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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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Xie J, Zhang Y. Diversity and Distribution of Mites (ACARI) Revealed by Contamination Survey in Public Genomic Databases. Animals (Basel) 2023; 13:3172. [PMID: 37893896 PMCID: PMC10603697 DOI: 10.3390/ani13203172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/24/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023] Open
Abstract
Acari (mites and ticks) are a biodiverse group of microarthropods within the Arachnida. Because of their diminutive size, mites are often overlooked. We hypothesized that mites, like other closely related microorganisms, could also contaminate public genomic database. Here, using a strategy based on DNA barcodes previously reported, we scanned contaminations related to mites (Acari, exclusive of Ixodida) in Genbank WGS/TSA database. In 22,114 assemblies (17,845 animal and 4269 plant projects), 1717 contigs in 681 assemblies (3.1%) were detected as mite contaminations. Additional taxonomic analysis showed the following: (1) most of the contaminants (1445/1717) were from the specimens of Magnoliopsida, Insecta and Pinopsida; (2) the contamination rates were higher in plant or TSA projects; (3) mite distribution among different classes of hosts varied considerably. Additional phylogenetic analysis of these contaminated contigs further revealed complicated mite-host associations. Overall, we conducted a first systemic survey and analysis of mite contaminations in public genomic database, and these DNA barcode related mite contigs will provide a valuable resource of information for understanding the diversity and phylogeny of mites.
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Affiliation(s)
- Jiazheng Xie
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
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3
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Chen L, Yu XY, Xue XF, Zhang F, Guo LX, Zhang HM, Hoffmann AA, Hong XY, Sun JT. The genome sequence of a spider mite, Tetranychus truncatus, provides insights into interspecific host range variation and the genetic basis of adaptation to a low-quality host plant. INSECT SCIENCE 2023; 30:1208-1228. [PMID: 37279769 DOI: 10.1111/1744-7917.13212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 06/08/2023]
Abstract
The phytophagous mite Tetranychus truncatus is a serious pest in East Asia but has a relatively narrower host range than the pest mite Tetranychus urticae, which can feed on over 1200 plant species. Here, we generated a high-quality chromosomal level genome of T. truncatus and compared it with that of T. urticae, with an emphasis on the genes related to detoxification and chemoreception, to explore the genomic basis underlying the evolution of host range. We also conducted population genetics analyses (in 86 females from 10 populations) and host transfer experiments (in 4 populations) to investigate transcription changes following transfer to a low-quality host (Solanum melongena, eggplant), and we established possible connections between fitness on eggplant and genes related to detoxification and chemoreception. We found that T. truncatus has fewer genes related to detoxification, transport, and chemoreception than T. urticae, with a particularly strong reduction in gustatory receptor (GR) genes. We also found widespread transcriptional variation among T. truncatus populations, which varied in fitness on eggplant. We characterized selection on detoxification-related genes through ω values and found a negative correlation between expression levels and ω values. Based on the transcription results, as well as the fitness and genetic differences among populations, we identified genes potentially involved in adaptation to eggplant in T. truncatus. Our work provides a genomic resource for this pest mite and new insights into mechanisms underlying the adaptation of herbivorous mites to host plants.
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Affiliation(s)
- Lei Chen
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Xin-Yue Yu
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Xiao-Feng Xue
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Feng Zhang
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Li-Xue Guo
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Hua-Meng Zhang
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Ary A Hoffmann
- Bio21 Institute, School of Biosciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Jing-Tao Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
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4
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Chetverikov PE, Bolton SJ, Craemer C, Gankevich VD, Zhuk AS. Atypically Shaped Setae in Gall Mites (Acariformes, Eriophyoidea) and Mitogenomics of the Genus Leipothrix Keifer (Eriophyidae). INSECTS 2023; 14:759. [PMID: 37754727 PMCID: PMC10531682 DOI: 10.3390/insects14090759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/28/2023]
Abstract
The setae in Eriophyoidea are filiform, slightly bent and thickened near the base. Confocal microscopy indicates that their proximal and distal parts differ in light reflection and autofluorescence. Approximately 50 genera have atypically shaped setae: bifurcated, angled or swollen. These modifications are known in the basal part of prosomal setae u', ft', ft″, d, v, bv, ve, sc and caudal setae h2. We assessed the distribution of atypically shaped setae in Eriophyoidea and showed that they are scattered in different phylogenetic lineages. We hypothesized that the ancestral setae of eriophyoid mites were bifurcated before later simplifying into filiform setae. We also proposed that hypo-furcating setae are a synapomorphy that unites Eriophyoidea with Nematalycidae. We analyzed four new mitochondrial genomes of Leipothrix, the largest genus with bifurcated d, and showed that it is monophyletic and has a unique mitochondrial gene order with translocated trnK. We exclude Cereusacarus juniperensisn. comb. Xue and Yin, 2020 from Leipothrix and transfer five Epitrimerus spp. to Leipothrix: L. aegopodii (Liro 1941) n. comb., L. femoralis (Liro 1941) n. comb., L. geranii (Liro 1941) n. comb., L. ranunculi (Liro 1941) n. comb., and L. triquetra (Meyer 1990) n. comb.
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Affiliation(s)
- Philipp E. Chetverikov
- Zoological Institute of Russian Academy of Sciences, Universitetskaya Naberezhnaya 1, 199034 St. Petersburg, Russia;
- Department of Invertebrate Zoology, St. Petersburg State University, Universitetskaya Naberezhnaya 7/9, 199034 St. Petersburg, Russia
| | - Samuel J. Bolton
- Florida State Collection of Arthropods, Division of Plant Industry, Florida Department of Agriculture and Consumer Services, Gainesville, FL 32608, USA;
| | - Charnie Craemer
- Landcare Research, 231 Morrin Road, Auckland 1072, New Zealand;
| | - Vladimir D. Gankevich
- Zoological Institute of Russian Academy of Sciences, Universitetskaya Naberezhnaya 1, 199034 St. Petersburg, Russia;
| | - Anna S. Zhuk
- Institute of Applied Computer Science, ITMO University, 197101 St. Petersburg, Russia;
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Bolton SJ, Chetverikov PE, Ochoa R, Klimov PB. Where Eriophyoidea (Acariformes) Belong in the Tree of Life. INSECTS 2023; 14:527. [PMID: 37367343 DOI: 10.3390/insects14060527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/28/2023]
Abstract
Over the past century and a half, the taxonomic placement of Eriophyoidea has been in flux. For much of this period, this group has been treated as a subtaxon within Trombidiformes. However, the vast majority of recent phylogenetic analyses, including almost all phylogenomic analyses, place this group outside Trombidiformes. The few studies that still place Eriophyoidea within Trombidiformes are likely to be biased by incomplete taxon/gene sampling, long branch attraction, the omission of RNA secondary structure in sequence alignment, and the inclusion of hypervariable expansion-contraction rRNA regions. Based on the agreement among a number of independent analyses that use a range of different datasets (morphology; multiple genes; mitochondrial/whole genomes), Eriophyoidea are almost certain to be closely related to Nematalycidae, a family of vermiform mites within Endeostigmata, a basal acariform grade. Much of the morphological evidence in support of this relationship was apparent after the discovery of Nematalycidae in the middle of the 20th century. However, this evidence has largely been disregarded until very recently, perhaps because of overconfidence in the placement of Eriophyoidea within Trombidiformes. Here, we briefly review and identify a number of biases, both molecular- and morphology-based, that can lead to erroneous reconstructions of the position of Eriophyoidea in the tree of life.
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Affiliation(s)
- Samuel J Bolton
- Florida State Collection of Arthropods, Division of Plant Industry, Florida Department of Agriculture and Consumer Services, Gainesville, FL 32608, USA
| | - Philipp E Chetverikov
- Zoological Institute of Russian Academy of Sciences, Universitetskaya nab., 1, St. Petersburg 199034, Russia
| | - Ronald Ochoa
- Agricultural Research Service, Systematic Entomology Laboratory, United States Department of Agriculture, Beltsville, MD 20705, USA
| | - Pavel B Klimov
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
- Institute of Environmental and Agricultural Biology (X-BIO), University of Tyumen, Tyumen 625003, Russia
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6
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Chetverikov PE, Craemer C, Gankevich VD, Zhuk AS. Integrative Taxonomy of the Gall Mite Nothopoda todeica n. sp. (Eriophyidae) from the Disjunct Afro-Australasian Fern Todea barbara: Morphology, Phylogeny, and Mitogenomics. INSECTS 2023; 14:507. [PMID: 37367323 DOI: 10.3390/insects14060507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/27/2023] [Accepted: 05/27/2023] [Indexed: 06/28/2023]
Abstract
Eriophyoidea is a group of phytoparasitic mites with poorly resolved phylogeny. Previous studies inferred Eriophyidae s.l. as the largest molecular clade of Eriophyoidea, and Nothopodinae as the basal divergence of Eriophyidae s.l. We investigate the morphology and molecular phylogeny of Nothopoda todeican. sp. (Nothopodinae, Nothopodini), associated with a disjunct Afro-Australasian fern Todea barbara (Osmundaceae) from South Africa. Our analyses (1) determine new erroneous sequences (KF782375, KF782475, KF782586) wrongly assigned to Nothopodinae instead of Phyllocoptinae, (2) confirm the basal position of Nothopodinae in Eriophyoidea s.l., (3) question the monophyly of the Colopodacini and Nothopodini tribes, and (4) show the nested position of African fern-associated Nothopoda within a clade dominated by Asian nothopodines from angiosperms, which implies (a) a secondary association of nothopodines with ferns and (b) no relation between geography (continents) and the phylogenetic relationships of Nothopodinae species. Finally, we obtained a first complete mitochondrial genome for Nothopodinae and revealed a new gene order in the mitogenome of N. todeican. sp., notably deviating from those in other investigated eriophyoids. Our results contribute to resolving the phylogeny of Eriophyoidea and provide an example of an integrative study of a new taxon belonging to an economically important group of acariform mites.
