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Jiao X, Shi J, Qin S, Huang D, Wang Y. Dataset of the transcriptomes of Urechis unicinctus to identify differentially expressed genes (DEGs) under different temperature and exposure to open air. Data Brief 2021; 35:106941. [PMID: 33842678 PMCID: PMC8020418 DOI: 10.1016/j.dib.2021.106941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 02/22/2021] [Accepted: 03/03/2021] [Indexed: 10/29/2022] Open
Abstract
Urechis unicinctus has a wide range of bioactive polypeptides with high edible, economic and medicinal values. As the key technical breakthrough, the artificial breeding is imperative. However, the seedling transport becomes a primary matter, which indicates the indispensability of realizing how Urechis unicinctus responses to various situations. We compared transcriptome of Urechis unicinctus under the dry and ultraviolet irradiation treatment and different temperature. The dataset of the organism in response to water-temperature variety was provided by using the Illumina Hiseq X Ten system, which will be helpful to understand the adaptation of Urechis unicinctus to changing temperature (low, high and room temperature) and open air (ultraviolet and desiccation). The assembly of the transcriptomes was carried out using the isoform sequencing (Iso-seq) method. The functions of expressed genes were annotated and categorized, while the DEGs were presented.
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Affiliation(s)
- Xudong Jiao
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Jiaxin Shi
- College of Oceanic and Atmospheric Sciences, Ocean University of China, Qingdao 266000, China
| | - Song Qin
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
| | - Dong Huang
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.,Agronomy College, Rudong University, Shandong, Yantai 264025, China
| | - Yinchu Wang
- Key Laboratory of Coastal Biology and Biological Resources Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China
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2
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Zhang QL, Jiang YH, Dong ZX, Li HW, Lin LB. Exposure to benzo[a]pyrene triggers distinct patterns of microRNA transcriptional profiles in aquatic firefly Aquatica wuhana (Coleoptera: Lampyridae). JOURNAL OF HAZARDOUS MATERIALS 2021; 401:123409. [PMID: 32763701 DOI: 10.1016/j.jhazmat.2020.123409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 06/25/2020] [Accepted: 07/03/2020] [Indexed: 06/11/2023]
Abstract
Larval aquatic fireflies in fresh water are adversely affected by water pollutants such as benzo(a)pyrene (BaP). However, their response to BaP stress at the microRNA (miRNA)-regulatory level remains unknown. Here, transcriptomes containing 31,872 genes and six miRNA transcriptional profiles were obtained for Aquatica wuhana larvae, and comparative analysis was performed between larvae exposed to BaP (0.01 mg/L) and unexposed controls. Fifteen of 114 miRNAs identified via bioinformatics were detected as differentially expressed (DEMs) upon BaP exposure. Analysis results of predicted target genes of DEM suggests that BaP exposure primarily triggered transcriptional changes of miRNA associated with five major regulatory categories: 1) osmotic balance, 2) energy metabolic efficiency, 3) development, 4) xenobiotic metabolism (oxidative stress), and 5) innate immune response. Based on six innate immune- and xenobiotic metabolism-related pathways enriched by the predicted DEM targets, 11 key BaP-responsive DEMs were further screened to investigate dynamic changes of expression in response to BaP stress at five time points, and also to validate the miRNA sequencing data using quantitative real-time PCR. This study provides valuable information for the protection of firefly resources and supplements the understanding of miRNA regulatory mechanisms in response to water deterioration.
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Affiliation(s)
- Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China; Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Kunming, 650500, China.
| | - Yu-Hang Jiang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Zhi-Xiang Dong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Hong-Wei Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China; Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Kunming, 650500, China.
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3
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de la Cruz-Ramos JM, Hernández-Triana LM, García-De la Peña C, González-Álvarez VH, Weger-Lucarelli J, Siller-Rodríguez QK, Sánchez Rámos FJ, Rodríguez AD, Ortega-Morales AI. Comparison of two DNA extraction methods from larvae, pupae, and adults of Aedes aegypti. Heliyon 2019; 5:e02660. [PMID: 31692696 PMCID: PMC6806409 DOI: 10.1016/j.heliyon.2019.e02660] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 09/13/2019] [Accepted: 10/11/2019] [Indexed: 11/29/2022] Open
Abstract
Mosquitoes are the most important arthropods from the point of view of public health, due to the fact that they can transmit a large number of pathogens which can cause diseases to humans and animals. Aedes aegypti (L.) is one of the most important vector species in the world, since it can transmit numerous pathogens such as dengue, Zika, and chikungunya. Therefore, studies involving the molecular aspects of this and other mosquitoes species are currently increasing. In this report, we describe the comparison between two DNA extraction techniques, Chelex and cetyltrimethylammonium bromide (CTAB), for carrying out DNA extraction in larvae, pupae and adult female of Ae. aegypti. The Chelex technique was superior in the amount and purity of DNA as compared to the CTAB technique in the three life stages we tested.
