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Ferguson KB, Visser S, Dalíková M, Provazníková I, Urbaneja A, Pérez‐Hedo M, Marec F, Werren JH, Zwaan BJ, Pannebakker BA, Verhulst EC. Jekyll or Hyde? The genome (and more) of Nesidiocoris tenuis, a zoophytophagous predatory bug that is both a biological control agent and a pest. INSECT MOLECULAR BIOLOGY 2021; 30:188-209. [PMID: 33305885 PMCID: PMC8048687 DOI: 10.1111/imb.12688] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 11/25/2020] [Accepted: 12/07/2020] [Indexed: 05/14/2023]
Abstract
Nesidiocoris tenuis (Reuter) is an efficient predatory biological control agent used throughout the Mediterranean Basin in tomato crops but regarded as a pest in northern European countries. From the family Miridae, it is an economically important insect yet very little is known in terms of genetic information and no genomic or transcriptomic studies have been published. Here, we use a linked-read sequencing strategy on a single female N. tenuis. From this, we assembled the 355 Mbp genome and delivered an ab initio, homology-based and evidence-based annotation. Along the way, the bacterial "contamination" was removed from the assembly. In addition, bacterial lateral gene transfer (LGT) candidates were detected in the N. tenuis genome. The complete gene set is composed of 24 688 genes; the associated proteins were compared to other hemipterans (Cimex lectularis, Halyomorpha halys and Acyrthosiphon pisum). We visualized the genome using various cytogenetic techniques, such as karyotyping, CGH and GISH, indicating a karyotype of 2n = 32. Additional analyses include the localization of 18S rDNA and unique satellite probes as well as pooled sequencing to assess nucleotide diversity and neutrality of the commercial population. This is one of the first mirid genomes to be released and the first of a mirid biological control agent.
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Affiliation(s)
- K. B. Ferguson
- Laboratory of GeneticsWageningen UniversityWageningenThe Netherlands
| | - S. Visser
- Biology Centre CASInstitute of EntomologyČeské BudějoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
| | - M. Dalíková
- Biology Centre CASInstitute of EntomologyČeské BudějoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
| | - I. Provazníková
- Biology Centre CASInstitute of EntomologyČeské BudějoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
- European Molecular Biology LaboratoryHeidelbergGermany
| | - A. Urbaneja
- Centro de Protección Vegetal y BiotecnologíaInstituto Valenciano de Investigaciones Agrarias (IVIA)MoncadaSpain
| | - M. Pérez‐Hedo
- Centro de Protección Vegetal y BiotecnologíaInstituto Valenciano de Investigaciones Agrarias (IVIA)MoncadaSpain
| | - F. Marec
- Biology Centre CASInstitute of EntomologyČeské BudějoviceCzech Republic
| | - J. H. Werren
- Department of BiologyUniversity of RochesterRochesterNew YorkUSA
| | - B. J. Zwaan
- Laboratory of GeneticsWageningen UniversityWageningenThe Netherlands
| | - B. A. Pannebakker
- Laboratory of GeneticsWageningen UniversityWageningenThe Netherlands
| | - E. C. Verhulst
- Laboratory of EntomologyWageningen UniversityWageningenThe Netherlands
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Ma M, Guo L, Tu C, Wang A, Xu L, Luo J. Comparative Analysis of Adelphocoris suturalis Jakovlev (Hemiptera: Miridae) Immune Responses to Fungal and Bacterial Pathogens. Front Physiol 2021; 12:646721. [PMID: 33815150 PMCID: PMC8012897 DOI: 10.3389/fphys.2021.646721] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 02/18/2021] [Indexed: 01/30/2023] Open
Abstract
The wide-spread culture of transgenic Bt cotton resisting the infamous cotton bollworms has reduced the adoption of broad-spectrum insecticides to a large extent. Consequently, the non-targeted insect Adelphocoris suturalis Jakovlev has become a major cotton pest in China. Entomopathogenic microbes show promising results for controlling this pest in the future, but A. suturalis innate immune responses to these pathogens are poorly understood. Here, we used the entomopathogenic fungus Beauveria bassiana and the Gram-negative pathogenic bacteria Enterobactor cloacae to infect A. suturalis nymphs, followed by high throughput RNA-seq to analyze the immune transcriptomes of A. suturalis in response to the two pathogens. A total of 150 immunity-related genes were identified, including pattern recognition receptors, extracellular signal modulators, signal pathways (Toll, IMD, JNK, and JAK/STAT), and response effectors. Further quantitative