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Affiliation(s)
- Philipp E Chetverikov
- Zoological Institute of Russian Academy of Sciences, Universitetskaya Nab. 1, 199034 St. Petersburg, Russia
| | - Charnie Craemer
- Manaaki Whenua-Landcare Research, 231 Morrin Road, Auckland 1072, New Zealand
| | - Vladimir D Gankevich
- Zoological Institute of Russian Academy of Sciences, Universitetskaya Nab. 1, 199034 St. Petersburg, Russia
| | - Anna S Zhuk
- Institute of Applied Computer Science, ITMO University, 191002 St. Petersburg, Russia
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7
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Sabroux R, Corbari L, Hassanin A. Phylogeny of sea spiders (Arthropoda: Pycnogonida) inferred from mitochondrial genome and 18S ribosomal RNA gene sequences. Mol Phylogenet Evol 2023; 182:107726. [PMID: 36754337 DOI: 10.1016/j.ympev.2023.107726] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 01/20/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023]
Abstract
The phylogeny of sea spiders has been debated for more than a century. Despite several molecular studies in the last twenty years, interfamilial relationships remain uncertain. In the present study, relationships within Pycnogonida are examined in the light of a new dataset composed of 160 mitochondrial genomes (including 152 new sequences) and 130 18S rRNA gene sequences (including 120 new sequences), from 141 sea spider morphospecies representing 26 genera and 9 families. Node congruence between mitochondrial and nuclear markers was analysed to identify the most reliable relationships. We also reanalysed a multilocus dataset previously published and showed that the high percentages of missing data make phylogenetic conclusions difficult and uncertain. Our results support the monophyly of most families currently accepted, except Callipallenidae and Nymphonidae, the monophyly of the superfamilies Ammotheoidea (Ammotheidae + Pallenopsidae), Nymphonoidea (Nymphonidae + Callipallenidae), Phoxichilidioidea (Phoxichilidiidae + Endeidae) and Colossendeoidea (Colossendeidae + Pycnogonidae + Rhynchothoracidae), and the sister-group relationship between Ammotheoidea and Phoxichilidioidea. We discuss the morphological evolution of sea spiders, identifying homoplastic characters and possible synapomorphies. We also discuss the palaeontological and phylogenetic arguments supporting either a radiation of sea spiders prior to Jurassic or a progressive diversification from Ordovician or Cambrian.
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Affiliation(s)
- Romain Sabroux
- Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, 57 rue Cuvier, CP 51, 75005 Paris, France
| | - Laure Corbari
- Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, 57 rue Cuvier, CP 51, 75005 Paris, France
| | - Alexandre Hassanin
- Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, UA, 57 rue Cuvier, CP 51, 75005 Paris, France.
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8
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Bi S, Song Y, Liu L, Wan J, Zhou Y, Zhu Q, Liu J. Complete Mitochondrial Genome of Piophila casei (Diptera: Piophilidae): Genome Description and Phylogenetic Implications. Genes (Basel) 2023; 14:genes14040883. [PMID: 37107641 PMCID: PMC10137744 DOI: 10.3390/genes14040883] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
Piophila casei is a flesh-feeding Diptera insect that adversely affects foodstuffs, such as dry-cured ham and cheese, and decaying human and animal carcasses. However, the unknown mitochondrial genome of P. casei can provide information on its genetic structure and phylogenetic position, which is of great significance to the research on its prevention and control. Therefore, we sequenced, annotated, and analyzed the previously unknown complete mitochondrial genome of P. casei. The complete mt genome of P. casei is a typical circular DNA, 15,785 bp in length, with a high A + T content of 76.6%. It contains 13 protein-coding genes (PCG), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and 1 control region. Phylogenetic analysis of 25 Diptera species was conducted using Bayesian and maximum likelihood methods, and their divergence times were inferred. The comparison of the mt genomes from two morphologically similar insects P. casei and Piophila megastigmata indicates a divergence time of 7.28 MYA between these species. The study provides a reference for understanding the forensic medicine, taxonomy, and genetics of P. casei.
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Affiliation(s)
- Shenghui Bi
- School of Liquor and Food Engineering, Guizhou University, Guiyang 550025, China
- Scientific Observing and Experimental Station of Crop Pest in Guiyang, Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Institute of Entomology, Guizhou University, Ministry of Agriculture, Guiyang 550025, China
| | - Yanfei Song
- Scientific Observing and Experimental Station of Crop Pest in Guiyang, Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Institute of Entomology, Guizhou University, Ministry of Agriculture, Guiyang 550025, China
| | - Linggao Liu
- School of Liquor and Food Engineering, Guizhou University, Guiyang 550025, China
| | - Jing Wan
- School of Liquor and Food Engineering, Guizhou University, Guiyang 550025, China
| | - Ying Zhou
- School of Liquor and Food Engineering, Guizhou University, Guiyang 550025, China
| | - Qiujin Zhu
- School of Liquor and Food Engineering, Guizhou University, Guiyang 550025, China
| | - Jianfeng Liu
- Scientific Observing and Experimental Station of Crop Pest in Guiyang, Guizhou Provincial Key Laboratory for Agricultural Pest Management of the Mountainous Region, Institute of Entomology, Guizhou University, Ministry of Agriculture, Guiyang 550025, China
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9
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Xia X, Peng CW, Ye QT, Bing XL, Hong XY. Rop plays conserved roles in the reproductive and digestive processes of spider mites. INSECT SCIENCE 2023; 30:351-364. [PMID: 35980307 DOI: 10.1111/1744-7917.13103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/19/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Ras opposite (Rop) is known to play an essential role in regulating vesicle trafficking, including synaptic transmission and general secretion. The fundamental roles of Rop have been confirmed by the observation that null mutations in many organisms generate lethal phenotypes during embryogenesis. However, the effects of Rop during the postembryonic stages, especially in non-model organisms, remain largely unknown. Here, we provide new data that enhance our understanding of Rop's roles in the adults of multiple species of Tetranychus spider mites (Acari: Tetranychidae), a class of notorious agricultural pests. Our in silico and experimental evidence demonstrated that Rop is under purifying selection and is highly conserved in Tetranychus spp. RNA interference experiments showed that Rop is required for maintaining normal fecundity but has no significant effect on survival. We further demonstrate that knockdown of Rop darkens the body color of spider mites and blocks the excretion of fecal pellets, which is likely to be related to an abnormality in the excretion of food waste in the digestive system. Overall, our findings clarify novel functions of a vesicle trafficking-related gene in the adult stage of multiple Tetranychus species and highlight the need to evaluate the roles of essential genes in various organisms.
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Affiliation(s)
- Xue Xia
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Chang-Wu Peng
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Qing-Tong Ye
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Xiao-Li Bing
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, China
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10
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Macroevolutionary analyses point to a key role of hosts in diversification of the highly speciose eriophyoid mite superfamily. Mol Phylogenet Evol 2023; 179:107676. [PMID: 36535519 DOI: 10.1016/j.ympev.2022.107676] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 12/05/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
The superfamily Eriophyoidea includes >5000 named species of very small phytophagous mites. As for many groups of phytophagous invertebrates, factors responsible for diversification of eriophyoid mites are unclear. Here, we used an inferred phylogeny of 566 putative species of eriophyoid mites based on fragments of two mitochondrial genes and two nuclear genes to examine factors associated with their massive evolutionary diversification through time. Our dated phylogeny indicates a Carboniferous origin for gymnosperm-associated Eriophyoidea with subsequent diversification involving multiple host shifts to angiosperms-first to dicots, and then to monocots or shifts back to gymnosperms-beginning in the Cretaceous period when angiosperms diverged. Speciation rates increased more rapidly in the Eriophyidae + Diptilomiopidae (mostly infesting angiosperms) than in the Phytoptidae (mostly infesting gymnosperms). Phylogenetic signal, speciation rates, dispersal and vicariance results combined with inferred topologies show that hosts played a key role in the evolution of eriophyoid mites. Speciation constrained by hosts was probably the main driver behind eriophyoid mite diversification worldwide. We demonstrate monophyly of the Eriophyoidea, whereas all three families, most subfamilies, tribes, and most genera are not monophyletic. Our time-calibrated tree provides a framework for further evolutionary studies of eriophyoid mites and their interactions with host plants as well as taxonomic revisions above the species level.
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11
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Khakestani N, Latifi M, Babaeian E, Knee W, Hosseini S. Structure and molecular evolution of the barcode fragment of cytochrome oxidase I (COI) in Macrocheles (Acari: Mesostigmata: Macrochelidae). Ecol Evol 2022; 12:e9553. [PMID: 36514552 PMCID: PMC9731855 DOI: 10.1002/ece3.9553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 10/24/2022] [Accepted: 11/09/2022] [Indexed: 12/13/2022] Open
Abstract
Consisting of approximately 320 species, Macrocheles is the most widely distributed genus in the family Macrochelidae. Though some studies have focused on the description of Macrochelidae using molecular techniques (e.g., RAPD) and sequencing of some genes, the interspecies relationships within Macrocheles still remain uncertain. As such, in the present study, we examine all publicly available data in GenBank to explore the evolutionary relationships, divergence times, and amino acid variations within Macrocheles. Exploring the patterns of variation in the secondary protein structure shows high levels of conservation in the second and last helices, emphasizing their involvement in the energy metabolism function of the cytochrome oxidase subunit I enzyme. According to our phylogenetic analysis, all available Macrocheles species are clustered in a monophyletic group. However, in the reconstructed trees, we subdivided M. merdarius and M. willowae into two well-supported intraspecific clades that are driven by geographic separation and host specificity. We also estimate the divergence time of selected species using calibration evidence from available fossils and previous studies. Thus, we estimate that the age of the Parasitiformes is 320.4 (273.3-384.3) Mya (Permian), and the Mesostigmata is 285.1 (270.8-286.4) Mya (Carboniferous), both with likely origins in the Paleozoic era. We also estimate that Macrocheles diverged from other Mesostigmata mites during the Mesozoic, approximately 222.9 Mya.
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Affiliation(s)
- Najme Khakestani
- Department of Plant Protection, Faculty of AgricultureVali‐e‐Asr University of RafsanjanRafsanjanIran
| | - Malihe Latifi
- Department of Plant Protection, Faculty of AgricultureVali‐e‐Asr University of RafsanjanRafsanjanIran
| | - Esmaeil Babaeian
- Centre for Biodiversity GenomicsUniversity of GuelphGuelphCanada
| | - Wayne Knee
- Canadian National Collection of Insects, Arachnids, and Nematodes, Agriculture and Agri‐Food CanadaOttawaOntarioCanada
| | - Samin Hosseini
- Department of Plant Protection, Faculty of AgricultureVali‐e‐Asr University of RafsanjanRafsanjanIran
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12
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Chetverikov PE, Bertone MA. First rhyncaphytoptine mite (Eriophyoidea, Diptilomiopidae) parasitizing American hazelnut (Corylus americana): molecular identification, confocal microscopy, and phylogenetic position. EXPERIMENTAL & APPLIED ACAROLOGY 2022; 88:75-95. [PMID: 36318416 DOI: 10.1007/s10493-022-00740-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
The plant genus Corylus is an economically important crop, valued especially for its nuts. Numerous pathogens and harmful phytophagous arthropods are known to damage hazelnuts. We report on a new eriophyoid mite, Rhyncaphytoptus corylivagrans n. sp., and the first record of Coptophylla lamimani both collected from leaves of American hazelnut (Corylus americana) in North Carolina, USA. Including our new data, the complex of eriophyoids from Corylus comprises 15 species from three families: Phytoptidae (2 spp.), Eriophyidae (11 spp.), and Diptilomiopidae (2 spp.). We obtained sequences of three genes (Cox1, D1-D5 28S, and ITS1-5.8S-ITS2), applied BLAST and tree-based approaches for identification of R. corylivagrans n. sp., and performed the first molecular phylogenetic analysis focused on Rhyncaphytoptinae. Among the three genes, Cox1 showed better power when used for BLAST searches. Combined molecular phylogenetic analyses inferred R. corylivagrans n. sp. as sister to R. betulae, determined several moderately supported host-specific lineages of rhyncaphytoptines, and indicated a close relationship of the new species with members of the genus Rhinotergum. In two Rhinotergum spp. from Rosaceae, confocal microscopy revealed a new structure, the needle-like anterior process of the prodorsal shield, which is absent in R. corylivagrans n. sp. Additionally, the elements of the anal secretory apparatus presumably associated with silk-production and hypothesized as a synapomorphy of Eriophyoidea, were detected in the new species, providing the first documented report of this structure in Diptilomiopidae. Our study contributes to knowledge on the biodiversity of phytoparasites associated with hazelnuts and calls for future comparative phylogenetics of Diptilomiopidae.
