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Mou CY, Li Q, Huang ZP, Ke HY, Zhao H, Zhao ZM, Duan YL, Li HD, Xiao Y, Qian ZM, Du J, Zhou J, Zhang L. PacBio single-molecule long-read sequencing provides new insights into the complexity of full-length transcripts in oriental river prawn, macrobrachium nipponense. BMC Genomics 2023; 24:340. [PMID: 37340366 DOI: 10.1186/s12864-023-09442-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 06/11/2023] [Indexed: 06/22/2023] Open
Abstract
BACKGROUND Oriental river prawn (Macrobrachium nipponense) is one of the most dominant species in shrimp farming in China, which is a rich source of protein and contributes to a significant impact on the quality of human life. Thus, more complete and accurate annotation of gene models are important for the breeding research of oriental river prawn. RESULTS A full-length transcriptome of oriental river prawn muscle was obtained using the PacBio Sequel platform. Then, 37.99 Gb of subreads were sequenced, including 584,498 circular consensus sequences, among which 512,216 were full length non-chimeric sequences. After Illumina-based correction of long PacBio reads, 6,599 error-corrected isoforms were identified. Transcriptome structural analysis revealed 2,263 and 2,555 alternative splicing (AS) events and alternative polyadenylation (APA) sites, respectively. In total, 620 novel genes (NGs), 197 putative transcription factors (TFs), and 291 novel long non-coding RNAs (lncRNAs) were identified. CONCLUSIONS In summary, this study offers novel insights into the transcriptome complexity and diversity of this prawn species, and provides valuable information for understanding the genomic structure and improving the draft genome annotation of oriental river prawn.
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Affiliation(s)
- Cheng-Yan Mou
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Qiang Li
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Zhi-Peng Huang
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Hong-Yu Ke
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Han Zhao
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Zhong-Meng Zhao
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Yuan-Liang Duan
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Hua-Dong Li
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Yu Xiao
- Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 610066, China
| | - Zhou-Ming Qian
- Chengdu Eaters Agricultural Group Co., Ltd, Chengdu, Sichuan, 610000, China
| | - Jun Du
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China
| | - Jian Zhou
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China.
| | - Lu Zhang
- Fisheries Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan, 611731, China.
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Li S, Li H, Chen C, Hao D. Tolerance to dietary linalool primarily involves co-expression of cytochrome P450s and cuticular proteins in Pagiophloeus tsushimanus (Coleoptera: Curculionidae) larvae using SMRT sequencing and RNA-seq. BMC Genomics 2023; 24:34. [PMID: 36658477 PMCID: PMC9854079 DOI: 10.1186/s12864-023-09117-7] [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: 09/02/2022] [Accepted: 01/05/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Pagiophloeus tsushimanus (Coleoptera: Curculionidae), an emerging forest pest exclusively infesting camphor trees, has recently caused severe ecological and economic damage in localized areas in China. Its population outbreak depends largely on the capacity to overcome the pressure of terpenoid-derived metabolites (e.g. linalool) from camphor trees. At present, the molecular basis of physiological adaptation of P. tsushimanus to dietary linalool is poorly understood, and there is no available reference genome or transcriptome. RESULTS Herein, we constructed the transcriptome profiling of P. tsushimanus larvae reared on linalool-infused diets using RNA sequencing and single-molecule real-time sequencing. A total of 20,325 high-quality full-length transcripts were identified as a reference transcriptome, of which 14,492 protein-coding transcripts including 130 transcription factors (TFs), and 5561 long non-coding RNAs (lncRNAs) were detected. Also, 30 alternative splicing events and 8049 simple sequence repeats were captured. Gene ontology enrichment of differential expressed transcripts revealed that overall up-regulation of both cytochrome P450s (CYP450s) and cuticular proteins (CPs), was the primary response characteristic against dietary linalool. Other physiological effects possibly caused by linalool exposure, such as increase in Reactive Oxygen Species (ROS) and hormetic stimulation, were compensated by a handful of induced genes encoding antioxidases, heat shock proteins (HSPs), juvenile hormone (JH) epoxide hydrolases, and digestive enzymes. Additionally, based on co-expression networks analysis, a diverse array of hub lncRNAs and TFs co-expressed with CYP450s and CPs were screened as the potential gene regulators. Temporal expression of candidate transcripts determined by quantitative real-time PCR also indicated a cooperative relationship between the inductions of CYP450s and CPs upon exposure to linalool. CONCLUSIONS Our present study provides an important transcriptome resource of P. tsushimanus, and lays a valuable foundation for understanding how this specialist pest copes with chemical challenges in its specific host environments.
