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Wang S, Raza SHA, Zhang K, Mei C, Alamoudi MO, Aloufi BH, Alshammari AM, Zan L. Selection signatures of Qinchuan cattle based on whole-genome sequences. Anim Biotechnol 2023; 34:1483-1491. [PMID: 35152846 DOI: 10.1080/10495398.2022.2033252] [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] [Indexed: 11/01/2022]
Abstract
Qinchuan cattle has gradually improved in body shape and growth rate in the long-term breeding process from the draft cattle to beef cattle. As the head of the five local yellow cattle in China, the Qinchuan cattle has been designated as a specialized beef cattle breed. We investigated the selection signatures using whole genome sequencing data in Qinchuan cattle. Based on Fst, we detected hundreds of candidate genes under selection across Qinchuan, Red Angus, and Japanese Black cattle. Through protein-protein interaction analysis and functional annotation of candidate genes, the results revealed that KMT2E, LTBP1 and NIPBL were related to brain size, body characteristics, and limb development, respectively, suggesting that these potential genes may affect the growth and development traits in Qinchuan cattle. ARIH2, DACT1 and DNM2, et al. are related to meat quality. Meanwhile, TBXA2R can be used as a gene associated with reproductive function, and USH2A affect coat color. This provided a glimpse into the formation of breeds and molecular genetic breeding. Our findings will promote genome-assisted breeding to improve animal production and health.
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Affiliation(s)
- Sihu Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | | | - Ke Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chugang Mei
- College of Grassland Agriculture, Northwest A&F University, Yangling, China
| | - Muna O Alamoudi
- Department of Biology, Faculty of Science, University of Hail, Hail, Saudi Arabia
| | - Bandar H Aloufi
- Department of Biology, Faculty of Science, University of Hail, Hail, Saudi Arabia
| | | | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
- National Beef Cattle Improvement Center, Yangling, China
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Nath A, Bora U. RNAinsecta: A tool for prediction of precursor microRNA in insects and search for their target in the model organism Drosophila melanogaster. PLoS One 2023; 18:e0287323. [PMID: 37812647 PMCID: PMC10561860 DOI: 10.1371/journal.pone.0287323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/03/2023] [Indexed: 10/11/2023] Open
Abstract
INTRODUCTION AND BACKGROUND Pre-MicroRNAs are the hairpin loops from which microRNAs are produced that have been found to negatively regulate gene expression in several organisms. In insects, microRNAs participate in several biological processes including metamorphosis, reproduction, immune response, etc. Numerous tools have been designed in recent years to predict novel pre-microRNA using binary machine learning classifiers where prediction models are trained with true and pseudo pre-microRNA hairpin loops. Currently, there are no existing tool that is exclusively designed for insect pre-microRNA detection. AIM Application of machine learning algorithms to develop an open source tool for prediction of novel precursor microRNA in insects and search for their miRNA targets in the model insect organism, Drosophila melanogaster. METHODS Machine learning algorithms such as Random Forest, Support Vector Machine, Logistic Regression and K-Nearest Neighbours were used to train insect true and false pre-microRNA features with 10-fold Cross Validation on SMOTE and Near-Miss datasets. miRNA targets IDs were collected from miRTarbase and their corresponding transcripts were collected from FlyBase. We used miRanda algorithm for the target searching. RESULTS In our experiment, SMOTE performed significantly better than Near-Miss for which it was used for modelling. We kept the best performing parameters after obtaining initial mean accuracy scores >90% of Cross Validation. The trained models on Support Vector Machine achieved accuracy of 92.19% while the Random Forest attained an accuracy of 80.28% on our validation dataset. These models are hosted online as web application called RNAinsecta. Further, searching target for the predicted pre-microRNA in Drosophila melanogaster has been provided in RNAinsecta.
