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Zhang Q, Lu YW, Liu XY, Li Y, Gao WN, Sun JT, Hong XY, Shao R, Xue XF. Phylogenomics resolves the higher-level phylogeny of herbivorous eriophyoid mites (Acariformes: Eriophyoidea). BMC Biol 2024; 22:70. [PMID: 38519936 PMCID: PMC10960459 DOI: 10.1186/s12915-024-01870-9] [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: 07/22/2023] [Accepted: 03/14/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND Eriophyoid mites (Eriophyoidea) are among the largest groups in the Acariformes; they are strictly phytophagous. The higher-level phylogeny of eriophyoid mites, however, remains unresolved due to the limited number of available morphological characters-some of them are homoplastic. Nevertheless, the eriophyoid mites sequenced to date showed highly variable mitochondrial (mt) gene orders, which could potentially be useful for resolving the higher-level phylogenetic relationships. RESULTS Here, we sequenced and compared the complete mt genomes of 153 eriophyoid mite species, which showed 54 patterns of rearranged mt gene orders relative to that of the hypothetical ancestor of arthropods. The shared derived mt gene clusters support the monophyly of eriophyoid mites (Eriophyoidea) as a whole and the monophylies of six clades within Eriophyoidea. These monophyletic groups and their relationships were largely supported in the phylogenetic trees inferred from mt genome sequences as well. Our molecular dating results showed that Eriophyoidea originated in the Triassic and diversified in the Cretaceous, coinciding with the diversification of angiosperms. CONCLUSIONS This study reveals multiple molecular synapomorphies (i.e. shared derived mt gene clusters) at different levels (i.e. family, subfamily or tribe level) from the complete mt genomes of 153 eriophyoid mite species. We demonstrated the use of derived mt gene clusters in unveiling the higher-level phylogeny of eriophyoid mites, and underlines the origin of these mites and their co-diversification with angiosperms.
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Affiliation(s)
- Qi Zhang
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yi-Wen Lu
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xin-Yu Liu
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Ye Li
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Wei-Nan Gao
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jing-Tao Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Renfu Shao
- Centre for Bioinnovation, School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, 4556, Australia
| | - Xiao-Feng Xue
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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Fang Y, Sun M, Fang Y, Zuo Z, Liu L, Chu L, Ding L, Hu C, Li F, Han R, Xia X, Zhou S, Sun E. Complete mitochondrial genomes of Thyreophagus entomophagus and Acarus siro (Sarcoptiformes: Astigmatina) provide insight into mitogenome features, evolution, and phylogeny among Acaroidea mites. EXPERIMENTAL & APPLIED ACAROLOGY 2022; 88:57-74. [PMID: 36255591 DOI: 10.1007/s10493-022-00745-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Mites from the Acaroidea (Sarcoptiformes: Astigmatina) are important pests of various stored products, posing potential threats to preserved foods. In addition, mites can cause allergic diseases. Complete mitochondrial genomes (mitogenomes) are valuable resources for different research fields, including comparative genomics, molecular evolutionary analysis, and phylogenetic inference. We sequenced and annotated the complete mitogenomes of Thyreophagus entomophagus and Acarus siro. A comparative analysis was made between mitogenomic sequences from 10 species representing nine genera within Acaroidea. The mitogenomes of T. entomophagus and A. siro contained 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and one control region. In Acaroidea species, mitogenomes have highly conserved gene size and order, and codon usage. Among Acaroidea mites, most PCGs were found to be under purifying selection, implying that most PCGs might have evolved slowly. Our findings showed that nad4 evolved most rapidly, whereas cox1 and cox3 evolved most slowly. The evolutionary rates of Acaroidea vary considerably across families. In addition, selection analyses were also performed in 23 astigmatid mite species, and the evolutionary rate of the same genes in different superfamilies exhibited large differences. Phylogenetic results are mostly consistent with those identified by previous phylogenetic studies on astigmatid mites. The monophyly of Acaroidea was rejected, and the Suidasiidae and Lardoglyphidae appeared to deviate from the Acaroidea branch. Our research proposed a review of the current Acaroidea classification system.
