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Chen W, Zhang H, Meng R, Zhang X, Duo H, Guo Z, Shen X, Chen C, Li Z, Fu Y. Genome-wide phylogenetic and genetic evolutionary analyses of mitochondria in Hypoderma bovis and H. sinense on the Qinghai-Tibetan Plateau. Parasitol Res 2023; 123:43. [PMID: 38095728 DOI: 10.1007/s00436-023-08060-6] [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: 07/26/2023] [Accepted: 10/27/2023] [Indexed: 12/18/2023]
Abstract
Hypoderma bovis (H. bovis) and Hypoderma sinense (H. sinense) are insects that cause hypodermosis in yaks and Bos taurus. Hypodermosis is a severe skin condition that not only impairs the development of local animal husbandry but also poses threats to human health as a zoonosis. The Qinghai-Tibetan Plateau (QTP) is known as the "Roof of the World." Its unique geographical environment and climate conditions have supported the growth of a wide range of mammals, providing favorable conditions for Hypoderma spp. to complete their life cycles. In this study, the whole mitochondrial genomes of H. bovis and H. sinense collected from the QTP were sequenced and phylogenetically analyzed. We found that the whole genomes of H. bovis and H. sinense are 16,283 bp and 16,300 bp in length, respectively. Both the H. bovis and H. sinense genomes have 37 mitochondrial genes, which include two rRNA genes (16S rRNA and 12S rRNA), 22 tRNA genes, the control region (D-loop region), the light chain replication initiation region, and 13 protein-coding genes (PCGs). The phylogenetic tree generated based on the 13 PCGs revealed close phylogenetic relationships between H. sinense, H. bovis, and Hypoderma lineatum. A similar result was also found in our phylogenetic analysis based on 18S rRNA and 28S rRNA. However, analysis of cytochrome oxidase subunit I (COI) showed cluster of H. bovis, H. sinense, and Cuterebra spp. on the same branch, all belonging to Oestridae. The differentiation time generated based on 13 PCGs indicates that H. bovis and H. sinense differentiated and formed ~4.69 million years ago (Mya) and ~4.06 Mya, respectively. This timing coincides with the differentiation and appearance of yak and Bos taurus in the Pliocene (~4.7 Mya), indicating that the parasites and mammals diverged in close temporal proximity. Of note, this period also witnessed a rapid uplift of the QTP, causing significant climate and environmental changes. Thus, we conjecture that the differentiation of Hypoderma spp. is potentially related to the differentiation of their host species, as well as climate changes caused by the uplift of the QTP. Overall, our study can provide valuable data to support further studies on the phylogeny and differentiation of Hypoderma spp. on the QTP.
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Affiliation(s)
- Wangkai Chen
- Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China
| | - Haining Zhang
- Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China
| | - Ru Meng
- Xining Animal Disease Control Center, Xining, People's Republic of China
| | - Xueyong Zhang
- Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China
| | - Hong Duo
- Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China
| | - Zhihong Guo
- Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China
| | - Xiuying Shen
- Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China
| | - Changjiang Chen
- Animal Husbandry and Veterinary Station of Huangyuan County, Xining, People's Republic of China
| | - Zhi Li
- Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China.
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China.
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, People's Republic of China.
| | - Yong Fu
- Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, People's Republic of China.
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Diseases and Green Technical Research for Prevention and Control, Xining, People's Republic of China.
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Wang J, Fan H, Li Y, Zhang TF, Liu YH. Trehalose-6-phosphate phosphatases are involved in trehalose synthesis and metamorphosis in Bactrocera minax. INSECT SCIENCE 2022; 29:1643-1658. [PMID: 35075784 DOI: 10.1111/1744-7917.13010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/24/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Trehalose is the principal sugar circulating in the hemolymph of insects, and trehalose synthesis is catalyzed by trehalose-6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP). Insect TPS is a fused enzyme containing both TPS domain and TPP domain. Thus, many insects do not possess TPP genes as TPSs have replaced the function of TPPs. However, TPPs are widely distributed across the dipteran insects, while the roles they play remain largely unknown. In this study, 3 TPP genes from notorious dipteran pest Bactrocera minax (BmiTPPB, BmiTPPC1, and BmiTPPC2) were identified and characterized. The different temporal-spatial expression patterns of 3 BmiTPPs implied that they exert different functions in B. minax. Recombinant BmiTPPs were heterologously expressed in yeast cells, and all purified proteins exhibited enzymatic activities, despite the remarkable disparity in performance between BmiTPPB and BmiTPPCs. RNA interference revealed that all BmiTPPs were successfully downregulated after double-stranded RNA injection, leading to decreased trehalose content and increased glucose content. Also, suppression of BmiTPPs significantly affected expression of downstream genes and increased the mortality and malformation rate. Collectively, these results indicated that all 3 BmiTPPs in B. minax are involved in trehalose synthesis and metamorphosis. Thus, these genes could be evaluated as insecticidal targets for managing B. minax, and even for other dipteran pests.
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Affiliation(s)
- Jia Wang
- College of Plant Protection, Southwest University, Chongqing, China
| | - Huan Fan
- College of Plant Protection, Southwest University, Chongqing, China
| | - Ying Li
- College of Plant Protection, Southwest University, Chongqing, China
| | - Tong-Fang Zhang
- College of Food Science, Southwest University, Chongqing, China
| | - Ying-Hong Liu
- College of Plant Protection, Southwest University, Chongqing, China
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Unfolding the mitochondrial genome structure of green semilooper (Chrysodeixis acuta Walker): An emerging pest of onion (Allium cepa L.). PLoS One 2022; 17:e0273635. [PMID: 36040876 PMCID: PMC9426943 DOI: 10.1371/journal.pone.0273635] [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: 05/02/2022] [Accepted: 08/12/2022] [Indexed: 11/19/2022] Open
Abstract
Onion is the most important crop challenged by a diverse group of insect pests in the agricultural ecosystem. The green semilooper (Chrysodeixis acuta Walker), a widespread tomato and soybean pest, has lately been described as an emergent onion crop pest in India. C. acuta whole mitochondrial genome was sequenced in this work. The circular genome of C. acuta measured 15,743 base pairs (bp) in length. Thirteen protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and one control region were found in the 37 sequence elements. With an average 395 bp gene length, the maximum and minimum gene length observed was 1749 bp and 63 bp of nad5 and trnR, respectively. Nine of the thirteen PCGs have (ATN) as a stop codon, while the other four have a single (T) as a stop codon. Except for trnS1, all of the tRNAs were capable of producing a conventional clover leaf structure. Conserved ATAGA motif sequences and poly-T stretch were identified at the start of the control region. Six overlapping areas and 18 intergenic spacer regions were found, with sizes ranged from 1 to 20 bp and 1 to 111 bp correspondingly. Phylogenetically, C. acuta belongs to the Plusiinae subfamily of the Noctuidae superfamily, and is closely linked to Trichoplusia ni species from the same subfamily. In the present study, the emerging onion pest C. acuta has its complete mitochondrial genome sequenced for the first time.
