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Wang S, Wei K, Wang X. The complete mitochondrial genome and phylogenetic analysis of Cyanopterus ninghais (Hymenoptera: Braconidae). Mitochondrial DNA B Resour 2024; 9:976-980. [PMID: 39105178 PMCID: PMC11299438 DOI: 10.1080/23802359.2024.2386423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 07/25/2024] [Indexed: 08/07/2024] Open
Abstract
Cyanopterus ninghais is an important gregarious ectoparasitoid during the larval stage of Monochamus alternatus, a key vector for pine wilt disease in Asia. In this study, the complete mitochondrial genome of C. ninghais was sequenced and analyzed. The mitochondrial genome of C. ninghais is 15,386 bp in length, comprising 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), and 2 ribosomal RNA genes (rRNAs). The nucleotide composition is 41.32% A, 8.29% G, 6.06% C, and 44.33% T. Phylogenetic trees of Braconidae were constructed using 13 PCG sequences via Bayesian inference (BI) and maximum likelihood (ML) analyses to determine their phylogenetic position. Both ML and BI analyses revealed that C. ninghais is closely related to Euurobracon yokahamae, Virgulibracon endoxylaphagus, and Habrobracon hebetor.
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Affiliation(s)
- Shaobo Wang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Ke Wei
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
| | - Xiaoyi Wang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
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Zhang CH, Wang HY, Wang Y, Chi ZH, Liu YS, Zu GH. The first two complete mitochondrial genomes for the genus Anagyrus (Hymenoptera, Encyrtidae) and their phylogenetic implications. Zookeys 2024; 1206:81-98. [PMID: 39006402 PMCID: PMC11245640 DOI: 10.3897/zookeys.1206.121923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 06/12/2024] [Indexed: 07/16/2024] Open
Abstract
Anagyrus, a genus of Encyrtidae (Hymenoptera, Chalcidoidea), represents a successful group of parasitoid insects that attack various mealybug pests of agricultural and forestry plants. Until now, only 20 complete mitochondrial genomes have been sequenced, including those in this study. To enrich the diversity of mitochondrial genomes in Encyrtidae and to gain insights into their phylogenetic relationships, the mitochondrial genomes of two species of Anagyrus were sequenced, and the mitochondrial genomes of these species were compared and analyzed. Encyrtid mitochondrial genomes exhibit similarities in nucleotide composition, gene organization, and control region patterns. Comparative analysis of protein-coding genes revealed varying molecular evolutionary rates among different genes, with six genes (ATP8, ND2, ND4L, ND6, ND4 and ND5) showing higher rates than others. A phylogenetic analysis based on mitochondrial genome sequences supports the monophyly of Encyrtidae; however, the two subfamilies, Encyrtinae and Tetracneminae, are non-monophyletic. This study provides valuable insights into the phylogenetic relationships within the Encyrtidae and underscores the utility of mitochondrial genomes in the systematics of this family.
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Affiliation(s)
- Cheng-Hui Zhang
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin 300392, ChinaTianjin Agricultural UniversityTianjinChina
| | - Hai-Yang Wang
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin 300392, ChinaTianjin Agricultural UniversityTianjinChina
| | - Yan Wang
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin 300392, ChinaTianjin Agricultural UniversityTianjinChina
| | - Zhi-Hao Chi
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin 300392, ChinaTianjin Agricultural UniversityTianjinChina
| | - Yue-Shuo Liu
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin 300392, ChinaTianjin Agricultural UniversityTianjinChina
| | - Guo-Hao Zu
- College of Horticulture and Landscape, Tianjin Agricultural University, Tianjin 300392, ChinaTianjin Agricultural UniversityTianjinChina
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Castañeda-Osorio R, Belokobylskij SA, Jasso-Martínez JM, Samacá-Sáenz E, Kula RR, Zaldívar-Riverón A. Mitogenome architecture supports the non-monophyly of the cosmopolitan parasitoid wasp subfamily Doryctinae (Hymenoptera: Braconidae) recovered by nuclear and mitochondrial phylogenomics. INVERTEBR SYST 2024; 38:IS24029. [PMID: 38740060 DOI: 10.1071/is24029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
Mitochondrial DNA gene organisation is an important source of phylogenetic information for various metazoan taxa at different evolutionary timescales, though this has not been broadly tested for all insect groups nor within a phylogenetic context. The cosmopolitan subfamily Doryctinae is a highly diverse group of braconid wasps mainly represented by ectoparasitoids of xylophagous beetle larvae. Previous molecular studies based on Sanger and genome-wide (ultraconserved elements, UCE; and mitochondrial genomes) sequence data have recovered a non-monophyletic Doryctinae, though the relationships involved have always been weakly supported. We characterised doryctine mitogenomes and conducted separate phylogenetic analyses based on mitogenome and UCE sequence data of ~100 representative doryctine genera to assess the monophyly and higher-level classification of the subfamily. We identified rearrangements of mitochondrial transfer RNAs (tRNAs) that support a non-monophyletic Doryctinae consisting of two separate non-related clades with strong geographic structure ('New World' and 'Old World' clades). This geographic structure was also consistently supported by the phylogenetic analyses preformed with mitogenome and UCE sequence data. These results highlight the utility of the mitogenome gene rearrangements as a potential source of phylogenetic information at different evolutionary timescales.
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Affiliation(s)
- Rubén Castañeda-Osorio
- Colección Nacional de Insectos, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, 3er circuito exterior s/n, Ciudad Universitaria, Coyoacán, Ciudad de México, México; and Posgrado en Ciencias Biológicas, Unidad de Posgrado, Edificio A, 1er Piso, Circuito de Posgrados, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Sergey A Belokobylskij
- Zoological Institute of the Russian Academy of Sciences, Universitetskaya Naberezhnaya 1, Saint Petersburg, Russian Federation
| | - Jovana M Jasso-Martínez
- Colección Nacional de Insectos, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, 3er circuito exterior s/n, Ciudad Universitaria, Coyoacán, Ciudad de México, México; and Department of Entomology, Smithsonian Institution, National Museum of Natural History, 10th Street & Constitution Avenue NW, Washington, DC, USA
| | - Ernesto Samacá-Sáenz
- Instituto de Investigaciones Biomédicas, Departamento de Biología Celular y Fisiología, Universidad Nacional Autónoma de México, 3er Circuito Exterior s/n, Ciudad Universitaria, Coyoacán, Ciudad de México, México
| | - Robert R Kula
- Systematic Entomology Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, US Department of Agriculture, c/o Department of Entomology, Smithsonian Institution, National Museum of Natural History, Washington, DC, USA
| | - Alejandro Zaldívar-Riverón
- Colección Nacional de Insectos, Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, 3er circuito exterior s/n, Ciudad Universitaria, Coyoacán, Ciudad de México, México
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Li Y, Yi H, Zhu Y. Novel insights into adaptive evolution based on the unusual AT-skew in Acheilognathus gracilis mitogenome and phylogenetic relationships of bitterling. Gene 2024; 902:148154. [PMID: 38218382 DOI: 10.1016/j.gene.2024.148154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/20/2023] [Accepted: 01/08/2024] [Indexed: 01/15/2024]
Abstract
Acheilognathus gracilis, a bitterling species, distribute in lower reaches of Yangtze River. They are identified as the top-priority bitterling species for conservation as having high evolutionary distinctiveness and are at risk of extinction. In present study, we first sequenced the complete mitogenome of A. gracilis and analyzed its phylogenetic position using 13 PCGs. The A. gracilis mitogenome is 16,774 bp in length, including 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, a control region and the origin of the light strand replication. The overall base composition of A. gracilis in descending order is T 27.9 %, A 27.7 %, C 26.1 % and G 18.3 %, shows a unusual AT-skew with slightly negative. Further investigation revealed A. gracilis uses excess T over A in NADH dehydrogenase 5 (nd5), whereas the most of other bitterlings are biased toward to use A not T, implying there is likely to be unique strategy of adaptive evolution in A. gracilis. We also compared 13 PCGs of 30 bitterling mitogenomes and the results exhibit highly conservative. Phylogenetic trees constructed by 13 PCGs strongly support the monophyly of Acheilognathus and the paraphyly of Rhodeus and Tanakia. Current results will provide valuable information for follow-up research on conservation of species facing with serious population decline and can provide novel insights into the phylogenetic analysis and evolutionary biology research.
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Affiliation(s)
- Yuxuan Li
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongbo Yi
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Yurong Zhu
- College of Fisheries, Engineering Research Center of Green development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China; Hubei Provincial Engineering Laboratory for Pond Aquaculture, Hubei, China.
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Lin JY, He J, Ma LJ, Yang HL, Wei SJ, Song F. The complete mitochondrial genome of Aphidius colemani (Hymenoptera: Braconidae: Aphidiinae). Mitochondrial DNA B Resour 2024; 9:257-261. [PMID: 38348095 PMCID: PMC10860412 DOI: 10.1080/23802359.2024.2311745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/24/2024] [Indexed: 02/15/2024] Open
Abstract
The genome-level features are crucial genetic resources for species identification and phylogenetic analysis. Here, the complete mitochondrial genome of Aphidius colemani Viereck 1912 (Hymenoptera: Braconidae: Aphidiinae) was sequenced, determined and analyzed. The circular genome is 16,372 bp in length with an overall base composition of 38.9% for A, 46.2% for T, 6.7% for C, and 8.2% for G. The mitochondrial genome of A. colemani contained 13 protein-coding genes that initiated by the ATN codon, 22 transfer RNA genes, two ribosomal RNA genes (rRNAs), and a control region (CR). It shared the same gene arrangement patterns that occurred in two tRNA clusters of trnI-trnQ-trnM and trnW-trnC-trnY with Aphidius gifuensis. Phylogenetic analyses using Bayesian inference and Maximum-likelihood methods supported that the two species of Aphidiinae formed a clade and sister to other subfamilies of Braconidae.
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Affiliation(s)
- Jia-Yu Lin
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jia He
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
- Institute of Plant Protection, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Li-Jun Ma
- Institute of Plant Protection, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Hai-Lin Yang
- Yuxi Branch, Yunnan Tobacco Company, Yuxi, China
| | - Shu-Jun Wei
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Fan Song
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
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Li YR, Wang ZW, Corlett RT, Yu WB. Comparative analyses of mitogenomes in the social bees with insights into evolution of long inverted repeats in the Meliponini. Zool Res 2024; 45:160-175. [PMID: 38199971 PMCID: PMC10839653 DOI: 10.24272/j.issn.2095-8137.2023.169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
The insect mitogenome is typically a compact circular molecule with highly conserved gene contents. Nonetheless, mitogenome structural variations have been reported in specific taxa, and gene rearrangements, usually the tRNAs, occur in different lineages. Because synapomorphies of mitogenome organizations can provide information for phylogenetic inferences, comparative analyses of mitogenomes have been given increasing attention. However, most studies use a very few species to represent the whole genus, tribe, family, or even order, overlooking potential variations at lower taxonomic levels, which might lead to some incorrect inferences. To provide new insights into mitogenome organizations and their implications for phylogenetic inference, this study conducted comparative analyses for mitogenomes of three social bee tribes (Meliponini, Bombini, and Apini) based on the phylogenetic framework with denser taxonomic sampling at the species and population levels. Comparative analyses revealed that mitogenomes of Apini and Bombini are the typical type, while those of Meliponini show diverse variations in mitogenome sizes and organizations. Large inverted repeats (IRs) cause significant gene rearrangements of protein coding genes (PCGs) and rRNAs in Indo-Malay/Australian stingless bee species. Molecular evolution analyses showed that the lineage with IRs have lower d N/ d S ratios for PCGs than lineages without IRs, indicating potential effects of IRs on the evolution of mitochondrial genes. The finding of IRs and different patterns of gene rearrangements suggested that Meliponini is a hotspot in mitogenome evolution. Unlike conserved PCGs and rRNAs whose rearrangements were found only in the mentioned lineages within Meliponini, tRNA rearrangements are common across all three tribes of social bees, and are significant even at the species level, indicating that comprehensive sampling is needed to fully understand the patterns of tRNA rearrangements, and their implications for phylogenetic inference.