real-time PCR analysis demonstrated that B. bassiana and E. cloacae were recognized by different receptors (GNBP and PGRP, respectively); activated Toll pathway and IMD pathway respectively; and both induced expression of the effector gene Defensin. However, melanization is suppressed in B. bassiana-infected nymphs. Collectively, this study provides a transcriptomic snapshot of the A. suturalis immune system, and at the genetic level, gains multifaceted insights of the immune response to fungal and Gram-negative bacterial pathogens. Ultimately this work pioneers the study of molecular mechanisms underlying immune interactions between A. suturalis and its pathogens and assists in the development of novel mitigation strategies to control this pest.
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Affiliation(s)
- Meiqi Ma
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Libin Guo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Chengjie Tu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Aoli Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Letian Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Jing Luo
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
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Fu S, Duan Y, Wang S, Ren Y, Bu W. Comparative Transcriptomic Analysis of Riptortus pedestris (Hemiptera: Alydidae) to Characterize Wing Formation across All Developmental Stages. INSECTS 2021; 12:insects12030226. [PMID: 33807991 PMCID: PMC7999114 DOI: 10.3390/insects12030226] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/28/2021] [Accepted: 03/01/2021] [Indexed: 12/13/2022]
Abstract
Simple Summary Riptortus pedestris is a widely distributed pest insect in East Asia that causes considerable economic losses. In this study, we applied the Illumina HiSeq6000 platform to construct and sequence the transcriptome libraries of R. pedestris during all life stages. First, a total of 60,058 unigenes were assembled from raw data, and then annotated and classified with various databases. Furthermore, different numbers of differentially expressed genes were calculated by pairwise comparisons of all life stages, and some of these DEGs were associated with various functions by GO and KEGG analysis. Additionally, a total number of 35,158 SSRs and 715,604 SNPs were identified from all the transcriptome libraries. Finally, we analyzed ten wing formation-related signaling pathways, and detected the molecular and expression characterization of five wing development-related genes by qRT-PCR for all developmental stages of R. pedestris. Collectively, all these data may pave the avenue for exploring the developmental processes of hemimetabolous insects and pest management. Abstract Riptortus pedestris (Hemiptera: Alydidae) is a major agricultural pest in East Asia that causes considerable economic losses to the soybean crop each year. However, the molecular mechanisms governing the growth and development of R. pedestris have not been fully elucidated. In this study, the Illumina HiSeq6000 platform was employed to perform de novo transcriptome assembly and determine the gene expression profiles of this species across all developmental stages, including eggs, first-, second-, third-, fourth-, and fifth-instar nymphs, and adults. In this study, a total of 60,058 unigenes were assembled from numerous raw reads, exhibiting an N50 length of 2126 bp and an average length of 1199 bp, and the unigenes were annotated and classified with various databases, such as the Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), and Gene Ontology (GO). Furthermore, various numbers of differentially expressed genes (DEGs) were calculated through pairwise comparisons of all life stages, and some of these DEGs were associated with immunity, metabolism, and development by GO and KEGG enrichment. In addition, 35,158 simple sequence repeats (SSRs) and 715,604 potential single nucleotide polymorphisms (SNPs) were identified from the seven transcriptome libraries of R. pedestris. Finally, we identified and summarized ten wing formation-related signaling pathways, and the molecular properties and expression levels of five wing development-related genes were analyzed using quantitative real-time PCR for all developmental stages of R. pedestris. Taken together, the results of this study may establish a foundation for future research investigating developmental processes and wing formation in hemimetabolous insects and may provide valuable data for pest control efforts attempting to reduce the economic damage caused by this pest.