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Affiliation(s)
- Adhiraj Nath
- Department of BSBE, IIT Guwahati, North Guwahati, Assam, India
| | - Utpal Bora
- Department of BSBE, IIT Guwahati, North Guwahati, Assam, India
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Chen Z, Fu T, Fu L, Liu B, Lin Y, Tang B, Hou Y. The Cellular Immunological Responses and Developmental Differences between Two Hosts Parasitized by Asecodes hispinarum. LIFE (BASEL, SWITZERLAND) 2022; 12:life12122025. [PMID: 36556390 PMCID: PMC9781599 DOI: 10.3390/life12122025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/20/2022] [Accepted: 12/01/2022] [Indexed: 12/09/2022]
Abstract
This study aims to investigate the developmental interactions of Asecodes hispinarum Bouček on Brontispa longissima Gestro and Octodonta nipae Maulik, as well as the cellular immune responses of B. longissima and O. nipae larvae in response to parasitism by A. hispinarum, with the hope of determining the reason for the difference in larval breeding of A. hispinarum in B. longissima and O. nipae. The effects of parasitism by A. hispinarum on the larval development, hemocyte count, and proportion of the hemocyte composition of the two hosts were carried out through selective assay and non-selective assay using statistical analysis and anatomical imaging. There was no significant difference in parasitic selection for A. hispinarum on the larvae of these two beetles; however, more eggs were laid to B. longissima larvae than to O. nipae larvae after parasitism by A. hispinarum. The eggs of A. hispinarum were able to grow and develop normally inside the larvae of B. longissima, and the parasitism caused the larvae of B. longissima become rigid within 7 d, with a high larval mortality rate of 98.88%. In contrast, the eggs of A. hispinarum were not able to develop normally inside the O. nipae larvae, with a high encapsulation rate of 99.05%. In addition, the parasitism by A. hispinarum caused a 15.31% mortality rate in O. nipae larvae and prolonged the larval stage by 5 d and the pupal stage by 1 d. The number of hemocytes during the 12, 24, 48, 72, and 96 h of the four instars from O. nipae larvae was 6.08 times higher than from B. longissima larvae of the same age. After 24 h of being parasitized by A. hispinarum, the total number of hemocytes and granulocyte proportion of B. longissima larvae increased significantly. However, the total number of hemocytes and plasmatocyte proportion of O. nipae increased significantly after 24, 72, and 96 h, and the proportion of granulocytes increased significantly after 12 h post-parasitism. The results in the present study indicated that A. hispinarum was unable to successfully reproduce offspring in O. nipae, but its spawning behavior had an adverse effect on the larval development of its host. In addition, the adequate number of hemocytes and more pronounced changes in the hemocyte count and hemocyte composition ratio in the larvae after parasitization may be important factors for the successful encapsulation in O. nipae larvae.
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Affiliation(s)
- Zhiming Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Integrated Technical Service Center of Rongcheng Customs, Fuzhou 350015, China
- Fujian Province Key Laboratory of Insect Ecology, Department of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Lab of Biopesticide and Chemical Biology, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tingting Fu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Province Key Laboratory of Insect Ecology, Department of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Lab of Biopesticide and Chemical Biology, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lang Fu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Province Key Laboratory of Insect Ecology, Department of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Lab of Biopesticide and Chemical Biology, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Bin Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Province Key Laboratory of Insect Ecology, Department of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Lab of Biopesticide and Chemical Biology, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yaping Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Province Key Laboratory of Insect Ecology, Department of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Lab of Biopesticide and Chemical Biology, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Baozhen Tang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Province Key Laboratory of Insect Ecology, Department of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Lab of Biopesticide and Chemical Biology, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Youming Hou
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Province Key Laboratory of Insect Ecology, Department of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Lab of Biopesticide and Chemical Biology, Ministerial and Provincial Joint Innovation Centre for Safety Production of Cross-Strait Crops, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Zhao X, Liu Y. Current Knowledge on Bee Innate Immunity Based on Genomics and Transcriptomics. Int J Mol Sci 2022; 23:ijms232214278. [PMID: 36430757 PMCID: PMC9692672 DOI: 10.3390/ijms232214278] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/28/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022] Open
Abstract
As important pollinators, bees play a critical role in maintaining the balance of the ecosystem and improving the yield and quality of crops. However, in recent years, the bee population has significantly declined due to various pathogens and environmental stressors including viruses, bacteria, parasites, and increased pesticide application. The above threats trigger or suppress the innate immunity of bees, their only immune defense system, which is essential to maintaining individual health and that of the colony. In addition, bees can be divided into solitary and eusocial bees based on their life traits, and eusocial bees possess special social immunities, such as grooming behavior, which cooperate with innate immunity to maintain the health of the colony. The omics approach gives us an opportunity to recognize the distinctive innate immunity of bees. In this regard, we summarize innate bee immunity from a genomic and transcriptomic perspective. The genetic characteristics of innate immunity were revealed by the multiple genomes of bees with different kinds of sociality, including honeybees, bumblebees, wasps, leaf-cutter bees, and so on. Further substantial transcriptomic data of different tissues from diverse bees directly present the activation or suppression of immune genes under the infestation of pathogens or toxicity of pesticides.