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Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies. Sci Rep 2022; 12:7028. [PMID: 35487927 PMCID: PMC9054809 DOI: 10.1038/s41598-022-10547-8] [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: 12/19/2018] [Accepted: 03/21/2022] [Indexed: 11/08/2022] Open
Abstract
Uziflies (Family: Tachinidae) are dipteran endoparasites of sericigenous insects which cause major economic loss in the silk industry globally. Here, we are presenting the first full mitogenome of Blepharipa sp. (Acc: KY644698, 15,080 bp, A + T = 78.41%), a dipteran parasitoid of Muga silkworm (Antheraea assamensis) found in the Indian states of Assam and Meghalaya. This study has confirmed that Blepharipa sp. mitogenome gene content and arrangement is similar to other Tachinidae and Sarcophagidae flies of Oestroidea superfamily, typical of ancestral Diptera. Although, Calliphoridae and Oestridae flies have undergone tRNA translocation and insertion, forming unique intergenic spacers (IGS) and overlapping regions (OL) and a few of them (IGS, OL) have been conserved across Oestroidea flies. The Tachinidae mitogenomes exhibit more AT content and AT biased codons in their protein-coding genes (PCGs) than the Oestroidea counterpart. About 92.07% of all (3722) codons in PCGs of this new species have A/T in their 3rd codon position. The high proportion of AT and repeats in the control region (CR) affects sequence coverage, resulting in a short CR (Blepharipa sp.: 168 bp) and a smaller tachinid mitogenome. Our research unveils those genes with a high AT content had a reduced effective number of codons, leading to high codon usage bias. The neutrality test shows that natural selection has a stronger influence on codon usage bias than directed mutational pressure. This study also reveals that longer PCGs (e.g., nad5, cox1) have a higher codon usage bias than shorter PCGs (e.g., atp8, nad4l). The divergence rates increase nonlinearly as AT content at the 3rd codon position increases and higher rate of synonymous divergence than nonsynonymous divergence causes strong purifying selection. The phylogenetic analysis explains that Blepharipa sp. is well suited in the family of insectivorous tachinid maggots. It's possible that biased codon usage in the Tachinidae family reduces the effective number of codons, and purifying selection retains the core functions in their mitogenome, which could help with efficient metabolism in their endo-parasitic life style and survival strategy.
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Wang J, Li XY, Du RB, Liu YH. The complete mitogenome of Chlorops oryzae Matsumura (Diptera: Chloropidae). Mitochondrial DNA B Resour 2021; 6:1844-1846. [PMID: 34124364 PMCID: PMC8183556 DOI: 10.1080/23802359.2021.1934171] [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] [Indexed: 11/26/2022] Open
Abstract
Chlorops oryzae Matsumura is an important pest of rice plants throughout Asia, and has even become a major pest in some regions. Here, we present the complete mitogenome of C. oryzae for the first time. The complete mitogenome is 17,313 bp in length and contains 37 genes (13 protein-coding genes, 22 transfer RNAs, and two ribosomal RNAs) and a control region. The overall base composition is 42.04% for A, 37.18% for T, 12.59% for C, and 8.29% for G, with a bias toward A + T (79.22%). Protein-coding genes cox1 features an atypical ACG start codon and cox2, nad5, and nad4 have incomplete stop codons T or TA. All tRNA genes present the typical clover leaf secondary structure except trnS1 (AGN), where the DHU arm is replaced by a loop. Phylogeny showed that C. oryzae was placed as the basal lineage in Brachycera clade, and shared a closer relationship to Acalyptrate species.
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Affiliation(s)
- Jia Wang
- College of Plant Protection, Southwest University, Chongqing, China
| | - Xian-Ya Li
- College of Plant Protection, Southwest University, Chongqing, China
| | - Run-Bang Du
- College of Plant Protection, Southwest University, Chongqing, China
| | - Ying-Hong Liu
- College of Plant Protection, Southwest University, Chongqing, China
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Wang J, Ran LL, Li Y, Liu YH. Comparative proteomics provides insights into diapause program of Bactrocera minax (Diptera: Tephritidae). PLoS One 2021; 15:e0244493. [PMID: 33382763 PMCID: PMC7774860 DOI: 10.1371/journal.pone.0244493] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/10/2020] [Indexed: 12/20/2022] Open
Abstract
The Chinese citrus fly, Bactrocera minax, is a notorious univoltine pest that causes damage to citrus. B. minax enters obligatory pupal diapause in each generation to resist harsh environmental conditions in winter. Despite the enormous efforts that have been made in the past decade, the understanding of pupal diapause of B. minax is currently still fragmentary. In this study, the 20-hydroxyecdysone solution and ethanol solvent was injected into newly-formed pupae to obtain non-diapause- (ND) and diapause-destined (D) pupae, respectively, and a comparative proteomics analysis between ND and D pupae was performed 1 and 15 d after injection. A total of 3,255 proteins were identified, of which 190 and 463 were found to be differentially abundant proteins (DAPs) in ND1 vs D1 and ND15 vs D15 comparisons, respectively. The reliability and accuracy of LFQ method was validated by qRT-PCR. Functional analyses of DAPs, including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and protein-protein interaction (PPI) network construction, were conducted. The results revealed that the diapause program of B. minax is closely associated with several physiological activities, such as phosphorylation, chitin biosynthesis, autophagy, signaling pathways, endocytosis, skeletal muscle formation, protein metabolism, and core metabolic pathways of carbohydrate, amino acid, and lipid conversion. The findings of this study provide insights into diapause program of B. minax and lay a basis for further investigation into its underlying molecular mechanisms.
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Affiliation(s)
- Jia Wang
- College of Plant Protection, Institute of Entomology, Southwest University, Chongqing, China
- * E-mail:
| | - Li-Lin Ran
- College of Plant Protection, Institute of Entomology, Southwest University, Chongqing, China
| | - Ying Li
- College of Plant Protection, Institute of Entomology, Southwest University, Chongqing, China
| | - Ying-Hong Liu
- College of Plant Protection, Institute of Entomology, Southwest University, Chongqing, China
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Lee J, Park J, Xi H, Park J. Comprehensive Analyses of the Complete Mitochondrial Genome of Figulus binodulus (Coleoptera: Lucanidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2020; 20:10. [PMID: 32976575 PMCID: PMC7583265 DOI: 10.1093/jisesa/ieaa090] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Indexed: 05/06/2023]
Abstract
Figulus binodulus Waterhouse is a small stag beetle distributed in East Asia. We determined the first mitochondrial genome of F. binodulus of which is 16,261-bp long including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large noncoding region of 1,717 bp. Gene order of F. binodulus is identical to the ancestral insect mitochondrial gene order as in most other stag beetle species. All of 22 tRNAs could be shaped into typical clover-leaf structure except trnSer1. Comparative analyses of 21 Lucanidae mitochondrial genomes was conducted in aspect of their length and AT-GC ratio. Nucleotide diversities analyses provide that cox1 and cox2 in Lucanidae are less diverse than those of Scarabaeoidea. Fifty simple sequence repeats (SSRs) were identified on F. binodulus mitochondrial genome. Comparative analysis of SSRs among five mitochondrial genomes displayed similar trend along with SSR types. Figulus binodulus was sister to all other available family Lucanidae species in the phylogenetic tree.