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Han X, Lu C, Geib SM, Zheng J, Wu S, Zhang F, Liang G. Characterization of Dendrolimus houi Lajonquiere (Lepidoptera: Lasiocampidae) Transcriptome across All Life Stages. INSECTS 2019; 10:insects10120442. [PMID: 31835398 PMCID: PMC6956129 DOI: 10.3390/insects10120442] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/28/2019] [Accepted: 12/03/2019] [Indexed: 12/22/2022]
Abstract
Dendrolimus houi Lajonquiere is a phytophagous caterpillar infesting many economically important coniferous tree species in China, causing serious economic and ecological environment losses. Based on previous research, it has one generation per year in South China and East China in contrast to two generations per year in Yunnan province in southwestern China. The species is potentially resilient to climatic extremes in these regions with the eggs and 1st instar larvae surviving in the winter (5 °C), older instar larvae and pupae surviving high temperatures in the summer (35 °C), suggesting some temperature stress tolerance during different developmental stages. However, little is known in this species at the genetic and genomic level. In this study, we used high throughput sequencing to obtain transcriptome data from different developmental stages (eggs, 1st-3rd instar larvae, 4th-5th instar larvae, 6th-7th instar larvae, pupae, male and female adults), which were collected from Fujian province. In total, we obtained approximately 90 Gb of data, from which 33,720 unigenes were assembled and 17,797 unigenes were annotated. We furtherly analyzed the differentially expressed genes (DGEs) across all stages, the largest number between the eggs and 1st instar larvae stage and gene expression varied significantly in different developmental stages. Furthermore, 4138 SSR genes and 114,977 SNP loci were screened from transcriptome data. This paper will be a foundation for further study towards improved integrated pest management strategies for this species.
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Affiliation(s)
- Xiaohong Han
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (S.W.)
| | - Ciding Lu
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (S.W.)
| | - Scott M. Geib
- Daniel K. Inouye US Pacific Basin Agricultural Research Center, USDA-ARS, 64 Nowelo, St.; Hilo, HI 96720, USA;
| | - Junxian Zheng
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (S.W.)
| | - Songqing Wu
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (S.W.)
- Provincial Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Feiping Zhang
- Provincial Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
| | - Guanghong Liang
- Forestry College, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.H.); (S.W.)
- Provincial Key Laboratory of Integrated Pest Management in Ecological Forests, Fujian Agriculture and Forestry University, Fuzhou 350002, China;
- Correspondence: ; Tel.: +86-0591-8385-1475
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Zhang QL, Wang F, Guo J, Deng XY, Chen JY, Lin LB. Characterization of ladybird Henosepilachna vigintioctopunctata transcriptomes across various life stages. Sci Data 2018; 5:180093. [PMID: 29870033 PMCID: PMC5987669 DOI: 10.1038/sdata.2018.93] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/27/2018] [Indexed: 12/17/2022] Open
Abstract
Henosepilachna vigintioctopunctata is a vegetable pest that has spread worldwide. It belongs to the Coccinellidae family, whose members exhibit remarkable diversity, both in terms of their diets and the colored spots that appear on the elytra in the adult stage. Transcriptomic data from H. vigintioctopunctata at different life stages would be useful for further investigating the genetic basis of this dietary diversity and the formation of the colored spots in ladybird beetles, as well as revealing the population dynamics of H. vigintioctopunctata, which could be useful in pest control. Here, we generated a comprehensive RNA-seq data set (a total of ~24 Gb of clean data) for H. vigintioctopunctata by sequencing samples collected at different life stages. We characterized the transcriptomes of each of the four life stages (egg, larva, pupa, adult) and generated a high-coverage pool by combining all the RNA-seq reads. Furthermore, we identified a catalog of simple sequence repeat (SSR) markers. This represents the first study to collect transcriptome data from all life stages of a ladybird beetle.