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Affiliation(s)
- Xiaomeng Zhao
- College of Engineering, Hebei Normal University, Shijiazhuang 050024, China
| | - Yanjie Liu
- Key Laboratory for Insect-Pollinator Biology of the Ministry of Agriculture and Rural Affairs, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
- Correspondence:
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Kamiyama T, Shimada-Niwa Y, Tanaka H, Katayama M, Kuwabara T, Mori H, Kunihisa A, Itoh T, Toyoda A, Niwa R. Whole-genome sequencing analysis and protocol for RNA interference of the endoparasitoid wasp Asobara japonica. DNA Res 2022; 29:6605221. [PMID: 35686927 PMCID: PMC9233498 DOI: 10.1093/dnares/dsac019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Asobara japonica is an endoparasitic wasp that parasitizes Drosophila flies. It synthesizes various toxic components in the venom gland and injects them into host larvae during oviposition. To identify and characterize these toxic components for enabling parasitism, we performed the whole-genome sequencing (WGS) and devised a protocol for RNA interference (RNAi) with A. japonica. Because it has a parthenogenetic lineage due to Wolbachia infection, we generated a clonal strain from a single wasp to obtain highly homogenous genomic DNA. The WGS analysis revealed that the estimated genome size was 322 Mb with a heterozygosity of 0.132%. We also performed RNA-seq analyses for gene annotation. Based on the qualified WGS platform, we cloned ebony-Aj, which encodes the enzyme N-β-alanyl dopamine synthetase, which is involved in melanin production. The microinjection of double-stranded RNA (dsRNA) targeting ebony-Aj led to body colour changes in adult wasps, phenocopying ebony-Dm mutants. Furthermore, we identified putative venom genes as a target of RNAi, confirming that dsRNA injection-based RNAi specifically suppressed the expression of the target gene in wasp adults. Taken together, our results provide a powerful genetic toolkit for studying the molecular mechanisms of parasitism.
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Affiliation(s)
- Takumi Kamiyama
- Graduate School of Life and Environmental Sciences, University of Tsukuba , Tsukuba 305-8577, Japan
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba , Tsukuba 305-8577, Japan
| | - Yuko Shimada-Niwa
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba , Tsukuba 305-8577, Japan
- Precursory Research for Embryonic Science and Technology (PREST), Japan Science and Technology Agency (JST) , Tokyo 102-0076, Japan
| | - Hiroyuki Tanaka
- Department of Biological Information, Tokyo Institute of Technology , Meguro, Tokyo 152-8550, Japan
| | - Minami Katayama
- Graduate School of Life and Environmental Sciences, University of Tsukuba , Tsukuba 305-8577, Japan
| | - Takayoshi Kuwabara
- College of Biological Sciences, University of Tsukuba , Tsukuba 305-8577, Japan
| | - Hitoha Mori
- College of Biological Sciences, University of Tsukuba , Tsukuba 305-8577, Japan
| | - Akari Kunihisa
- College of Biological Sciences, University of Tsukuba , Tsukuba 305-8577, Japan
| | - Takehiko Itoh
- Department of Biological Information, Tokyo Institute of Technology , Meguro, Tokyo 152-8550, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics , Mishima, Shizuoka 411-8540, Japan
| | - Ryusuke Niwa
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba , Tsukuba 305-8577, Japan
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Chen L, Feng C, Wang R, Nong X, Deng X, Chen X, Yu H. A chromosome-level genome assembly of the pollinating fig wasp Valisia javana. DNA Res 2022; 29:6589890. [PMID: 35595238 PMCID: PMC9160881 DOI: 10.1093/dnares/dsac014] [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: 02/21/2022] [Indexed: 12/02/2022] Open
Abstract
Fig wasp has always been thought the species-specific pollinator for their host fig (Moraceae, Ficus) and constitute a model system with its host to study co-evolution and co-speciation. The availability of a high-quality genome will help to further reveal the mechanisms underlying these characteristics. Here, we present a high-quality chromosome-level genome for Valisa javana developed by a combination of PacBio long-read and Illumina short-read. The assembled genome size is 296.34 Mb from 13 contigs with a contig N50 length of 26.76 kb. Comparative genomic analysis revealed expanded and positively selected genes related to biological features that aid fig wasps living in syconium of its highly specific host. Protein-coding genes associated with chemosensory, detoxification and venom genes were identified. Several differentially expressed genes in transcriptome data of V. javana between odor-stimulated samples and the controls have been identified in some olfactory signal transduction pathways, e.g. olfactory transduction, cAMP, cGMP-PKG, Calcim, Ras and Rap1. This study provides a valuable genomic resource for a fig wasp, and sheds insight into further revealing the mechanisms underlying their adaptive traits to their hosts in different places and co-speciation with their host.
