphological structures in adult male and pupal stages, however, molecular methods are needed to verify the placement of this subgenus within Cricotopus. We obtained mitogenomes of C. (Pseudocricotopus) cf. montanus and nine other Cricotopus species for phylogenetic analysis, coupled with two Rheocricotopus species and one Synorthocladius species as outgroups. The structure of the mitogenome was similar among these Cricotopus species, exhibiting A+T bias and retaining ancestral gene order. Mutation rate, estimated as Ka/Ks, varied among genes, and was highest for ATP8 and lowest for COI. The phylogenetic relationships among species of Cricotopus, Rheocricotopus and Synorthocladius was reconstructed using Bayesian inference and maximum likelihood estimation. The phylogenetic trees confirmed placement of subgenus Pseudocricotopus, represented by Cricotopus cf. montanus, within Cricotopus. Our study increases the library of chironomid mitogenomes and provides insight into the properties of their constituent genes.
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Affiliation(s)
- Shu-Yi Li
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Meng-Han Chen
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Li Sun
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Rui-Hao Wang
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Chen-Hong Li
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Susan Gresens
- Department of Biological Sciences, Towson University, Towson, Maryland, USA
| | - Zhao Li
- China National Environmental Monitoring Centre, Beijing, China
| | - Xiao-Long Lin
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
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4
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Chesters D, Ferrari RR, Lin X, Orr MC, Staab M, Zhu CD. Launching insectphylo.org; a new hub facilitating construction and use of synthesis molecular phylogenies of insects. Mol Ecol Resour 2023; 23:1556-1573. [PMID: 37265018 DOI: 10.1111/1755-0998.13817] [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: 11/13/2022] [Revised: 05/07/2023] [Accepted: 05/17/2023] [Indexed: 06/03/2023]
Abstract
The Holy Grail of an Insect Tree of Life can only be 'discovered' through extensive collaboration among taxon specialists, phylogeneticists and centralized frameworks such as Open Tree of Life, but insufficient effort from stakeholders has so far hampered this promising approach. The resultant unavailability of synthesis phylogenies is an unfortunate situation given the numerous practical usages of phylogenies in the near term and against the backdrop of the ongoing biodiversity crisis. To resolve this issue, we establish a new online hub that centralizes the collation of relevant phylogenetic data and provides the resultant synthesis molecular phylogenies. This is achieved through key developments in a proposed pipeline for the construction of a species-level insect phylogeny. The functionality of the framework is demonstrated through the construction of a highly supported, species-comprehensive phylogeny of Diptera, built from integrated omics data, COI DNA barcodes, and a compiled database of over 100 standardized, published Diptera phylogenies. Machine-readable forms of the phylogeny (and subsets thereof) are publicly available at insectphylo.org, a new public repository for species-comprehensive phylogenies for biological research.
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Affiliation(s)
- Douglas Chesters
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- International College, University of Chinese Academy of Sciences, Beijing, China
| | - Rafael R Ferrari
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xiaolong Lin
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Michael C Orr
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Entomologie, Staatliches Museum für Naturkunde Stuttgart, Stuttgart, Germany
| | - Michael Staab
- Ecological Networks, Technische Universität Darmstadt, Darmstadt, Germany
| | - Chao-Dong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- International College, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Biological Sciences, University of Chinese Academy of Sciences, Beijing, China
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5
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Qi Y, Bu WJ, Zheng CG, Lin XL, Jiao KL. New data on mitogenomes of Thienemanniella Kieffer, 1911 (Diptera: Chironomidae, Orthocladiinae). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2023; 114:1-9. [PMID: 37672308 DOI: 10.1002/arch.22051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/07/2023]
Abstract
The mitochondrial genome (mitogenome) has been widely used as a powerful marker in phylogenetic and evolutionary studies of various Dipteran groups. However, only a few mitogenomes from the Thienemanniella genus have been reported till now. Furthermore, there is still indeterminacy in the phylogenetic relationships of the genus Thienemanniella. In this study, mitogenomes of five Thienemanniella species were sequenced and analyzed newly. Combined with the published mitogenome of Thienemanniella nipponica, the obtained results showed that mitogenomes of Thienemanniella were conserved in structure, and all genes were observed to be arranged in the same gene order as the ancestral mitogenome. Nucleotide composition varied significantly among different genes, and the control region displayed the highest A + T content. All protein coding genes are subjected to purification selection, and the fastest evolving gene is ATP8. Maximum likelihood and Bayesian inference analyses showed the phylogeny of Thienemanniella which was supported in five topologies. Our present study provides valuable insight into the phylogenetic relationships of Thienemanniella species.