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Affiliation(s)
- Qi-Lin Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210023, China
| | - Feng Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Jun Guo
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Xian-Yu Deng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
| | - Jun-Yuan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210023, China
- LPS, Nanjing Institute of Geology and Paleontology, CAS, Nanjing 210008, China
| | - Lian-Bing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China
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Chen D, Chen F, Chen C, Chen X, Mao Y. Transcriptome analysis of three cotton pests reveals features of gene expressions in the mesophyll feeder Apolygus lucorum. SCIENCE CHINA-LIFE SCIENCES 2017; 60:826-838. [PMID: 28730342 DOI: 10.1007/s11427-017-9065-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 04/05/2017] [Indexed: 11/27/2022]
Abstract
The green mirid bug Apolygus lucorum is an agricultural pest that is known to cause damage to more than 150 plant species. Here, we report the transcriptomes of A. lucorum at three different developmental stages (the second and fifth instar nymphs and adults). A total of 98,236 unigenes with an average length of 1,335 nt was obtained, of which 50,640 were annotated, including those encoding digestive enzymes and cytochrome P450s. Comparisons with cotton bollworm and cotton aphid transcriptomes revealed distinct features of A. lucorum as a mesophyll feeder. The gene expression dynamics varied during development from young nymphs to adults. The high-quality transcriptome data and the gene expression dynamics reported here provide valuable data for a more comprehensive understanding of the physiology and development of mirid bugs, and for mining targets for their control.
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Affiliation(s)
- Dianyang Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fangyan Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunyu Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoya Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Yingbo Mao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
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Bian HX, Ma HF, Zheng XX, Peng MH, Li YP, Su JF, Wang H, Li Q, Xia RX, Liu YQ, Jiang XF. Characterization of the Adult Head Transcriptome and Identification of Migration and Olfaction Genes in the Oriental Armyworm Mythimna separate. Sci Rep 2017; 7:2324. [PMID: 28539591 PMCID: PMC5443819 DOI: 10.1038/s41598-017-02513-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/12/2017] [Indexed: 01/20/2023] Open
Abstract
The oriental armyworm Mythimna separate is an economically important insect with a wide distribution and strong migratory activity. However, knowledge about the molecular mechanisms regulating the physiological and behavioural responses of the oriental armyworm is scarce. In the present study, we took a transcriptomic approach to characterize the gene network in the adult head of M. separate. The sequencing and de novo assembly yielded 63,499 transcripts, which were further assembled into 46,459 unigenes with an N50 of 1,153 bp. In the head transcriptome data, unigenes involved in the 'signal transduction mechanism' are the most abundant. In total, 937 signal transduction unigenes were assigned to 22 signalling pathways. The circadian clock, melanin synthesis, and non-receptor protein of olfactory gene families were then identified, and phylogenetic analyses were performed with these M. separate genes, the model insect Bombyx mori and other insects. Furthermore, 1,372 simple sequence repeats of 2-6 bp in unit length were identified. The transcriptome data represent a comprehensive molecular resource for the adult head of M. separate, and these identified genes can be valid targets for further gene function research to address the molecular mechanisms regulating the migratory and olfaction genes of the oriental armyworm.