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Affiliation(s)
- Lianfu Chen
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of Sciences , Guangzhou 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, The Chinese Academy of Sciences , Guangzhou 510650, China
| | - Chao Feng
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of Sciences , Guangzhou 510650, China
| | - Rong Wang
- School of Ecological and Environmental Sciences, Tiantong National Station for Forest Ecosystem Research, East China Normal University , Shanghai 200241, China
| | - Xiaojue Nong
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of Sciences , Guangzhou 510650, China
| | - Xiaoxia Deng
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of Sciences , Guangzhou 510650, China
| | - Xiaoyong Chen
- School of Ecological and Environmental Sciences, Tiantong National Station for Forest Ecosystem Research, East China Normal University , Shanghai 200241, China
| | - Hui Yu
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, The Chinese Academy of Sciences , Guangzhou 510650, China
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, The Chinese Academy of Sciences , Guangzhou 510650, China
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Chen K, Song J, Song Q, Dou X, Wang Y, Wei Y, Chen J, Wang L, Alradi MF, Liu X, Han Z, Feng C. Transcriptomic analysis provides insights into the immune responses and nutrition in Ostrinia furnacalis larvae parasitized by Macrocentrus cingulum. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2022; 109:e21863. [PMID: 34967472 DOI: 10.1002/arch.21863] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/06/2021] [Accepted: 12/15/2021] [Indexed: 06/14/2023]
Abstract
Macrocentrus cingulum is a principal endoparasite of Ostrinia furnacalis larvae. M. cingulum larvae repress host immune responses for survival and ingest host nutrients for development until emerging. However, most investigations focused on the mechanisms of how wasps repress the host immunity, the triggered immune responses and nutrient status altered by wasps in host are neglected. In this study, we found that parasitized O. furnacalis larvae activated fast recognition responses and produced some effectors such as lysozyme and antimicrobial peptides, along with more consumption of trehalose, glucose, and even lipid to defend against the invading M. cingulum. However, the expression of peroxidase 6 and superoxide dismutase 2 (SOD 2) was upregulated, and the messenger RNA (mRNA) levels of cellular immunity-related genes such as thioester-containing protein 2 (TEP 2) and hemocytin were also reduced, suggesting that some immune responses were selectively shut down by wasp parasitization. Taken together, all the results indicated that parasitized O. furnacalis larvae selectively activate the immune recognition response, and upregulate effector genes, but suppress ROS reaction and cellular immunity, and invest more energy to fuel certain immune responses to defend against the wasp invading. This study provides useful information for further identifying key components of the nutrition and innate immune repertoire which may shape host-parasitoid coevolutionary dynamics.