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Affiliation(s)
- Yan Qi
- Department of Plant Protection, College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin, China
| | - Wen-Jun Bu
- College of Life Sciences, Nankai University, Tianjin, China
| | | | - Xiao-Long Lin
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai, China
| | - Ke-Long Jiao
- Department of Plant Protection, College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin, China
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6
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Di X, Lei T, Mou K, Song C, Qi X. Complete mitochondrial genome of the non-biting midge Polypedilum henicurum Wang, 1995 (Diptera: Chironomidae). Mitochondrial DNA B Resour 2023; 8:908-911. [PMID: 37645474 PMCID: PMC10461503 DOI: 10.1080/23802359.2023.2246597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 08/04/2023] [Indexed: 08/31/2023] Open
Abstract
The complete mitochondrial genome of Polypedilum henicurum was sequenced and analyzed. The whole mitogenome is 15,964 bp in length and contains 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), and two ribosomal RNAs (rRNAs). The overall nucleotide composition is 39.5% A, 39.0% T, 13.1% C, and 8.4% G. Most PCGs start with ATN codon excluding COX1 (TTG) and all PCGs end with TAA codon. Gene arrangement stays the same with the ancestral mitochondrial genome. Bayesian inference phylogenetic tree supports its close relationship with P. unifascium. This work enriches the library of Chironomidae mitochondrial genomes and provides a valuable resource for understanding the evolutionary history of Polypedilum.
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Affiliation(s)
- Xuanru Di
- College of Life Sciences, Taizhou University, Taizhou, China
| | - Teng Lei
- College of Life Sciences, Taizhou University, Taizhou, China
- Institute of Soil and Waste Treatment and Biodiversity Protection, Taizhou University, Taizhou, China
| | - Kunlun Mou
- Xianju Branch of Taizhou Municipal Ecology and Environment Bureau, Taizhou, China
| | - Chao Song
- College of Life Sciences, Taizhou University, Taizhou, China
| | - Xin Qi
- College of Life Sciences, Taizhou University, Taizhou, China
- Institute of Soil and Waste Treatment and Biodiversity Protection, Taizhou University, Taizhou, China
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7
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Fang X, Wang X, Mao B, Xiao Y, Shen M, Fu Y. Comparative mitogenome analyses of twelve non-biting flies and provide insights into the phylogeny of Chironomidae (Diptera: Culicomorpha). Sci Rep 2023; 13:9200. [PMID: 37280228 DOI: 10.1038/s41598-023-36227-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/31/2023] [Indexed: 06/08/2023] Open
Abstract
The family Chironomidae is represented by seven subfamilies in China, among which Chironominae and Orthocladiinae are the most diverse. To gain a better understanding of the architecture and evolution of the mitogenomes of Chironomidae, we sequenced mitogenomes of twelve species (including two published species) of the two subfamilies Chironominae and Orthocladiinae, and comparative mitogenomic analyses were performed. Thus, we identified highly conserved genome organization of twelve species with regard to genome content, nucleotide and amino acid composition, codon usage, and gene characteristics. The Ka/Ks values of most protein-coding genes were far smaller than 1, indicating that these genes were evolving under purifying selection. Phylogenetic relationships between the family Chironomidae were reconstructed using 23 species representing six subfamilies, based on protein-coding genes and rRNAs using Bayesian Inference and Maximum Likelihood. Our results suggested the following relationship within the Chironomidae: (Podonominae + Tanypodinae) + (Diamesinae + (Prodiamesinae + (Orthocladiinae + Chironominae))). This study contributes to the mitogenomic database of Chironomidae, which will be significant for studing the mitogenome evolution of Chironomidae.