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Affiliation(s)
- Yu-Ran Li
- Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants & Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- University of Chinese Academy of Sciences, Shijingshan District, Beijing 100049, China
| | - Zheng-Wei Wang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
| | - Richard T Corlett
- Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants & Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China. E-mail:
| | - Wen-Bin Yu
- Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants & Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan 666303, China
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Mengla, Yunnan 666303, China. E-mail:
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Wang J, Tai J, Zhang W, He K, Lan H, Liu H. Comparison of seven complete mitochondrial genomes from Lamprologus and Neolamprologus (Chordata, Teleostei, Perciformes) and the phylogenetic implications for Cichlidae. Zookeys 2023; 1184:115-132. [PMID: 38314327 PMCID: PMC10838552 DOI: 10.3897/zookeys.1184.107091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 10/27/2023] [Indexed: 02/06/2024] Open
Abstract
In this study, mitochondrial genomes (mitogenomes) of seven cichlid species (Lamprologuskungweensis, L.meleagris, L.ornatipinnis, Neolamprologusbrevis, N.caudopunctatus, N.leleupi, and N.similis) are characterized for the first time. The newly sequenced mitogenomes contained 37 typical genes [13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs) and 22 transfer RNA genes (tRNAs)]. The mitogenomes were 16,562 ~ 16,587 bp in length with an A + T composition of 52.1~58.8%. The cichlid mitogenomes had a comparable nucleotide composition, A + T content was higher than the G + C content. The AT-skews of most mitogenomes were inconspicuously positive and the GC-skews were negative, indicating higher occurrences of C than G. Most PCGs started with the conventional start codon, ATN. There was no essential difference in the codon usage patterns of these seven species. Using Ka/Ks, we found the fastest-evolving gene were atp8. But the results of p-distance indicated that the fastest-evolving gene was nad6. Phylogenetic analysis revealed that L.meleagris did not cluster with Lamprologus species, but with species from the genus Neolamprologus. The novel information obtained about these mitogenomes will contribute to elucidating the complex relationships among cichlid species.
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Affiliation(s)
- Jiachen Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China Nanjing Forestry University Nanjing China
| | - Jingzhe Tai
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China Nanjing Forestry University Nanjing China
| | - Wenwen Zhang
- Institute of Environmental Sciences, Ministry of Ecology and Environment of China State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains Research Center for Biodiversity Conservation and Biosafety, Nanjing 210042, China Institute of Environmental Sciences, Ministry of Ecology and Environment of China State Environmental Protection Scientific Observation and Research Station for Ecological Environment of Wuyi Mountains Research Center for Biodiversity Conservation and Biosafety Nanjing China
| | - Ke He
- Zhejiang Agriculture and Forestry University, Hangzhou 311300, China Zhejiang Agriculture and Forestry University Hangzhou China
| | - Hong Lan
- Zhejiang Open University, Hangzhou 310012, China Zhejiang Open University Hangzhou China
| | - Hongyi Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China Nanjing Forestry University Nanjing China
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Wang SH, Hu SY, Li M, Liu M, Sun H, Zhao JR, Chen WT, Yuan ML. Comparative Mitogenomic Analyses of Darkling Beetles (Coleoptera: Tenebrionidae) Provide Evolutionary Insights into tRNA-like Sequences. Genes (Basel) 2023; 14:1738. [PMID: 37761878 PMCID: PMC10530909 DOI: 10.3390/genes14091738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/25/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
Tenebrionidae is widely recognized owing to its species diversity and economic importance. Here, we determined the mitochondrial genomes (mitogenomes) of three Tenebrionidae species (Melanesthes exilidentata, Anatolica potanini, and Myladina unguiculina) and performed a comparative mitogenomic analysis to characterize the evolutionary characteristics of the family. The tenebrionid mitogenomes were highly conserved with respect to genome size, gene arrangement, base composition, and codon usage. All protein-coding genes evolved under purifying selection. The largest non-coding region (i.e., control region) showed several unusual features, including several conserved repetitive fragments (e.g., A+T-rich regions, G+C-rich regions, Poly-T tracts, TATA repeat units, and longer repetitive fragments) and tRNA-like structures. These tRNA-like structures can bind to the appropriate anticodon to form a cloverleaf structure, although base-pairing is not complete. We summarized the quantity, types, and conservation of tRNA-like sequences and performed functional and evolutionary analyses of tRNA-like sequences with various anticodons. Phylogenetic analyses based on three mitogenomic datasets and two tree inference methods largely supported the monophyly of each of the three subfamilies (Stenochiinae, Pimeliinae, and Lagriinae), whereas both Tenebrioninae and Diaperinae were consistently recovered as polyphyletic. We obtained a tenebrionid mitogenomic phylogeny: (Lagriinae, (Pimeliinae, ((Tenebrioninae + Diaperinae), Stenochiinae))). Our results provide insights into the evolution and function of tRNA-like sequences in tenebrionid mitogenomes and contribute to our general understanding of the evolution of Tenebrionidae.
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Affiliation(s)
- Su-Hao Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Shi-Yun Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou 730020, China
| | - Min Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Min Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou 730020, China
| | - Hao Sun
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou 730020, China
| | - Jia-Rui Zhao
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Wen-Ting Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Ming-Long Yuan
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Lanzhou University, Lanzhou 730020, China; (S.-H.W.); (S.-Y.H.); (M.L.); (M.L.); (H.S.); (J.-R.Z.); (W.-T.C.)
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Lanzhou University, Lanzhou 730020, China
- College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China
- National Demonstration Center for Experimental Grassland Science Education, Lanzhou University, Lanzhou 730020, China
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9
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Huang Y, Yang Y, Qi L, Hu H, Rasplus JY, Wang X. Novel Gene Rearrangement Pattern in Pachycrepoideus vindemmiae Mitochondrial Genome: New Gene Order in Pteromalidae (Hymenoptera: Chalcidoidea). Animals (Basel) 2023; 13:1985. [PMID: 37370495 DOI: 10.3390/ani13121985] [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: 04/18/2023] [Revised: 06/05/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
The mitochondrial genomes of Muscidifurax similadanacus, M. sinesensilla, Nasonia vitripennis, and Pachycrepoideus vindemmiae were sequenced to better understand the structural evolution of Pteromalidae mitogenomes. These newly sequenced mitogenomes all contained 37 genes. Nucleotide composition was AT-biased and the majority of the protein-coding genes exhibited a negative AT skew. All 13 protein-coding genes (PCGs) initiated with the standard start codon of ATN, excepted for nad1 of N. vitripennis, which started with TTG, and terminated with a typical stop codon TAA/TAG or an incomplete stop codon T. All transfer RNA (tRNA) genes were predicted to fold into the typical clover-leaf secondary structures, except for trnS1, which lacks the DHU arm in all species. In P. vindemmiae, trnR and trnQ lack the DHU arm and TΨC arm, respectively. Although most genes evolved under a strong purifying selection, the Ka/Ks value of the atp8 gene of P. vindemmiae was greater than 1, indicating putative positive selection. A novel transposition of trnR in P. vindemmiae was revealed, which was the first of this kind to be reported in Pteromalidae. Two kinds of datasets (PCG12 and AA) and two inference methods (maximum likelihood and Bayesian inference) were used to reconstruct a phylogenetic hypothesis for the newly sequenced mitogenomes of Pteromalidae and those deposited in GenBank. The topologies obtained recovered the monophyly of the three subfamilies included. Pachyneurinae and Pteromalinae were recovered as sister families, and both appeared sister to Sycophaginae. The pairwise breakpoint distances of mitogenome rearrangements were estimated to infer phylogeny among pteromalid species. The topology obtained was not totally congruent with those reconstructed using the ML and BI methods.
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Affiliation(s)
- Yixin Huang
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
| | - Yuanhan Yang
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, China
| | - Liqing Qi
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, China
| | - Haoyuan Hu
- Collaborative Innovation Center of Recovery and Reconstruction of Degraded Ecosystem in Wanjiang Basin Co-founded by Anhui Province and Ministry of Education, School of Ecology and Environment, Anhui Normal University, Wuhu 241000, China
| | - Jean-Yves Rasplus
- Centre de Biologie pour la Gestion des Populations (CBGP), INRAE, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, 34398 Montpellier, France
| | - Xu Wang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources, College of Life Sciences, Anhui Normal University, Wuhu 241000, China
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10
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Yuan Y, Zhang L, Li K, Hong Y, Storey KB, Zhang J, Yu D. Nine Mitochondrial Genomes of Phasmatodea with Two Novel Mitochondrial Gene Rearrangements and Phylogeny. INSECTS 2023; 14:insects14050485. [PMID: 37233113 DOI: 10.3390/insects14050485] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/27/2023]
Abstract
The classification of stick and leaf insects (Order Phasmatodea) is flawed at various taxonomic ranks due to a lack of robust phylogenetic relationships and convergent morphological characteristics. In this study, we sequenced nine new mitogenomes that ranged from 15,011 bp to 17,761 bp in length. In the mitogenome of Carausis sp., we found a translocation of trnR and trnA, which can be explained by the tandem duplication/random loss (TDRL) model. In the Stheneboea repudiosa Brunner von Wattenwyl, 1907, a novel mitochondrial structure of 12S rRNA-CR1-trnI-CR2-trnQ-trnM was found for the first time in Phasmatodea. Due to the low homology of CR1 and CR2, we hypothesized that trnI was inverted through recombination and then translocated into the middle of the control region. Control region repeats were frequently detected in the newly sequenced mitogenomes. To explore phylogenetic relationships in Phasmatodea, mtPCGs from 56 Phasmatodean species (composed of 9 stick insects from this study, 31 GenBank data, and 16 data derived from transcriptome splicing) were used for Bayesian inference (BI), and maximum likelihood (ML) analyses. Both analyses supported the monophyly of Lonchodinae and Necrosciinae, but Lonchodidae was polyphyletic. Phasmatidae was monophyletic, and Clitumninae was paraphyletic. Phyllidae was located at the base of Neophasmatodea and formed a sister group with the remaining Neophasmatodea. Bacillidae and Pseudophasmatidae were recovered as a sister group. Heteroptergidae was monophyletic, and the Heteropteryginae sister to the clade (Obriminae + Dataminae) was supported by BI analysis and ML analysis.
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Affiliation(s)
- Yani Yuan
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
| | - Lihua Zhang
- Taishun County Forestry Bureau, Wenzhou 325500, China
| | - Ke Li
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
| | - Yuehuan Hong
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
| | - Kenneth B Storey
- Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada
| | - Jiayong Zhang
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
| | - Danna Yu
- College of Life Science, Zhejiang Normal University, Jinhua 321004, China
- Key Lab of Wildlife Biotechnology, Conservation and Utilization of Zhejiang Province, Zhejiang Normal University, Jinhua 321004, China
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11
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Xu S, Li W, Liu Q, Wang Y, Li X, Duan X, He J, Song F. The mitochondrial genome of Binodoxys acalephae (Hymenoptera: Braconidae) with unique gene rearrangement and phylogenetic implications. Mol Biol Rep 2023; 50:2641-2649. [PMID: 36639523 PMCID: PMC10011326 DOI: 10.1007/s11033-022-08232-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 12/22/2022] [Indexed: 01/15/2023]
Abstract
BACKGROUND Species in the subfamily Aphidiinae from the Braconidae of Hymenoptera are endoparasitic wasps that exclusively utilize aphids as hosts. Some Aphidiinae species are widely used as biological agents. However, there were only one species with determined complete mitochondrial genome from this subfamily. METHODS AND RESULTS In this study, we sequenced and annotated the mitochondrial genome (mitogenome) of Binodoxys acalephae, which was 15,116 bp in size and contained 37 genes. The start codon of 13 protein-coding genes was ATN, and the complete stop codon TAA and TAG was widely assigned to 11 protein-coding genes. The lrRNA contains 43 stem-loop structures, and srRNA contains 25 stem-loop structures. Translocation and inversion of tRNA genes was found to be dominant in B. acalephae. In contrast to Aphidius gifuensis from the same subfamily Aphidiinae, inverted tRNALeu1 was translocated to the gene cluster between tRNALeu2 and COX2, and the control region between tRNAIle and tRNAMet was deleted in the mitogenome of B. acalephae. Within Braconidae, gene clusters tRNATrp-tRNACys-tRNATyr and CR-tRNAIle-tRNAGln-tRNAMet were hotspots for gene rearrangement. Phylogenetic analysis showed that both Bayesian and maximum-likelihood methods recovered the monophyly of Aphidiinae and suggested that Aphidiinae formed sister clades with the remaining subfamilies. The phylogenetic analyses of nine subfamilies supported the monophyly of Cyclostomes and Noncyclostomes in Braconidae. CONCLUSION The arrangement of mitochondrial genes and the phylogenetic relationships among nine Braconidae subfamilies were constructed better to understand the diversity and evolution of Aphidiinae mitogenomes.