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Affiliation(s)
- Kangkang Chen
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, China
| | - Jiahui Song
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, China
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, Missouri, USA
| | - Xiaoyi Dou
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Yin Wang
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Youheng Wei
- Department of Biotechnology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Jiaqian Chen
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, China
| | - Libao Wang
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, China
| | - Mohamed F Alradi
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xu Liu
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zhaoyang Han
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, China
| | - Congjing Feng
- Department of Plant Protection, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu, China
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8
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Burke GR, Hines HM, Sharanowski BJ. The Presence of Ancient Core Genes Reveals Endogenization from Diverse Viral Ancestors in Parasitoid Wasps. Genome Biol Evol 2021; 13:evab105. [PMID: 33988720 PMCID: PMC8325570 DOI: 10.1093/gbe/evab105] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2021] [Indexed: 12/12/2022] Open
Abstract
The Ichneumonoidea (Ichneumonidae and Braconidae) is an incredibly diverse superfamily of parasitoid wasps that includes species that produce virus-like entities in their reproductive tracts to promote successful parasitism of host insects. Research on these entities has traditionally focused upon two viral genera Bracovirus (in Braconidae) and Ichnovirus (in Ichneumonidae). These viruses are produced using genes known collectively as endogenous viral elements (EVEs) that represent historical, now heritable viral integration events in wasp genomes. Here, new genome sequence assemblies for 11 species and 6 publicly available genomes from the Ichneumonoidea were screened with the goal of identifying novel EVEs and characterizing the breadth of species in lineages with known EVEs. Exhaustive similarity searches combined with the identification of ancient core genes revealed sequences from both known and novel EVEs. One species harbored a novel, independently derived EVE related to a divergent large double-stranded DNA (dsDNA) virus that manipulates behavior in other hymenopteran species. Although bracovirus or ichnovirus EVEs were identified as expected in three species, the absence of ichnoviruses in several species suggests that they are independently derived and present in two younger, less widespread lineages than previously thought. Overall, this study presents a novel bioinformatic approach for EVE discovery in genomes and shows that three divergent virus families (nudiviruses, the ancestors of ichnoviruses, and Leptopilina boulardi Filamentous Virus-like viruses) are recurrently acquired as EVEs in parasitoid wasps. Virus acquisition in the parasitoid wasps is a common process that has occurred in many more than two lineages from a diverse range of arthropod-infecting dsDNA viruses.
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Affiliation(s)
- Gaelen R Burke
- Department of Entomology, University of Georgia, Athens, Georgia, USA
| | - Heather M Hines
- Department of Biology and Department of Entomology, Pennsylvania State University, University Park, Pennsylvania, USA
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9
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Li B, Du Z, Tian L, Zhang L, Huang Z, Wei S, Song F, Cai W, Yu Y, Yang H, Li H. Chromosome-level genome assembly of the aphid parasitoid Aphidius gifuensis using Oxford Nanopore sequencing and Hi-C technology. Mol Ecol Resour 2021; 21:941-954. [PMID: 33314728 PMCID: PMC7986076 DOI: 10.1111/1755-0998.13308] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 12/04/2020] [Accepted: 12/08/2020] [Indexed: 12/14/2022]
Abstract
Aphidius gifuensis is a parasitoid wasp that has been commercially bred and released in large scale as a biocontrol agent for the management of aphid pests. As a highly efficient endoparasitoid, it is also an important model for exploring mechanisms of parasitism. Currently, artificially bred populations of this wasp are facing rapid decline with undetermined cause, and mechanisms underlying its parasitoid strategy remain poorly understood. Exploring the mechanism behind its population decline and the host–parasitoid relationship is impeded partly due to the lack of a comprehensive genome data for this species. In this study, we constructed a high‐quality reference genome of A. gifuensis using Oxford Nanopore sequencing and Hi‐C (proximity ligation chromatin conformation capture) technology. The final genomic assembly was 156.9 Mb, with a contig N50 length of 3.93 Mb, the longest contig length of 10.4 Mb and 28.89% repetitive sequences. 99.8% of genome sequences were anchored onto six linkage groups. A total of 11,535 genes were predicted, of which 90.53% were functionally annotated. Benchmarking Universal Single‐Copy Orthologs (BUSCO) analysis showed the completeness of assembled genome is 98.3%. We found significantly expanded gene families involved in metabolic processes, transmembrane transport, cell signal communication and oxidoreductase activity, in particular ATP‐binding cassette (ABC) transporter, Cytochrome P450 and venom proteins. The olfactory receptors (ORs) showed significant contraction, which may be associated with the decrease in host recognition. Our study provides a solid foundation for future studies on the molecular mechanisms of population decline as well as host–parasitoid relationship for parasitoid wasps.