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Affiliation(s)
- Jungmo Lee
- InfoBoss Inc., Ltd., Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
| | - Jonghyun Park
- InfoBoss Inc., Ltd., Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
| | - Hong Xi
- InfoBoss Inc., Ltd., Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
| | - Jongsun Park
- InfoBoss Inc., Ltd., Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Seolleung-ro, Gangnam-gu, Seoul, Republic of Korea
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Krosch MN, Strutt F, Blacket MJ, Batovska J, Starkie M, Clarke AR, Cameron SL, Schutze MK. Development of internal COI primers to improve and extend barcoding of fruit flies (Diptera: Tephritidae: Dacini). INSECT SCIENCE 2020; 27:143-158. [PMID: 29873880 DOI: 10.1111/1744-7917.12612] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 04/30/2018] [Accepted: 05/17/2018] [Indexed: 06/08/2023]
Abstract
Accurate species-level identifications underpin many aspects of basic and applied biology; however, identifications can be hampered by a lack of discriminating morphological characters, taxonomic expertise or time. Molecular approaches, such as DNA "barcoding" of the cytochrome c oxidase (COI) gene, are argued to overcome these issues. However, nuclear encoding of mitochondrial genes (numts) and poor amplification success of suboptimally preserved specimens can lead to erroneous identifications. One insect group for which these molecular and morphological problems are significant are the dacine fruit flies (Diptera: Tephritidae: Dacini). We addressed these issues associated with COI barcoding in the dacines by first assessing several "universal" COI primers against public mitochondrial genome and numt sequences for dacine taxa. We then modified a set of four primers that more closely matched true dacine COI sequence and amplified two overlapping portions of the COI barcode region. Our new primers were tested alongside universal primers on a selection of dacine species, including both fresh preserved and decades-old dry specimens. Additionally, Bactrocera tryoni mitochondrial and nuclear genomes were compared to identify putative numts. Four numt clades were identified, three of which were amplified using existing universal primers. In contrast, our new primers preferentially amplified the "true" mitochondrial COI barcode in all dacine species tested. The new primers also successfully amplified partial barcodes from dry specimens for which full length barcodes were unobtainable. Thus we recommend these new primers be incorporated into the suites of primers used by diagnosticians and quarantine labs for the accurate identification of dacine species.
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Affiliation(s)
- Matt N Krosch
- School of Earth, Environmental & Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Plant Biosecurity Co-operative Research Centre, Bruce, Australian Capital Territory, Australia
| | - Francesca Strutt
- School of Earth, Environmental & Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Plant Biosecurity Co-operative Research Centre, Bruce, Australian Capital Territory, Australia
| | - Mark J Blacket
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Jana Batovska
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Melissa Starkie
- School of Earth, Environmental & Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Anthony R Clarke
- School of Earth, Environmental & Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Stephen L Cameron
- School of Earth, Environmental & Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Plant Biosecurity Co-operative Research Centre, Bruce, Australian Capital Territory, Australia
- Department of Entomology, Purdue University, West Lafayette, Indiana, USA
| | - Mark K Schutze
- School of Earth, Environmental & Biological Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
- Plant Biosecurity Co-operative Research Centre, Bruce, Australian Capital Territory, Australia
- Department of Agriculture & Fisheries, Queensland Primary Industries Insect Collection (QDPC), Dutton Park, Queensland, Australia
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Drosopoulou E, Syllas A, Goutakoli P, Zisiadis GA, Konstantinou T, Pangea D, Sentis G, van Sauers-Muller A, Wee SL, Augustinos AA, Zacharopoulou A, Bourtzis K. Τhe Complete Mitochondrial Genome of Bactrocera carambolae (Diptera: Tephritidae): Genome Description and Phylogenetic Implications. INSECTS 2019; 10:E429. [PMID: 31795125 PMCID: PMC6955806 DOI: 10.3390/insects10120429] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 11/15/2019] [Accepted: 11/21/2019] [Indexed: 01/09/2023]
Abstract
Bactrocera carambolae is one of the approximately 100 sibling species of the Bactrocera dorsalis complex and considered to be very closely related to B. dorsalis. Due to their high morphological similarity and overlapping distribution, as well as to their economic impact and quarantine status, the development of reliable markers for species delimitation between the two taxa is of great importance. Here we present the complete mitochondrial genome of B. carambolae sourced from its native range in Malaysia and its invaded territory in Suriname. The mitogenome of B. carambolae presents the typical organization of an insect mitochondrion. Comparisons of the analyzed B. carambolae sequences to all available complete mitochondrial sequences of B. dorsalis revealed several species-specific polymorphic sites. Phylogenetic analysis based on Bactrocera mitogenomes supports that B. carambolae is a differentiated taxon though closely related to B. dorsalis. The present complete mitochondrial sequences of B. carambolae could be used, in the frame of Integrative Taxonomy, for species discrimination and resolution of the phylogenetic relationships within this taxonomically challenging complex, which would facilitate the application of species-specific population suppression strategies, such as the sterile insect technique.
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Affiliation(s)
- Elena Drosopoulou
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.S.); (P.G.); (G.-A.Z.); (T.K.); (D.P.); (G.S.)
| | - Alexandros Syllas
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.S.); (P.G.); (G.-A.Z.); (T.K.); (D.P.); (G.S.)
| | - Panagiota Goutakoli
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.S.); (P.G.); (G.-A.Z.); (T.K.); (D.P.); (G.S.)
| | - Georgios-Alkis Zisiadis
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.S.); (P.G.); (G.-A.Z.); (T.K.); (D.P.); (G.S.)
| | - Theodora Konstantinou
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.S.); (P.G.); (G.-A.Z.); (T.K.); (D.P.); (G.S.)
| | - Dimitra Pangea
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.S.); (P.G.); (G.-A.Z.); (T.K.); (D.P.); (G.S.)
| | - George Sentis
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece; (A.S.); (P.G.); (G.-A.Z.); (T.K.); (D.P.); (G.S.)
| | - Alies van Sauers-Muller
- Consultant, retired from Ministry of Agriculture, Animal Husbandry and Fisheries, Carambola Fruit Fly Project, Damboentong 282, Tijgerkreek, Saramacca, Suriname;
| | - Suk-Ling Wee
- Center for Insect Systematics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia;
| | - Antonios A. Augustinos
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Seibersdorf, A-1400 Vienna, Austria; (A.A.A.); (K.B.)
| | | | - Kostas Bourtzis
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Seibersdorf, A-1400 Vienna, Austria; (A.A.A.); (K.B.)
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The first two complete mitochondrial genome of Dacus bivittatus and Dacus ciliatus (Diptera: Tephritidae) by next-generation sequencing and implications for the higher phylogeny of Tephritidae. Int J Biol Macromol 2019; 140:469-476. [DOI: 10.1016/j.ijbiomac.2019.08.076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 07/22/2019] [Accepted: 08/07/2019] [Indexed: 11/18/2022]
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11
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Hong F, Gao L, Han HL, Wang P, Wang J, Wei D, Liu Y. Population Genetics of Bactrocera minax (Diptera: Tephritidae) in China Based on nad4 Gene Sequence. INSECTS 2019; 10:E236. [PMID: 31382425 PMCID: PMC6723541 DOI: 10.3390/insects10080236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/25/2019] [Accepted: 07/30/2019] [Indexed: 11/21/2022]
Abstract
Bactrocera minax (Enderlein) (Diptera: Tephritidae) is an important citrus pest in Asia with a non-uniform distribution. In some locations, it had been reported to occur but was either eradicated or disappeared itself. To understand species dispersal of B. minax, we collected and analyzed 359 individuals from 18 localities in China. One mitochondrial DNA gene fragment (nad4) was used to investigate the genetic diversity and population genetic structure of B. minax. The populations were divided by phylogenetic analyses and statistical parsimony haplotype networks into three branches: a Central China (CC) branch, a Western China (WC) branch, and a Southern China (SC) branch. A total of 93 variable sites (15.6% of the 595 bp alignment) and 91 unique haplotypes were observed in the 359 individuals scored from the nad4 gene of the 18 B. minax populations. This indicated that B. minax had a high level of genetic diversity. These populations also showed a discrete distribution in both the scatter plots of genetic versus geographical distance for pairwise population comparisons and the median-joining network of haplotypes, which revealed the strong genetic structure of B. minax.