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Affiliation(s)
- Xiangliang Fang
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Zhongke Research Institute of Industrial Technology, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang City, 438000, Hubei, People's Republic of China
| | - Xinhua Wang
- College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Bin Mao
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Zhongke Research Institute of Industrial Technology, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang City, 438000, Hubei, People's Republic of China
| | - Yunli Xiao
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Zhongke Research Institute of Industrial Technology, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang City, 438000, Hubei, People's Republic of China
| | - Mi Shen
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Zhongke Research Institute of Industrial Technology, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang City, 438000, Hubei, People's Republic of China
| | - Yue Fu
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Hubei Zhongke Research Institute of Industrial Technology, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang City, 438000, Hubei, People's Republic of China.
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8
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Zhang D, He FX, Li XB, Aishan Z, Lin XL. New Mitogenomes of the Polypedilum Generic Complex (Diptera: Chironomidae): Characterization and Phylogenetic Implications. INSECTS 2023; 14:238. [PMID: 36975923 PMCID: PMC10054901 DOI: 10.3390/insects14030238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Mitochondrial genomics, as a useful marker for phylogenetics and systematics of organisms, are important for molecular biology studies. The phylogenetic relationships of the Polypedilum generic complex remains controversial, due to lack taxonomy and molecular information. In this study, we newly sequenced mitogenomes of 14 species of the Polypedilum generic complex. Coupled with three recently published sequences, we analyzed the nucleotide composition, sequence length, and evolutionary rate of this generic complex. The control region showed the highest AT content. The evolution rate of protein coding genes was as follows: ATP8 > ND6 > ND5 > ND3 > ND2 > ND4L > ND4 > COX1 > ND1 > CYTB > APT6 > COX2 > COX3. We reconstructed the phylogenetic relationships among the genera within the Polypedilum generic complex based on 19 mitochondrial genomes (seventeen ingroups and two outgroups), using Bayesian Inference (BI) and Maximum Likelihood (ML) methods for all databases. Phylogenetic analysis of 19 mitochondrial genomes demonstrated that the Endochironomus + Synendotendipes was sister to Phaenopsectra + Sergentia.
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Affiliation(s)
- Dan Zhang
- Characteristic Laboratory of Forensic Science in Universities of Shandong Province, Shandong University of Political Science and Law, Jinan 250014, China
| | - Fei-Xiang He
- Dongting Lake Eco-Environmental Monitoring Center of Hunan Province, Yueyang 414000, China
| | - Xue-Bo Li
- Characteristic Laboratory of Forensic Science in Universities of Shandong Province, Shandong University of Political Science and Law, Jinan 250014, China
| | - Zhulidezi Aishan
- College of Life Science and Technology, Xinjiang University, Urumqi 830017, China
| | - Xiao-Long Lin
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
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Li SY, Zhao YM, Guo BX, Li CH, Sun BJ, Lin XL. Comparative Analysis of Mitogenomes of Chironomus (Diptera: Chironomidae). INSECTS 2022; 13:1164. [PMID: 36555075 PMCID: PMC9784984 DOI: 10.3390/insects13121164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/18/2022] [Accepted: 11/18/2022] [Indexed: 06/17/2023]
Abstract
(1) Background: Chironomids are biological indicators, playing an important role in monitoring and assessing the changes in water ecosystems. Mitochondrial genomes have been widely applied as a molecular marker to analyze the taxonomy and phylogeny of insects. However, knowledge of the mitogenomes of Chironomus species is scarce at present, which limits our understanding of the evolutionary relationships among Chironomus. (2) Methods: In our study, the mitogenomes and their basic structure of 12 Chironomus species and one Microchironomus species were newly sequenced. Combined with reported mitogenomes, a total of 15 mitogenomes of Chironomus were selected for a comparative mitogenomic analysis and phylogenetic reconstruction of Chironomus. (3) Results: Each mitogenome of the Chironomus species has the typical 37 genes and a control region. The basic structure of the whole mitogenomes of Chironomus species is relatively conservative, and the genetic arrangements stay the same as the ancestral mitogenome. (4) Conclusions: Our study enriches the library of mitogenomes of chironomids and provides a valuable resource for understanding the evolutionary history of Chironomus.