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Affiliation(s)
- Philipp E Chetverikov
- Saint-Petersburg State University, Universitetskaya nab. 7/9, 199034, St. Petersburg, Russia.
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, 199034,, St. Petersburg, Russia.
| | - Matthew A Bertone
- Department of Entomology and Plant Pathology, North Carolina State University, Campus Box 7613, 27695, Raleigh, NC, USA.
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13
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Abstract
Acari harbor numerous minute species of agricultural economic importance, mainly Tetranychidae and Phytoseiidae. Great efforts have been established by means of recovering morphological, molecular, and phylogenetic traits for species identification. Traditional identification still relies on external diagnostic characters, which are limited and usually exhibit large phenotypic plasticity within the species, rendering them useless for species delimitation and identification. We decided to increase the number of sequences of the Acari mitochondrial COI (Cytochrome C oxidase I) marker and ITS nuclear ribosomal DNA region for species identification in Tetranychidae and Phytoseiidae. The molecular data allow us to establish species boundaries and phylogenetic relationships among several clades of Acari, mainly Tetranychidae and Phytoseiidae. Sequence comparisons between complete COI and the Acari mitochondrial COI, ITS1-5,8S-ITS2, and ITS2 among all Acari sequences have demonstrated that the selected regions, even small, gave enough informative positions for both species’ identification and phylogenetic studies. Analyses of both DNA regions have unveiled their use as species identification characters, with special emphasis on Acari mitochondrial COI for Tetranychidae and Phytoseiidae species in comparison with the Folmer fragment, which has been universally used as a barcode marker. We demonstrated that the Acari mitochondrial COI region is also a suitable marker to establish a barcode dataset for Acari identification. Our phylogenetic analyses are congruent with other recent works, showing that Acari is a monophyletic group, of which Astigmata, Ixodida, Mesostigmata, Oribatida, and Prostigmata are also monophyletic.
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14
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Ban XC, Shao ZK, Wu LJ, Sun JT, Xue XF. Highly diversified mitochondrial genomes provide new evidence for interordinal relationships in the Arachnida. Cladistics 2022; 38:452-464. [PMID: 35349189 DOI: 10.1111/cla.12504] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2022] [Indexed: 12/11/2022] Open
Abstract
Arachnida is an exceptionally diverse class in the Arthropoda, consisting of 20 orders and playing crucial roles in the terrestrial ecosystems. However, their interordinal relationships have been debated for over a century. Rearranged or highly rearranged mitochondrial genomes (mitogenomes) were consistently found in this class, but their various extent in different lineages and efficiency for resolving arachnid phylogenies are unclear. Here, we reconstructed phylogenetic trees using mitogenome sequences of 290 arachnid species to decipher interordinal relationships as well as diversification through time. Our results recovered monophyly of ten orders (i.e. Amblypygi, Araneae, Ixodida, Mesostigmata, Opiliones, Pseudoscorpiones, Ricinulei, Sarcoptiformes, Scorpiones and Solifugae), while rejecting monophyly of the Trombidiformes due to the unstable position of the Eriophyoidea. The monophyly of Acari (subclass) was rejected, possibly due to the long-branch attraction of the Pseudoscorpiones. The monophyly of Arachnida was further rejected because the Xiphosura nested within arachnid orders with unstable positions. Mitogenomes that are highly rearranged in mites but less rearranged or conserved in the remaining lineages point to their exceptional diversification in mite orders; however, shared derived mitochondrial (mt) gene clusters were found within superfamilies rather than interorders, confusing phylogenetic signals in arachnid interordinal relationships. Molecular dating results show that arachnid orders have ancient origins, ranging from the Ordovician to the Carboniferous, yet have significantly diversified since the Cretaceous in orders Araneae, Mesostigmata, Sarcoptiformes, and Trombidiformes. By summarizing previously resolved key positions of some orders, we propose a plausible arachnid tree of life. Our results underline a more precise framework for interordinal phylogeny in the Arachnida and provide new insights into their ancient evolution.
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Affiliation(s)
- Xin-Chao Ban
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zi-Kai Shao
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Li-Jun Wu
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Jing-Tao Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Xiao-Feng Xue
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
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15
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Klimov PB, Chetverikov PE, Dodueva IE, Vishnyakov AE, Bolton SJ, Paponova SS, Lutova LA, Tolstikov AV. Symbiotic bacteria of the gall-inducing mite Fragariocoptes setiger (Eriophyoidea) and phylogenomic resolution of the eriophyoid position among Acari. Sci Rep 2022; 12:3811. [PMID: 35264574 PMCID: PMC8907322 DOI: 10.1038/s41598-022-07535-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/17/2022] [Indexed: 12/13/2022] Open
Abstract
Eriophyoid mites represent a hyperdiverse, phytophagous lineage with an unclear phylogenetic position. These mites have succeeded in colonizing nearly every seed plant species, and this evolutionary success was in part due to the mites' ability to induce galls in plants. A gall is a unique niche that provides the inducer of this modification with vital resources. The exact mechanism of gall formation is still not understood, even as to whether it is endogenic (mites directly cause galls) or exogenic (symbiotic microorganisms are involved). Here we (i) investigate the phylogenetic affinities of eriophyoids and (ii) use comparative metagenomics to test the hypothesis that the endosymbionts of eriophyoid mites are involved in gall formation. Our phylogenomic analysis robustly inferred eriophyoids as closely related to Nematalycidae, a group of deep-soil mites belonging to Endeostigmata. Our comparative metagenomics, fluorescence in situ hybridization, and electron microscopy experiments identified two candidate endosymbiotic bacteria shared across samples, however, it is unlikely that they are gall inducers (morphotype1: novel Wolbachia, morphotype2: possibly Agrobacterium tumefaciens). We also detected an array of plant pathogens associated with galls that may be vectored by the mites, and we determined a mite pathogenic virus (Betabaculovirus) that could be tested for using in biocontrol of agricultural pest mites.
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Affiliation(s)
- Pavel B Klimov
- X-BIO Institute, Tyumen State University, Tyumen, Russia, 625003.
| | | | - Irina E Dodueva
- Saint-Petersburg State University, St. Petersburg, Russia, 199034
| | | | - Samuel J Bolton
- Florida Department of Agriculture and Consumer Services, Gainesville, FL, USA
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Bajda SA, De Clercq P, Van Leeuwen T. Selectivity and molecular stress responses to classical and botanical acaricides in the predatory mite Phytoseiulus persimilis Athias-Henriot (Acari: Phytoseiidae). PEST MANAGEMENT SCIENCE 2022; 78:881-895. [PMID: 34862726 DOI: 10.1002/ps.6747] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/28/2021] [Accepted: 12/04/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND Acaricide application remains an integral component of integrated pest management (IPM) for the two-spotted spider mite Tetranychus urticae. Species and strains of phytoseiid predatory mites vary significantly in their response to acaricides. For the success of IPM, it is imperative to identify the determinants of selectivity and molecular stress responses of acaricides in predatory mites. RESULTS The three classical acaricides bifenazate, cyflumetofen, and fenbutatin oxide did not affect the survival and fecundity of Phytoseiulus persimilis regardless of the route of exposure. Selectivity of the orange oil and terpenoid blend-based botanical acaricides was low via a combination of direct exposure, acaricide-laced diet, and residual exposure but improved when limiting exposure only to diet. To gain insights into the molecular stress responses, the transcriptome of P. persimilis was assembled. Subsequent gene expression analysis of predatory mites orally exposed to fenbutatin oxide and orange oil yielded only a limited xenobiotic stress response. In contrast, P. persimilis exhibited target-site resistance mutations, including I260M in SdhB, I1017M in CHS1, and kdr and super-kdr in VGSC. Extending the screen using available Phytoseiidae sequences uncovered I136T, S141F in cytb, G119S in AChE, and A2083V in ACC, well-known target-sites of acaricides. CONCLUSION Selectivity of the tested botanical acaricides to P. persimilis was low but could be enhanced by restricting exposure to a single route. Differential gene expression analysis did not show a robust induced stress response after sublethal exposure. In contrast, this study uncovered target-site mutations that may help to explain the physiological selectivity of several classical acaricides to phytoseiid predators.
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Affiliation(s)
- Sabina A Bajda
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Patrick De Clercq
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Thomas Van Leeuwen
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Chetverikov PE, Rector BG, Tonkel K, Dimitri L, Cheglakov DS, Romanovich AE, Amrine J. Phylogenetic Position of a New Trisetacus Mite Species (Nalepellidae) Destroying Seeds of North American Junipers and New Hypotheses on Basal Divergence of Eriophyoidea. INSECTS 2022; 13:insects13020201. [PMID: 35206774 PMCID: PMC8876007 DOI: 10.3390/insects13020201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 01/27/2023]
Abstract
Simple Summary Eriophyoid mites are microscopic herbivores associated with higher plants. Some of them are serious pests due to their ability to vector viruses and cause other damage to host plants. Mites of the genus Trisetacus are widespread parasites of conifers. They usually live in buds, cones, and rarely within needles of Pinaceae (pine family) and Cupressaceae (cypress family). We discovered a new species, Trisetacus indelisn. sp., severely damaging seeds of three North American junipers in the western USA. This species possesses two morphologically different forms of females and has two deletion mutations in the gene cytochrome oxidase subunit I (Cox1). Such mutations are rare in eriophyoids and were previously detected only in two pestiferous species from palms and hazelnut. Our molecular-phylogenetic analyses determine the closest known relatives of the new species and suggest that Old and New World Trisetacus independently transitioned to living in seeds of junipers. Additionally we show that reconstruction of the phylogeny of Eriophyoidea based on one gene, Cox1, produces a poorly-resolved but biologically consistent tree topology to hypothesize the evolution of Eriophyoidea. Overall, our study improves our understanding of the diversity of conifer-inhabiting mites and indicates further needs in investigating the phylogeny of Eriophyoidea. Abstract Eriophyoid mites of the genus Trisetacus Keifer are widespread parasites of conifers. A new oligophagous species, T. indelis n. sp., was discovered severely damaging seeds of North American junipers (Juniperus osteosperma, J. occidentalis, and J. californica) in the western USA. It has two codon deletions in the mitochondrial gene Cox1 rarely detected in Eriophyoidea and includes distinct morphological dimorphism of females. A phylogenetic analysis based on amino acid alignment of translated Cox1 sequences using a large set of out-groups (a) determined that two North American congeners, T. batonrougei and T. neoquadrisetus, were the closest known relatives of T. indelis n. sp., and (b) indicated that Old and New World seed-inhabiting Trisetacus from junipers do not form a distinct clade, suggesting a possible independent transition to living in seeds of junipers in America and Eurasia by Trisetacus spp. Our analysis produced a new topology consistent with a scenario assuming gradual reduction of prodorsal shield setation in Eriophyoidea and an ancient switch from gymnosperms to other hosts. Additionally, our analysis did not support monophyly of Trisetacus; recovered a new host-specific, moderately supported clade comprising Trisetacus and Nalepellinae (Nalepella + Setoptus) associated with Pinaceae; and questioned the monophyly of Trisetacus associated with Cupressaceae.