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Affiliation(s)
- Feng Hong
- College of Agriculture, Xinyang Agriculture and Forestry University, Xinyang 464000, China
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Lizhi Gao
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Hong-Liang Han
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Pan Wang
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Jia Wang
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, China
| | - Dong Wei
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
| | - Yinghong Liu
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, China.
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12
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Wang J, Fan H, Wang P, Liu YH. Expression Analysis Reveals the Association of Several Genes with Pupal Diapause in Bactrocera minax (Diptera: Tephritidae). INSECTS 2019; 10:insects10060169. [PMID: 31200584 PMCID: PMC6628110 DOI: 10.3390/insects10060169] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/03/2019] [Accepted: 06/11/2019] [Indexed: 11/18/2022]
Abstract
The Chinese citrus fly, Bactrocera minax, is a devastating pest of citrus, which enters the obligatory diapause in overwintering pupae to resist harsh environmental conditions. However, little is known about the molecular mechanisms underlying pupal diapause. The previous transcriptomic analysis revealed that a large number of genes were regulated throughout the pupal stage. Of these genes, 12 and six ones that are remarkably up- and downregulated, respectively, specifically in intense diapause were manually screened out in present study. To validate the expression of these genes throughout the pupal stage, the quantitative real-time PCR (qRT-PCR) was conducted, and the genes displaying different expression patterns with those of previous study were excluded. Then, the expressions of remaining genes were compared between diapause-destined and non-diapause-destined pupae to reveal their association with diapause using qRT-PCR and semiquantitative PCR. Finally, five genes, TTLL3B, Cyp6a9, MSTA, Fru, and UC2, and two genes, KSPI and LYZ1, were demonstrated to be positively and negatively associated with diapause, respectively. These findings provide a solid foundation for the further investigation of molecular mechanisms underlying B. minax pupal diapause.
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Affiliation(s)
- Jia Wang
- College of Plant Protection, Southwest University, Chongqing 400716, China.
| | - Huan Fan
- College of Plant Protection, Southwest University, Chongqing 400716, China.
| | - Pan Wang
- College of Plant Protection, Southwest University, Chongqing 400716, China.
| | - Ying-Hong Liu
- College of Plant Protection, Southwest University, Chongqing 400716, China.
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13
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Jiang F, Liang L, Li Z, Yu Y, Wang J, Wu Y, Zhu S. A conserved motif within cox 2 allows broad detection of economically important fruit flies (Diptera: Tephritidae). Sci Rep 2018; 8:2077. [PMID: 29391551 PMCID: PMC5794786 DOI: 10.1038/s41598-018-20555-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 01/19/2018] [Indexed: 11/09/2022] Open
Abstract
The genera Anastrepha, Bactrocera, Ceratitis, Dacus and Rhagoletis in the family Tephritidae order Diptera are economically important, worldwide distributed and cause damage to a large number of commercially produced fruits and vegetables. China had regulated these five genera as quarantine pests, including the species Carpomya vesuviana. An accurate molecular method not depending on morphology able to detect all the quarantine fruit flies simultaneously is required for quarantine monitoring. This study contributes a comparative analysis of 146 mitochondrial genomes of Diptera species and found variable sites at the mt DNA cox2 gene only conserved in economically important fruit flies species. Degenerate primers (TephFdeg/TephR) were designed specific for the economically important fruit flies. A 603 bp fragment was amplified after testing each of the 40 selected representative species belonging to each economically important Tephritid genera, no diagnostic fragments were detected/amplified in any of the other Tephritidae and Diptera species examined. PCR sensitivity assays demonstrated the limit of detection of targeted DNA was 0.1 ng/μl. This work contributes an innovative approach for detecting all reported economically important fruit flies in a single-step PCR specific for reported fruit fly species of quarantine concern in China.
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Affiliation(s)
- Fan Jiang
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Liang Liang
- Key Laboratory of Agro-Products Postharvest Handling, Ministry of Agriculture, Chinese Academy of Agricultural Engineering, Beijing, 100121, China
| | - Zhihong Li
- College of Plant Protection, China Agricultural University, Beijing, 100193, China.
| | - Yanxue Yu
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Jun Wang
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, China
| | - Yuping Wu
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, China.
| | - Shuifang Zhu
- Chinese Academy of Inspection and Quarantine, Beijing, 100176, China.
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14
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Wang J, Fan H, Xiong KC, Liu YH. Transcriptomic and metabolomic profiles of Chinese citrus fly, Bactrocera minax (Diptera: Tephritidae), along with pupal development provide insight into diapause program. PLoS One 2017; 12:e0181033. [PMID: 28704500 PMCID: PMC5507520 DOI: 10.1371/journal.pone.0181033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 06/26/2017] [Indexed: 12/15/2022] Open
Abstract
The Chinese citrus fly, Bactrocera minax (Enderlein), is a devastating citrus pest in Asia. This univoltine insect enters obligatory pupal diapause in each generation, while little is known about the course and the molecular mechanisms of diapause. In this study, the course of diapause was determined by measuring the respiratory rate throughout the pupal stage. In addition, the variation of transcriptomic and metabolomic profiles of pupae at five developmental stages (pre-, early-, middle-, late-, and post-diapause) were evaluated by next-generation sequencing technology and 1H nuclear magnetic resonance spectroscopy (NMR), respectively. A total of 4,808 genes were significantly altered in ten pairwise comparisons, representing major shifts in metabolism and signal transduction as well as endocrine system and digestive system. Gene expression profiles were validated by qRT-PCR analysis. In addition, 48 metabolites were identified and quantified by 1H NMR. Nine of which significantly contributed to the variation in the metabolomic profiles, especially proline and trehalose. Moreover, the samples collected within diapause maintenance (early-, middle-, and late-diapause) only exhibited marginal transcriptomic and metabolomic variation with each other. These findings greatly improve our understanding of B. minax diapause and lay the foundation for further pertinent studies.
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Affiliation(s)
- Jia Wang
- Institute of Entomology, College of Plant Protection, Southwest University, Chongqing, China
| | - Huan Fan
- Institute of Entomology, College of Plant Protection, Southwest University, Chongqing, China
| | - Ke-Cai Xiong
- Institute of Entomology, College of Plant Protection, Southwest University, Chongqing, China
| | - Ying-Hong Liu
- Institute of Entomology, College of Plant Protection, Southwest University, Chongqing, China
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15
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Liu JH, Jia PF, Liu LL, Wang QM, Zhang YX, Ruan SQ. Complete mitochondrial genome of stripped fruit fly, Bactrocera (Zeugodacus) scutellata (Diptera: Tephritidae) from Anshun, Southwest China. Mitochondrial DNA B Resour 2017; 2:387-388. [PMID: 33490452 PMCID: PMC7800262 DOI: 10.1080/23802359.2017.1347899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 06/24/2017] [Indexed: 11/16/2022] Open
Abstract
The striped fruit fly, Bactrocera (Zeugodacus) scutellata occurred in East and Southeast Asia and is one of the most serious pest insects in China. Complete mitochondrial genome was sequenced and characterized for the fruit fly from Anshun, Guizhou Province in Southwest China. The pest fruit fly has a total length of 15,904 bp, consisting of 13 protein-coding genes (PCGs), 22 tRNA, 2 rRNA genes and a non-coding region (A + T-rich control region). The phylogenetic position of B. scutellata was closely clustered with B. cucurbitae, B. tau, B. caudata and B. diaphora. The all species of the subgenus Zeugodacus formed a sister group which was monophyletic. The complete mitochondrial genome of B. scutellata will provide helpful information for genetics, systematics and phylogeny of tephritid fruit flies, Particularly Bactrocera genus.