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Affiliation(s)
- Hai-Xu Bian
- Insect Resource Center for Engineering and Technology of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, China
| | - Hong-Fang Ma
- Insect Resource Center for Engineering and Technology of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xi-Xi Zheng
- Insect Resource Center for Engineering and Technology of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, China
| | - Ming-Hui Peng
- Insect Resource Center for Engineering and Technology of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yu-Ping Li
- Insect Resource Center for Engineering and Technology of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, China
| | - Jun-Fang Su
- School of Basic Medicine, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Huan Wang
- Insect Resource Center for Engineering and Technology of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, China
| | - Qun Li
- Insect Resource Center for Engineering and Technology of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, China
| | - Run-Xi Xia
- Insect Resource Center for Engineering and Technology of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yan-Qun Liu
- Insect Resource Center for Engineering and Technology of Liaoning Province, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Xing-Fu Jiang
- State Key laboratory for Biology of Plant Diseases and Insect Pest, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Tang PA, Wu HJ, Xue H, Ju XR, Song W, Zhang QL, Yuan ML. Characterization of transcriptome in the Indian meal moth Plodia interpunctella (Lepidoptera: Pyralidae) and gene expression analysis during developmental stages. Gene 2017; 622:29-41. [PMID: 28412460 DOI: 10.1016/j.gene.2017.04.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 12/01/2016] [Accepted: 04/12/2017] [Indexed: 12/18/2022]
Abstract
The Indian meal moth Plodia interpunctella (Lepidoptera: Pyralidae) is a worldwide pest that causes serious damage to stored foods. Although many efforts have been conducted on this species due to its economic importance, the study of genetic basis of development, behavior and insecticide resistance has been greatly hampered due to lack of genomic information. In this study, we used high throughput sequencing platform to perform a de novo transcriptome assembly and tag-based digital gene expression profiling (DGE) analyses across four different developmental stages of P. interpunctella (egg, third-instar larvae, pupae and adult). We obtained approximate 9gigabyte (GB) of clean data and recovered 84,938 unigenes, including 37,602 clusters and 47,336 singletons. These unigenes were annotated using BLAST against the non-redundant protein databases and then functionally classified based on Gene Ontology (GO), Clusters of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes databases (KEGG). A large number of differentially expressed genes were identified by pairwise comparisons among different developmental stages. Gene expression profiles dramatically changed between developmental stage transitions. Some of these differentially expressed genes were related to digestion and cuticularization. Quantitative real-time PCR results of six randomly selected genes conformed the findings in the DGEs. Furthermore, we identified over 8000 microsatellite markers and 97,648 single nucleotide polymorphisms which will be useful for population genetics studies of P. interpunctella. This transcriptomic information provided insight into the developmental basis of P. interpunctella and will be helpful for establishing integrated management strategies and developing new targets of insecticides for this serious pest.
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Affiliation(s)
- Pei-An Tang
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, China.
| | - Hai-Jing Wu
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, China
| | - Hao Xue
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, China
| | - Xing-Rong Ju
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, China
| | - Wei Song
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing 210023, China
| | - Qi-Lin Zhang
- Evo-devo Institute, School of Life Sciences, Nanjing University, Nanjing 210008, China
| | - Ming-Long Yuan
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730020, China.
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Guo Y, Chai Y, Zhang L, Zhao Z, Gao LL, Ma R. Transcriptome Analysis and Identification of Major Detoxification Gene Families and Insecticide Targets in Grapholita Molesta (Busck) (Lepidoptera: Tortricidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2017; 17:3075266. [PMID: 28365764 PMCID: PMC5469388 DOI: 10.1093/jisesa/iex014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Indexed: 05/12/2023]
Abstract
The oriental fruit moth, Grapholita molesta (Busck) (Lepidoptera: Tortricidae), is an important pest of most stone and pome fruits and causes serious damage to the fruit industry worldwide. This insect pest has been primarily controlled through the application of insecticides; as a result, G. molesta has developed resistance to many different types of insecticides. To identify detoxification genes, we have, de novo, sequenced the transcriptome of G. molesta (Lepidoptera: Tortricidae) and yielded 58,970 unigenes of which 26,985 unigenes matched to known proteins. In total, 2,040 simple sequence repeats have been identified. The comprehensive transcriptome data set has permitted us to identify members of important gene families related to detoxification in G. molesta, including 77 unigenes of putative cytochrome P450s, 28 of glutathione S-transferases, 46 of Carboxylesterases, and 31 of insecticide targets. Orthologs of some of these unigenes have shown to play a pivotal role in insecticide resistance in other insect species and those unigenes likely have similar functions in G. molesta.
