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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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Lienhard A, Schäffer S. Extracting the invisible: obtaining high quality DNA is a challenging task in small arthropods. PeerJ 2019; 7:e6753. [PMID: 30997294 PMCID: PMC6463856 DOI: 10.7717/peerj.6753] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 03/09/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The application of an appropriate extraction method is a relevant factor for the success of all molecular studies. METHODS Seven different DNA extraction methods suitable for high-throughput DNA sequencing with very small arthropods were compared by applying nine different protocols: three silica gel based spin methods, two cetyltrimethyl ammonium bromide (CTAB) based ones (one with an additional silica membrane), a protein precipitation method and a method based on a chelating resin (applying different protocols). The quantity (concentration) and quality (degradation, contamination, polymerase chain reaction (PCR) and sequencing success) of the extracted DNA as well as the costs, preparation times, user friendliness, and required supplies were compared across these methods. To assess the DNA quantity, two different DNA concentration measurements were applied. Additionally, the effect of varying amounts of starting material (different body sizes), variable lysis temperatures and mixing during DNA extraction was evaluated. RESULTS Although low DNA concentrations were measured for all methods, the results showed that-with the exception of two methods-the PCR success was 100%. However, other parameters show vast differences. The time taken to perform DNA extraction varied from 20 min to 2.5 h (Chelex vs. CTAB) and the costs from 0.02 to 3.46 € (Chelex vs. QIAamp kit) per sample. High quality genomic DNA was only gained from four methods. Results of DNA quantity measurements further indicated that some devices cannot deal with small amounts of DNA and show variant results. DISCUSSION In conclusion, using Chelex (chelating resin) turned out as a rapid, low-cost method which can provide high quality DNA for different kinds of molecular investigations.
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Lee CC, Wang J. Rapid Expansion of a Highly Germline-Expressed Mariner Element Acquired by Horizontal Transfer in the Fire Ant Genome. Genome Biol Evol 2018; 10:3262-3278. [PMID: 30304394 PMCID: PMC6307670 DOI: 10.1093/gbe/evy220] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2018] [Indexed: 12/25/2022] Open
Abstract
Transposable elements (TEs) are present in almost all organisms and affect the host in various ways. TE activity can increase genomic variation and thereby affect host evolution. Currently active TEs are particularly interesting because they are likely generating new genomic diversity. These active TEs have been poorly studied outside of model organisms. In this study, we aimed to identify currently active TEs of a notorious invasive species, the red imported fire ant Solenopsis invicta. Using RNA profiling of male and female germline tissues, we found that the majority of TE-containing transcripts in the fire ant germline belong to the IS630-Tc1-Mariner superfamily. Subsequent genomic characterization of fire ant mariner content, molecular evolution analysis, and population comparisons revealed a highly expressed and highly polymorphic mariner element that is rapidly expanding in the fire ant genome. Additionally, using comparative genomics of multiple insect species we showed that this mariner has undergone several recent horizontal transfer events (<5.1 My). Our results document a rare case of a currently active TE originating from horizontal transfer.