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Affiliation(s)
- Jian-Hong Liu
- Yunnan Provincial Key Laboratory of Forest Disaster Warning and Control, Southwest Forestry University, Kunming, China
| | - Ping-Fan Jia
- Yunnan Provincial Key Laboratory of Forest Disaster Warning and Control, Southwest Forestry University, Kunming, China
| | - Lan-Lan Liu
- Yunnan Provincial Key Laboratory of Forest Disaster Warning and Control, Southwest Forestry University, Kunming, China
| | - Qing-Mei Wang
- Yunnan Provincial Key Laboratory of Forest Disaster Warning and Control, Southwest Forestry University, Kunming, China
| | - Yu-Xin Zhang
- Yunnan Provincial Key Laboratory of Forest Disaster Warning and Control, Southwest Forestry University, Kunming, China
| | - Shi-Qin Ruan
- School of Agriculture, Anshun University, Anshun, China
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16
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Drosopoulou E, Pantelidou C, Gariou-Papalexiou A, Augustinos AA, Chartomatsidou T, Kyritsis GA, Bourtzis K, Mavragani-Tsipidou P, Zacharopoulou A. The chromosomes and the mitogenome of Ceratitis fasciventris (Diptera: Tephritidae): two genetic approaches towards the Ceratitis FAR species complex resolution. Sci Rep 2017; 7:4877. [PMID: 28687799 PMCID: PMC5501848 DOI: 10.1038/s41598-017-05132-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/25/2017] [Indexed: 11/29/2022] Open
Abstract
Ceratitis fasciventris is a serious agricultural pest of the Tephritidae family that belongs to the African Ceratitis FAR species complex. Species limits within the FAR complex are obscure and multidisciplinary approaches have attempted to resolve phylogenetic relationships among its members. These studies support the existence of at least three additional species in the complex, C. anonnae, C. rosa and C. quilicii, while they indicate the presence of two structured populations (F1 and F2) within the C. fasciventris species. In the present study we present the mitotic karyotype, polytene chromosome maps, in situ hybridization data and the complete mitochondrial genome sequence of an F2 population of C. fasciventris. This is the first polytene chromosome map and complete mitogenome of a member of the FAR complex and only the second reported for the Ceratitis genus. Both polytene chromosomes and mitochondrial sequence could provide valuable information and be used as reference for comparative analysis among the members of the complex towards the clarification of their phylogenetic relationships.
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Affiliation(s)
- Elena Drosopoulou
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece.
| | - Christina Pantelidou
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Antonios A Augustinos
- Department of Biology, University of Patras, Patras, Greece.,Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Seibersdorf, Vienna, Austria
| | - Tatiana Chartomatsidou
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Georgios A Kyritsis
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Seibersdorf, Vienna, Austria
| | - Kostas Bourtzis
- Insect Pest Control Laboratory, Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Seibersdorf, Vienna, Austria
| | - Penelope Mavragani-Tsipidou
- Department of Genetics, Development and Molecular Biology, School of Biology, Faculty of Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
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17
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Li X, Li W, Ding S, Cameron SL, Mao M, Shi L, Yang D. Mitochondrial Genomes Provide Insights into the Phylogeny of Lauxanioidea (Diptera: Cyclorrhapha). Int J Mol Sci 2017; 18:E773. [PMID: 28420076 PMCID: PMC5412357 DOI: 10.3390/ijms18040773] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/23/2017] [Accepted: 04/01/2017] [Indexed: 11/17/2022] Open
Abstract
The superfamily Lauxanioidea is a significant dipteran clade including over 2500 known species in three families: Lauxaniidae, Celyphidae and Chamaemyiidae. We sequenced the first five (three complete and two partial) lauxanioid mitochondrial (mt) genomes, and used them to reconstruct the phylogeny of this group. The lauxanioid mt genomes are typical of the Diptera, containing all 37 genes usually present in bilaterian animals. A total of three conserved intergenic sequences have been reported across the Cyclorrhapha. The inferred secondary structure of 22 tRNAs suggested five substitution patterns among the Cyclorrhapha. The control region in the Lauxanioidea has apparently evolved very fast, but four conserved structural elements were detected in all three complete mt genome sequences. Phylogenetic relationships based on the mt genome data were inferred by Maximum Likelihood and Bayesian methods. The traditional relationships between families within the Lauxanioidea, (Chamaemyiidae + (Lauxaniidae + Celyphidae)), were corroborated; however, the higher-level relationships between cyclorrhaphan superfamilies are mostly poorly supported.
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Affiliation(s)
- Xuankun Li
- Department of Entomology, China Agricultural University, Beijing 100193, China.
| | - Wenliang Li
- College of Forestry, Henan University of Science and Technology, Luoyang 471023, China.
| | - Shuangmei Ding
- Department of Entomology, China Agricultural University, Beijing 100193, China.
| | - Stephen L Cameron
- Department of Entomology, Purdue University, West Lafayette, IN 47907, USA.
| | - Meng Mao
- Department of Plant and Environmental Protection Science, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
| | - Li Shi
- College of Agronomy, Inner Mongolia Agricultural University, Hohhot 010018, China.
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing 100193, China.
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18
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Pu DQ, Liu HL, Gong YY, Ji PC, Li YJ, Mou FS, Wei SJ. Mitochondrial genomes of the hoverflies Episyrphus balteatus and Eupeodes corollae (Diptera: Syrphidae), with a phylogenetic analysis of Muscomorpha. Sci Rep 2017; 7:44300. [PMID: 28276531 PMCID: PMC5343577 DOI: 10.1038/srep44300] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 02/06/2017] [Indexed: 12/11/2022] Open
Abstract
The hoverflies Episyrphus balteatus and Eupeodes corollae (Diptera: Muscomorpha: Syrphidae) are important natural aphid predators. We obtained mitochondrial genome sequences from these two species using methods of PCR amplification and sequencing. The complete Episyrphus mitochondrial genome is 16,175 bp long while the incomplete one of Eupeodes is 15,326 bp long. All 37 typical mitochondrial genes are present in both species and arranged in ancestral positions and directions. The two mitochondrial genomes showed a biased A/T usage versus G/C. The cox1, cox2, cox3, cob and nad1 showed relatively low level of nucleotide diversity among protein-coding genes, while the trnM was the most conserved one without any nucleotide variation in stem regions within Muscomorpha. Phylogenetic relationships among the major lineages of Muscomorpha were reconstructed using a complete set of mitochondrial genes. Bayesian and maximum likelihood analyses generated congruent topologies. Our results supported the monophyly of five species within the Syrphidae (Syrphoidea). The Platypezoidea was sister to all other species of Muscomorpha in our phylogeny. Our study demonstrated the power of the complete mitochondrial gene set for phylogenetic analysis in Muscomorpha.