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Affiliation(s)
- Josué M de la Cruz-Ramos
- Universidad Autónoma Agraria Antonio Narro Unidad Laguna, Periférico y carretera Santa Fe, 27084, Torreón, Coahuila, Mexico.,Unidad de Investigaciones Entomológicas y de Bioensayos del estado de Durango, Periférico y carretera Santa Fe, 27084, Torreón, Coahuila, Mexico
| | - Luis M Hernández-Triana
- Animal and Plant Health Agency, Virology Department, Wildlife Zoonoses and Vector Borne Diseases Research Group, Woodham Lane, New Haw, Addlestone, Surrey, KT153NB, UK
| | - Cristina García-De la Peña
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, Av. Universidad, 35010, Gómez Palacio, Durango, Mexico
| | - Vicente H González-Álvarez
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma de Guerrero, Ciajinicuilapa, Guerrero, Mexico
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Quetzaly Karmy Siller-Rodríguez
- Facultad de Ciencias Biológicas, Universidad Juárez del Estado de Durango, Av. Universidad, 35010, Gómez Palacio, Durango, Mexico
| | - Francisco J Sánchez Rámos
- Universidad Autónoma Agraria Antonio Narro Unidad Laguna, Periférico y carretera Santa Fe, 27084, Torreón, Coahuila, Mexico
| | - Américo D Rodríguez
- Centro Regional de Investigación en Salud Publica, Instituto Nacional de Salud Publica, Tapachula, Chiapas, Mexico
| | - Aldo I Ortega-Morales
- Universidad Autónoma Agraria Antonio Narro Unidad Laguna, Periférico y carretera Santa Fe, 27084, Torreón, Coahuila, Mexico.,Unidad de Investigaciones Entomológicas y de Bioensayos del estado de Durango, Periférico y carretera Santa Fe, 27084, Torreón, Coahuila, Mexico
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Wei Y, Yan R, Zhou Q, Qiao L, Zhu G, Chen M. Monitoring and Mechanisms of Chlorantraniliprole Resistance in Chilo suppressalis (Lepidoptera: Crambidae) in China. JOURNAL OF ECONOMIC ENTOMOLOGY 2019; 112:1348-1353. [PMID: 30715398 DOI: 10.1093/jee/toz001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Indexed: 06/09/2023]
Abstract
Chlorantraniliprole, an anthranilic diamide insecticide, is widely used for controlling lepidopteran pests, because of its high insecticidal activity. However, overuse of chlorantraniliprole has led to the selection of resistance in many insect pests, including Chilo suppressalis (Lepidoptera:Crambidae), one of the most damaging rice pests in China. In this study, resistance levels to chlorantraniliprole for C. suppressalis was surveyed from eight populations of three provinces in China. The levels of resistance were ranged from 34.4-fold to 284.0-fold compared with a susceptible population. Then, a 15402 bp fragment of the full-length cDNA of ryanodine receptor gene (CsRyR) from the XS strain, the highest resistant population, and a 1992 bp fragment of CsRyR cDNA encoding the carboxyl-terminal of CsRyR gene from the other seven populations were sequenced. A common previously identified mutation that was associated with chlorantraniliprole resistance against C. suppressalis, G4910E, was not detected in any of the eight populations in this study. However, another mutation I4758M was found in all seven resistant populations. Furthermore, the relative mRNA expression levels of CsRyR gene in the seven resistant populations were all reduced compared with susceptible strain. Our study provides new insights into the basis of monitoring the development of resistance and the mechanism of resistance to chlorantraniliprole in C. suppressalis.
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Affiliation(s)
- Yanbing Wei
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Ru Yan
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Qiaoling Zhou
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Liya Qiao
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Guonian Zhu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Mengli Chen
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
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Xu Q, Liu H, Yuan P, Zhang X, Chen Q, Jiang X, Zhou Y. Development of a simplified RT-PCR without RNA isolation for rapid detection of RNA viruses in a single small brown planthopper (Laodelphax striatellus Fallén). Virol J 2017; 14:90. [PMID: 28468626 PMCID: PMC5415734 DOI: 10.1186/s12985-017-0732-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 03/16/2017] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND The small brown planthopper (SBPH) is an important pest of cereal crops and acts as a transmission vector for multiple RNA viruses. Rapid diagnosis of virus in the vector is crucial for efficient forecast and control of viral disease. Reverse transcription polymerase chain reaction (RT-PCR) is a rapid, sensitive and reliable method for virus detection. The traditional RT-PCR contains a RNA isolation step and is widely used for virus detection in insect. However, using the traditional RT-PCR for detecting RNA virus in individual SBPHs becomes challenging because of the expensive reagents and laborious procedure associated with RNA isolation when processing a large number of samples. RESULTS We established a simplified RT-PCR method without RNA isolation for RNA virus detection in a single SBPH. This method is achieved by grinding a single SBPH in sterile water and using the crude extract directly as the template for RT-PCR. The crude extract containing the virus RNA can be prepared in approximately two minutes. Rice stripe virus (RSV), rice black streaked dwarf virus (RBSDV) and Himetobi P virus (HiPV) were successfully detected using this simplified method. The detection results were validated by sequencing and dot immunobinding assay, indicating that this simplified method is reliable for detecting different viruses in insects. The evaluation of the sensitivity of this method showed that both RSV and HiPV can be detected when the cDNA from the crude extract was diluted up to 103 fold. Compared to the traditional RT-PCR with RNA isolation, the simplified RT-PCR method greatly reduces the sample processing time, decreases the detection cost, and improves the efficiency by avoiding RNA isolation. CONCLUSIONS A simplified RT-PCR method is developed for rapid detection of RNA virus in a single SBPH without the laborious RNA isolation step. It offers a convenient alternative to the traditional RT-PCR method.