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Affiliation(s)
- Philipp E. Chetverikov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab. 1, 199034 St. Petersburg, Russia;
- Department of Invertebrate Zoology, St. Petersburg State University, Universitetskaya Nab. 7/9, 199034 St. Petersburg, Russia;
- Correspondence:
| | - Brian G. Rector
- USDA-ARS-GBRRU, 920 Valley Road, Reno, NV 89512, USA; (B.G.R.); (K.T.); (L.D.)
| | - Kirk Tonkel
- USDA-ARS-GBRRU, 920 Valley Road, Reno, NV 89512, USA; (B.G.R.); (K.T.); (L.D.)
| | - Lindsay Dimitri
- USDA-ARS-GBRRU, 920 Valley Road, Reno, NV 89512, USA; (B.G.R.); (K.T.); (L.D.)
| | - Denis S. Cheglakov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab. 1, 199034 St. Petersburg, Russia;
- Department of Invertebrate Zoology, St. Petersburg State University, Universitetskaya Nab. 7/9, 199034 St. Petersburg, Russia;
| | - Anna E. Romanovich
- Department of Invertebrate Zoology, St. Petersburg State University, Universitetskaya Nab. 7/9, 199034 St. Petersburg, Russia;
| | - James Amrine
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506, USA;
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18
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Thia JA, Young ND, Korhnen PK, Yang Q, Gasser RB, Umina PA, Hoffmann AA. The mitogenome of Halotydeus destructor (Tucker) and its relationships with other trombidiform mites as inferred from nucleotide sequences and gene arrangements. Ecol Evol 2021; 11:14162-14174. [PMID: 34707848 PMCID: PMC8525180 DOI: 10.1002/ece3.8133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/25/2021] [Accepted: 09/01/2021] [Indexed: 01/02/2023] Open
Abstract
The redlegged earth mite, Halotydeus destructor (Tucker, 1925: Trombidiformes, Eupodoidea, Penthaleidae), is an invasive mite species. In Australia, this mite has become a pest of winter pastures and grain crops. We report the complete mitogenome for H. destructor, the first to represent the family Penthaleidae, superfamily Eupodoidea. The mitogenome of H. destructor is 14,691 bp in size, and has a GC content of 27.87%, 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. We explored evolutionary relationships of H. destructor with other members of the Trombidiformes using phylogenetic analyses of nucleotide sequences and the order of protein-coding and rRNA genes. We found strong, consistent support for the superfamily Tydeoidea being the sister taxon to the superfamily Eupodoidea based on nucleotide sequences and gene arrangements. Moreover, the gene arrangements of Eupodoidea and Tydeoidea are not only identical to each other but also identical to that of the hypothesized arthropod ancestor, showing a high level of conservatism in the mitogenomic structure of these mite superfamilies. Our study illustrates the utility of gene arrangements for providing complementary information to nucleotide sequences with respect to inferring the evolutionary relationships of species within the order Trombidiformes. The mitogenome of H. destructor provides a valuable resource for further population genetic studies of this important agricultural pest. Given the co-occurrence of closely related, morphologically similar Penthaleidae mites with H. destructor in the field, a complete mitogenome provides new opportunities to develop metabarcoding tools to study mite diversity in agro-ecosystems. Moreover, the H. destructor mitogenome fills an important taxonomic gap that will facilitate further study of trombidiform mite evolution.
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Affiliation(s)
- Joshua A. Thia
- Bio 21 Institute, School of BioSciencesThe University of MelbourneMelbourneVictoriaAustralia
| | - Neil D. Young
- Department of Veterinary Biosciences, Melbourne Veterinary SchoolThe University of MelbourneMelbourneVictoriaAustralia
| | - Pasi K. Korhnen
- Department of Veterinary Biosciences, Melbourne Veterinary SchoolThe University of MelbourneMelbourneVictoriaAustralia
| | - Qiong Yang
- Bio 21 Institute, School of BioSciencesThe University of MelbourneMelbourneVictoriaAustralia
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary SchoolThe University of MelbourneMelbourneVictoriaAustralia
| | - Paul A. Umina
- Bio 21 Institute, School of BioSciencesThe University of MelbourneMelbourneVictoriaAustralia
- Cesar AustraliaBrunswickVictoriaAustralia
| | - Ary A. Hoffmann
- Bio 21 Institute, School of BioSciencesThe University of MelbourneMelbourneVictoriaAustralia
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19
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Duan DY, Chen Z, Fu YT, Liu GH, Cheng TY. Characterization of the complete mitochondrial genomes of two Ixodes ticks, I. nipponensis and Ixodes (Pholeoixodes) sp. MEDICAL AND VETERINARY ENTOMOLOGY 2021; 35:513-522. [PMID: 33931902 DOI: 10.1111/mve.12523] [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: 07/07/2020] [Revised: 04/10/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
In this study, the authors sequenced and characterized the complete mitochondrial (mt) genomes of two hard ticks of the genus Ixodes, I. nipponensis and Ixodes (Pholeoixodes) sp., which were 14 505 and 14 543 bp in length, respectively. Their mt genomes encoded 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA genes and two ribosomal RNA genes, and have only one non-coding region. The gene order in their mt genomes was the same as that of other Ixodes spp. mt genomes. The average sequence identity, combined nucleotide diversity, non-synonymous/synonymous substitutions ratio analyses consistently demonstrated that cox1, rrnS, cox2, cox3 and cytb were the most conserved and atp8, nad6 and nad2 were the most variable genes across Ixodes mitogenomes. Phylogeny of the present Ixodes spp., and other selected hard tick species, based on concatenated amino acid sequences of PCGs, confirmed their position within the genus Ixodes and sub-family Ixodinae. The novel mt markers described herein will be useful for further studies of the population genetics, molecular epidemiology and systematics of hard ticks.
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Affiliation(s)
- D-Y Duan
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, China
- Hunan Co-Innovation Center of Animal Production Safety, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, China
| | - Z Chen
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, China
| | - Y-T Fu
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, China
| | - G-H Liu
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, China
- Hunan Co-Innovation Center of Animal Production Safety, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, China
| | - T-Y Cheng
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, China
- Hunan Co-Innovation Center of Animal Production Safety, College of Veterinary Medicine, Hunan Agricultural University, Changsha, Hunan Province, China
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20
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Druciarek T, Lewandowski M, Tzanetakis I. Molecular phylogeny of Phyllocoptes associated with roses discloses the presence of a new species. INFECTION GENETICS AND EVOLUTION 2021; 95:105051. [PMID: 34450295 DOI: 10.1016/j.meegid.2021.105051] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/16/2021] [Accepted: 08/22/2021] [Indexed: 11/17/2022]
Abstract
There are few plant maladies as devastating as rose rosette, a disease caused by an eriophyoid -transmitted virus. Rosette annihilates roses across North America, and to date, there is a single verified vector of the virus, Phyllocoptes fructiphilus Keifer. In direct contrast to the importance of rose for the ornamental industry there is limited knowledge on the eriophyoids that inhabit roses in North America and even less information on their vectoring capacities. This study dissects the genetic diversity of the eriophyoid fauna in rosette-affected hotspots and provides evidence of the existence of an undescribed species named Phyllocoptes arcani sp. nov., that could potentially be a second vector of the rosette virus.
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Affiliation(s)
- Tobiasz Druciarek
- Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System Fayetteville, AR 72701, United States.
| | - Mariusz Lewandowski
- Section of Applied Entomology, Department of Plant Protection, Institute of Horticultural Sciences, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Ioannis Tzanetakis
- Entomology and Plant Pathology, Division of Agriculture, University of Arkansas System Fayetteville, AR 72701, United States.
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21
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Liu Q, Deng Y, Song A, Xiang Y, Chen D, Wei L. Comparative analysis of mite genomes reveals positive selection for diet adaptation. Commun Biol 2021; 4:668. [PMID: 34083730 PMCID: PMC8175442 DOI: 10.1038/s42003-021-02173-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/30/2021] [Indexed: 02/06/2023] Open
Abstract
Diet is a powerful evolutionary force for species adaptation and diversification. Acari is one of the most abundant clades of Arachnida, exhibiting diverse dietary types, while the underlying genetic adaptive mechanisms are not fully understood. Based on comparative analyses of 15 Acari genomes, we found genetic bases for three specialized diets. Herbivores experienced stronger selection pressure than other groups; the olfactory genes and gene families involving metabolizing toxins showed strong adaptive signals. Genes and gene families related to anticoagulation, detoxification, and haemoglobin digestion were found to be under strong selection pressure or significantly expanded in the blood-feeding species. Lipid metabolism genes have a faster evolutionary rate and been subjected to greater selection pressures in fat-feeding species; one positively selected site in the fatty-acid amide hydrolases 2 gene was identified. Our research provides a new perspective for the evolution of Acari and offers potential target loci for novel pesticide development.
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Affiliation(s)
- Qiong Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yuhua Deng
- Clinical Research Institute, The First People's Hospital of Foshan, Foshan, China
| | - An Song
- ShaanXi JunDa Forensic Medicine Expertise Station, The Fourth Military Medical University, Xi'an, China
| | - Yifan Xiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - De Chen
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China.
| | - Lai Wei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.