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Affiliation(s)
- Shu-Yi Li
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
| | - Yan-Min Zhao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing 100012, China
| | - Bing-Xin Guo
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
| | - Chen-Hong Li
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
| | - Bing-Jiao Sun
- China National Environmental Monitoring Centre, Beijing 100012, China
| | - Xiao-Long Lin
- Engineering Research Center of Environmental DNA and Ecological Water Health Assessment, Shanghai Ocean University, Shanghai 201306, China
- Shanghai Universities Key Laboratory of Marine Animal Taxonomy and Evolution, Shanghai Ocean University, Shanghai 201306, China
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10
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Mitochondrial Genomes Provide New Phylogenetic and Evolutionary Insights into Psilidae (Diptera: Brachycera). INSECTS 2022; 13:insects13060518. [PMID: 35735855 PMCID: PMC9224655 DOI: 10.3390/insects13060518] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/29/2022] [Accepted: 05/30/2022] [Indexed: 02/05/2023]
Abstract
Psilidae (Diptera: Brachycera) is a moderate-sized family currently placed in the superfamily Diopsoidea and contains some destructive agricultural and forestry pests. The systematic position and intrafamilial classification of rust flies are in need of further study, and the available molecular data of Psilidae are still limited. In this study, we present the mitochondrial genomes of 6 Psilidae species (Chamaepsilatestudinaria Wang and Yang, Chyliza bambusae Wang and Yang, Chy. chikuni Wang, Loxocera lunata Wang and Yang, L. planivena Wang and Yang and L. sinica Wang and Yang). Comparative analyses show a conserved genome structure, in terms of gene composition and arrangement, and a highly Adenine plus Thymine biased nucleotide composition of the 6 psilid mitogenomes. Mitochondrial evolutionary rates vary among the 6 species, with species of Chylizinae exhibiting a slower average rate than species of Psilinae. The length, the nucleotide composition, and the copy number of repeat units of the control region are variable among the 6 species, which may offer useful information for phylogenetic and evolutionary studies of Psilidae. Phylogenetic analyses based on 4 mitogenomic datasets (AA, PCG, PCG12RNA, and PCGRNA) support the monophyly of Psilidae, and the sister relationship between Chylizinae and Psilinae, while Diopsoidea is suggested to be non-monophyletic. Our study enlightens the future application of mitogenomic data in the phylogenetic and evolutionary studies of Psilidae, based on denser taxon sampling.
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Lin X, Liu Z, Yan L, Duan X, Bu W, Wang X, Zheng C. Mitogenomes provide new insights of evolutionary history of Boreheptagyiini and Diamesini (Diptera: Chironomidae: Diamesinae). Ecol Evol 2022; 12:e8957. [PMID: 35646319 PMCID: PMC9130564 DOI: 10.1002/ece3.8957] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 04/16/2022] [Accepted: 05/06/2022] [Indexed: 01/11/2023] Open
Abstract
Mitogenomes have been widely used for phylogenetic reconstruction of various Dipteran groups, but specifically for chironomid, they have not been carried out to resolve the relationships. Diamesinae (Diptera: Chironomidae) are important bioindicators for freshwater ecosystem monitoring, but its evolutionary history remains uncertain for lack of information. Here, coupled with one previously published and 30 new mitogenomes of Diamesinae, we carried out comparative mitogenomic analysis and phylogenetic analysis. Mitogenomes of Diamesinae were conserved in structure, and all genes arranged in the same order as the ancestral insect mitogenome. All protein-coding genes in Diamesinae were under stronger purifying selection than those of other nonbiting midge species, which may exhibit signs of adaptation to life at cold living conditions. Phylogenetic analyses strongly supported the monophyly of Diamesinae, with Boreheptagyiini deeply nested within Diamesini. In addition, phylogenetic relationship of selected six genera was resolved, except Sympotthastia remained unstable. Our study revealed that the mitogenomes of Diamesinae are highly conserved, and they are practically useful for phylogenetic inference.