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Affiliation(s)
- Shouyin Li
- grid.410625.40000 0001 2293 4910Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu China ,grid.410625.40000 0001 2293 4910College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu China
| | - Hui Li
- grid.410625.40000 0001 2293 4910Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu China ,grid.410625.40000 0001 2293 4910College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu China
| | - Cong Chen
- grid.410625.40000 0001 2293 4910Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu China ,grid.410625.40000 0001 2293 4910College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu China
| | - Dejun Hao
- grid.410625.40000 0001 2293 4910Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu China ,grid.410625.40000 0001 2293 4910College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu China
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Li M, Yang X, Fan F, Ge Y, Hong D, Wang Z, Lu C, Chen S, Wei G. De novo genome assembly of Bradysia cellarum (Diptera: Sciaridae), a notorious pest in traditional special vegetables in China. INSECT MOLECULAR BIOLOGY 2022; 31:508-518. [PMID: 35389542 DOI: 10.1111/imb.12776] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 02/28/2022] [Accepted: 04/04/2022] [Indexed: 06/14/2023]
Abstract
Bradysia cellarum (Diptera: Sciaridae) is a destructive vegetable insect pest infesting more than 30 species of host plants from seven families in Asia and Europe. B. cellarum causes grave problems in Chinese chive, which originated in China and is cultivated widely in East Asia. The B. cellarum infestation results in economic losses and subsequent severe food safety problems in farm productions, insecticide resistance and environmental pollution. The genomic and molecular information of B. cellarum to delineate the biological features, insecticide resistance, evolution remains poorly understood. Herein, we decode the whole genome of B. cellarum to delineate the underlying molecular mechanisms causing insecticide resistance. We constructed a highly reliable genome for B. cellarum using PacBio, Illumina and 10X Genomics sequencing platforms. The genome size of B. cellarum was 375.91 Mb with a contig N50 of 1.57 Mb. A total of 16,231 genes were identified, among which 93.8% were functionally annotated, and 42.06% were repeat sequences. According to phylogenetic analysis, B. cellarum diverged from the common ancestor of Drosophila melanogaster and Musca domestica ~139.3-191.0 million years ago. Moreover, some important genes responsible for significant insecticide resistance, such as cytochrome P450s, ABC transporters and those involved in glutathione metabolism, were expanded in B. cellarum. We assembled a high-quality B. cellarum genome to provide valuable insights into their life history strategies, insecticide resistance and biological behaviours. It also lays the foundation for exploring gene structure and functional evolution, as well as comparative genomics of B. cellarum and other model insect species.
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Affiliation(s)
- Mengyao Li
- College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Xiaofan Yang
- Plant protection Institute, Hebei Academy of Agricultural and Forestry Sciences, Baoding, China
| | - Fan Fan
- College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Yafei Ge
- College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Dawei Hong
- College of Plant Science, Tibet Agricultural and Animal Husbandry University, Nyingchi, Tibet, China
| | - Zhongyan Wang
- The Technical Education Centre of Nangong City, Xingtai, China
| | - Chenyan Lu
- College of Plant Science&Technology, Huazhong Agricultural University, Wuhan, China
| | - Suyi Chen
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Guoshu Wei
- College of Plant Protection, Hebei Agricultural University, Baoding, China
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Ding Q, Xu X, Sang Z, Wang R, Ullah F, Gao X, Song D. Characterization of the insecticide detoxification carboxylesterase Boest1 from Bradysia odoriphaga Yang et Zhang (Diptera: Sciaridae). PEST MANAGEMENT SCIENCE 2022; 78:591-602. [PMID: 34596943 DOI: 10.1002/ps.6667] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/19/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND In insects, carboxylesterases (CarEs) are enzymes involved in the detoxification of insecticides. However, the molecular mechanism of CarE-mediated insecticide metabolism in Bradysia odoriphaga, a serious agricultural pest, remains unclear. The aim of this study is to investigate the detoxification process of malathion, bifenthrin, and imidacloprid by B. odoriphaga carboxylesterase (Boest1). RESULTS An alpha class CarE gene Boest1 was cloned from B. odoriphaga. The results of real-time quantitative polymerase chain reaction showed that Boest1 is up-regulated with age during the larval stage, and the level of transcription of Boest1 is higher in the midgut and Malpighian tubule than in other tissues. The expression level of Boest1 was significantly increased after exposure to malathion and bifenthrin. Recombinant BoEST1 expressed in vitro showed high catalytic activity toward α-naphthyl acetate, which was substantially inhibited by malathion and triphenyl phosphate. The in vitro metabolism assays showed that BoEST1 demonstrates hydrolytic capacity toward malathion and bifenthrin but not imidacloprid. The binding free energy analysis indicates that BoEST1 has a higher affinity for malathion and bifenthrin than imidacloprid. CONCLUSION These results suggest that BoEST1 plays a role in the breakdown of insecticides and may be involved in the development of resistance in the Chinese chive pest B. odoriphaga; our findings also provide data for better pest management and perspectives for new pesticides development. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Qian Ding
- Department of Entomology, China Agricultural University, Beijing, China
| | - Xiao Xu
- Department of Entomology, China Agricultural University, Beijing, China
| | - Zitong Sang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Ruijie Wang
- Department of Entomology, China Agricultural University, Beijing, China
| | - Farman Ullah
- Department of Entomology, China Agricultural University, Beijing, China
| | - Xiwu Gao
- Department of Entomology, China Agricultural University, Beijing, China