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Affiliation(s)
- De-qiang Pu
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610300, China
| | - Hong-ling Liu
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Yi-yun Gong
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610300, China
| | - Pei-cheng Ji
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610300, China
| | - Yue-jian Li
- Institute of Horticulture Research, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Fang-sheng Mou
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610300, China
| | - Shu-jun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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19
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Jeong SY, Kim MJ, Kim JS, Kim I. Complete mitochondrial genome of the pumpkin fruit fly, Bactrocera depressa (Diptera: Tephritidae). Mitochondrial DNA B Resour 2017; 2:85-87. [PMID: 33473724 PMCID: PMC7800232 DOI: 10.1080/23802359.2017.1285212] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In this study, we sequenced the complete mitochondrial genome (mitogenome) of the pumpkin fruit fly, Bactrocera depressa (Diptera: Tephritidae), which is an economically damaging pest of pumpkin and turban squash. The 15,832-bp-long complete mitogenome of the species consists of a typical set of genes, with an arrangement typical of insects. Of the 13 protein-coding genes (PCGs), 12 have a typical ATN start codon, whereas the COI gene begins with TCG, which has been identified as the start codon for all Bactrocera COI genes. The 1004-bp A + T-rich region of B. depressa is the third longest, after B. minax and B. scutellata, of the Bactrocera species for which the whole mitogenome has been sequenced. Phylogenetic analysis using the 13 PCGs of Bactrocera species indicated that B. depressa is a sister to the sister group containing B. tau and B. cucurbitae with the highest nodal support (Bayesian posterior probability =1.0).
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Affiliation(s)
- Su Yeon Jeong
- College of Agriculture & Life Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Min Jee Kim
- College of Agriculture & Life Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Jong Seok Kim
- College of Agriculture & Life Sciences, Chonnam National University, Gwangju, Republic of Korea
| | - Iksoo Kim
- College of Agriculture & Life Sciences, Chonnam National University, Gwangju, Republic of Korea
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20
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Jiang F, Pan X, Li X, Yu Y, Zhang J, Jiang H, Dou L, Zhu S. The first complete mitochondrial genome of Dacus longicornis (Diptera: Tephritidae) using next-generation sequencing and mitochondrial genome phylogeny of Dacini tribe. Sci Rep 2016; 6:36426. [PMID: 27812024 PMCID: PMC5095552 DOI: 10.1038/srep36426] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/14/2016] [Indexed: 11/09/2022] Open
Abstract
The genus Dacus is one of the most economically important tephritid fruit flies. The first complete mitochondrial genome (mitogenome) of Dacus species - D. longicornis was sequenced by next-generation sequencing in order to develop the mitogenome data for this genus. The circular 16,253 bp mitogenome is the typical set and arrangement of 37 genes present in the ancestral insect. The mitogenome data of D. longicornis was compared to all the published homologous sequences of other tephritid species. We discovered the subgenera Bactrocera, Daculus and Tetradacus differed from the subgenus Zeugodacus, the genera Dacus, Ceratitis and Procecidochares in the possession of TA instead of TAA stop codon for COI gene. There is a possibility that the TA stop codon in COI is the synapomorphy in Bactrocera group in the genus Bactrocera comparing with other Tephritidae species. Phylogenetic analyses based on the mitogenome data from Tephritidae were inferred by Bayesian and Maximum-likelihood methods, strongly supported the sister relationship between Zeugodacus and Dacus.
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MESH Headings
- Animals
- Base Sequence
- Bayes Theorem
- Codon, Terminator
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/isolation & purification
- DNA, Mitochondrial/metabolism
- Electron Transport Complex IV/chemistry
- Electron Transport Complex IV/genetics
- Genome, Mitochondrial
- High-Throughput Nucleotide Sequencing
- Mitochondria/genetics
- Phylogeny
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- Sequence Analysis, DNA
- Tephritidae/classification
- Tephritidae/genetics
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Affiliation(s)
- Fan Jiang
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Xubin Pan
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Xuankun Li
- Australian National Insect Collection, CSIRO National Research Collections Australia, Canberra, ACT 2601, Australia
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Yanxue Yu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Junhua Zhang
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Hongshan Jiang
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Liduo Dou
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Shuifang Zhu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
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21
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Wang J, Xiong KC, Liu YH. De novo Transcriptome Analysis of Chinese Citrus Fly, Bactrocera minax (Diptera: Tephritidae), by High-Throughput Illumina Sequencing. PLoS One 2016; 11:e0157656. [PMID: 27331903 PMCID: PMC4917245 DOI: 10.1371/journal.pone.0157656] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 06/02/2016] [Indexed: 12/30/2022] Open
Abstract
The Chinese citrus fly, Bactrocera minax (Enderlein), is one of the most devastating pests of citrus in the temperate areas of Asia. So far, studies involving molecular biology and physiology of B. minax are still scarce, partly because of the lack of genomic information and inability to rear this insect in laboratory. In this study, de novo assembly of a transcriptome was performed using Illumina sequencing technology. A total of 20,928,907 clean reads were obtained and assembled into 33,324 unigenes, with an average length of 908.44 bp. Unigenes were annotated by alignment against NCBI non-redundant protein (Nr), Swiss-Prot, Clusters of Orthologous Groups (COG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG) database. Genes potentially involved in stress tolerance, including 20 heat shock protein (Hsps) genes, 26 glutathione S-transferases (GSTs) genes, and 2 ferritin subunit genes, were identified. These genes may play roles in stress tolerance in B. minax diapause stage. It has previously been found that 20E application on B. minax pupae could avert diapause, but the underlying mechanisms remain unknown. Thus, genes encoding enzymes in 20E biosynthesis pathway, including Neverland, Spook, Phantom, Disembodied, Shadow, Shade, and Cyp18a1, and genes encoding 20E receptor proteins, ecdysone receptor (EcR) and ultraspiracle (USP), were identified. The expression patterns of 20E-related genes among developmental stages and between 20E-treated and untreated pupae demonstrated their roles in diapause program. In addition, 1,909 simple sequence repeats (SSRs) were detected, which will contribute to molecular marker development. The findings in this study greatly improve our genetic understanding of B. minax, and lay the foundation for future studies on this species.
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Affiliation(s)
- Jia Wang
- Institute of Entomology, College of Plant Protection, Southwest University, Chongqing, P. R. China
- * E-mail:
| | - Ke-Cai Xiong
- Institute of Entomology, College of Plant Protection, Southwest University, Chongqing, P. R. China
| | - Ying-Hong Liu
- Institute of Entomology, College of Plant Protection, Southwest University, Chongqing, P. R. China
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22
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Shi X, Zhu Q, Wu N, Tu J, Yang D, Xu H, Yao Y, Yang M, Li D. The complete nucleotide sequence of the mitochondrial genome of Drosophila formosana (Diptera: Drosophilidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4316-4317. [PMID: 26544023 DOI: 10.3109/19401736.2015.1089480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Drosophila formosana (Diptera: Drosophilidae) belongs to the Drosophilidae group of Drosophila. The mitochondrial genome sequence of Drosophila formosana is determined in this study. Mitochondrion of D. formosana is a circular DNA molecule of the 16 100 nucleotide pairs (bp) that contains one encoding region including 37 genes and 1 non-coding A + T-rich region. The similarity and typicality have been showed by the structure and organization analysis. All genes are arranged in the circular DNA molecule. In addition to DN5 that use GTG start codon, all other protein-coding genes (PCGs) start with an ATN start codon. Ten protein-coding genes stop with the termination codon TAN, while other protein-coding genes (PCGs) used incomplete termination codon TA- (cox2, nad5, nad1). The A + T-rich region with a length of 1088 bp is located between rrnS and trnI. The mitochondrial genome of D. formosana has been completely sequenced for the first time in this study.