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Affiliation(s)
- Qiufang Xu
- Institute of Plant Protection; Jiangsu Academy of Agricultural Sciences; Jiangsu Technical Service Center of Diagnosis and Detection for Plant Virus Diseases, Nanjing, Jiangsu, People's Republic of China
| | - Haoqiu Liu
- Institute of Plant Protection; Jiangsu Academy of Agricultural Sciences; Jiangsu Technical Service Center of Diagnosis and Detection for Plant Virus Diseases, Nanjing, Jiangsu, People's Republic of China
| | - Pingping Yuan
- Institute of Plant Protection; Jiangsu Academy of Agricultural Sciences; Jiangsu Technical Service Center of Diagnosis and Detection for Plant Virus Diseases, Nanjing, Jiangsu, People's Republic of China
- College of Agriculture, Guizhou University, Guiyang, Guizhou, People's Republic of China
| | - Xiaoxia Zhang
- Institute of Plant Protection; Jiangsu Academy of Agricultural Sciences; Jiangsu Technical Service Center of Diagnosis and Detection for Plant Virus Diseases, Nanjing, Jiangsu, People's Republic of China
| | - Qingqing Chen
- Institute of Plant Protection; Jiangsu Academy of Agricultural Sciences; Jiangsu Technical Service Center of Diagnosis and Detection for Plant Virus Diseases, Nanjing, Jiangsu, People's Republic of China
| | - Xuanli Jiang
- College of Agriculture, Guizhou University, Guiyang, Guizhou, People's Republic of China
| | - Yijun Zhou
- Institute of Plant Protection; Jiangsu Academy of Agricultural Sciences; Jiangsu Technical Service Center of Diagnosis and Detection for Plant Virus Diseases, Nanjing, Jiangsu, People's Republic of China.
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Ridgeway JA, Timm AE. Reference gene selection for quantitative real-time PCR normalization in larvae of three species of Grapholitini (Lepidoptera: Tortricidae). PLoS One 2015; 10:e0129026. [PMID: 26030743 PMCID: PMC4450875 DOI: 10.1371/journal.pone.0129026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 05/04/2015] [Indexed: 12/02/2022] Open
Abstract
Despite the agricultural importance of species in the Grapholitini (Lepidoptera: Tortricidae), and the value of gene expression analysis for improved population management, few gene expression studies based on quantitative real-time PCR (qPCR) have been conducted for this tribe. Part of the reason for this lack of information is that suitable reference genes, which are fundamental for accurate normalization of qPCR studies, have not been identified for the tribe. Thus, the expression stability of six potential reference genes (ACT, AK, COI, EF1, ENO and TUB) was assessed in three different tissues (whole body, midgut and cuticle) of Cryptophlebia peltastica (Meyrick), Cydia pomonella (L.) and Thaumatotibia leucotreta (Meyrick). Additionally, these reference genes were tested using T. leucotreta at different temperatures (15°C, 25°C and 35°C) with and without baculovirus infection. Suitable reference genes were identified for the whole body and midgut tissue of all three species, and for cuticle tissue of Cy. pomonella and T. leucotreta. When T. leucotreta was infected with the virus at all temperature conditions ACT, AK and EF1 were found to be the most suitable reference genes for experimental normalization. In general, for all tissue types, species and stress conditions, AK and EF1 were the best-performing reference genes. However, even though the three species analysed were closely related and within the same tribe, each species required varying gene combinations for suitable normalization. This study provides the first reference gene evaluation for the Tortricidae, and paves the way for future qPCR analysis in Tortricidae.
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Affiliation(s)
- Jaryd A. Ridgeway
- Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
| | - Alicia E. Timm
- Department of Zoology and Entomology, Rhodes University, Grahamstown, South Africa
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