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Affiliation(s)
- Shiwen Xu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, 100193 Beijing, China
| | - Weiwei Li
- Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, China
- Yunnan Agricultural University, 650201 Kunming, China
| | - Qiannan Liu
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, 100193 Beijing, China
| | - Yunming Wang
- Yuxi Branch, Yunnan Tobacco Company, 653100 Yuxi, China
| | - Xiaoling Li
- Yuxi Branch, Yunnan Tobacco Company, 653100 Yuxi, China
| | - Xiaoqian Duan
- Yuxi Branch, Yunnan Tobacco Company, 653100 Yuxi, China
| | - Jia He
- Institute of Plant Protection, Academy of Ningxia Agriculture and Forestry Science, 750002 Yinchuan, China
- Ningxia Key Laboratory of Plant Disease and Pest Control, 750002 Yinchuan, China
| | - Fan Song
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, 100193 Beijing, China
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12
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Shu X, Yuan R, Xia Z, Gao G, Yang L, Sun Z, Mu Q, Tang P, Chen X. Comparative mitogenomes reveal diverse and novel gene rearrangements in the genus Meteorus (Hymenoptera: Braconidae). Front Genet 2023; 14:1132606. [PMID: 36861128 PMCID: PMC9968957 DOI: 10.3389/fgene.2023.1132606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/03/2023] [Indexed: 02/15/2023] Open
Abstract
Meteorus Haliday, 1835 is a cosmopolitan genus within Braconidae (Hymenoptera). They are koinobiont endoparasitoids of Coleoptera or Lepidoptera larvae. Only one mitogenome of this genus was available. Here, we sequenced and annotated three mitogenomes of Meteorus species, and found that the tRNA gene rearrangements in these mitogenomes were rich and diverse. Compared with the ancestral organization, only seven tRNAs (trnW, trnY, trnL2, trnH, trnT, trnP and trnV) were conserved and trnG had its own unique location in the four mitogenomes. This dramatic tRNA rearrangement was not observed in mitogenomes of other insect groups before. In addition, the tRNA cluster (trnA-trnR-trnN-trnS1-trnE-trnF) between nad3 and nad5 was rearranged into two patterns, i.e., trnE-trnA-trnR-trnN-trnS1 and trnA-trnR-trnS1-trnE-trnF-trnN. The phylogenetic results showed that the Meteorus species formed a clade within the subfamily Euphorinae, and were close to Zele (Hymenoptera, Braconidae, Euphorinae). In the Meteorus, two clades were reconstructed: M. sp. USNM and Meteorus pulchricornis forming one clade while the remaining two species forming another clade. This phylogenetic relationship also matched the tRNA rearrangement patterns. The diverse and phylogenetic signal of tRNA rearrangements within one genus provided insights into tRNA rearrangements of the mitochondrial genome at genus/species levels in insects.
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Affiliation(s)
- Xiaohan Shu
- Hainan Institute, Zhejiang University, Sanya, China,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China,State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China,Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Ruizhong Yuan
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China,State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China,Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhilin Xia
- Guizhou Province Tobacco Companies Qian xinan Municipal Tobacco Company, Xingyi, China
| | - Gui Gao
- Guizhou Province Tobacco Companies Qian xinan Municipal Tobacco Company, Xingyi, China
| | - Lei Yang
- Guizhou Province Tobacco Companies Qian xinan Municipal Tobacco Company, Xingyi, China,Tobacco Leaf Purchase Center, Hunan China Tobacco Industry Co., Ltd., Changsha, China
| | - Zhirong Sun
- Guizhou Province Tobacco Companies Qian xinan Municipal Tobacco Company, Xingyi, China
| | - Qing Mu
- Guizhou Province Tobacco Companies Qian xinan Municipal Tobacco Company, Xingyi, China,*Correspondence: Qing Mu, ; Pu Tang,
| | - Pu Tang
- Hainan Institute, Zhejiang University, Sanya, China,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China,State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China,Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China,*Correspondence: Qing Mu, ; Pu Tang,
| | - Xuexin Chen
- Hainan Institute, Zhejiang University, Sanya, China,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China,State Key Lab of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China,Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
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13
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Comparative analysis of the mitochondrial genome of Dermacentor steini from different regions in China. Parasitology 2023; 150:195-205. [PMID: 36482713 PMCID: PMC10090625 DOI: 10.1017/s0031182022001639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ticks are a group of blood-sucking ectoparasites that play an important role in human health and livestock production development as vectors of zoonotic diseases. The phylogenetic tree of single genes cannot accurately reflect the true kinship between species. Based on the complete mitochondrial genome analysis one can help to elucidate the phylogenetic relationships among species. In this study, the complete mitochondrial genome of Dermacentor steini (isolate Longyan) was sequenced and compared with the mitochondrial genes of 3 other Chinese isolates (Nanchang, Jinhua and Yingtan). In Dermacentor steini 4 isolates had identical or similar mitochondrial genome lengths and an overall variation of 0.76% between sequences. All nucleotide compositions showed a distinct AT preference. The most common initiation and stop codons were ATG and TAA, respectively. Fewer base mismatches were found in the tRNA gene of D. steini (isolate Longyan), and the vicinity of the control region and tRNA gene was a hot rearrangement region of the genus Dermacentor. Maximum likelihood trees and Bayesian trees indicate that D. steini is most closely related to Dermacentor auratus. The results enrich the mitochondrial genomic data of species in the genus Dermacentor and provide novel insights for further studies on the phylogeographic classification and molecular evolution of ticks.
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14
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Xiao D, Wang Z, Zhu J, Zhou X, Tang P, Chen X. The Mitochondrial Genomes of Two Parasitoid Wasps Protapanteles immunis and Parapanteles hyposidrae (Hymenoptera: Braconidae) with Phylogenetic Implications and Novel Gene Rearrangements. Genes (Basel) 2023; 14:genes14010230. [PMID: 36672971 PMCID: PMC9859417 DOI: 10.3390/genes14010230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/08/2023] [Accepted: 01/10/2023] [Indexed: 01/19/2023] Open
Abstract
Parapanteles hypsidrae (Wilkinson, 1928) and Protapanteles immunis (Haliday, 1834) are the most important parasitic wasps of Ectropis grisescens Warren and Ectropis obliqua (Prout). We sequenced and annotated the mitochondrial genomes of Pa. hyposidrae and Pr. immunis, which are 17,063 bp and 16,397 bp in length, respectively, and possess 37 mitochondrial genes. We discovered two novel types of gene rearrangement, the local inversion of nad4L in Pa. hyposidrae and the remote inversion of the block cox3-nad3-nad5-nad4 in Pr. immunis, within the mitogenomes of Braconidae. The phylogenetic analysis supported the subfamily Microgastrinae is a monophyletic group, but the tribes Apantelini and Cotesiini within this subfamily are paraphyletic groups.
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Affiliation(s)
- Dandan Xiao
- Hainan Institute, Zhejiang University, Sanya 572025, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ziqi Wang
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jiachen Zhu
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xiaogui Zhou
- Ministry of Agriculture Key Laboratory of Tea Quality and Safety Control, Tea Research Institute of Chinese Academy of Agricultural Sciences, Hangzhou 310008, China
| | - Pu Tang
- Hainan Institute, Zhejiang University, Sanya 572025, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Correspondence:
| | - Xuexin Chen
- Hainan Institute, Zhejiang University, Sanya 572025, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- State Key Laboratory of Rice Biology, Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, and Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
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15
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Fiteha YG, Rashed MA, Ali RA, Abd El-Moneim D, Alshanbari FA, Magdy M. Mitogenomic Features and Evolution of the Nile River Dominant Tilapiine Species (Perciformes: Cichlidae). BIOLOGY 2022; 12:biology12010040. [PMID: 36671733 PMCID: PMC9855864 DOI: 10.3390/biology12010040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022]
Abstract
To better understand the diversity and evolution of cichlids, we sequenced, assembled, and annotated the complete mitochondrial genomes of three Nile tilapiine species (Coptodon zillii, Oreochromis niloticus, and Sarotherodon galilaeus) dominating the Nile River waters. Our results showed that the general mitogenomic features were conserved among the Nile tilapiine species. The genome length ranged from 16,436 to 16,631 bp and a total of 37 genes were identified (two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), 13 protein-coding genes (PCGs), and 1 control region). The ND6 was the only CDS that presented a negative AT skew and a positive GC skew. The most extended repeat sequences were in the D-loop followed by the pseudogenes (trnSGCU). The ND5 showed relatively high substitution rates whereas ATP8 had the lowest substitution rate. The codon usage bias displayed a greater quantity of NNA and NNC at the third position and anti-bias against NNG. The phylogenetic relationship based on the complete mitogenomes and CDS was able to differentiate the three species as previously reported. This study provides new insight into the evolutionary connections between various subfamilies within cichlids while providing new molecular data that can be applied to discriminate between Nile tilapiine species and their populations.
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Affiliation(s)
- Yosur G. Fiteha
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
- Department of Zoology, Faculty of Women for Art, Science and Education, Ain Shams University, Cairo 11566, Egypt
| | - Mohamed A. Rashed
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
| | - Ramadan A. Ali
- Department of Zoology, Faculty of Women for Art, Science and Education, Ain Shams University, Cairo 11566, Egypt
| | - Diaa Abd El-Moneim
- Department of Plant Production (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish 45511, Egypt
| | - Fahad A. Alshanbari
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52266, Saudi Arabia
| | - Mahmoud Magdy
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
- Correspondence:
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16
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A Compositional Heterogeneity Analysis of Mitochondrial Phylogenomics in Chalcidoidea Involving Two Newly Sequenced Mitogenomes of Eupelminae (Hymenoptera: Chalcidoidea). Genes (Basel) 2022; 13:genes13122340. [PMID: 36553606 PMCID: PMC9778353 DOI: 10.3390/genes13122340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
As next-generation sequencing technology becomes more mature and the cost of sequencing continues to fall, researchers are increasingly using mitochondrial genomes to explore phylogenetic relationships among different groups. In this study, we sequenced and analyzed the complete mitochondrial genomes of Eupelmus anpingensis and Merostenus sp. We predicted the secondary-structure tRNA genes of these two species and found that 21 of the 22 tRNA genes in Merostenus sp. exhibited typical clover-leaf structures, with trnS1 being the lone exception. In E. anpingensis, we found that, in addition to trnS1, the secondary structure of trnE was also incomplete, with only DHU arms and anticodon loop remaining. In addition, we found that compositional heterogeneity and variable rates of evolution are prevalent in Chalcidoidea. Under the homogeneity model, a Eupelmidae + Encyrtidae sister group relationship was proposed. Different datasets based on the heterogeneity model produced different tree topologies, but all tree topologies contained Chalcididae and Trichogrammatidae in the basal position of the tree. This is the first study to consider the phylogenetic relationships of Chalcidoidea by comparing a heterogeneity model with a homogeneity model.
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17
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Yuan R, Zhou J, Shu X, Ye X, Tang P, Chen X. The mitochondrial genome of Chelonus formosanus (Hymenoptera: Braconidae) with novel gene orders and phylogenetic implications. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2022; 111:e21870. [PMID: 35089615 PMCID: PMC9539690 DOI: 10.1002/arch.21870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/06/2022] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Chelonus formosanus Sonan is an important egg-larval parasitoid of noctuid moths and a potential candidate for understanding interactions between host and parasitoid mediated by polydnavirues (PDVs). We sequenced and annotated the mitochondrial genome of C. formosanus, which is 15,466 bp in length and possesses 38 mitochondrial genes. However, unlike most animal mitochondrial genomes, it contains one extra trnF gene. There are five transfer RNA (tRNA) rearrangement events compared with the ancestral gene order, which is a novel rearrangement type in Hymenoptera for all published mitogenomes so far. Phylogenetic trees supported C. formosanus from the subfamily Cheloninae was closely related to the subfamily Cardiochilinae and Microgastrinae.