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22
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Plazzi F, Puccio G, Passamonti M. HERMES: An improved method to test mitochondrial genome molecular synapomorphies among clades. Mitochondrion 2021; 58:285-295. [PMID: 33639269 DOI: 10.1016/j.mito.2021.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 01/10/2021] [Accepted: 02/12/2021] [Indexed: 02/06/2023]
Abstract
Mitochondrial chromosomes have diversified among eukaryotes and many different architectures and features are now acknowledged for this genome. Here we present the improved HERMES index, which can measure and quantify the amount of molecular change experienced by mitochondrial genomes. We test the improved approach with ten molecular phylogenetic studies based on complete mitochondrial genomes, representing six bilaterian Phyla. In most cases, HERMES analysis spotted out clades or single species with peculiar molecular synapomorphies, allowing to identify phylogenetic and ecological patterns. The software presented herein handles linear, circular, and multi-chromosome genomes, thus widening the HERMES scope to the complete eukaryotic domain.
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Affiliation(s)
- Federico Plazzi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3, 40126 Bologna, Italy.
| | - Guglielmo Puccio
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3, 40126 Bologna, Italy.
| | - Marco Passamonti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, via Selmi, 3, 40126 Bologna, Italy.
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23
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Chetverikov PE, Craemer C, Cvrković T, Klimov PB, Petanović RU, Romanovich AE, Sukhareva SI, Zukoff SN, Bolton S, Amrine J. Molecular phylogeny of the phytoparasitic mite family Phytoptidae (Acariformes: Eriophyoidea) identified the female genitalic anatomy as a major macroevolutionary factor and revealed multiple origins of gall induction. EXPERIMENTAL & APPLIED ACAROLOGY 2021; 83:31-68. [PMID: 33201392 DOI: 10.1007/s10493-020-00571-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 11/07/2020] [Indexed: 06/11/2023]
Abstract
Phytoptidae s.str. is a lineage of eriophyoid mites associated with angiosperms. Based on representative taxon sampling and four gene markers (COI, HSP70, 18S, and 28S), we inferred the molecular phylogeny of this group and performed comparative analyses of cuticle-lined female internal genitalia. Although basal relationships were unclear, several well supported clades were recovered. These clades were supported by geography, host associations, and female genital anatomy, but contradicted the current morphology-based systematics. The monophyly of each of five conventional supraspecific groupings (Fragariocoptes, Phytoptus, Phytoptinae, Sierraphytoptinae, and Sierraphytoptini) is rejected based on a series of statistical tests. Additionally, four morphological characters (the absence of tibial solenidion φ and opisthosomal seta c1, presence of telosomal pseudotagma, and 'morphotype') were found to be homoplasies that cannot be used to confidently delimit supraspecific lineages of phytoptids. However, our molecular topology was highly congruent with female genital characters. Eight molecular clades were unambiguously supported by the shapes and topography of the spermathecal apparatus and genital apodemes. This suggests that the female genital anatomy could be an important factor affecting cladogenesis in Phytoptidae, a conclusion contrasting with the general expectation that host characteristics should be a major macroevolutionary force influencing the evolution of host-specific symbionts. Indeed, despite the high host-specificity, there were no apparent cophylogenetic patterns. Furthermore, we show that gall-inducing ability evolved multiple times in phytoptids. Because gall formation creates nearly instantaneous niche partitioning and the potential loss or reduction of gene flow, we hypothesize that it could be an important evolutionary factor affecting speciation within different host-associated clades of phytoptid mites.
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Affiliation(s)
- Philipp E Chetverikov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, St. Petersburg, Russia, 199034.
- Saint-Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, Russia, 199034.
| | - Charnie Craemer
- ARC-Plant Protection Research Institute, Queenswood, P/Bag X134, Pretoria, 0121, South Africa
| | - Tatjana Cvrković
- Department of Plant Pests, Institute for Plant Protection and Environment, Banatska 33, 11080, Zemun, Serbia
| | - Pavel B Klimov
- Department of Ecology and Evolutionary Biology, University of Michigan, 1109 Geddes Ave, Ann Arbor, MI, 48109-1079, USA
| | - Radmila U Petanović
- Serbian Academy of Sciences and Arts, Knez Mihailova 35, 11000, Belgrade, Serbia
- Faculty of Agriculture, University of Belgrade, Nemanjina 6, 11080, Zemun, Serbia
| | - Anna E Romanovich
- Resource Center for Development of Molecular and Cellular Technologies, St. Petersburg State University, Universitetskaya Nab., 7/9, St. Petersburg, Russia, 199034
| | - Sogdiana I Sukhareva
- Saint-Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, Russia, 199034
| | - Sarah N Zukoff
- Southwest Research and Extension Center, Kansas State University, 4500 E. Mary Street, Garden City, KS, 67846, USA
| | - Samuel Bolton
- Division of Plant Industry, Florida Department of Agriculture and Consumer Services, 1911 SW 34th St, Gainesville, FL, 32614-7100, USA
| | - James Amrine
- Division of Plant and Soil Sciences, West Virginia University, P.O. Box 6108, Morgantown, WV, 26506-6108, USA
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24
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Pachl P, Uusitalo M, Scheu S, Schaefer I, Maraun M. Repeated convergent evolution of parthenogenesis in Acariformes (Acari). Ecol Evol 2021; 11:321-337. [PMID: 33437432 PMCID: PMC7790623 DOI: 10.1002/ece3.7047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 10/19/2020] [Accepted: 10/30/2020] [Indexed: 11/30/2022] Open
Abstract
The existence of old species-rich parthenogenetic taxa is a conundrum in evolutionary biology. Such taxa point to ancient parthenogenetic radiations resulting in morphologically distinct species. Ancient parthenogenetic taxa have been proposed to exist in bdelloid rotifers, darwinulid ostracods, and in several taxa of acariform mites (Acariformes, Acari), especially in oribatid mites (Oribatida, Acari). Here, we investigate the diversification of Acariformes and their ancestral mode of reproduction using 18S rRNA. Because parthenogenetic taxa tend to be more frequent in phylogenetically old taxa of Acariformes, we sequenced a wide range of members of this taxon, including early-derivative taxa of Prostigmata, Astigmata, Endeostigmata, and Oribatida. Ancestral character state reconstruction indicated that (a) Acariformes as well as Oribatida evolved from a sexual ancestor, (b) the primary mode of reproduction during evolution of Acariformes was sexual; however, species-rich parthenogenetic taxa radiated independently at least four times (in Brachychthonioidea (Oribatida), Enarthronota (Oribatida), and twice in Nothrina (Oribatida), (c) parthenogenesis additionally evolved frequently in species-poor taxa, for example, Tectocepheus, Oppiella, Rostrozetes, Limnozetes, and Atropacarus, and (d) sexual reproduction likely re-evolved at least three times from species-rich parthenogenetic clusters, in Crotonia (Nothrina), in Mesoplophora/Apoplophora (Mesoplophoridae, Enarthronota), and in Sphaerochthonius/Prototritia (Protoplophoridae, Enarthronota). We discuss possible reasons that favored the frequent diversification of parthenogenetic taxa including the continuous long-term availability of dead organic matter resources as well as generalist feeding of species as indicated by natural variations in stable isotope ratios.
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Affiliation(s)
- Patrick Pachl
- JFB Institute of Zoology and AnthropologyUniversity of GöttingenGöttingenGermany
| | - Matti Uusitalo
- Zoological MuseumCentre for Biodiversity of TurkuTurkuFinland
| | - Stefan Scheu
- JFB Institute of Zoology and AnthropologyUniversity of GöttingenGöttingenGermany
- Centre of Biodiversity and Sustainable Land UseUniversity of GöttingenGöttingenGermany
| | - Ina Schaefer
- JFB Institute of Zoology and AnthropologyUniversity of GöttingenGöttingenGermany
| | - Mark Maraun
- JFB Institute of Zoology and AnthropologyUniversity of GöttingenGöttingenGermany
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25
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Arribas P, Andújar C, Moraza ML, Linard B, Emerson BC, Vogler AP. Mitochondrial Metagenomics Reveals the Ancient Origin and Phylodiversity of Soil Mites and Provides a Phylogeny of the Acari. Mol Biol Evol 2020; 37:683-694. [PMID: 31670799 DOI: 10.1093/molbev/msz255] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
High-throughput DNA methods hold great promise for phylogenetic analysis of lineages that are difficult to study with conventional molecular and morphological approaches. The mites (Acari), and in particular the highly diverse soil-dwelling lineages, are among the least known branches of the metazoan Tree-of-Life. We extracted numerous minute mites from soils in an area of mixed forest and grassland in southern Iberia. Selected specimens representing the full morphological diversity were shotgun sequenced in bulk, followed by genome assembly of short reads from the mixture, which produced >100 mitochondrial genomes representing diverse acarine lineages. Phylogenetic analyses in combination with taxonomically limited mitogenomes available publicly resulted in plausible trees defining basal relationships of the Acari. Several critical nodes were supported by ancestral-state reconstructions of mitochondrial gene rearrangements. Molecular calibration placed the minimum age for the common ancestor of the superorder Acariformes, which includes most soil-dwelling mites, to the Cambrian-Ordovician (likely within 455-552 Ma), whereas the origin of the superorder Parasitiformes was placed later in the Carboniferous-Permian. Most family-level taxa within the Acariformes were dated to the Jurassic and Triassic. The ancient origin of Acariformes and the early diversification of major extant lineages linked to the soil are consistent with a pioneering role for mites in building the earliest terrestrial ecosystems.
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Affiliation(s)
- Paula Arribas
- Island Ecology and Evolution Research Group, IPNA-CSIC, La Laguna, Tenerife, Spain.,Department of Life Sciences, Natural History Museum, London, United Kingdom.,Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - Carmelo Andújar
- Island Ecology and Evolution Research Group, IPNA-CSIC, La Laguna, Tenerife, Spain.,Department of Life Sciences, Natural History Museum, London, United Kingdom.,Department of Life Sciences, Imperial College London, Ascot, United Kingdom
| | - María Lourdes Moraza
- Departamento de Biología Ambiental, Universidad de Navarra, Facultad de Ciencias, Pamplona, Spain
| | - Benjamin Linard
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,LIRMM, Université de Montpellier, CNRS, Montpellier, France.,ISEM, Université de Montpellier, CNRS, IRD, EPHE, CIRAD, INRAP, Montpellier, France
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, IPNA-CSIC, La Laguna, Tenerife, Spain
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Department of Life Sciences, Imperial College London, Ascot, United Kingdom
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26
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Greenhalgh R, Dermauw W, Glas JJ, Rombauts S, Wybouw N, Thomas J, Alba JM, Pritham EJ, Legarrea S, Feyereisen R, Van de Peer Y, Van Leeuwen T, Clark RM, Kant MR. Genome streamlining in a minute herbivore that manipulates its host plant. eLife 2020; 9:56689. [PMID: 33095158 PMCID: PMC7738191 DOI: 10.7554/elife.56689] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022] Open
Abstract
The tomato russet mite, Aculops lycopersici, is among the smallest animals on earth. It is a worldwide pest on tomato and can potently suppress the host's natural resistance. We sequenced its genome, the first of an eriophyoid, and explored whether there are genomic features associated with the mite's minute size and lifestyle. At only 32.5 Mb, the genome is the smallest yet reported for any arthropod and, reminiscent of microbial eukaryotes, exceptionally streamlined. It has few transposable elements, tiny intergenic regions, and is remarkably intron-poor, as more than 80% of coding genes are intronless. Furthermore, in accordance with ecological specialization theory, this defense-suppressing herbivore has extremely reduced environmental response gene families such as those involved in chemoreception and detoxification. Other losses associate with this species' highly derived body plan. Our findings accelerate the understanding of evolutionary forces underpinning metazoan life at the limits of small physical and genome size.