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Affiliation(s)
- Yanqiong Guo
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi 030801, China (; ; ; )
| | - Yanping Chai
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi 030801, China (; ; ; )
| | - Lijun Zhang
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi 030801, China (; ; ; )
| | - Zhiguo Zhao
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi 030801, China (; ; ; )
| | - Ling-Ling Gao
- CSIRO Agriculture & Food, Private Bag 5, Wembley, WA 6913, Australia, and
| | - Ruiyan Ma
- College of Agriculture, Shanxi Agricultural University, Taigu, Shanxi 030801, China (; ; ; )
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Ji R, Wang Y, Cheng Y, Zhang M, Zhang HB, Zhu L, Fang J, Zhu-Salzman K. Transcriptome Analysis of Green Peach Aphid ( Myzus persicae): Insight into Developmental Regulation and Inter-Species Divergence. FRONTIERS IN PLANT SCIENCE 2016; 7:1562. [PMID: 27812361 PMCID: PMC5072348 DOI: 10.3389/fpls.2016.01562] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 10/04/2016] [Indexed: 06/06/2023]
Abstract
Green peach aphid (Myzus persicae) and pea aphid (Acyrthosiphon pisum) are two phylogenetically closely related agricultural pests. While pea aphid is restricted to Fabaceae, green peach aphid feeds on hundreds of plant species from more than 40 families. Transcriptome comparison could shed light on the genetic factors underlying the difference in host range between the two species. Furthermore, a large scale study contrasting gene expression between immature nymphs and fully developed adult aphids would fill a previous knowledge gap. Here, we obtained transcriptomic sequences of green peach aphid nymphs and adults, respectively, using Illumina sequencing technology. A total of 2244 genes were found to be differentially expressed between the two developmental stages, many of which were associated with detoxification, hormone production, cuticle formation, metabolism, food digestion, and absorption. When searched against publically available pea aphid mRNA sequences, 13,752 unigenes were found to have no homologous counterparts. Interestingly, many of these unigenes that could be annotated in other databases were involved in the "xenobiotics biodegradation and metabolism" pathway, suggesting the two aphids differ in their adaptation to secondary metabolites of host plants. Conversely, 3989 orthologous gene pairs between the two species were subjected to calculations of synonymous and nonsynonymous substitutions, and 148 of the genes potentially evolved in response to positive selection. Some of these genes were predicted to be associated with insect-plant interactions. Our study has revealed certain molecular events related to aphid development, and provided some insight into biological variations in two aphid species, possibly as a result of host plant adaptation.