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Affiliation(s)
- Rui‐Zhong Yuan
- State Key Lab of Rice BiologyZhejiang UniversityHangzhouChina
- Institute of Insect Sciences, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Jin‐Jin Zhou
- State Key Lab of Rice BiologyZhejiang UniversityHangzhouChina
- Institute of Insect Sciences, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- Hainan InstituteZhejiang UniversitySanyaChina
| | - Xiao‐Han Shu
- State Key Lab of Rice BiologyZhejiang UniversityHangzhouChina
- Institute of Insect Sciences, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- Hainan InstituteZhejiang UniversitySanyaChina
| | - Xi‐Qian Ye
- State Key Lab of Rice BiologyZhejiang UniversityHangzhouChina
- Institute of Insect Sciences, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
| | - Pu Tang
- State Key Lab of Rice BiologyZhejiang UniversityHangzhouChina
- Institute of Insect Sciences, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
| | - Xue‐Xin Chen
- State Key Lab of Rice BiologyZhejiang UniversityHangzhouChina
- Institute of Insect Sciences, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- Hainan InstituteZhejiang UniversitySanyaChina
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
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18
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Ge X, Zang H, Ye X, Peng L, Wang B, Lian G, Sun C. Comparative Mitogenomic Analyses of Hydropsychidae Revealing the Novel Rearrangement of Protein-Coding Gene and tRNA (Trichoptera: Annulipalpia). INSECTS 2022; 13:759. [PMID: 36135460 PMCID: PMC9501032 DOI: 10.3390/insects13090759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/17/2022] [Accepted: 08/20/2022] [Indexed: 06/16/2023]
Abstract
Gene rearrangement of the mitochondrial genome of insects, especially the rearrangement of protein-coding genes, has long been a hot topic for entomologists. Although mitochondrial gene rearrangement is common within Annulipalpia, protein-coding gene rearrangement is relatively rare. As the largest family in Annulipalpia, the available mitogenomes from Hydropsychidae Curtis, 1835 are scarce, and thus restrict our interpretation of the mitogenome characteristic. In this study, we obtained 19 novel mitogenomes of Hydropsychidae, of which the mitogenomes of the genus Arctopsyche are published for the first time. Coupled with published hydropsychid mitogenome, we analyzed the nucleotide composition evolutionary rates and gene rearrangements of the mitogenomes among subfamilies. As a result, we found two novel gene rearrangement patterns within Hydropsychidae, including rearrangement of protein-coding genes. Meanwhile, our results consider that the protein-coding gene arrangement of Potamyia can be interpreted by the tandem duplication/random loss (TDRL) model. In addition, the phylogenetic relationships within Hydropsychidae constructed by two strategies (Bayesian inference and maximum likelihood) strongly support the monophyly of Arctopscychinae, Diplectroninae, Hydropsychinae, and Macronematinae. Our study provides new insights into the mechanisms and patterns of mitogenome rearrangements in Hydropsychidae.
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Affiliation(s)
- Xinyu Ge
- Lab of Taxonomy & Aquatic Insects, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Haoming Zang
- Lab of Taxonomy & Aquatic Insects, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoyun Ye
- Environmental Monitoring Station of Qingtian County, Lishui 323999, China
| | - Lang Peng
- Lab of Taxonomy & Aquatic Insects, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Beixin Wang
- Lab of Taxonomy & Aquatic Insects, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Gang Lian
- Zhejiang Key Laboratory of Ecological and Environmental Monitoring, Forewarning and Quality Control, Zhejiang Province Ecological Environment Monitoring Centre, Hangzhou 310012, China
| | - Changhai Sun
- Lab of Taxonomy & Aquatic Insects, Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
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Huang L, Sun HQ, Li CJ, Zhao WX, Yao YX. The complete mitochondrial genome of Platygaster robiniae (Hymenoptera: Platygastridae): A novel tRNA secondary structure, gene rearrangements and phylogenetic implications. Int J Parasitol Parasites Wildl 2022; 18:249-259. [PMID: 35800109 PMCID: PMC9253838 DOI: 10.1016/j.ijppaw.2022.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/14/2022] [Accepted: 06/20/2022] [Indexed: 01/04/2023]
Abstract
Platygaster robiniae is economically important as a highly specific parasitoid of the invasive pest Obolodiplosis robiniae which was introduced into the Euro-Asia region in the last decade. Despite being a critical and specific parasitoid of the invasive pest O. robiniae and its use as an effective biocontrol agent, the absence of sequence information from P. robiniae have limited its genetic applications for pest management in forests. Mitochondrial (mt) genomes generally contain abundant nucleotide information and thus are helpful for understanding species history. Here, we sequenced the complete mt genome of P. robiniae using next generation sequencing, and annotated 13 protein-coding, 22 tRNA, and 2 rRNA genes and a 702 bp noncoding region. Comparative analysis indicated that this mt genome has a normal A + T content and codons use, however possessed both the expected and unique rearrangements. Ten tRNAs at four gene blocks COII-ATP8, COIII-ND3, ND3-ND5 and the A + T-rich region-ND2 were rearranged, including gene shuffles, transpositions and inversions. Notably, two genes tRNASer(UCN) and tRNALeu(CUN) had undergone long-range inversions, which is the first record of this rearrangement type in the superfamily Platygastroidea. The D-loops of both tRNAIle and tRNALeu(CUN) were absent from the tRNA secondary structure, which has not been reported from hymenopteran previously. Phylogenetic analysis based with the maximum likelihood and Bayesian methods showed that P. robiniae grouped with other species of Platygastridae, and that the superfamily Platygastridea is sister to the other Proctotrupomorpha superfamilies. Our tree strongly supports the monophyly of the five superfamilies of Proctotrupomorpha. This study discovered some unique characters of P. robiniae, and contributes to our understanding of genome rearrangements in the order Hymenoptera. Assemble the complete mitochondria genome of the obligate parasitoid (Platygaster robiniae) of Obolodiplosis robiniae. Discover some unique tRNA secondary structures. Discover some unique rearrangements of Platygaster robiniae and Platygastroidea. The abundance rearrangements in the order Hymenoptera.
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Kamiyama T, Shimada-Niwa Y, Tanaka H, Katayama M, Kuwabara T, Mori H, Kunihisa A, Itoh T, Toyoda A, Niwa R. Whole-genome sequencing analysis and protocol for RNA interference of the endoparasitoid wasp Asobara japonica. DNA Res 2022; 29:6605221. [PMID: 35686927 PMCID: PMC9233498 DOI: 10.1093/dnares/dsac019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Asobara japonica is an endoparasitic wasp that parasitizes Drosophila flies. It synthesizes various toxic components in the venom gland and injects them into host larvae during oviposition. To identify and characterize these toxic components for enabling parasitism, we performed the whole-genome sequencing (WGS) and devised a protocol for RNA interference (RNAi) with A. japonica. Because it has a parthenogenetic lineage due to Wolbachia infection, we generated a clonal strain from a single wasp to obtain highly homogenous genomic DNA. The WGS analysis revealed that the estimated genome size was 322 Mb with a heterozygosity of 0.132%. We also performed RNA-seq analyses for gene annotation. Based on the qualified WGS platform, we cloned ebony-Aj, which encodes the enzyme N-β-alanyl dopamine synthetase, which is involved in melanin production. The microinjection of double-stranded RNA (dsRNA) targeting ebony-Aj led to body colour changes in adult wasps, phenocopying ebony-Dm mutants. Furthermore, we identified putative venom genes as a target of RNAi, confirming that dsRNA injection-based RNAi specifically suppressed the expression of the target gene in wasp adults. Taken together, our results provide a powerful genetic toolkit for studying the molecular mechanisms of parasitism.
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Affiliation(s)
- Takumi Kamiyama
- Graduate School of Life and Environmental Sciences, University of Tsukuba , Tsukuba 305-8577, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba , Tsukuba 305-8577, Japan
| | - Yuko Shimada-Niwa
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba , Tsukuba 305-8577, Japan
- Precursory Research for Embryonic Science and Technology (PREST), Japan Science and Technology Agency (JST) , Tokyo 102-0076, Japan
| | - Hiroyuki Tanaka
- Department of Biological Information, Tokyo Institute of Technology , Meguro, Tokyo 152-8550, Japan
| | - Minami Katayama
- Graduate School of Life and Environmental Sciences, University of Tsukuba , Tsukuba 305-8577, Japan
| | - Takayoshi Kuwabara
- College of Biological Sciences, University of Tsukuba , Tsukuba 305-8577, Japan
| | - Hitoha Mori
- College of Biological Sciences, University of Tsukuba , Tsukuba 305-8577, Japan
| | - Akari Kunihisa
- College of Biological Sciences, University of Tsukuba , Tsukuba 305-8577, Japan
| | - Takehiko Itoh
- Department of Biological Information, Tokyo Institute of Technology , Meguro, Tokyo 152-8550, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics , Mishima, Shizuoka 411-8540, Japan
| | - Ryusuke Niwa
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba , Tsukuba 305-8577, Japan
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Novel Gene Rearrangements in the Mitochondrial Genomes of Cynipoid Wasps (Hymenoptera: Cynipoidea). Genes (Basel) 2022; 13:genes13050914. [PMID: 35627299 PMCID: PMC9140913 DOI: 10.3390/genes13050914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 12/04/2022] Open
Abstract
Cynipoidea is a medium-sized superfamily of Hymenoptera with diverse lifestyles. In this study, 16 mitochondrial genomes were newly sequenced, 11 of which were the first obtained mitochondrial genomes in the family Liopteridae and four subfamilies (Anacharitinae, Aspicerinae, Figitinae, and Parnipinae) of Figitidae. All of the newly sequenced mitogenomes have unique rearrangement types within Cynipoidea, whereas some gene patterns are conserved in several groups. nad5-nad4-nad4L-nad6-cytb was remotely inverted and two rRNA genes were translocated to nad3 downstream in Ibaliidae and three subfamilies (Anacharitinae, Eucoilinae, and Parnipinae within Figitidae); two rRNA genes in Aspicerinae, Figitinae, and Liopteridae were remotely inverted to the cytb-nad1 junction; rrnL-rrnS was translocated to the cytb-nad1 junction in Cynipidae. Phylogenetic inference suggested that Figitidae was a polyphyletic group, while the Ibaliidae nested deep within Cynipoidea and was a sister-group to the Figitidae. These results will improve our understanding of the gene rearrangement of the mitogenomes and the phylogenetic relationships in the Cynipoidea.
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Jasso-Martínez JM, Santos BF, Zaldívar-Riverón A, Fernandez-Triana J, Sharanowski BJ, Richter R, Dettman JR, Blaimer BB, Brady SG, Kula RR. Phylogenomics of braconid wasps (Hymenoptera, Braconidae) sheds light on classification and the evolution of parasitoid life history traits. Mol Phylogenet Evol 2022; 173:107452. [DOI: 10.1016/j.ympev.2022.107452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 02/17/2022] [Accepted: 03/01/2022] [Indexed: 01/05/2023]
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Zheng B, Han Y, Yuan R, Liu J, Tang P, van Achterberg C, Chen X. Mitochondrial Genomes Yield Insights into the Basal Lineages of Ichneumonid Wasps (Hymenoptera: Ichneumonidae). Genes (Basel) 2022; 13:genes13020218. [PMID: 35205263 PMCID: PMC8872219 DOI: 10.3390/genes13020218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/26/2021] [Accepted: 01/19/2022] [Indexed: 02/05/2023] Open
Abstract
We obtained four mitochondrial genomes of Odontocolon sp., Xorides funiuensis, Euceros kiushuensis and Euceros serricornis, which represent the first two representatives from subfamily Eucerotinae and Xoridinae (Ichneumonidae), respectively. All of the 4 newly sequenced mitochondrial genomes contain 13 protein-coding genes (PCGs) and most 24 RNA genes. Furthermore, they all have novel tRNA rearrangement patterns comparing with published mitogenomes in Ichneumonidae. For the tRNA cluster trnI-trnQ-trnM, X. funiuensis is shuffled as trnM-trnI-trnQ with trnQ inversed, while Odontocolon sp. with a remote translocation of trnK, shuffling as trnI-trnM-trnQ. E. kiushuensis and E. serricornis shared the same cluster trnQ-trnY-trnW-trnC. Finally, we reconstructed the phylogenetic relationships among the sequenced subfamilies of Ichneumonidae based on nucleotides and amino acids sequences of 13 PCGs in mitochondrial genomes, and the results of both the maximum likelihood and Bayesian inference analyses highly support that Eucerotinae is the basal ichneumonid lineage rather than Xoridinae.
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Affiliation(s)
- Boying Zheng
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yuanyuan Han
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ruizhong Yuan
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Jingxian Liu
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China;
| | - Pu Tang
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Correspondence:
| | - Cornelis van Achterberg
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xuexin Chen
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China; (B.Z.); (Y.H.); (R.Y.); (C.v.A.); (X.C.)