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Affiliation(s)
- Chih-Chi Lee
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Laboratory of Insect Ecology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Japan
- Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto, Japan
| | - John Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
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Xue XF, Deng W, Qu SX, Hong XY, Shao R. The mitochondrial genomes of sarcoptiform mites: are any transfer RNA genes really lost? BMC Genomics 2018; 19:466. [PMID: 29914378 PMCID: PMC6006854 DOI: 10.1186/s12864-018-4868-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 06/13/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Mitochondrial (mt) genomes of animals typically contain 37 genes for 13 proteins, two ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes. In sarcoptiform mites, the entire set of mt tRNA genes is present in Aleuroglyphus ovatus, Caloglyphus berlesei, Dermatophagoides farinae, D. pteronyssinus, Histiostoma blomquisti and Psoroptes cuniculi. Loss of 16 mt tRNA genes, however, was reported in Steganacarus magnus; loss of 2-3 tRNA genes was reported in Tyrophagus longior, T. putrescentiae and Sarcoptes scabiei. Nevertheless, convincing evidence for mt gene loss is lacking in these mites. RESULTS We sequenced the mitochondrial genomes of two sarcoptiform mites, Histiostoma feroniarum (13,896 bp) and Rhizoglyphus robini (14,244 bp). Using tRNAScan and ARWEN programs, we identified 16 and 17 tRNA genes in the mt genomes of H. feroniarum and R. robini, respectively. The other six mt tRNA genes in H. feroniarum and five mt tRNA genes in R. robini can only be identified manually by sequence comparison when alternative anticodons are considered. We applied this manual approach to other mites that were reported previously to have lost mt tRNA genes. We were able to identify all of the 16 mt tRNA genes that were reported as lost in St. magnus, two of the three mt tRNA genes that were reported as lost in T. longior and T. putrescentiae, and the two mt tRNA genes that were reported as lost in Sa. scabiei. All of the tRNA genes inferred from these manually identified genes have truncation in the arms and mismatches in the stems. CONCLUSIONS Our results reveal very unconventional tRNA structures in sarcoptiform mites and do not support the loss of mt tRNA genes in these mites. The functional implication of the drastic structural changes in these tRNA genes remains to be investigated.
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Affiliation(s)
- Xiao-Feng Xue
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Wei Deng
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Shao-Xuan Qu
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 Jiangsu China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Renfu Shao
- GeneCology Research Centre, Centre for Animal Health Innovation, School of Science and Engineering, University of the Sunshine Coast, Maroochydore, QLD 4556 Australia
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The mitochondrial genome of the oribatid mite Paraleius leontonychus: new insights into tRNA evolution and phylogenetic relationships in acariform mites. Sci Rep 2018; 8:7558. [PMID: 29765106 PMCID: PMC5954100 DOI: 10.1038/s41598-018-25981-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 05/02/2018] [Indexed: 01/06/2023] Open
Abstract
Bilaterian mitochondrial (mt) genomes are circular molecules that typically contain 37 genes. To date, only a single complete mitogenome sequence is available for the species-rich sarcoptiform mite order Oribatida. We sequenced the mitogenome of Paraleius leontonychus, another species of this suborder. It is 14,186 bp long and contains 35 genes, including only 20 tRNAs, lacking tRNAGly and tRNATyr. Re-annotation of the mitogenome of Steganacarus magnus increased the number of mt tRNAs for this species to 12. As typical for acariform mites, many tRNAs are highly truncated in both oribatid species. The total number of tRNAs and the number of tRNAs with a complete cloverleaf-like structure in P. leontonychus, however, clearly exceeds the numbers previously reported for Sarcoptiformes. This indicates, contrary to what has been previously assumed, that reduction of tRNAs is not a general characteristic for sarcoptiform mites. Compared to other Sarcoptiformes, the two oribatid species have the least rearranged mt genome with respect to the pattern observed in Limulus polyphemus, a basal arachnid species. Phylogenetic analysis of the newly sequenced mt genome and previously published data on other acariform mites confirms paraphyly of the Oribatida and an origin of the Astigmata within the Oribatida.
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Han YD, Min GS. Complete mitochondrial genome of the feather mite Ardeacarus ardeae (Acari, Sarcoptiformes, Pterolichidae). Mitochondrial DNA B Resour 2017; 2:41-42. [PMID: 33473710 PMCID: PMC7800169 DOI: 10.1080/23802359.2017.1289345] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In this study, we determined the mitogenome sequence of Ardeacarus ardeae (Canestrini, 1878) in the family Pterolichidae (Acari, Sarcoptiformes), which is the first complete mitogenome sequence in feather mite. The mitogenome of A. ardeae is 14,069 bp in length and contains 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), 2 ribosomal RNAs (rRNAs), and a control region (CR). The phylogenetic tree shows that A. ardeae belong to the supercohort Desmonomatides within the order Sarcoptiformes.
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Affiliation(s)
- Yeong-Deok Han
- Department of Biological Sciences, Inha University, Incheon, South Korea
| | - Gi-Sik Min
- Department of Biological Sciences, Inha University, Incheon, South Korea
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