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Affiliation(s)
- Xian Shi
- a Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University , Chengdu , P.R. China
| | - Qing Zhu
- a Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University , Chengdu , P.R. China
| | - Nan Wu
- a Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University , Chengdu , P.R. China
| | - Jianbo Tu
- a Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University , Chengdu , P.R. China
| | - Deying Yang
- a Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University , Chengdu , P.R. China
| | - Huailiang Xu
- a Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University , Chengdu , P.R. China
| | - Yongfang Yao
- a Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University , Chengdu , P.R. China
| | - Mingyao Yang
- a Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University , Chengdu , P.R. China
| | - Diyan Li
- a Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University , Chengdu , P.R. China
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23
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Liu JH, Xu J, Li YH, Dan W, Pan Y. Complete mitochondrial genome of the guava fruit fly, Bactrocera correcta (Diptera: Tephritidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4553-4554. [PMID: 26513144 DOI: 10.3109/19401736.2015.1101559] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Bactrocera correcta (Diptera: Tephritidae) is one of the most serious pest insects in south China and surrounding Southeast Asian countries. The family Tephritidae includes over 4257 species distributed worldwide, so the complete mitochondrial genome would be helpful for bio-identification, biogeography and phylogeny. The B. correcta genome consists of 15 936 bp. Annotation indicated that the structure and orientation of 13 protein-coding genes (PCGs), 22 tRNA and 2 rRNA sequences were typical of, and similar to, the ten closely related tephritid species. The nucleotide composition shows heavily biased toward As and Ts accounting 73.2% and exhibits a slightly positive AT skew, which is similar to other known tephritid species and other insects. The phylogenetic tree indicated the presence of three distinct families (Tephritidae, Muscidae, Drosophilidae) in Order Diptera.
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Affiliation(s)
- Jian-Hong Liu
- a College of Forestry, Southwest Forestry University , Kunming , China.,b Yunnan Provincial Key Laboratory of Forest Disaster Warning and Control , Kunming , China , and
| | - Jin Xu
- c Agriculture School, Yunnan University , Kunming , China
| | - Yong-He Li
- a College of Forestry, Southwest Forestry University , Kunming , China.,b Yunnan Provincial Key Laboratory of Forest Disaster Warning and Control , Kunming , China , and
| | - Wenli Dan
- a College of Forestry, Southwest Forestry University , Kunming , China
| | - Yongzhi Pan
- a College of Forestry, Southwest Forestry University , Kunming , China.,b Yunnan Provincial Key Laboratory of Forest Disaster Warning and Control , Kunming , China , and
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24
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Yong HS, Song SL, Lim PE, Chan KG, Chow WL, Eamsobhana P. Complete mitochondrial genome of Bactrocera arecae (Insecta: Tephritidae) by next-generation sequencing and molecular phylogeny of Dacini tribe. Sci Rep 2015; 5:15155. [PMID: 26472633 PMCID: PMC4607999 DOI: 10.1038/srep15155] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 09/15/2015] [Indexed: 11/09/2022] Open
Abstract
The whole mitochondrial genome of the pest fruit fly Bactrocera arecae was obtained from next-generation sequencing of genomic DNA. It had a total length of 15,900 bp, consisting of 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a non-coding region (A + T-rich control region). The control region (952 bp) was flanked by rrnS and trnI genes. The start codons included 6 ATG, 3 ATT and 1 each of ATA, ATC, GTG and TCG. Eight TAA, two TAG, one incomplete TA and two incomplete T stop codons were represented in the protein-coding genes. The cloverleaf structure for trnS1 lacked the D-loop, and that of trnN and trnF lacked the TΨC-loop. Molecular phylogeny based on 13 protein-coding genes was concordant with 37 mitochondrial genes, with B. arecae having closest genetic affinity to B. tryoni. The subgenus Bactrocera of Dacini tribe and the Dacinae subfamily (Dacini and Ceratitidini tribes) were monophyletic. The whole mitogenome of B. arecae will serve as a useful dataset for studying the genetics, systematics and phylogenetic relationships of the many species of Bactrocera genus in particular, and tephritid fruit flies in general.
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Affiliation(s)
- Hoi-Sen Yong
- Institute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia.,Chancellery High Impact Research, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Sze-Looi Song
- Chancellery High Impact Research, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Phaik-Eem Lim
- Institute of Ocean and Earth Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kok-Gan Chan
- Institute of Biological Sciences, University of Malaya, 50603 Kuala Lumpur, Malaysia.,Chancellery High Impact Research, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Wan-Loo Chow
- Science Vision Sdn Bhd, Setia Avenue, 33A-4 Jalan Setia Prima S, U13/S, Setia Alam, Seksyen U13, 40170 Shah Alam, Selangor Darul Ehsan, Malaysia
| | - Praphathip Eamsobhana
- Department of Parasitology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
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25
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Zhang KJ, Liu L, Rong X, Zhang GH, Liu H, Liu YH. The complete mitochondrial genome of Bactrocera diaphora (Diptera: Tephtitidae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4314-4315. [PMID: 26462416 DOI: 10.3109/19401736.2015.1089479] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We sequenced and annotated the complete mitochondrial genome (mitogenome) of Bactrocera diaphora (Diptera: Tephtitidae), which is an economically important pest in the southwest area of China, India, Sri Lanka, Vietnam and Malaysia. This mitogenome is 15 890 bp in length with an A + T content of 74.103%, and contains 37 typical animal mitochondrial genes that are arranged in the same order as that of the inferred ancestral insects. All protein-coding genes (PCGs) start with a typical ATN codon, except cox1 that begins with TCG. Ten PCGs stop with termination codon TAA or TAG, whereas cox1, nad1 and nad5 have single T-- as the incomplete stop codon. All of the transfer RNA genes present the typical clover leaf secondary structure except trnS1 (AGN) with a looping D-arm. The A + T-rich region is located between rrnS and trnI with a length of 946 bp, and contains a 20 bp poly-T stretch and 22 bp poly-A stretch. Except the control region, the longest intergenic spacer is located between trnR and trnN that is 94 bp long with an excessive high A + T content (95.74%) and a microsatellite-like region (TA)13.