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China
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Bessa MH, Ré FCD, Moura RDD, Loreto EL, Robe LJ. Comparative mitogenomics of Drosophilidae and the evolution of the Zygothrica genus group (Diptera, Drosophilidae). Genetica 2021; 149:267-281. [PMID: 34609625 DOI: 10.1007/s10709-021-00132-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 09/08/2021] [Indexed: 11/27/2022]
Abstract
The Zygothrica genus group of Drosophilidae encompasses more than 437 species and five genera. Although knowledge regarding its diversity has increased, uncertainties about its monophyly and position within Drosophilidae remain. Genomic approaches have been widely used to address different phylogenetic questions and analyses involving the mitogenome have revealed a cost-efficient tool to these studies. Thus, this work aims to characterize mitogenomes of three species of the Zygothrica genus group (from the Hirtodrosophila, Paraliodrosophila and Zygothrica genera), while comparing them with orthologous sequences from other 23 Drosophilidae species and addressing their phylogenetic position. General content concerning gene order and overlap, nucleotide composition, start and stop codon, codon usage and tRNA structures were compared, and phylogenetic trees were constructed under different datasets. The complete mitogenomes characterized for H. subflavohalterata affinis H002 and P. antennta present the PanCrustacea gene order with 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, 13 protein coding genes and an A+T rich region with two T-stretched elements. Some peculiarities such as the almost complete overlap of genes tRNAH/ND4, tRNAF/ND5 and tRNAS2/ND1 are reported for different Drosophilidae species. Non-canonical secondary structures were encountered for tRNAS1 and tRNAY, revealing patterns that apply at different phylogenetic scales. According to the best depiction of the mitogenomes evolutionary history, the three Neotropical species of the Zygothrica genus group encompass a monophyletic lineage sister to Zaprionus, composing with this genus a clade that is sister to the Drosophila subgenus.
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Affiliation(s)
- Maiara Hartwig Bessa
- Programa de Pós-Graduação Em Biodiversidade Animal, Universidade Federal de Santa Maria - UFSM, Santa Maria, RS, Brazil
| | - Francine Cenzi de Ré
- Programa de Pós-Graduação Em Biodiversidade Animal, Universidade Federal de Santa Maria - UFSM, Santa Maria, RS, Brazil
| | - Rafael Dias de Moura
- Curso de Ciências Biológicas, Universidade Federal de Santa Maria - UFSM, Santa Maria, RS, Brazil
| | - Elgion Lucio Loreto
- Programa de Pós-Graduação Em Biodiversidade Animal, Universidade Federal de Santa Maria - UFSM, Santa Maria, RS, Brazil
| | - Lizandra Jaqueline Robe
- Programa de Pós-Graduação Em Biodiversidade Animal, Universidade Federal de Santa Maria - UFSM, Santa Maria, RS, Brazil.
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Mitochondrial Genomic Landscape: A Portrait of the Mitochondrial Genome 40 Years after the First Complete Sequence. Life (Basel) 2021; 11:life11070663. [PMID: 34357035 PMCID: PMC8303319 DOI: 10.3390/life11070663] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 12/11/2022] Open
Abstract
Notwithstanding the initial claims of general conservation, mitochondrial genomes are a largely heterogeneous set of organellar chromosomes which displays a bewildering diversity in terms of structure, architecture, gene content, and functionality. The mitochondrial genome is typically described as a single chromosome, yet many examples of multipartite genomes have been found (for example, among sponges and diplonemeans); the mitochondrial genome is typically depicted as circular, yet many linear genomes are known (for example, among jellyfish, alveolates, and apicomplexans); the chromosome is normally said to be “small”, yet there is a huge variation between the smallest and the largest known genomes (found, for example, in ctenophores and vascular plants, respectively); even the gene content is highly unconserved, ranging from the 13 oxidative phosphorylation-related enzymatic subunits encoded by animal mitochondria to the wider set of mitochondrial genes found in jakobids. In the present paper, we compile and describe a large database of 27,873 mitochondrial genomes currently available in GenBank, encompassing the whole eukaryotic domain. We discuss the major features of mitochondrial molecular diversity, with special reference to nucleotide composition and compositional biases; moreover, the database is made publicly available for future analyses on the MoZoo Lab GitHub page.
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Comparative mitogenomes of three species in Moenkhausia: Rare irregular gene rearrangement within Characidae. Int J Biol Macromol 2021; 183:1079-1086. [PMID: 33984380 DOI: 10.1016/j.ijbiomac.2021.05.049] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 04/22/2021] [Accepted: 05/06/2021] [Indexed: 11/22/2022]
Abstract
Generally, a teleostean group possesses only one type or a set of similar mitochondrial gene arrangements. However, a new type of gene arrangement has been identified in the mitochondrial genomes (mitogenomes) of Moenkhausia. Here, three newly sequenced complete mitogenomes of tetras (Characidae: Moenkhausia) are presented (M. costae, M. pittieri, and M. sanctaefilomenae). The three mitogenomes had a classical circular structure, with total lengths ranging from 15,811 to 18,435 bp. Base composition analysis indicated that the sequences were biased toward adenine (A) and thymine (T), with A + T content of 54.63% in M. costae, 58.47% in M. pittieri, and 59.98% in M. sanctaefilomenae. The gene order and organization of M. sanctaefilomenae differed from those of typical teleostean mitogenomes. The genes tRNA-Ile, tRNA-Gln, and tRNA-Pro were translocated between tRNA-Trp and tRNA-Asn. One extra tRNA-Met and an extra CR were also discovered in the mitogenome. BI and ML analyses based on sequences of 38 different mitogenomes showed that M. costae and M. pittieri were classified together, and M. sanctaefilomenae was slightly further from other fish of the same genus. These results provide insight into the gene arrangement features of Characidae mitogenomes and lay the foundation for further phylogenetic studies on Characidae.
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Comparative mitogenomics and phylogenetics of the stinging wasps (Hymenoptera: Aculeata). Mol Phylogenet Evol 2021; 159:107119. [PMID: 33609704 DOI: 10.1016/j.ympev.2021.107119] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/22/2021] [Accepted: 02/09/2021] [Indexed: 11/22/2022]
Abstract
The stinging wasps (Hymenoptera: Aculeata) include diverse groups such as vespid wasps, ants and bees. Phylogenetic relationships among major lineages of stinging wasps have been inferred from molecular and morphological data. However, the genomic features of the mitochondrial genomes and their phylogenetic utility remain to be explored. In this study, we determined 23 mitochondrial genomes from the Aculeata. Four Mutillidae species showed relatively low A + T content compared to other species of the Aculeata (69.7%-77.4%). Eleven out of 44 species, mainly from the Chrysididae and the Pompilidae, showed reversals of GC skews. Gene rearrangements occurred across the species. Patterns of tRNA rearrangement were conserved in some groups, including the Chrysididae, Bethylidae, Pompilidae, Scolioidea and Vespoidea. Rearrangement of protein-coding genes were found in 12 out of 44 species of the Aculeata, including all four species from the Chrysididae, both species from the Bethylidae, one species from the Dryinidae, all three Scolioidea species and two Apoidea species. Phylogenetic inference showed a long branch in species with unusual genomic features, such as in the Mutillidae and Bethylidae. By excluding these species, we found paraphyly of the Chrysidoidea and a sister group relationship between the Formicoidea and Vespoidea. These results improve our understanding of the evolution of mitochondrial genomes in the Aculeata and, in general, the evolution across this subclade.
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Yu P, Zhou L, Yang WT, Miao LJ, Li Z, Zhang XJ, Wang Y, Gui JF. Comparative mitogenome analyses uncover mitogenome features and phylogenetic implications of the subfamily Cobitinae. BMC Genomics 2021; 22:50. [PMID: 33446100 PMCID: PMC7809818 DOI: 10.1186/s12864-020-07360-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 12/29/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Loaches of Cobitinae, widely distributed in Eurasian continent, have high economic, ornamental and scientific value. However, the phylogeny of Cobitinae fishes within genera or family level remains complex and controversial. Up to now, about 60 Cobitinae mitogenomes had been deposited in GenBank, but their integrated characteristics were not elaborated. RESULTS In this study, we sequenced and analyzed the complete mitogenomes of a female Cobits macrostigma. Then we conducted a comparative mitogenome analysis and revealed the conserved and unique characteristics of 58 Cobitinae mitogenomes, including C. macrostigma. Cobitinae mitogenomes display highly conserved tRNA secondary structure, overlaps and non-coding intergenic spacers. In addition, distinct base compositions were observed among different genus and significantly negative linear correlation between AT% and AT-skew were found among Cobitinae, genus Cobitis and Pangio mitogenomes, respectively. A specific 3 bp insertion (GCA) in the atp8-atp6 overlap was identified as a unique feature of loaches, compared to other Cypriniformes fish. Additionally, all protein coding genes underwent a strong purifying selection. Phylogenetic analysis strongly supported the paraphyly of Cobitis and polyphyly of Misgurnus. The strict molecular clock predicted that Cobitinae might have split into northern and southern lineages in the late Eocene (42.11 Ma), furthermore, mtDNA introgression might occur (14.40 Ma) between ancestral species of Cobitis and ancestral species of Misgurnus. CONCLUSIONS The current study represents the first comparative mitogenomic and phylogenetic analyses within Cobitinae and provides new insights into the mitogenome features and evolution of fishes belonging to the cobitinae family.
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Affiliation(s)
- Peng Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Tao Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Jun Miao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, the Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Powell C, Caleca V, Rhode C, Teixeira da Costa L, van Asch B. New Mitochondrial Gene Rearrangement in Psyttalia concolor, P. humilis and P. lounsburyi (Hymenoptera: Braconidae), Three Parasitoid Species of Economic Interest. INSECTS 2020; 11:E854. [PMID: 33276418 PMCID: PMC7761351 DOI: 10.3390/insects11120854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 12/02/2022]
Abstract
The family Braconidae consists mostly of specialized parasitoids, some of which hold potential in biocontrol of agricultural pests. Psyttalia concolor, Psyttalia humilis and Psyttalia lounsburyi are parasitoids associated with Bactrocera oleae, a major pest of cultivated olives. The native range of Psyttalia concolor is the Mediterranean, and P. humilis and P. lounsburyi are native to sub-Saharan Africa. This study reports the mitochondrial genomes of the three species, thus laying the foundation for mitogenomic analyses in the genus Psyttalia. Comparative mitogenomics within Braconidae showed a novel gene arrangement in Psyttalia in involving translocation and inversion of transfer RNA genes. The placement of Psyttalia in the subfamily Opiinae was well-supported, and the divergence between Psyttalia and its closest relative (Diachasmimorpha longicaudata) was at ~55 MYA [95% highest posterior density (HPD): 34-83 MYA]. Psyttalia lounsburyi occupied the most basal position among the three Psyttalia, having diverged from the other two species ~11 MYA (95% HPD: 6-17 MYA). Psyttalia concolor and P. humilis were recovered as sister species diverged at ~2 MYA (95% HPD: 1.1-3.6 MYA). This phylogeny combining new sequences and a set of 31 other cyclostomes and non-cyclostomes highlights the importance of a comprehensive taxonomic coverage of Braconidae mitogenomes to overcome the lack of robustness in the placement of several subfamilies.
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Affiliation(s)
- Chanté Powell
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; (C.P.); (C.R.)
| | - Virgilio Caleca
- Department of Agricultural, Food and Forest Sciences, Università degli Studi di Palermo, Viale delle Scienze, Edificio 5, 90128 Palermo, Italy;
| | - Clint Rhode
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; (C.P.); (C.R.)
| | - Luis Teixeira da Costa
- Unit for Cardiac and Cardiovascular Genetics, Department of Medical Genetics, Oslo University Hospital, Postboks 4956 Nydalen, 0424 Oslo, Norway
- Norsk Entomologisk Forening, Naturhistorisk Museum, Universitetet i Oslo, Postboks 1172 Blindern, 0318 Oslo, Norway
| | - Barbara van Asch
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; (C.P.); (C.R.)