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Affiliation(s)
- Robert Greenhalgh
- School of Biological Sciences, University of Utah, Salt Lake City, United States
| | - Wannes Dermauw
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Joris J Glas
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Nicky Wybouw
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jainy Thomas
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Juan M Alba
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Ellen J Pritham
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, United States
| | - Saioa Legarrea
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - René Feyereisen
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.,Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium.,Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Thomas Van Leeuwen
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Richard M Clark
- School of Biological Sciences, University of Utah, Salt Lake City, United States.,Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, United States
| | - Merijn R Kant
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
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27
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de Lillo E, Fanelli E, Valenzano D, Monfreda R, Troccoli A, Vovlas A, De Luca F. Characterisation of Aceria massalongoi and a histopathological study of the leaf galls induced on chaste trees. EXPERIMENTAL & APPLIED ACAROLOGY 2020; 82:33-57. [PMID: 32870432 DOI: 10.1007/s10493-020-00518-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 06/23/2020] [Indexed: 06/11/2023]
Abstract
The eriophyoid mite Aceria massalongoi (Canestrini) was collected from globoid leaf galls on severely injured chaste trees, Vitex agnus-castus L. (Lamiaceae), in Bari and Bernalda (southern Italy), and on the Ionian island Leukade (Greece). Female, male and nymph were described in detail, following the current morphometric descriptive scheme, supplementing older and incomplete descriptions. Molecular characterization of A. massalongoi from Italy and Greece was conducted by amplifying and sequencing the ribosomal ITS, the D2-D3 expansion domains of the 28S rRNA gene and the mitochondrial COI, for the first time. Phylogenetic trees based on the three molecular markers showed congruent results, confirming that Italian and Greek A. massalongoi populations are the same species that cluster together with some intraspecific variability. Galls, ranging from 0.5 to 2.8 mm in diameter, were randomly distributed on both leaf surfaces, and protruded ca. 1 mm from the leaf surface. Sometimes they were closely aggregated on midrib and leaves, which, consequently, appeared strongly deformed. Close-up observations revealed that gall induction causes hyperplastic proliferation of leaf tissues around the gall chamber hosting mites. The uniserial cell lining inside this chamber provides the nutritional tissue for the mites. All feeding cells contained one or more (frequently 2-3) hypertrophied nuclei and dense granular cytoplasm.
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Affiliation(s)
- Enrico de Lillo
- Entomology and Zoology Section, Department of Soil, Plant and Food Sciences (Di.S.S.P.A.), University of Bari Aldo Moro, 70126, Bari, Italy.
| | - Elena Fanelli
- Istituto per la Protezione Sostenibile delle Piante (I.P.S.P.), Consiglio Nazionale delle Ricerche, 70126, Bari, Italy
| | - Domenico Valenzano
- Entomology and Zoology Section, Department of Soil, Plant and Food Sciences (Di.S.S.P.A.), University of Bari Aldo Moro, 70126, Bari, Italy
| | - Rosita Monfreda
- Entomology and Zoology Section, Department of Soil, Plant and Food Sciences (Di.S.S.P.A.), University of Bari Aldo Moro, 70126, Bari, Italy
| | - Alberto Troccoli
- Istituto per la Protezione Sostenibile delle Piante (I.P.S.P.), Consiglio Nazionale delle Ricerche, 70126, Bari, Italy
| | - Alessio Vovlas
- A. P. S. Polyxena, Via Donizetti 12, Conversano, 70014, Bari, Italy
| | - Francesca De Luca
- Istituto per la Protezione Sostenibile delle Piante (I.P.S.P.), Consiglio Nazionale delle Ricerche, 70126, Bari, Italy.
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28
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Sullivan GT, Ozman‐Sullivan SK. Alarming evidence of widespread mite extinctions in the shadows of plant, insect and vertebrate extinctions. AUSTRAL ECOL 2020. [DOI: 10.1111/aec.12932] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Gregory T. Sullivan
- School of Earth and Environmental Sciences The University of Queensland St. Lucia Brisbane QLD4072Australia
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29
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Chetverikov PE, Cvrković T, Efimov PG, Klimov PB, Petanović RU, Romanovich AE, Schubert MA, Sukhareva SI, Zukoff SN, Amrine J. Molecular phylogenetic analyses reveal a deep dichotomy in the conifer-inhabiting genus Trisetacus (Eriophyoidea: Nalepellidae), with the two lineages differing in their female genital morphology and host associations. EXPERIMENTAL & APPLIED ACAROLOGY 2020; 81:287-316. [PMID: 32514877 DOI: 10.1007/s10493-020-00503-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 05/14/2020] [Indexed: 06/11/2023]
Abstract
We analyzed the phylogenetic relationships of the genus Trisetacus using two genes [cytochrome c oxidase subunit I (COI) and D1-D2 region of 28S rDNA (D1-D2 28S)], a representive taxon sampling (nearly 40% of known diversity), and a large set of close and distant outgroups. Our analyses suggest the presence of a dichotomy between Trisetacus associated with Cupressaceae and Pinaceae. The following smaller molecular clades were found: Pin-1 (bud mites, twig sheath mites, bark gall mites, and endoparasitic mites from pinaceans), Pin-2 (needle sheath mites from pines), Pin-2a (putative Nearctic group of needle sheath mites), Pin-2b (putative Palearctic group of needle sheath mites), Cup-1 and 2 (bud, cone, seed mites and mites living under bark scales from cupressaceans). The monophyly of the recently proposed subgenus Brevithecus nested within clade Cup-2 was confirmed. Ancestral character reconstruction analyses recovered: (1) Pinaceae as the ancestral hosts of Nalepellidae and Trisetacus, (2) repetitive reductions of the spermathecal tube independently occurred in two lineages of Trisetacus from Cupressaceae, and (3) several mite habitats on host (galls, cones, twig sheaths, seeds, inside leaves, and under scales) are evolutionarily derived states, whereas living in buds or needle sheaths are ancestral states for Trisetacus clades Cup and Pin. Using confocal microscopy, we identified six basic types of the female internal genitalia of Trisetacus based on shapes of the spermatheca and spermathecal tube. These genitalic types are strongly correlated with lineages recovered by molecular phylogenetic analyses, suggesting that the female genital morphology is both evolutionarily conserved and is a factor influencing macroevolutionary patterns in this group of mites.
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Affiliation(s)
- Philipp E Chetverikov
- Saint-Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, Russia, 199034.
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. 1, St. Petersburg, Russia, 199034.
| | - Tatjana Cvrković
- Department of Plant Pests, Institute for Plant Protection and Environment, Banatska 33, 11080, Zemun, Serbia
| | - Petr G Efimov
- Komarov Botanical Institute of the Russian Academy of Sciences, Prof. Popov str. 2, St. Petersburg, Russia, 197376
| | - Pavel B Klimov
- Department of Ecology and Evolutionary Biology, University of Michigan, 1109 Geddes Ave, Ann Arbor, MI, 48109-1079, USA
| | - Radmila U Petanović
- Serbian Academy of Sciences and Arts, Knez Mihailova 35, 11000, Belgrade, Serbia
- Faculty of Agriculture, University of Belgrade, Nemanjina 6, 11080, Zemun, Serbia
| | - Anna E Romanovich
- Resource Center for Development of Molecular and Cellular Technologies, St. Petersburg State University, Universitetskaya nab., 7/9, St. Petersburg, Russia, 199034
| | - Maria A Schubert
- Saint-Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, Russia, 199034
| | - Sogdiana I Sukhareva
- Saint-Petersburg State University, Universitetskaya nab. 7/9, St. Petersburg, Russia, 199034
| | - Sarah N Zukoff
- Southwest Research and Extension Center, Kansas State University, 4500 E. Mary Street, Garden City, KS, 67846, USA
| | - James Amrine
- Division of Plant & Soil Sciences, West Virginia University, P.O. Box 6108, Morgantown, WV, 26506-6108, USA
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30
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Yin Y, Yao LF, Zhang Q, Hebert PDN, Xue XF. Using multiple lines of evidence to delimit protogynes and deutogynes of four-legged mites: a case study on Epitrimerus sabinae s.l. (Acari : Eriophyidae). INVERTEBR SYST 2020. [DOI: 10.1071/is20014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Accurate species delimitation is essential for the study of biodiversity, but morphological approaches often provide a limited ability to connect different life stages, sexes or other phenotypic variants in eriophyoid mites because many species possess two phenotypically distinct forms: protogynes and deutogynes. In this study, we analysed the morphological variation in 26 populations of the eriophyoid mite, Epitrimerus sabinae Xue & Hong, 2005 s.l., from sites across its entire known distribution and revealed three morphotypes (LNS: large, normal palp seta d; MBS: medium, bifurcated palp seta d; SBS: small, bifurcated palp seta d) distinguished by body size and structure of dorsal pedipalp genual seta. Five lines of evidence (morphometrics, DNA-based species delimitation, phylogenetics, haplotype network, mitochondrial genome architecture) indicated that the MBS and SBS groups were very distinct from LNS (E. sabinae s.s.). In fact, the MBS and SBS morphotypes are properly placed in the genus Leipothrix with the MBS lineage representing the protogyne of L. juniperensis, sp. nov., whereas the SBS lineage is its deutogyne. By expanding the approaches used to link protogynes and deutogynes of eriophyoid mites, this study provides a way to accelerate the delineation of species boundaries in this important group of plant pests.