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Affiliation(s)
- Rui Ji
- Institute of Plant Protection, Jiangsu Academy of Agricultural SciencesNanjing, China
- Department of Entomology, Texas A&M UniversityCollege Station, TX, USA
| | - Yujun Wang
- Ministry of Agriculture Key Laboratory of Agricultural Entomology, Institute of Insect Sciences, Zhejiang UniversityHangzhou, China
| | - Yanbin Cheng
- Department of Plant Pathology and Microbiology, Texas A&M UniversityCollege Station, TX, USA
| | - Meiping Zhang
- Department of Soil and Crop Sciences, Texas A&M UniversityCollege Station, TX, USA
| | - Hong-Bin Zhang
- Department of Soil and Crop Sciences, Texas A&M UniversityCollege Station, TX, USA
| | - Li Zhu
- Biotechnology Research Institute, Chinese Academy of Agricultural SciencesBeijing, China
| | - Jichao Fang
- Institute of Plant Protection, Jiangsu Academy of Agricultural SciencesNanjing, China
| | - Keyan Zhu-Salzman
- Department of Entomology, Texas A&M UniversityCollege Station, TX, USA
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11
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Li F, Wang R, Qu C, Fu N, Luo C, Xu Y. Sequencing and Characterization of the Invasive Sycamore Lace Bug Corythucha ciliata (Hemiptera: Tingidae) Transcriptome. PLoS One 2016; 11:e0160609. [PMID: 27494615 PMCID: PMC4975459 DOI: 10.1371/journal.pone.0160609] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 07/21/2016] [Indexed: 11/19/2022] Open
Abstract
The sycamore lace bug, Corythucha ciliata (Hemiptera: Tingidae), is an invasive forestry pest rapidly expanding in many countries. This pest poses a considerable threat to the urban forestry ecosystem, especially to Platanus spp. However, its molecular biology and biochemistry are poorly understood. This study reports the first C. ciliata transcriptome, encompassing three different life stages (Nymphs, adults female (AF) and adults male (AM)). In total, 26.53 GB of clean data and 60,879 unigenes were obtained from three RNA-seq libraries. These unigenes were annotated and classified by Nr (NCBI non-redundant protein sequences), Nt (NCBI non-redundant nucleotide sequences), Pfam (Protein family), KOG/COG (Clusters of Orthologous Groups of proteins), Swiss-Prot (A manually annotated and reviewed protein sequence database), and KO (KEGG Ortholog database). After all pairwise comparisons between these three different samples, a large number of differentially expressed genes were revealed. The dramatic differences in global gene expression profiles were found between distinct life stages (nymphs and AF, nymphs and AM) and sex difference (AF and AM), with some of the significantly differentially expressed genes (DEGs) being related to metamorphosis, digestion, immune and sex difference. The different express of unigenes were validated through quantitative Real-Time PCR (qRT-PCR) for 16 randomly selected unigenes. In addition, 17,462 potential simple sequence repeat molecular markers were identified in these transcriptome resources. These comprehensive C. ciliata transcriptomic information can be utilized to promote the development of environmentally friendly methodologies to disrupt the processes of metamorphosis, digestion, immune and sex differences.
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Affiliation(s)
- Fengqi Li
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, P. R. China
| | - Ran Wang
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, P. R. China
| | - Cheng Qu
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, P. R. China
| | - Ningning Fu
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, P. R. China
| | - Chen Luo
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, P. R. China
- * E-mail:
| | - Yihua Xu
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, P. R. China
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12
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Jia BY, Ba HX, Wang GW, Yang Y, Cui XZ, Peng YH, Zheng JJ, Xing XM, Yang FH. Transcriptome analysis of sika deer in China. Mol Genet Genomics 2016; 291:1941-53. [PMID: 27423230 DOI: 10.1007/s00438-016-1231-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 07/11/2016] [Indexed: 12/17/2022]
Abstract
Sika deer is of great commercial value because their antlers are used in tonics and alternative medicine and their meat is healthy and delicious. The goal of this study was to generate transcript sequences from sika deer for functional genomic analyses and to identify the transcripts that demonstrate tissue-specific, age-dependent differential expression patterns. These sequences could enhance our understanding of the molecular mechanisms underlying sika deer growth and development. In the present study, we performed de novo transcriptome assembly and profiling analysis across ten tissue types and four developmental stages (juvenile, adolescent, adult, and aged) of sika deer, using Illumina paired-end tag (PET) sequencing technology. A total of 1,752,253 contigs with an average length of 799 bp were generated, from which 1,348,618 unigenes with an average length of 590 bp were defined. Approximately 33.2 % of these (447,931 unigenes) were then annotated in public protein databases. Many sika deer tissue-specific, age-dependent unigenes were identified. The testes have the largest number of tissue-enriched unigenes, and some of them were prone to develop new functions for other tissues. Additionally, our transcriptome revealed that the juvenile-adolescent transition was the most complex and important stage of the sika deer life cycle. The present work represents the first multiple tissue transcriptome analysis of sika deer across four developmental stages. The generated data not only provide a functional genomics resource for future biological research on sika deer but also guide the selection and manipulation of genes controlling growth and development.