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Li R, Zhang W, Ma Z, Zhou C. Novel gene rearrangement pattern in the mitochondrial genomes of Torleya mikhaili and Cincticostella fusca (Ephemeroptera: Ephemerellidae). Int J Biol Macromol 2020; 165:3106-3114. [PMID: 33098898 DOI: 10.1016/j.ijbiomac.2020.10.124] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 10/23/2022]
Abstract
The mayfly family Ephemerellidae (Insecta: Ephemeroptera) is distributed around the world and has very high species diversity. However, its evolution pattern of mitogenome and phylogenetic relationships within Ephemeroptera remain unclear. In this study, the complete mitochondrial genomes (mitogenomes) of Torleya mikhaili (15,042 bp) and Cincticostella fusca (15,135 bp) were firstly determined and analyzed. Two ephemerellid mitogenomes shared similar gene organization with 37 typical genes as well as a putative control region. Compared with other reported mitogenomes of mayflies, the unique gene order (I'-CR-Q-M) was found in these two mitogenomes. Although the observed rearrangement pattern is novel within ephemeropteran mitogenomes, it could be explained presumably by the mechanisms of tandem duplication-random loss and recombination. The phylogenetic analyses using both Bayesian inference (BI) and maximum likelihood (ML) methods based on four nucleotide datasets placed three ephemerellid species together. Furthermore, the phylogenetic relationships of the three genera were recovered as ((Ephemerella + Cincticostella) + Torleya).
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Affiliation(s)
- Ran Li
- The Key Laboratory of Jiangsu Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, PR China
| | - Wei Zhang
- The Key Laboratory of Jiangsu Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, PR China
| | - Zhenxing Ma
- The Key Laboratory of Jiangsu Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, PR China
| | - Changfa Zhou
- The Key Laboratory of Jiangsu Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, PR China.
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Yu K, Xiong S, Xu G, Ye X, Yao H, Wang F, Fang Q, Song Q, Ye G. Identification of Neuropeptides and Their Receptors in the Ectoparasitoid, Habrobracon hebetor. Front Physiol 2020; 11:575655. [PMID: 33178044 PMCID: PMC7596734 DOI: 10.3389/fphys.2020.575655] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/16/2020] [Indexed: 12/20/2022] Open
Abstract
Neuropeptides are a group of signal molecules that regulate many physiological and behavioral processes by binding to corresponding receptors, most of which are G-protein-coupled receptors (GPCRs). Using bioinformatic methods, we screened genomic and transcriptomic data of the ectoparasitoid wasp, Habrobracon hebetor, and annotated 34 neuropeptide candidate precursor genes and 44 neuropeptide receptor candidate genes. The candidate neuropeptide genes were found to encode all known insect neuropeptides except allatotropin, neuropeptide F, pigment dispersing factor, and CCHamides. When compared with the endoparasitic wasp Pteromalus puparum and the ectoparasitic wasp Nasonia vitripennis, trissin and FMRFamide were found only in H. hebetor. A similar result held for the neuropeptide receptor genes, for the receptors were found in H. hebetor except the receptors of CCHamides and neuroparsin. Furthermore, we compared and analyzed the differences in neuropeptides in eight Braconidae wasps and identified natalisin in H. hebetor, Diachasma alloeum, Fopius arisanus and Microplitis demolitor, but not in the other wasps. We also analyzed the transcriptome data and qRT-PCR data from different developmental stages and tissues to reveal the expression patterns of the neuropeptides and their receptors. In this study, we revealed composition of neuropeptides and neuropeptide receptors in H. hebetor, which may contribute to future neurobiological studies.
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Affiliation(s)
- Kaili Yu
- State Key Laboratory of Rice Biology and Key Laboratory of Agricultural Entomology of Ministry of Agriculture, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Shijiao Xiong
- State Key Laboratory of Rice Biology and Key Laboratory of Agricultural Entomology of Ministry of Agriculture, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Gang Xu
- State Key Laboratory of Rice Biology and Key Laboratory of Agricultural Entomology of Ministry of Agriculture, Institute of Insect Sciences, Zhejiang University, Hangzhou, China.,College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Xinhai Ye
- State Key Laboratory of Rice Biology and Key Laboratory of Agricultural Entomology of Ministry of Agriculture, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Hongwei Yao
- State Key Laboratory of Rice Biology and Key Laboratory of Agricultural Entomology of Ministry of Agriculture, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fang Wang
- State Key Laboratory of Rice Biology and Key Laboratory of Agricultural Entomology of Ministry of Agriculture, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Qi Fang
- State Key Laboratory of Rice Biology and Key Laboratory of Agricultural Entomology of Ministry of Agriculture, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Qisheng Song
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO, United States
| | - Gongyin Ye
- State Key Laboratory of Rice Biology and Key Laboratory of Agricultural Entomology of Ministry of Agriculture, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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32
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Mitogenome of Tolypocladium guangdongense. Appl Microbiol Biotechnol 2020; 104:9295-9308. [PMID: 32918580 DOI: 10.1007/s00253-020-10889-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 08/27/2020] [Accepted: 09/04/2020] [Indexed: 01/08/2023]
Abstract
Tolypocladium guangdongense is a high-value edible fungus with various medicinal and food safety properties. However, its evolutionary and genetic information is still limited. Mitochondrial genomes are potential models for molecular evolution and phylogenetic studies. In this study, we sequenced the complete mitogenome of T. guangdongense, demonstrating circular sequence of 46,102 bp, containing 14 standard protein-coding genes (PCGs), 2 ribosomal RNA subunit genes, and 28 tRNA genes. Phylogenetic analysis based on mitochondrial genes indicated that T. guangdongense was clustered into the Tolypocladium genus with high support value, based on the core PCG dataset. In addition, rps3 is also a suitable marker in the phylogenetic analysis in Hypocreales. Gene rearrangement analysis indicated that the gene order of PCGs was highly consistent in Hypocreales, and tRNA rearrangement events occurred in most species of Hypocreales; however, the rearrangement rates were not taxonomically correlated. Divergence time estimation based on the old fossil record and previous reports revealed that T. guangdongense originated approximately in the middle Cenozoic (42 Mya, 95% highest posterior density interval: 43-116) with the Tolypocladium genus differentiation. Our results provided more mitogenomic information of T. guangdongense and shed new insights into evolution of the Tolypocladium genus. KEY POINTS: • The general and unique features of T. guangdongense mitogenome are firstly reported. • Phylogenetic analysis further verified the taxonomic status of T. guangdongense. • Divergence time estimation provides more evolutionary information of T. guangdongense.
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33
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Feng Z, Wu Y, Yang C, Gu X, Wilson JJ, Li H, Cai W, Yang H, Song F. Evolution of tRNA gene rearrangement in the mitochondrial genome of ichneumonoid wasps (Hymenoptera: Ichneumonoidea). Int J Biol Macromol 2020; 164:540-547. [PMID: 32693134 DOI: 10.1016/j.ijbiomac.2020.07.149] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 12/21/2022]
Abstract
Gene rearrangements in the mitochondrial genome (mt genome) are common in certain insect groups and can be an informative character for phylogenetic reconstruction. However, knowledge of the mechanism and biases of gene rearrangement in insect mt genomes is still limited. With an accelerated rate of gene rearrangements, Hymenoptera is an important group for mt genome rearrangements diversity and for understanding the gene rearrangement evolution in mt genomes. Here, we sequenced the complete mt genome of Aphidius gifuensis and analyzed the evolution of tRNA gene rearrangements in the mt genomes of ichneumonoid wasps. Two control regions were detected in A. gifuensis and most of the tRNA rearrangement events occurred around these control regions. tRNA gene rearrangements occurred in almost all of the sequenced mt genomes of Ichneumonoidea and the gene block CR-trnI-trnQ-trnM-ND2-trnW-trnC-trnY was the main hot spot of gene rearrangement. Mapped over the backbone phylogeny of Ichneumonoidea, we found that the inversion and translocation of both trnI and trnM is likely a synapomorphic rearrangement in Braconidae. Our study also demonstrated that the gene block CR-trnI-trnQ-trnM-ND2-trnW-trnC-trnY was important for inferring the gene rearrangement dynamics in Ichneumonoidea.
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Affiliation(s)
- Zengbei Feng
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yunfei Wu
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Chun Yang
- Tobacco Company, Yuxi 653100, Yunnan, China
| | - Xinghui Gu
- Tobacco Company, Yuxi 653100, Yunnan, China
| | - John James Wilson
- Vertebrate Zoology at World Museum, National Museums Liverpool, Liverpool, UK; Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok, Thailand
| | - Hu Li
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Wanzhi Cai
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Hailin Yang
- Tobacco Company, Yuxi 653100, Yunnan, China.
| | - Fan Song
- Department of Entomology, MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing 100193, China.
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Su H, Lyu B, Meng R, Lu H, Tang J. The mitochondrial genome of an ectoparasitoid wasp, Habrobracon hebetor (Hymenoptera: Braconidae: Braconinae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:2790-2791. [PMID: 33457950 PMCID: PMC7783055 DOI: 10.1080/23802359.2020.1787268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In this study, we sequenced the mitogenome of Habrobracon hebetor, and obtained almost complete mitogenome of it. The mitogenome contains 14,629 bp which consists of 13 protein-coding genes (PCGs), 20 transfer RNA genes (trnI and trnM are absent), and 2 ribosomal RNA genes (GenBank accession no. MT558946). Gene rearrangement events occurred in this species, five tRNA genes with changes in positions or/and directions are found. All of 13 PCGs started with ATN. Eight PCGs used the typical stop codon ‘TAA’, five PCGs terminated with incomplete stop codons (T). Phylogenetic analyses within the Cyclostomes were performed based on mitochondrial PCGs.
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Affiliation(s)
- Hao Su
- College of Plant Protection, Hainan University, Haikou, China
| | - Baoqian Lyu
- China Academy of Tropical Agriculture Sciences/Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Haikou, China
| | - Rui Meng
- Post-Entry Quarantine Station for Tropical Plant, Haikou, PR China.,Hainan Province Engineering Research Center for Quarantine, Prevention and Control of Exotic Pests, Haikou, PR China
| | - Hui Lu
- China Academy of Tropical Agriculture Sciences/Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Haikou, China
| | - Jihong Tang
- China Academy of Tropical Agriculture Sciences/Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Environment and Plant Protection Institute, Haikou, China
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35
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Dennis AB, Ballesteros GI, Robin S, Schrader L, Bast J, Berghöfer J, Beukeboom LW, Belghazi M, Bretaudeau A, Buellesbach J, Cash E, Colinet D, Dumas Z, Errbii M, Falabella P, Gatti JL, Geuverink E, Gibson JD, Hertaeg C, Hartmann S, Jacquin-Joly E, Lammers M, Lavandero BI, Lindenbaum I, Massardier-Galata L, Meslin C, Montagné N, Pak N, Poirié M, Salvia R, Smith CR, Tagu D, Tares S, Vogel H, Schwander T, Simon JC, Figueroa CC, Vorburger C, Legeai F, Gadau J. Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum. BMC Genomics 2020; 21:376. [PMID: 32471448 PMCID: PMC7257214 DOI: 10.1186/s12864-020-6764-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/30/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Parasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biological control. Their success depends on adapting to develop inside aphids and overcoming both host aphid defenses and their protective endosymbionts. RESULTS We present the de novo genome assemblies, detailed annotation, and comparative analysis of two closely related parasitoid wasps that target pest aphids: Aphidius ervi and Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae). The genomes are small (139 and 141 Mbp) and the most AT-rich reported thus far for any arthropod (GC content: 25.8 and 23.8%). This nucleotide bias is accompanied by skewed codon usage and is stronger in genes with adult-biased expression. AT-richness may be the consequence of reduced genome size, a near absence of DNA methylation, and energy efficiency. We identify missing desaturase genes, whose absence may underlie mimicry in the cuticular hydrocarbon profile of L. fabarum. We highlight key gene groups including those underlying venom composition, chemosensory perception, and sex determination, as well as potential losses in immune pathway genes. CONCLUSIONS These findings are of fundamental interest for insect evolution and biological control applications. They provide a strong foundation for further functional studies into coevolution between parasitoids and their hosts. Both genomes are available at https://bipaa.genouest.org.
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Affiliation(s)
- Alice B Dennis
- Department of Aquatic Ecology, Eawag, 8600, Dübendorf, Switzerland.
- Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland.
- Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.
| | - Gabriel I Ballesteros
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centre for Molecular and Functional Ecology in Agroecosystems, Universidad de Talca, Talca, Chile
- Laboratorio de Control Biológico, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Stéphanie Robin
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
- Université de Rennes 1, INRIA, CNRS, IRISA, 35000, Rennes, France
| | - Lukas Schrader
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Jens Bast
- Department of Ecology and Evolution, Université de Lausanne, 1015, Lausanne, Switzerland
- Institute of Zoology, Universität zu Köln, 50674, Köln, Germany
| | - Jan Berghöfer
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Leo W Beukeboom
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Maya Belghazi
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, PINT, PFNT, Marseille, France
| | - Anthony Bretaudeau
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
- Université de Rennes 1, INRIA, CNRS, IRISA, 35000, Rennes, France
| | - Jan Buellesbach
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Elizabeth Cash
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, CA, 94720, USA
| | | | - Zoé Dumas
- Department of Ecology and Evolution, Université de Lausanne, 1015, Lausanne, Switzerland
| | - Mohammed Errbii
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | | | - Jean-Luc Gatti
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Elzemiek Geuverink
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Joshua D Gibson
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, CA, 94720, USA
- Department of Biology, Georgia Southern University, Statesboro, GA, 30460, USA
| | - Corinne Hertaeg
- Department of Aquatic Ecology, Eawag, 8600, Dübendorf, Switzerland
- Department of Environmental Systems Sciences, D-USYS, ETH Zürich, Zürich, Switzerland
| | - Stefanie Hartmann
- Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Emmanuelle Jacquin-Joly
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université Paris Diderot, Institute of Ecology and Environmental Sciences of Paris, iEES-Paris, F-78000, Versailles, France
| | - Mark Lammers
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Blas I Lavandero
- Laboratorio de Control Biológico, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Ina Lindenbaum
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | | | - Camille Meslin
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université Paris Diderot, Institute of Ecology and Environmental Sciences of Paris, iEES-Paris, F-78000, Versailles, France
| | - Nicolas Montagné
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université Paris Diderot, Institute of Ecology and Environmental Sciences of Paris, iEES-Paris, F-78000, Versailles, France
| | - Nina Pak
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Marylène Poirié
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Rosanna Salvia
- Department of Sciences, University of Basilicata, 85100, Potenza, Italy
| | - Chris R Smith
- Department of Biology, Earlham College, Richmond, IN, 47374, USA
| | - Denis Tagu
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
| | - Sophie Tares
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Tanja Schwander
- Department of Ecology and Evolution, Université de Lausanne, 1015, Lausanne, Switzerland
| | | | - Christian C Figueroa
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centre for Molecular and Functional Ecology in Agroecosystems, Universidad de Talca, Talca, Chile
| | - Christoph Vorburger
- Department of Aquatic Ecology, Eawag, 8600, Dübendorf, Switzerland
- Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Fabrice Legeai
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
- Université de Rennes 1, INRIA, CNRS, IRISA, 35000, Rennes, France
| | - Jürgen Gadau
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany.
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Sun H, Zhao W, Lin R, Zhou Z, Huai W, Yao Y. The conserved mitochondrial genome of the jewel beetle (Coleoptera: Buprestidae) and its phylogenetic implications for the suborder Polyphaga. Genomics 2020; 112:3713-3721. [PMID: 32360911 DOI: 10.1016/j.ygeno.2020.04.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 04/22/2020] [Accepted: 04/27/2020] [Indexed: 01/04/2023]
Abstract
In this study, we sequenced the mitochondrial (mt) genome of Agrilus mali (Coleoptera: Buprestidae) using next-generation sequencing, and accordingly annotated 13 protein-coding, 22 tRNA, and 2 rRNA genes and a 1458-bp non-coding region. Comparative analysis indicated that the mt genome of A. mali is relatively conserved, with a typical gene content and order identical to those of other coleopterans. However, the newly sequenced mt genome is characterized by a relatively higher A + T content compared with that of other species within the family Buprestidae. Phylogenetic analysis based on Bayesian inference revealed that the evolutionary relationship among the six infraorders of the suborder Polyphaga is (Scirtiformia + (Elateriformia + ((Scarabaeiformia + Staphyliniformia) + (Bostrichiformia + (Cucujiformia))))). However, the topology indicated that the family Buprestidae is a sister group to other Polyphaga infraorders, excluding Scirtiformia as a monophyly, and thus the monophyly of Elateriformia was not supported. This study not only presents the mt genome of a species in the family Buprestidae and a comparative analysis of jewel beetles but also examines the contribution of mt genomes in elucidating phylogenetic relationships within the suborder Polyphaga of Coleoptera.
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Affiliation(s)
- Huiquan Sun
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration/Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Wenxia Zhao
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration/Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Ruozhu Lin
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration/Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Zhongfu Zhou
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration/Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Wenxia Huai
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration/Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China
| | - Yanxia Yao
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration/Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing 100091, China.
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Novel gene rearrangement pattern in Cynoglossus melampetalus mitochondrial genome: New gene order in genus Cynoglossus (Pleuronectiformes: Cynoglossidae). Int J Biol Macromol 2020; 149:1232-1240. [DOI: 10.1016/j.ijbiomac.2020.02.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/31/2019] [Accepted: 02/03/2020] [Indexed: 11/24/2022]
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Comparative Analysis of Complete Mitochondrial Genomes of Three Gerres Fishes (Perciformes: Gerreidae) and Primary Exploration of Their Evolution History. Int J Mol Sci 2020; 21:ijms21051874. [PMID: 32182936 PMCID: PMC7084342 DOI: 10.3390/ijms21051874] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/05/2020] [Accepted: 03/07/2020] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial genome is a powerful molecule marker to explore phylogenetic relationships and reveal molecular evolution in ichthyological studies. Gerres species play significant roles in marine fishery, but its evolution has received little attention. To date, only two Gerres mitochondrial genomes were reported. In the present study, three mitogenomes of Gerres (Gerres filamentosus, Gerres erythrourus, and Gerres decacanthus) were systemically investigated. The lengths of the mitogenome sequences were 16,673, 16,728, and 16,871 bp for G. filamentosus, G. erythrourus, and G. decacanthus, respectively. Most protein-coding genes (PCGs) were initiated with the typical ATG codon and terminated with the TAA codon, and the incomplete termination codon T/TA could be detected in the three species. The majority of AT-skew and GC-skew values of the 13 PCGs among the three species were negative, and the amplitude of the GC-skew was larger than the AT-skew. The genetic distance and Ka/Ks ratio analyses indicated 13 PCGs were suffering purifying selection and the selection pressures were different from certain deep-sea fishes, were which most likely due to the difference in their living environment. The phylogenetic tree was constructed by molecular method (Bayesian Inference (BI) and maximum Likelihood (ML)), providing further supplement to the scientific classification of fish. Three Gerres species were differentiated in late Cretaceous and early Paleogene, and their evolution might link with the geological events that could change their survival environment.
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Comparative mitogenomics of Hymenoptera reveals evolutionary differences in structure and composition. Int J Biol Macromol 2020; 144:460-472. [DOI: 10.1016/j.ijbiomac.2019.12.135] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 11/06/2019] [Accepted: 12/15/2019] [Indexed: 01/26/2023]
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40
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Novel gene rearrangement in the mitochondrial genome of Pachyneuron aphidis (Hymenoptera: Pteromalidae). Int J Biol Macromol 2020; 149:1207-1212. [PMID: 32018006 DOI: 10.1016/j.ijbiomac.2020.01.308] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/04/2020] [Accepted: 01/31/2020] [Indexed: 11/21/2022]
Abstract
Species in Hymenoptera usually show exceptionally high rates of mitochondrial molecular evolution and dramatic gene rearrangements, which has been attributed to their parasitic lifestyle. However, mitochondrial genome (mitogenome) of chalcidoid wasps is still poorly understood and the evolution of gene rearrangements is still unclear. In this study, the nearly complete mitogenome of Pachyneuron aphidis, a chalcidoid wasp mainly hyperparasitizes the Aphidius gifuensis, was sequenced using a next-generation sequencing strategy. This genome is 15,137 bp in length, including 13 PCGs, 22 tRNAs, two rRNAs and a partial control region. Alignment with other Chalcidoidea mitogenomes revealed a novel inversion in the srRNA-trnV gene cluster in P. aphidis, which is the first of its kind to be reported in Chalcidoidea. Breakpoint distances analysis showed the high value of chalcidoid wasps compare to the ancestral arrangement pattern, which reflected as extensive gene rearrangements. Despite the high frequency of gene rearrangements in these insects, analyses of gene rearrangement and phylogenetic trees showed that species from the same family and the genus tent to have similar gene orders, and the conserved gene blocks (ND3-trnG, srRNA-trnV and COIII-ATP6-ATP8-trnD-trnK-COII-trnL2-COI) can usually be identified, especially at the family level of chalcidoid wasps.
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Five mitochondrial genomes of black fungus gnats (Sciaridae) and their phylogenetic implications. Int J Biol Macromol 2020; 150:200-205. [PMID: 32004603 DOI: 10.1016/j.ijbiomac.2020.01.271] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 01/26/2020] [Accepted: 01/27/2020] [Indexed: 11/21/2022]
Abstract
Sciaridae is a family of great species diversity, distributed worldwide, that includes important agricultural pests of cultivated mushrooms and plants produced in greenhouses. Here we sequenced five nearly complete mitochondrial genomes representing three subfamilies of Sciaridae. The lengths of these mitogenomes range from 13,849 bp to 16,923 bp with 13 protein-coding genes (PCGs), 20-22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a control region (CR). Compared with other dipteran species, rearrangements in Sciaridae are more common. Inversion or transition is observed frequently of trnL2, and in the tRNA clusters trnI-trnQ-trnM, trnW-trnC-trnY, and trnA-trnR-trnN-trnS1-trnE-trnF. Phylogenetic relationships within the family were reconstructed based on these newly sequenced species, combined with the published mitogenomes of related families, and recovered the topology within Sciaroidea as Cecidomyiidae + (Sciaridae + Keroplatidae). Relationships recovered within Sciaridae were Sciarinae + ('Pseudolycoriella group' + Megalosphyinae).
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Lyu B, Meng R, Cai B, Su H. Complete mitochondrial genome of a parasitic wasp Microplitis pallidipes (Hymenoptera: Braconidae: Microgastrinae). MITOCHONDRIAL DNA PART B-RESOURCES 2020; 5:871-872. [PMID: 33366790 PMCID: PMC7748814 DOI: 10.1080/23802359.2020.1715893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The complete mitochondrial genome of Microplitis pallidipes contains 15931 bp, with an A + T content of 86.5% and consists of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a control region (GenBank accession no. MN892396). All of the 22 tRNA genes displayed an usual clover-leaf structure. Gene rearrangement events occurred in this species, there are eight tRNA genes changed their positions or/and directions. 13 PCGs started with ATN. Ten PCGs used the typical stop codon ‘TAA’ and ‘TAG’, three PCGs terminated with incomplete stop codons (TA). Phylogenetic analyses within the microgastroid complex were performed based on mitochondrial protein-coding genes.