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Affiliation(s)
- Xiao‐Long Lin
- College of Life SciencesNankai UniversityTianjinChina
| | - Zheng Liu
- Geological Museum of ChinaBeijingChina
| | - Li‐Ping Yan
- School of Ecology and Nature ConservationBeijing Forestry UniversityBeijingChina
| | - Xin Duan
- Department of Plant ProtectionCollege of Horticulture and LandscapeTianjin Agricultural UniversityTianjinChina
| | - Wen‐Jun Bu
- College of Life SciencesNankai UniversityTianjinChina
| | - Xin‐Hua Wang
- College of Life SciencesNankai UniversityTianjinChina
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12
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First Report on Mitochondrial Gene Rearrangement in Non-Biting Midges, Revealing a Synapomorphy in Stenochironomus Kieffer (Diptera: Chironomidae). INSECTS 2022; 13:insects13020115. [PMID: 35206689 PMCID: PMC8875173 DOI: 10.3390/insects13020115] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 01/25/2023]
Abstract
Simple Summary Gene rearrangement is an additional type of data to support relationships of taxa, with rearrangement synapomorphies identified across multiple orders and at many different taxonomic levels. The concept to use mitochondrial gene rearrangements as phylogenetic markers has been proposed since the mid-1980s, the synapomorphic gene rearrangements have been identified from many lineages. However, mitochondrial gene rearrangement has never been observed in the non-biting midges (Diptera: Chironomidae). Here, seven new mitogenomes of the genus Stenochironomus were sequenced and analyzed. Coupled with published data, phylogenetic analyses were performed within Chironominae. The present study showed that mitogenomes of Stenochironomus are showing a higher A+T bias than other chironomid species. A synapomorphic gene rearrangement that the gene order rearranges from trnI-trnQ-trnM to trnI-trnM-trnQ was identified within Stenochironomus, which is the first instance of mitochondrial gene rearrangement discovered in the Chironomidae. The monophyly of the genus Stenochironomus was strongly supported by mitogenomes. Our study provides new insights into the mitochondrial gene order of Chironomidae, and provides a valuable resource for understanding synapomorphic gene rearrangements. Abstract (1) Background: Gene rearrangement of mitochondrial genome, especially those with phylogenetic signals, has long fascinated evolutionary biologists. The synapomorphic gene rearrangements have been identified across multiple orders and at many different taxonomic levels, supporting the monophyletic or systematic relationships of related lineages. However, mitochondrial gene rearrangement has never been observed in the non-biting midges (Diptera: Chironomidae); (2) methods: in this study, the complete mitogenomes of seven Stenochironomus species were sequenced and analyzed for the first time; (3) results: each mitogenome of Stenochironomus contains 37 typical genes and a control region. The whole mitogenomes of Stenochironomus species exhibit a higher A+T bias than other published chironomid species. The gene order rearranges from trnI-trnQ-trnM to trnI-trnM-trnQ in all the seven mitogenomes of Stenochironomus, which might be act as a synapomorphy of the genus, supporting the monophyletic of Stenochironomus species. In addition, another derived gene cluster: trnA-trnG-ND3-trnR exists in Stenochironomus tobaduodecimus. The derived gene orders described above are the first case of mitochondrial gene rearrangement in Chironomidae. Coupled with published data, phylogenetic relationships were reconstructed within Chironominae, and strongly supported the monophyly of Stenochironomus; (4) conclusions: our study provides new insights into the mitochondrial gene order of Chironomidae, and provides a valuable resource for understanding the synapomorphic gene rearrangements.
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