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Affiliation(s)
- Bo-Yin Jia
- State Key Laboratory for Molecular Biology of Special Economical Animals, Institute of Special Economic Animals and Plants, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun, 130112, China
| | - Heng-Xing Ba
- State Key Laboratory for Molecular Biology of Special Economical Animals, Institute of Special Economic Animals and Plants, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun, 130112, China
| | - Gui-Wu Wang
- State Key Laboratory for Molecular Biology of Special Economical Animals, Institute of Special Economic Animals and Plants, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun, 130112, China
| | - Ying Yang
- State Key Laboratory for Molecular Biology of Special Economical Animals, Institute of Special Economic Animals and Plants, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun, 130112, China
| | - Xue-Zhe Cui
- State Key Laboratory for Molecular Biology of Special Economical Animals, Institute of Special Economic Animals and Plants, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun, 130112, China
| | - Ying-Hua Peng
- State Key Laboratory for Molecular Biology of Special Economical Animals, Institute of Special Economic Animals and Plants, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun, 130112, China
| | - Jun-Jun Zheng
- State Key Laboratory for Molecular Biology of Special Economical Animals, Institute of Special Economic Animals and Plants, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun, 130112, China
| | - Xiu-Mei Xing
- State Key Laboratory for Molecular Biology of Special Economical Animals, Institute of Special Economic Animals and Plants, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun, 130112, China
| | - Fu-He Yang
- State Key Laboratory for Molecular Biology of Special Economical Animals, Institute of Special Economic Animals and Plants, Chinese Academy of Agricultural Sciences, 4899 Juye Street, Changchun, 130112, China.
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13
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Chen MS, Liu S, Wang H, Cheng X, El Bouhssini M, Whitworth RJ. Massive Shift in Gene Expression during Transitions between Developmental Stages of the Gall Midge, Mayetiola Destructor. PLoS One 2016; 11:e0155616. [PMID: 27224654 PMCID: PMC4880318 DOI: 10.1371/journal.pone.0155616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/02/2016] [Indexed: 11/18/2022] Open
Abstract
Mayetiola destructor is a destructive pest of wheat and has six developmental stages. Molecular mechanisms controlling the transition between developmental stages remain unknown. Here we analyzed genes that were expressed differentially between two successive developmental stages, including larvae at 1, 3, 5, and 7 days, pupae, and adults. A total of 17,344 genes were expressed during one or more of these studied stages. Among the expressed genes, 38-68% were differently expressed between two successive stages, with roughly equal percentages of up- and down-regulated genes. Analysis of the functions of the differentially expressed genes revealed that each developmental stage had some unique types of expressed genes that are characteristic of the physiology at that stage. This is the first genome-wide analysis of genes differentially expressed in different stages in a gall midge. The large dataset of up- and down-regulated genes in each stage of the insect shall be very useful for future research to elucidate mechanisms regulating insect development and other biological processes.
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Affiliation(s)
- Ming-Shun Chen
- Hard Winter Wheat Genetics Research Unit, USDA-ARS, Kansas State University, Manhattan, Kansas, United States of America
- Department of Entomology, Kansas State University, Manhattan, Kansas, United States of America
- * E-mail:
| | - Sanzhen Liu
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
| | - Haiyan Wang
- Department of Statistics, Kansas State University, Manhattan, Kansas, United States of America
| | - Xiaoyan Cheng
- Department of Entomology, Kansas State University, Manhattan, Kansas, United States of America
| | | | - R. Jeff Whitworth
- Department of Entomology, Kansas State University, Manhattan, Kansas, United States of America
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