| | - Dunlun Song
- Department of Entomology, China Agricultural University, Beijing, China
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5
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Fu H, Huang T, Yin C, Xu Z, Li C, Liu C, Wu T, Song F, Feng F, Yang F. Selection and Validation of Reference Genes for RT-qPCR Normalization in Bradysia odoriphaga (Diptera: Sciaridae) Under Insecticides Stress. Front Physiol 2022; 12:818210. [PMID: 35087425 PMCID: PMC8786907 DOI: 10.3389/fphys.2021.818210] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/08/2021] [Indexed: 01/08/2023] Open
Abstract
Bradysia odoriphaga (Diptera: Sciaridae) is the most serious root maggot pest which causes substantial damage to the Chinese chive. Organophosphate (OP) and neonicotinoid insecticides are widely used chemical pesticides and play important roles in controlling B. odoriphaga. However, a strong selection pressure following repeated pesticide applications has led to the development of resistant populations of this insect. To understand the insecticide resistance mechanism in B. odoriphaga, gene expression analysis might be required. Appropriate reference gene selection is a critical prerequisite for gene expression studies, as the expression stability of reference genes can be affected by experimental conditions, resulting in biased or erroneous results. The present study shows the expression profile of nine commonly used reference genes [elongation factor 1α (EF-1α), actin2 (ACT), elongation factor 2α (EF-2α), glucose-6-phosphate dehydrogenase (G6PDH), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), ribosomal protein L10 (RPL10), ribosomal protein S3 (RPS3), ubiquitin-conjugating enzyme (UBC), and α-tubulin (TUB)] was systematically analyzed under insecticide stress. Moreover, we also evaluated their expression stability in other experimental conditions, including developmental stages, sexes, and tissues. Five programs (NormFinder, geNorm, BestKeeper, RefFinder, and ΔCt) were used to validate the suitability of candidate reference genes. The results revealed that the most appropriate sets of reference genes were RPL10 and ACT across phoxim; ACT and TUB across chlorpyrifos and chlorfluazuron; EF1α and TUB across imidacloprid; EF1α and EF2α across developmental stages; RPL10 and TUB across larvae; EF1α and ACT across tissues, and ACT and G6PDH across sex. These results will facilitate the standardization of RT-qPCR and contribute to further research on B. odoriphaga gene function under insecticides stress.
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Affiliation(s)
- Haiyan Fu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China.,Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, China.,College of Life Science, Northeast Forestry University, Harbin, China
| | - Tubiao Huang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China.,Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, China
| | - Cheng Yin
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China.,Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, China
| | - Zhenhua Xu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China.,Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, China
| | - Chao Li
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China.,Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, China
| | - Chunguang Liu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China.,Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, China
| | - Tong Wu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China.,Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, China
| | - Fuqiang Song
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China.,Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, China
| | - Fujuan Feng
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Fengshan Yang
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China.,Heilongjiang Provincial Key Laboratory of Ecological Restoration and Resource Utilization for Cold Region, School of Life Sciences, Heilongjiang University, Harbin, China
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Tang B, Dai W, Qi L, Du S, Zhang C. Functional Characterization of an α-Esterase Gene Associated with Malathion Detoxification in Bradysia odoriphaga. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:6076-6083. [PMID: 32401500 DOI: 10.1021/acs.jafc.0c01486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Carboxylesterases (CarEs) are a multigene superfamily of metabolic enzymes involved in metabolic detoxification of xenobiotics. In this study, an α-esterase gene (BoαE1) was identified from Bradysia odoriphaga. Phylogenetic analysis classified BoαE1 into the α-esterase clade. Developmental expression analysis indicated that BoαE1 was significantly expressed in the second to fourth larval stages. Tissue-specific expression analysis indicated that BoαE1 was highly expressed in the larval midgut. After exposure to LC30 of malathion, the CarE activity of B. odoriphaga was induced and the transcriptional level of BoαE1 was significantly up-regulated. Silencing of BoαE1 significantly increased the susceptibility of B. odoriphaga larvae to malathion. Inhibition assays in vitro indicated that malathion significantly inhibited BoαE1 activity. GC-MS assay showed that BoαE1 possesses hydrolase activity toward malathion and participates in the detoxification of malathion. These results strongly suggest that BoαE1 plays a crucial role in detoxification of malathion in B. odoriphaga.
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Affiliation(s)
- Bowen Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas, and Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Wu Dai
- State Key Laboratory of Crop Stress Biology for Arid Areas, and Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Lijun Qi
- State Key Laboratory of Crop Stress Biology for Arid Areas, and Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Shaokai Du
- State Key Laboratory of Crop Stress Biology for Arid Areas, and Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Chunni Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, and Key Laboratory of Integrated Pest Management on Crops in Northwestern Loess Plateau, Ministry of Agriculture, College of Plant Protection, Northwest A&F University, Yangling 712100, Shaanxi, China
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