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Affiliation(s)
- Baoqian Lyu
- Environment and Plant Protection Institute, Ministry of Agriculture and Rural Affairs, China Academy of Tropical Agriculture Sciences/Key Laboratory of Integrated Pest Management on Tropical Crops, Haikou, China
| | - Rui Meng
- Post-Entry Quarantine Station for Tropical Plant, Haikou Customs District P. R. China/Hainan Province Engineering Research Center for Quarantine, Prevention and Control of Exotic Pests, Haikou, China
| | - Bo Cai
- Post-Entry Quarantine Station for Tropical Plant, Haikou Customs District P. R. China/Hainan Province Engineering Research Center for Quarantine, Prevention and Control of Exotic Pests, Haikou, China
| | - Hao Su
- Environment and Plant Protection Institute, Ministry of Agriculture and Rural Affairs, China Academy of Tropical Agriculture Sciences/Key Laboratory of Integrated Pest Management on Tropical Crops, Haikou, China
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Samacá-Sáenz E, Meza-Lázaro RN, Branstetter MG, Zaldívar-Riverón A. Phylogenomics and mitochondrial genome evolution of the gall-associated doryctine wasp genera (Hymenoptera: Braconidae). SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1685608] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Ernesto Samacá-Sáenz
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, 3er. circuito exterior s/n, Cd. Universitaria, Coyoacán, A. P. 70-233, C. P. 04510, Ciudad de México, México
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Circuito de Posgrados, Universidad Nacional Autónoma de México, Coyoacán, C. P. 04510, Ciudad de México, México
| | - Rubi N. Meza-Lázaro
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, 3er. circuito exterior s/n, Cd. Universitaria, Coyoacán, A. P. 70-233, C. P. 04510, Ciudad de México, México
| | - Michael G. Branstetter
- USDA-ARS Pollinating Insects Research Unit, Utah State University, 5310 Old Main Hill, Logan, UT 84322-5310, USA
| | - Alejandro Zaldívar-Riverón
- Colección Nacional de Insectos, Instituto de Biología, Universidad Nacional Autónoma de México, 3er. circuito exterior s/n, Cd. Universitaria, Coyoacán, A. P. 70-233, C. P. 04510, Ciudad de México, México
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Wang XY, Wang JJ, Fan ZH, Dai RH. Complete mitogenome of Olidiana ritcheriina (Hemiptera: Cicadellidae) and phylogeny of Cicadellidae. PeerJ 2019; 7:e8072. [PMID: 31788356 PMCID: PMC6883956 DOI: 10.7717/peerj.8072] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 10/21/2019] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Coelidiinae, a relatively large subfamily within the family Cicadellidae, includes 129 genera and ∼1,300 species distributed worldwide. However, the mitogenomes of only two species (Olidiana sp. and Taharana fasciana) in the subfamily Coelidiinae have been assembled. Here, we report the first complete mitogenome assembly of the genus Olidiana. METHODS Specimens were collected from Wenxian County (Gansu Province, China) and identified on the basis of their morphology. Mitogenomes were sequenced by next-generation sequencing, following which an NGS template was generated, and this was confirmed using polymerase chain reaction and Sanger sequencing. Phylogenic trees were constructed using maximum likelihood and Bayesian analyses. RESULTS The mitogenome of O. ritcheriina was 15,166 bp long, with an A + T content of 78.0%. Compared with the mitogenome of other Cicadellidae sp., the gene order, gene content, gene size, base composition, and codon usage of protein-coding genes (PCGs) in O. ritcheriina were highly conserved. The standard start codon of all PCGs was ATN and stop codon was TAA or TAG; COII, COIII, and ND4L ended with a single T. All tRNA genes showed the typical cloverleaf secondary structure, except for trnSer, which did not have the dihydrouridine arm. Furthermore, the secondary structures of rRNAs (rrnL and rrnS) in O. ritcheriina were predicted. Overall, five domains and 42 helices were predicted for rrnL (domain III is absent in arthropods), and three structural domains and 27 helices were predicted for rrnS. Maximum likelihood and Bayesian analyses indicated that O. ritcheriina and other Coelidiinae members were clustered into a clade, indicating the relationships among their subfamilies; the main topology was as follows: (Deltocephalinae + ((Coelidiinae + Iassinae) + ((Typhlocybinae + Cicadellinae) + (Idiocerinae + (Treehopper + Megophthalminae))))). The phylogenetic relationships indicated that the molecular taxonomy of O. ritcheriina is consistent with the current morphological classification.
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Affiliation(s)
- Xian-Yi Wang
- Institute of Entomology, Guizhou University, The Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Guizhou, Guiyang, China
| | - Jia-Jia Wang
- Institute of Entomology, Guizhou University, The Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Guizhou, Guiyang, China
| | - Zhi-Hua Fan
- Jingtanggang Customs House, Tangshan, Hebei, Tangshan, China
| | - Ren-Huai Dai
- Institute of Entomology, Guizhou University, The Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Guizhou, Guiyang, China
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Complete mitochondrial genome of Ophichthus brevicaudatus reveals novel gene order and phylogenetic relationships of Anguilliformes. Int J Biol Macromol 2019; 135:609-618. [PMID: 31132441 DOI: 10.1016/j.ijbiomac.2019.05.139] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/30/2019] [Accepted: 05/21/2019] [Indexed: 11/20/2022]
Abstract
Generally, a teleostean group possesses only one type or a set of similar mitochondrial gene arrangement. However, two types of gene arrangement have been identified in the mitochondrial genomes (mitogenomes) of Anguilliformes. Here, a newly sequenced mitogenome of Ophichthus brevicaudatus (Anguilliformes; Ophichthidae) was presented. The total length of the O. brevicaudatus mitogenome was 17,773 bp, and it contained 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNA (tRNA) genes, and two identical control regions (CRs). The gene order differed from that of the typical vertebrate mitogenomes. The genes ND6 and the conjoint trnE were translocated to the location between trnT and trnP, and one of the duplicated CR was translocated to the upstream of the ND6. The duplication-random loss model was adopted to explain the gene rearrangement events in this mitogenome. The most comprehensive phylogenetic trees of Anguilliformes based on complete mitogenome was constructed. The non-monophyly of Congridae was well supported, whereas the non-monophyly of Derichthyidae and Chlopsidae was not supported. These results provide insight into gene arrangement features of anguilliform mitogenomes and lay the foundation for further phylogenetic studies on Anguilliformes.
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Yu P, Zhou L, Zhou XY, Yang WT, Zhang J, Zhang XJ, Wang Y, Gui JF. Unusual AT-skew of Sinorhodeus microlepis mitogenome provides new insights into mitogenome features and phylogenetic implications of bitterling fishes. Int J Biol Macromol 2019; 129:339-350. [PMID: 30738158 DOI: 10.1016/j.ijbiomac.2019.01.200] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/17/2019] [Accepted: 01/29/2019] [Indexed: 12/25/2022]
Abstract
Sinorhodeus microlepis (S. microlepis) is recently described as a new species and represents a new genus Sinorhodeu of the subfamily Acheilognathinae. In this study, we first sequenced the complete mitogenome of S. microlepis and compared with the other 29 bitterling mitogenomes. The S. microlepis mitogenome is 16,591 bp in length and contains 37 genes. Gene distribution pattern is identical among 30 bitterling mitogenomes. A significant linear correlation between A+T% and AT-skew were found among 29 bitterling mitogenomes, except S. microlepis shows unusual AT-skew with slightly negative in tRNAs and PCGs. Bitterling mitogenomes exhibit highly conserved usage bias of start codon, relative synonymous codons and amino acids, overlaps and non-coding intergenic spacers. Phylogenetic trees constructed by 13 PCGs strongly support the polyphyly of the genus Acheilognathus and the paraphyly of Rhodeus and Tanakia. Together with the unusual characters of S. microlepis mitogenomes and phylogenetic trees, S. microlepis should be a sister species to the genus Rhodeu that might diverge about 13.69 Ma (95% HPD: 12.96-14.48 Ma).
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Affiliation(s)
- Peng Yu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China; College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Ya Zhou
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Wen-Tao Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Du S, Niu G, Nyman T, Wei M. Characterization of the mitochondrial genome of Arge bella Wei & Du sp. nov. (Hymenoptera: Argidae). PeerJ 2018; 6:e6131. [PMID: 30595984 PMCID: PMC6305119 DOI: 10.7717/peerj.6131] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 11/17/2018] [Indexed: 01/27/2023] Open
Abstract
We describe Arge bella Wei & Du sp. nov., a large and beautiful species of Argidae from south China, and report its mitochondrial genome based on high-throughput sequencing data. We present the gene order, nucleotide composition of protein-coding genes (PCGs), and the secondary structures of RNA genes. The nearly complete mitochondrial genome of A. bella has a length of 15,576 bp and a typical set of 37 genes (22 tRNAs, 13 PCGs, and 2 rRNAs). Three tRNAs are rearranged in the A. bella mitochondrial genome as compared to the ancestral type in insects: trnM and trnQ are shuffled, while trnW is translocated from the trnW-trnC-trnY cluster to a location downstream of trnI. All PCGs are initiated by ATN codons, and terminated with TAA, TA or T as stop codons. All tRNAs have a typical cloverleaf secondary structure, except for trnS1. H821 of rrnS and H976 of rrnL are redundant. A phylogenetic analysis based on mitochondrial genome sequences of A. bella, 21 other symphytan species, two apocritan representatives, and four outgroup taxa supports the placement of Argidae as sister to the Pergidae within the symphytan superfamily Tenthredinoidea.
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Affiliation(s)
- Shiyu Du
- Central South University of Forestry and Technology, Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education, Changsha, Hunan, China
| | - Gengyun Niu
- Jiangxi Normal University, Life Science College, Nanchang, Jiangxi, China
| | - Tommi Nyman
- Norwegian Institute of Bioeconomy Research, Department of Ecosystems in the Barents Region, Svanhovd Research Station, Svanvik, Norway
| | - Meicai Wei
- Central South University of Forestry and Technology, Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees (Central South University of Forestry and Technology), Ministry of Education, Changsha, Hunan, China
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Gene arrangement and sequence of mitochondrial genomes yield insights into the phylogeny and evolution of bees and sphecid wasps (Hymenoptera: Apoidea). Mol Phylogenet Evol 2018; 124:1-9. [DOI: 10.1016/j.ympev.2018.02.028] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 02/12/2018] [Accepted: 02/27/2018] [Indexed: 11/21/2022]
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Zhu JC, Tang P, Zheng BY, Wu Q, Wei SJ, Chen XX. The first two mitochondrial genomes of the family Aphelinidae with novel gene orders and phylogenetic implications. Int J Biol Macromol 2018; 118:386-396. [PMID: 29932999 DOI: 10.1016/j.ijbiomac.2018.06.087] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 06/17/2018] [Accepted: 06/18/2018] [Indexed: 11/17/2022]
Abstract
Chalcidoidea is one of the most diverse group in Hymenoptera by possessing striking mitochondrial gene arrangement. By using next generation sequencing method, the first two nearly complete mitochondrial genomes in the family Aphelinidae (Insecta, Hymenopetra, Chalcidoidea) were obtained in this study. Almost all previously sequenced mitochondrial genome of Chalcidoidea species have a large inversion including six genes (atp6-atp8-trnD-trnK-cox2-trnL2-cox1) as compared with ancestral mitochondrial genome, but these two Encarsia mitochondrial genomes had a large inversion including nine genes (nad3-trnG-atp6-atp8-trnD-trnK-cox2-trnL2-cox1), which was only congruent with the species in the genus Nasonia. Moreover, we found that one shuffling changes (trnD and trnK) happened in the species E. obtusiclava but not in another species E. formosa within the same genus, of which such shuffling within the same genus at this region was only detected in Polisters within Insecta. Phylogenetic analysis displayed that different data matrix (13PCG+ 2 rRNA or 13 PCG) and inference methods (BI or ML) indicate the identical topology with high nodal supports that Aphelinidae formed a sister group with (Trichogrammatidae + Aganoidae) and the monophyly of Pteramalidae. Our results also indicated the validity of assembling and feasibility of next-generation technology to obtain the mitochondrial genomes of parasitic Hymenoptera.
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Affiliation(s)
- Jia-Chen Zhu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Plant Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Pu Tang
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Plant Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Bo-Ying Zheng
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Plant Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qiong Wu
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Plant Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shu-Jun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xue-Xin Chen
- State Key Laboratory of Rice Biology and Ministry of Agriculture Key Lab of Molecular Biology of Plant Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China.
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Chen L, Chen PY, Xue XF, Hua HQ, Li YX, Zhang F, Wei SJ. Extensive gene rearrangements in the mitochondrial genomes of two egg parasitoids, Trichogramma japonicum and Trichogramma ostriniae (Hymenoptera: Chalcidoidea: Trichogrammatidae). Sci Rep 2018; 8:7034. [PMID: 29728615 PMCID: PMC5935716 DOI: 10.1038/s41598-018-25338-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 04/20/2018] [Indexed: 12/01/2022] Open
Abstract
Animal mitochondrial genomes usually exhibit conserved gene arrangement across major lineages, while those in the Hymenoptera are known to possess frequent rearrangements, as are those of several other orders of insects. Here, we sequenced two complete mitochondrial genomes of Trichogramma japonicum and Trichogramma ostriniae (Hymenoptera: Chalcidoidea: Trichogrammatidae). In total, 37 mitochondrial genes were identified in both species. The same gene arrangement pattern was found in the two species, with extensive gene rearrangement compared with the ancestral insect mitochondrial genome. Most tRNA genes and all protein-coding genes were encoded on the minority strand. In total, 15 tRNA genes and seven protein-coding genes were rearranged. The rearrangements of cox1 and nad2 as well as most tRNA genes were novel. Phylogenetic analysis based on nucleotide sequences of protein-coding genes and on gene arrangement patterns produced identical topologies that support the relationship of (Agaonidae + Pteromalidae) + Trichogrammatidae in Chalcidoidea. CREx analysis revealed eight rearrangement operations occurred from presumed ancestral gene order of Chalcidoidea to form the derived gene order of Trichogramma. Our study shows that gene rearrangement information in Chalcidoidea can potentially contribute to the phylogeny of Chalcidoidea when more mitochondrial genome sequences are available.
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Affiliation(s)
- Long Chen
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng-Yan Chen
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.,Department of Entomology, South China Agricultural University, Guangzhou, 510640, China
| | - Xiao-Feng Xue
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Hai-Qing Hua
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuan-Xi Li
- Department of Entomology, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Fan Zhang
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Shu-Jun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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