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Affiliation(s)
- Yu Fang
- Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, 241002, China
- Department of Medical Parasitology, Wannan Medical College, Wuhu, China
| | - Mingzhong Sun
- Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, 241002, China
| | - Ying Fang
- Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, 241002, China
| | - Zetao Zuo
- Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, 241002, China
| | - Luyao Liu
- Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, 241002, China
| | - Lingmiao Chu
- Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, 241002, China
| | - Lan Ding
- Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, 241002, China
| | - Caixiao Hu
- Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, 241002, China
| | - Feiyan Li
- Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, 241002, China
| | - Renrui Han
- Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, 241002, China
| | - Xingquan Xia
- College of Life Science, The Provincial Key Lab of the Conservation and Exploitation Research of Biological Resources in Anhui, Anhui Normal University, Wuhu, China.
| | - Shulin Zhou
- Department of Medical Parasitology, Wannan Medical College, Wuhu, China.
| | - Entao Sun
- Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, 241002, China.
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Dong F, Fang W, Fang Y, Zhan X, Tao D, Su X, Xu J, Wang Y, Liu F, Liu Y, Chen B, Xia X, Sun E. The Complete Mitochondrial Genome of Suidasia nesbitti and Phylogenetic Relationships of Astigmata. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Fang WX, Dong FY, Sun ET, Tao DD, Wang Y, Xu JY, Fang Y, Zhan XB, Ye CJ. De novo sequence of the mitochondrial genome of Tyrophagus putrescentiae (Acari: Sarcoptiformes) including 22 tRNA sequences and the largest non-coding region. EXPERIMENTAL & APPLIED ACAROLOGY 2020; 80:521-530. [PMID: 32162137 DOI: 10.1007/s10493-020-00477-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 02/29/2020] [Indexed: 06/10/2023]
Abstract
In this study, we de novo sequenced and analyzed the circular mitochondrial genome (mitogenome) of Tyrophagus putrescentiae. It was 14,156 bp long and contained a complete set of 37 genes, contrary to the initial published sequences; it included 22 tRNA sequences and the largest non-coding region. The mtDNA gene order of T. putrescentiae was found to be identical to that of Aleuroglyphus ovatus, Caloglyphus berlesei, and Rhizoglyphus robini (all Acaroidea). Most tRNAs of T. putrescentiae lack at least a D-arm or T-arm. Tyrophagus putrescentiae tRNAs also shared considerable structural and sequence similarity with the tRNAs of other reported Acaroidea species that have the full set of tRNAs. The largest non-coding region was located between trnF and trnS1, and it contained a microsatellite-like (AT)n sequence, short palindromic sequences, and several hairpin loops, as observed in other reported Acaroidea species (excepting Tyrophagus longior).
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Affiliation(s)
- Wei-Xi Fang
- Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, 241002, China
| | - Fang-Yuan Dong
- Department of Pathology, Wannan Medical College, Wuhu, China
| | - En-Tao Sun
- Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, 241002, China.
| | - Dong-Dong Tao
- Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, 241002, China
| | - Yan Wang
- Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, 241002, China
| | - Jiao-Yang Xu
- Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, 241002, China
| | - Yu Fang
- Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, 241002, China
| | - Xue-Bing Zhan
- Department of Pathology, Wannan Medical College, Wuhu, China
| | - Chang-Jiang Ye
- Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, 241002, China
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Li WN, Xue XF. Mitochondrial genome reorganization provides insights into the relationship between oribatid mites and astigmatid mites (Acari: Sarcoptiformes: Oribatida). Zool J Linn Soc 2019. [DOI: 10.1093/zoolinnean/zlz044] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Oribatida s.l. represents one of the most species-rich mite lineages, including two recognized groups: oribatid mites (Oribatida s.s., non-astigmatan oribatids) and astigmatid mites (Astigmata). However, the relationship between these two groups has been debated. Here, we sequenced the complete mitochondrial (mt) genome of one oribatid mite and one astigmatid mite, retrieved complete mt genomes of three oribatid mites, and compared them with two other oribatid mites and 12 astigmatid mites sequenced previously. We find that gene orders in the mt genomes of both oribatid mites and astigmatid mites are rearranged relative to the hypothetical ancestral arrangement of the arthropods. Based on the shared derived gene clusters in each mt genome group, rearranged mt genomes are roughly divided into two groups corresponding to each mite group (oribatid mites or astigmatid mites). Phylogenetic results show that Astigmata nested in Oribatida. The monophyly of Astigmata is recovered, while paraphyly of Oribatida s.s. is observed. Our results show that rearranged gene orders in the mt genomes characterize various lineages of oribatid mites and astigmatid mites, and have potential phylogenetic information for resolving the high-level (cohort or supercohort) phylogeny of Oribatida.
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Affiliation(s)
- Wei-Ning Li
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
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