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31
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Zhang YX, Chen X, Wang JP, Zhang ZQ, Wei H, Yu HY, Zheng HK, Chen Y, Zhang LS, Lin JZ, Sun L, Liu DY, Tang J, Lei Y, Li XM, Liu M. Genomic insights into mite phylogeny, fitness, development, and reproduction. BMC Genomics 2019; 20:954. [PMID: 31818245 PMCID: PMC6902594 DOI: 10.1186/s12864-019-6281-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 11/13/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Predatory mites (Acari: Phytoseiidae) are the most important beneficial arthropods used in augmentative biological pest control of protected crops around the world. However, the genomes of mites are far less well understood than those of insects and the evolutionary relationships among mite and other chelicerate orders are contested, with the enigmatic origin of mites at one of the centres in discussion of the evolution of Arachnida. RESULTS We here report the 173 Mb nuclear genome (from 51.75 Gb pairs of Illumina reads) of the predatory mite, Neoseiulus cucumeris, a biocontrol agent against pests such as mites and thrips worldwide. We identified nearly 20.6 Mb (~ 11.93% of this genome) of repetitive sequences and annotated 18,735 protein-coding genes (a typical gene 2888 bp in size); the total length of protein-coding genes was about 50.55 Mb (29.2% of this assembly). About 37% (6981) of the genes are unique to N. cucumeris based on comparison with other arachnid genomes. Our phylogenomic analysis supported the monophyly of Acari, therefore rejecting the biphyletic origin of mites advocated by other studies based on limited gene fragments or few taxa in recent years. Our transcriptomic analyses of different life stages of N. cucumeris provide new insights into genes involved in its development. Putative genes involved in vitellogenesis, regulation of oviposition, sex determination, development of legs, signal perception, detoxification and stress-resistance, and innate immune systems are identified. CONCLUSIONS Our genomics and developmental transcriptomics analyses of N. cucumeris provide invaluable resources for further research on the development, reproduction, and fitness of this economically important mite in particular and Arachnida in general.
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Affiliation(s)
- Yan-Xuan Zhang
- Research Center of Engineering and Technology of Natural Enemy Resource of Crop Pest in Fujian, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, 350003 People’s Republic of China
| | - Xia Chen
- Research Center of Engineering and Technology of Natural Enemy Resource of Crop Pest in Fujian, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, 350003 People’s Republic of China
| | - Jie-Ping Wang
- Agricultural Bio-Resources Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350013 People’s Republic of China
| | - Zhi-Qiang Zhang
- Landcare Research, Auckland and School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Hui Wei
- Research Center of Engineering and Technology of Natural Enemy Resource of Crop Pest in Fujian, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, 350003 People’s Republic of China
| | - Hai-Yan Yu
- Biomarker Technologies Corporation, Beijing, 101300 People’s Republic of China
| | - Hong-Kun Zheng
- Biomarker Technologies Corporation, Beijing, 101300 People’s Republic of China
| | - Yong Chen
- Research Center of Engineering and Technology of Natural Enemy Resource of Crop Pest in Fujian, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, 350003 People’s Republic of China
| | - Li-Sheng Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193 People’s Republic of China
| | - Jian-Zhen Lin
- Fujian Yanxuan Bio-preventing and Technology Biocontrol Corporation, Fuzhou, People’s Republic of China
| | - Li Sun
- Research Center of Engineering and Technology of Natural Enemy Resource of Crop Pest in Fujian, Institute of Plant Protection, Fujian Academy of Agricultural Sciences, Fuzhou, 350003 People’s Republic of China
| | - Dong-Yuan Liu
- Biomarker Technologies Corporation, Beijing, 101300 People’s Republic of China
| | - Juan Tang
- Biomarker Technologies Corporation, Beijing, 101300 People’s Republic of China
| | - Yan Lei
- Biomarker Technologies Corporation, Beijing, 101300 People’s Republic of China
| | - Xu-Ming Li
- Biomarker Technologies Corporation, Beijing, 101300 People’s Republic of China
| | - Min Liu
- Biomarker Technologies Corporation, Beijing, 101300 People’s Republic of China
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32
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Jin PY, Sun JT, Hoffmann A, Guo YF, Zhou JC, Zhu YX, Chen L, Hong XY. Phylogenetic signals in pest abundance and distribution range of spider mites. BMC Evol Biol 2019; 19:223. [PMID: 31805865 PMCID: PMC6896397 DOI: 10.1186/s12862-019-1548-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/27/2019] [Indexed: 11/21/2022] Open
Abstract
Background Attributes of pest species like host range are frequently reported as being evolutionarily constrained and showing phylogenetic signal. Because these attributes in turn could influence the abundance and impact of species, phylogenetic information could be useful in predicting the likely status of pests. In this study, we used regional (China) and global datasets to investigate phylogenetic patterns in occurrence patterns and host ranges of spider mites, which constitute a pest group of many cropping systems worldwide. Results We found significant phylogenetic signal in relative abundance and distribution range both at the regional and global scales. Relative abundance and range size of spider mites were positively correlated with host range, although these correlations became weaker after controlling for phylogeny. Conclusions The results suggest that pest impacts are evolutionarily constrained. Information that is easily obtainable – including the number of known hosts and phylogenetic position of the mites – could therefore be useful in predicting future pest risk of species.
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Affiliation(s)
- Peng-Yu Jin
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jing-Tao Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Ary Hoffmann
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Victoria, Australia
| | - Yan-Fei Guo
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jin-Cheng Zhou
- School of Plant Protection, Shenyang Agricultural University, Shenyang, 110866, Liaoning, China
| | - Yu-Xi Zhu
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Lei Chen
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Xiao-Yue Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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33
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Liu Q, Yuan YM, Lai Y, Wang GQ, Xue XF. Unravelling the phylogeny, cryptic diversity and morphological evolution of Diptilomiopus mites (Acari: Eriophyoidea). EXPERIMENTAL & APPLIED ACAROLOGY 2019; 79:323-344. [PMID: 31786687 DOI: 10.1007/s10493-019-00443-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 11/20/2019] [Indexed: 06/10/2023]
Abstract
The Eriophyoidea, notable for specific morphological characters (four-legged mites) and gall-formation in host plants (gall mites), is one of the most species-rich superfamilies of Acari. Monophyly of the superfamily Eriophyoidea is accepted by all acarologists; however, monophyly of most genera has not been evaluated in a molecular phylogenetic network. Furthermore, most eriophyoid mites, especially species in the genus Diptilomiopus, are morphologically similar, challenging their identification. Here we test the phylogeny and cryptic diversity of Diptilomiopus species using fragments of two mitochondrial (COI and 12S) and two nuclear (18S and 28S) genes. Our results revealed the monophyly of Diptilomiopus. Sequence distance, barcode gap, and species delimitation analyses of the COI gene allowed us to resolve cryptic diversity of Diptilomiopus species. Additionally, we supposed that characteristics of genu fused with femur on both legs and seta ft' absent on leg II evolved only once within Diptilomiopus, which are potential morphological synapomorphies. In contrast, characteristics of both setae ft' and ft″ divided into a short branch and a long branch were supposed evolving multiple times independently. Our findings contribute to the understanding of phylogeny and morphological evolution of Diptilomiopus species and provide a DNA-based approach for species delimitation of Diptilomiopus mites.
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Affiliation(s)
- Qing Liu
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yan-Mei Yuan
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Yan Lai
- Department of Plant Protection, Guangxi University, Nanning, 530005, Guangxi, China
| | - Guo-Quan Wang
- Department of Plant Protection, Guangxi University, Nanning, 530005, Guangxi, China
| | - Xiao-Feng Xue
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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34
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Wybouw N, Kurlovs AH, Greenhalgh R, Bryon A, Kosterlitz O, Manabe Y, Osakabe M, Vontas J, Clark RM, Van Leeuwen T. Convergent evolution of cytochrome P450s underlies independent origins of keto-carotenoid pigmentation in animals. Proc Biol Sci 2019; 286:20191039. [PMID: 31311468 DOI: 10.1098/rspb.2019.1039] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Keto-carotenoids contribute to many important traits in animals, including vision and coloration. In a great number of animal species, keto-carotenoids are endogenously produced from carotenoids by carotenoid ketolases. Despite the ubiquity and functional importance of keto-carotenoids in animals, the underlying genetic architectures of their production have remained enigmatic. The body and eye colorations of spider mites (Arthropoda: Chelicerata) are determined by β-carotene and keto-carotenoid derivatives. Here, we focus on a carotenoid pigment mutant of the spider mite Tetranychus kanzawai that, as shown by chromatography, lost the ability to produce keto-carotenoids. We employed bulked segregant analysis and linked the causal locus to a single narrow genomic interval. The causal mutation was fine-mapped to a minimal candidate region that held only one complete gene, the cytochrome P450 monooxygenase CYP384A1, of the CYP3 clan. Using a number of genomic approaches, we revealed that an inactivating deletion in the fourth exon of CYP384A1 caused the aberrant pigmentation. Phylogenetic analysis indicated that CYP384A1 is orthologous across mite species of the ancient Trombidiformes order where carotenoids typify eye and body coloration, suggesting a deeply conserved function of CYP384A1 as a carotenoid ketolase. Previously, CYP2J19, a cytochrome P450 of the CYP2 clan, has been identified as a carotenoid ketolase in birds and turtles. Our study shows that selection for endogenous production of keto-carotenoids led to convergent evolution, whereby cytochrome P450s were independently co-opted in vertebrate and invertebrate animal lineages.
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Affiliation(s)
- Nicky Wybouw
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Andre H Kurlovs
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.,School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA
| | - Robert Greenhalgh
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA
| | - Astrid Bryon
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Olivia Kosterlitz
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA
| | - Yuki Manabe
- Laboratory of Technology of Marine Bioproducts, Kyoto University, Kyoto 606-8502, Japan
| | - Masahiro Osakabe
- Laboratory of Ecological Information, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - John Vontas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 73100 Heraklion, Greece.,Department of Crop Science, Pesticide Science Lab, Agricultural University of Athens, 11855 Athens, Greece
| | - Richard M Clark
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA.,Center for Cell and Genome Science, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA
| | - Thomas Van Leeuwen
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
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35
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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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36
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Li W, Shao R, Zhang Q, Deng W, Xue X. Mitochondrial genome reorganization characterizes various lineages of mesostigmatid mites (Acari: Parasitiformes). ZOOL SCR 2019. [DOI: 10.1111/zsc.12369] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wei‐Ning Li
- Department of Entomology Nanjing Agricultural University Nanjing China
| | - Renfu Shao
- School of Science and Engineering, GeneCology Research Centre, Animal Research Centre University of the Sunshine Coast Sippy Downs Queensland Australia
| | - Qi Zhang
- Department of Entomology Nanjing Agricultural University Nanjing China
| | - Wei Deng
- Department of Entomology Nanjing Agricultural University Nanjing China
| | - Xiao‐Feng Xue
- Department of Entomology Nanjing Agricultural University Nanjing China
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37
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Duarte ME, de Mendonça RS, Skoracka A, Silva ES, Navia D. Integrative taxonomy of Abacarus mites (Eriophyidae) associated with hybrid sugarcane plants, including description of a new species. EXPERIMENTAL & APPLIED ACAROLOGY 2019; 78:373-401. [PMID: 31278610 DOI: 10.1007/s10493-019-00388-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/30/2019] [Indexed: 06/09/2023]
Abstract
Phytophagous mites belonging to the Eriophyoidea are extremely diverse and highly host-specific. Their accurate morphological identification is hampered by their reduced size and simplified bodies and by the existence of cryptic species complexes. Previous studies have demonstrated the urgency of applying multisource methods to accurate taxonomic identification of eriophyoid mites, especially species belonging to the genus Abacarus. This genus comprises 65 species, of which 37 are associated with grasses and four with sugarcane Saccharum (Poaceae). Recently, Abacarus specimens very similar to Abacarus sacchari were collected from the sugarcane crop in Brazil; however, their taxonomic placement was uncertain. In this study, we used an integrative approach to determine whether A. aff. sacchari specimens belong to A. sacchari or constitute a cryptic species. Morphological data were combined with molecular phylogeny based on the nucleotide sequences of three markers, one mitochondrial (COI) and two nuclear (D2 region of 28S and ITS). Morphological differences were observed between A. aff. sacchari, A. sacchari and A. doctus. The phylogenetic relationships among these three taxa and the genetic distances separating them revealed an interspecific divergence. The results of the morphological and molecular methods were congruent and supported the existence of a new species: Abacarus neosacchari n. sp. Duarte and Navia, herein described. This species belongs to the Abacarus cryptic species complex associated with sugarcane in the Americas. The results of this study, presenting the occurrence of multiple Abacarus species associated with sugarcane, contribute to the knowledge on plants and mites diversity by adding up one more clue highlighting that plant hybridization can be an important mechanism contributing to the speciation of plant-feeding arthropods.