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Affiliation(s)
- Kai-Jun Zhang
- a Key Laboratory of Entomology and Pest Control Engineering , College of Plant Protection, Southwest University , Beibei District , Chongqing , China
| | - Lei Liu
- a Key Laboratory of Entomology and Pest Control Engineering , College of Plant Protection, Southwest University , Beibei District , Chongqing , China
| | - Xia Rong
- a Key Laboratory of Entomology and Pest Control Engineering , College of Plant Protection, Southwest University , Beibei District , Chongqing , China
| | - Guo-Hao Zhang
- a Key Laboratory of Entomology and Pest Control Engineering , College of Plant Protection, Southwest University , Beibei District , Chongqing , China
| | - Huai Liu
- a Key Laboratory of Entomology and Pest Control Engineering , College of Plant Protection, Southwest University , Beibei District , Chongqing , China
| | - Ying-Hong Liu
- a Key Laboratory of Entomology and Pest Control Engineering , College of Plant Protection, Southwest University , Beibei District , Chongqing , China
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26
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Choudhary JS, Naaz N, Prabhakar CS, Rao MS, Das B. The mitochondrial genome of the peach fruit fly, Bactrocera zonata (Saunders) (Diptera: Tephritidae): Complete DNA sequence, genome organization, and phylogenetic analysis with other tephritids using next generation DNA sequencing. Gene 2015; 569:191-202. [PMID: 26031235 DOI: 10.1016/j.gene.2015.05.066] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 05/13/2015] [Accepted: 05/27/2015] [Indexed: 02/01/2023]
Abstract
Mitochondrial genome can provide information for genomic structure as well as for phylogenetic analysis and evolutionary biology. The complete 15,935 bp mitochondrial genome of Bactrocera zonata (Diptera: Tephritidae), is assembled from Illumina MiSeq read data. The mitogenome information for B. zonata was compared to the homologous sequences of other tephritids. Annotation indicated that the structure and orientation of 13 protein coding genes (PCGs), 22 tRNA and 2 rRNA sequences were typical of, and similar to, the ten closely related tephritid species. The nucleotide composition shows heavily biased toward As and Ts accounting 73.34% and exhibits a slightly positive AT skew, which is similar to other known tephritid species. All PCGs are initiated by ATN codons, except for cox1 with TCG and atp8 with GTG. Nine PCGs use a common stop codon of TAA or TAG, whereas the remaining four use an incomplete termination codon T or TA likely to be completed by adenylation. All tRNAs have the typical clover-leaf structure, with an exception for trnS((AGN)). Four short intergenic spacers showed high degree of conservation among B. zonata and other ten tephritids. A poly(T) stretch at the 5' end followed by [TA(A)]n-like stretch and a tandem repeats of 39 bp has been observed in CR. The analysis of gene evolutionary rate revealed that the cox1 and atp6 exhibits lowest and highest gene substitution rates, respectively than other genes. The phylogenetic relationships based on Maximum Likelihood method using all protein-coding genes and two ribosomal RNA genes confirmed that B. zonata is closely related to Bactrocera correcta, Bactrocera carambolae, Bactrocera papayae, and Bactrocera philippinensis and Bactrocera dorsalis belonging to B. dorsalis species complex forms a monophyletic clade, which is in accordance with the traditional morphological classification and recent molecular works.
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Affiliation(s)
- Jaipal S Choudhary
- ICAR Research Complex for Eastern Region, Research Centre, Plandu, Ranchi 834 010, Jharkhand, India.
| | - Naiyar Naaz
- ICAR Research Complex for Eastern Region, Research Centre, Plandu, Ranchi 834 010, Jharkhand, India.
| | - Chandra S Prabhakar
- ICAR Research Complex for Eastern Region, Research Centre, Plandu, Ranchi 834 010, Jharkhand, India; Department of Entomology, Bihar Agricultural University, Sabour, Bhagalpur 813 210, Bihar, India.
| | - Mathukumalli Srinivasa Rao
- Central Research Institute for Dryland Agriculture (CRIDA), Santoshnagar, Saidabad PO, Hyderabad 500 059, India.
| | - Bikash Das
- ICAR Research Complex for Eastern Region, Research Centre, Plandu, Ranchi 834 010, Jharkhand, India.
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27
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Li X, Ding S, Cameron SL, Kang Z, Wang Y, Yang D. The first mitochondrial genome of the sepsid fly Nemopoda mamaevi Ozerov, 1997 (Diptera: Sciomyzoidea: Sepsidae), with mitochondrial genome phylogeny of cyclorrhapha. PLoS One 2015; 10:e0123594. [PMID: 25826648 PMCID: PMC4380458 DOI: 10.1371/journal.pone.0123594] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Accepted: 02/20/2015] [Indexed: 11/18/2022] Open
Abstract
Sepsid flies (Diptera: Sepsidae) are important model insects for sexual selection research. In order to develop mitochondrial (mt) genome data for this significant group, we sequenced the first complete mt genome of the sepsid fly Nemopoda mamaevi Ozerov, 1997. The circular 15,878 bp mt genome is typical of Diptera, containing all 37 genes usually present in bilaterian animals. We discovered inaccurate annotations of fly mt genomes previously deposited on GenBank and thus re-annotated all published mt genomes of Cyclorrhapha. These re-annotations were based on comparative analysis of homologous genes, and provide a statistical analysis of start and stop codon positions. We further detected two 18 bp of conserved intergenic sequences from tRNAGlu-tRNAPhe and ND1-tRNASer(UCN) across Cyclorrhapha, which are the mtTERM binding site motifs. Additionally, we compared automated annotation software MITOS with hand annotation method. Phylogenetic trees based on the mt genome data from Cyclorrhapha were inferred by Maximum-likelihood and Bayesian methods, strongly supported a close relationship between Sepsidae and the Tephritoidea.
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Affiliation(s)
- Xuankun Li
- Department of Entomology, China Agricultural University, Beijing, China
| | - Shuangmei Ding
- Department of Entomology, China Agricultural University, Beijing, China
| | - Stephen L Cameron
- Earth, Environmental & Biological Sciences School, Science & Engineering Faculty, Queensland University of Technology, Brisbane, Australia
| | - Zehui Kang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Yuyu Wang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing, China
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Wu YP, He QS, Xie JL, Guo XF, Li HY. The complete mitochondrial genome sequence of Hemibagrus nemurus (Siluriformes: Bagridae). Mitochondrial DNA A DNA Mapp Seq Anal 2014; 27:1829-30. [PMID: 25319306 DOI: 10.3109/19401736.2014.971245] [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: 11/13/2022]
Abstract
Hemibagrus nemurus (Valenciennes, 1840) is a kind of tropical freshwater catfish which is native to Asian waters. It is economically valued for its importance in fisheries and aquaculture. At present, there exist some confusion in species identification in Bagridae. In this paper, we sequenced and characterize the complete mitogenome of H. nemurus. The genome was 16,526 bp in length, and typically consists of 37 genes, including 13 protein-coding genes, 2 rRNAs, 22 tRNA, 1 origin of replication on the light-strand (OL) and a single large control region (CR). The gene organization is identical to that of a typical bony fish. The overall base composition was 31.5%, 26.6%, 26.7%, and 15.2% for A, T, C, and G, respectively, with a slight bias on AT content (58.1%). This result is expected to provide useful molecular data and contribute to further taxonomic and phylogenetic studies of Hemibagrus and Bagridae.
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Affiliation(s)
- Yu-Peng Wu
- a College of Environment and Safety, Taiyuan University of Science and Technology , Taiyuan , P.R. China
| | - Qiu-Sheng He
- a College of Environment and Safety, Taiyuan University of Science and Technology , Taiyuan , P.R. China
| | - Jian-Lin Xie
- a College of Environment and Safety, Taiyuan University of Science and Technology , Taiyuan , P.R. China
| | - Xiao-Fang Guo
- a College of Environment and Safety, Taiyuan University of Science and Technology , Taiyuan , P.R. China
| | - Hong-Yan Li
- a College of Environment and Safety, Taiyuan University of Science and Technology , Taiyuan , P.R. China
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