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Affiliation(s)
- Mércia Elias Duarte
- Embrapa Recursos Genéticos e Biotecnologia, Brasilia, Distrito Federal, 70770-900, Brazil
| | - Renata Santos de Mendonça
- Faculdade de Agronomia e Medicina Veterinária, Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF, 70297-400, Brazil
| | - Anna Skoracka
- Population Ecology Lab, Faculty of Biology, Institute of Environmental Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, Poznań, 61-614, Poland
| | - Edmilson Santos Silva
- Universidade Federal de Alagoas, Campus Arapiraca, Arapiraca, 57309-005, Brazil
- Universidade Federal de Alagoas, Centro de Ciências Agrárias (CECA), Alagoas, 57100-000, Brazil
| | - Denise Navia
- Embrapa Recursos Genéticos e Biotecnologia, Brasilia, Distrito Federal, 70770-900, Brazil.
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38
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Zedek F, Bureš P. Pest Arthropods with Holocentric Chromosomes are More Resistant to Sterilizing Ionizing Radiation. Radiat Res 2019; 191:255-261. [PMID: 30702973 DOI: 10.1667/rr15208.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
It has been hypothesized that species with holocentric chromosomes have a selective evolutionary advantage for developmental and reproductive success because holocentric chromosomes are less susceptible to chromosome breakage than monocentric chromosomes. We analyzed data on sterilizing doses of ionizing radiation for more than 250 species of arthropods to test whether the minimal dose for reproductive sterilization is higher for species with holocentric chromosomes than for species with monocentric chromosomes. Using linear mixed models that account for phylogeny, we show that holocentric arthropods are more tolerant of sterilizing radiation than monocentrics. Moreover, higher dose rates correlate with lower sterilizing doses in monocentrics, but not in holocentrics, which is a novel finding that may be of importance for radiosanitation practice. Under the dose rate of 1 Gy/min, holocentric arthropods are sterilized on average with a 2.9 times higher minimal dose than monocentrics. Life stage and sex have significant but considerably weaker effects on sterilizing dose than chromosome type. Adults and males require 1.2 and 1.4 times higher sterilizing doses than juveniles and females, respectively. These results support the hypothesis that holocentric lineages may originate and thrive better in times of increased exposure to chromosome-breaking factors.
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Affiliation(s)
- František Zedek
- Department of Botany and Zoology, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
| | - Petr Bureš
- Department of Botany and Zoology, Masaryk University, Kotlarska 2, 611 37 Brno, Czech Republic
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39
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Sun JT, Jin PY, Hoffmann AA, Duan XZ, Dai J, Hu G, Xue XF, Hong XY. Evolutionary divergence of mitochondrial genomes in two Tetranychus species distributed across different climates. INSECT MOLECULAR BIOLOGY 2018; 27:698-709. [PMID: 29797479 DOI: 10.1111/imb.12501] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
There is increasing evidence that mitochondrial genomes (mitogenomes) can be under selection, whereas the selective regimes shaping mitogenome evolution remain largely unclear. To test for mitogenome evolution in relation to the climate adaptation, we explored mtDNA variation in two spider mite (Tetranychus) species that distribute across different climates. We sequenced 26 complete mitogenomes of Tetranychus truncates, which occurs in both warm and cold regions, and nine complete mitogenomes of Tetranychus pueraricola, which is restricted to warm regions. Patterns of evolution in the two species' mitogenomes were compared through a series of dN /dS methods and physicochemical profiles of amino acid replacements. We found that: (1) the mitogenomes of both species were under widespread purifying selection; (2) elevated directional adaptive selection was observed in the T. truncatus mitogenome, perhaps linked to the cold climates adaptation of T. truncatus; and (3) the strength of selection varied across genes, and diversifying positive selection detected on ND4 and ATP6 pointed to their crucial roles during adaptation to different climatic conditions. This study gained insight into the mitogenome evolution in relation to the climate adaptation.
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Affiliation(s)
- J-T Sun
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - P-Y Jin
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - A A Hoffmann
- School of BioSciences, Bio21 Institute, The University of Melbourne, Victoria, Australia
| | - X-Z Duan
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - J Dai
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - G Hu
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - X-F Xue
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - X-Y Hong
- Department of Entomology, Nanjing Agricultural University, Nanjing, Jiangsu, China
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40
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Laska A, Majer A, Szydło W, Karpicka-Ignatowska K, Hornyák M, Labrzycka A, Skoracka A. Cryptic diversity within grass-associated Abacarus species complex (Acariformes: Eriophyidae), with the description of a new species, Abacarus plumiger n. sp. EXPERIMENTAL & APPLIED ACAROLOGY 2018; 76:1-28. [PMID: 30171478 DOI: 10.1007/s10493-018-0291-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/24/2018] [Indexed: 05/20/2023]
Abstract
Accurate estimation of species richness is often complex as genetic divergence is not always accompanied by appreciable morphological differentiation. In consequence, cryptic lineages or species evolve. Cryptic speciation is common especially in taxa characterized by small and simplified bodies, what makes their proper identification challenging. The cereal rust mite, Abacarus hystrix, was regarded for a long time as a species associated with a wide range of grass hosts, whereas wide host ranges are rather rare in eriophyoid mites. Therefore, the generalist status of A. hystrix was questioned. In this paper we demonstrate that the diversity within Abacarus species associated with grasses is more complex than it was previously thought. The 78 Abacarus mtDNA COI sequences used in this study formed 10 highly supported clades (bootstrap value 99%) and four more distinct genetic lineages were represented by unique sequences. The genetic distances between them ranged from 6.6 to 26.5%. Moreover, morphological study and genetic approach based on the combination of the Poisson Tree Processes model for species delimitation (PTP) and a Bayesian implementation of PTP (bPTP), and Neighbour Joining analyses led to delimitation of a new species within the Abacarus complex: Abacarus plumiger, specialized on smooth brome (Bromus inermis). Furthermore, our analyses demonstrated a pattern of host-associated differentiation within the complex. Overall, our study indicates that cryptic speciation occurs in the grass-associated Abacarus genus, and suggests the need for more extensive sampling using integrative methods.
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Affiliation(s)
- Alicja Laska
- Population Ecology Lab, Faculty of Biology, Adam Mickiewicz University, Poznań, Umultowska 89, 61-614, Poznań, Poland.
| | - Agnieszka Majer
- Population Ecology Lab, Faculty of Biology, Adam Mickiewicz University, Poznań, Umultowska 89, 61-614, Poznań, Poland
| | - Wiktoria Szydło
- Department of Entomology, University of Nebraska-Lincoln, 103 Entomology Hall, Lincoln, NE, 68583-0816, USA
| | - Kamila Karpicka-Ignatowska
- Population Ecology Lab, Faculty of Biology, Adam Mickiewicz University, Poznań, Umultowska 89, 61-614, Poznań, Poland
| | - Marta Hornyák
- Department of Plant Physiology, Faculty of Agriculture and Economics, University of Agriculture in Krakow, Podłużna 3, 30-239, Kraków, Poland
| | - Anna Labrzycka
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University, Poznań, Umultowska 89, 61-614, Poznań, Poland
| | - Anna Skoracka
- Population Ecology Lab, Faculty of Biology, Adam Mickiewicz University, Poznań, Umultowska 89, 61-614, Poznań, Poland
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Cheng TY, Chen Z, Li ZB, Liu GH. First Report of Ixodes nipponensis Infection in Goats in China. Vector Borne Zoonotic Dis 2018; 18:575-578. [PMID: 29741996 DOI: 10.1089/vbz.2017.2263] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ticks are obligate blood-sucking ectoparasites that infect a wide range of animals and humans, causing a variety of both human and animal diseases around the world. Ixodes nipponensis is the most commonly reported tick in Korea and Japan, but it is very rare in China. In this study, six I. nipponensis samples were collected from three black goats in Hunan province, China. Ticks identified morphologically as I. nipponensis were then examined by PCR with two different molecular markers: mitochondrial cox1 and the second internal transcribed spacer of ribosomal DNA genes. Sequence comparison and phylogenetic analysis of the cox1 sequences confirmed that all of the examined hard Ixodes ticks represented I. nipponensis. This finding indicates a potential risk of zoonotic I. nipponensis infection in humans and animals in China. To our knowledge, this is the first report documenting the occurrence of I. nipponensis infection in goats in China.
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Affiliation(s)
- Tian-Yin Cheng
- 1 Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University , Changsha, People's Republic of China
- 2 Hunan Co-Innovation Center of Animal Production Safety , Changsha, Hunan Province, People's Republic of China
| | - Zhen Chen
- 1 Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University , Changsha, People's Republic of China
| | - Zhong-Bo Li
- 1 Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University , Changsha, People's Republic of China
| | - Guo-Hua Liu
- 1 Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University , Changsha, People's Republic of China
- 2 Hunan Co-Innovation Center of Animal Production Safety , Changsha, Hunan Province, People's Republic of China
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42
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Comprehensive phylogeny of acariform mites (Acariformes) provides insights on the origin of the four-legged mites (Eriophyoidea), a long branch. Mol Phylogenet Evol 2018; 119:105-117. [DOI: 10.1016/j.ympev.2017.10.017] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 10/13/2017] [Accepted: 10/22/2017] [Indexed: 11/19/2022]
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