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Affiliation(s)
- Bingyan Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhenyong Du
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Li Tian
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | | | | | - Shujun Wei
- Institute of Plant and Environmental Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Fan Song
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Wanzhi Cai
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
| | - Yanbi Yu
- Yunnan Tobacco Company of China National Tobacco Corporation, Kunming, China
| | | | - Hu Li
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, China
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Stoldt M, Klein L, Beros S, Butter F, Jongepier E, Feldmeyer B, Foitzik S. Parasite Presence Induces Gene Expression Changes in an Ant Host Related to Immunity and Longevity. Genes (Basel) 2021; 12:95. [PMID: 33451085 PMCID: PMC7828512 DOI: 10.3390/genes12010095] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/22/2020] [Accepted: 01/12/2021] [Indexed: 12/14/2022] Open
Abstract
Most species are either parasites or exploited by parasites, making parasite-host interactions a driver of evolution. Parasites with complex life cycles often evolve strategies to facilitate transmission to the definitive host by manipulating their intermediate host. Such manipulations could explain phenotypic changes in the ant Temnothorax nylanderi, the intermediate host of the cestode Anomotaenia brevis. In addition to behavioral and morphological alterations, infected workers exhibit prolonged lifespans, comparable to that of queens, which live up to two decades. We used transcriptomic data from cestodes and ants of different castes and infection status to investigate the molecular underpinnings of phenotypic alterations in infected workers and explored whether the extended lifespan of queens and infected workers has a common molecular basis. Infected workers and queens commonly upregulated only six genes, one of them with a known anti-aging function. Both groups overexpressed immune genes, although not the same ones. Our findings suggest that the lifespan extension of infected workers is not achieved via the expression of queen-specific genes. The analysis of the cestodes' transcriptome revealed dominant expression of genes of the mitochondrial respiratory transport chain, which indicates an active metabolism and shedding light on the physiology of the parasite in its cysticercoid stage.
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Affiliation(s)
- Marah Stoldt
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, 55128 Mainz, Germany; (L.K.); (S.F.)
| | - Linda Klein
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, 55128 Mainz, Germany; (L.K.); (S.F.)
| | - Sara Beros
- Max Planck Institute for the Biology of Ageing, 50931 Cologne, Germany;
| | - Falk Butter
- Institute for Molecular Biology, Johannes Gutenberg University Mainz, 55128 Mainz, Germany;
| | - Evelien Jongepier
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany;
| | - Barbara Feldmeyer
- Senckenberg Biodiversity and Climate Research Center (SBiK-F), Molecular Ecology, 60325 Frankfurt, Germany;
| | - Susanne Foitzik
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University Mainz, 55128 Mainz, Germany; (L.K.); (S.F.)
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Quicke DLJ, Butcher BA. Review of Venoms of Non-Polydnavirus Carrying Ichneumonoid Wasps. BIOLOGY 2021; 10:50. [PMID: 33445639 PMCID: PMC7828074 DOI: 10.3390/biology10010050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 12/23/2022]
Abstract
Parasitoids are predominantly insects that develop as larvae on or inside their host, also usually another insect, ultimately killing it after various periods of parasitism when both parasitoid larva and host are alive. The very large wasp superfamily Ichneumonoidea is composed of parasitoids of other insects and comprises a minimum of 100,000 species. The superfamily is dominated by two similarly sized families, Braconidae and Ichneumonidae, which are collectively divided into approximately 80 subfamilies. Of these, six have been shown to release DNA-containing virus-like particles, encoded within the wasp genome, classified in the virus family Polydnaviridae. Polydnaviruses infect and have profound effects on host physiology in conjunction with various venom and ovarial secretions, and have attracted an immense amount of research interest. Physiological interactions between the remaining ichneumonoids and their hosts result from adult venom gland secretions and in some cases, ovarian or larval secretions. Here we review the literature on the relatively few studies on the effects and chemistry of these ichneumonoid venoms and make suggestions for interesting future research areas. In particular, we highlight relatively or potentially easily culturable systems with features largely lacking in currently studied systems and whose study may lead to new insights into the roles of venom chemistry in host-parasitoid relationships as well as their evolution.
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Affiliation(s)
- Donald L. J. Quicke
- Integrative Ecology Laboratory, Department of Biology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan 10330, Thailand;
- Center of Excellence in Entomology, Bee Biology, Diversity of Insects and Mites, Chulalongkorn University, Phayathai Road, Pathumwan 10330, Thailand
| | - Buntika A. Butcher
- Integrative Ecology Laboratory, Department of Biology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan 10330, Thailand;
- Center of Excellence in Entomology, Bee Biology, Diversity of Insects and Mites, Chulalongkorn University, Phayathai Road, Pathumwan 10330, Thailand
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12
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Salvia R, Scieuzo C, Grimaldi A, Fanti P, Moretta A, Franco A, Varricchio P, Vinson SB, Falabella P. Role of Ovarian Proteins Secreted by Toxoneuron nigriceps (Viereck) (Hymenoptera, Braconidae) in the Early Suppression of Host Immune Response. INSECTS 2021; 12:insects12010033. [PMID: 33466542 PMCID: PMC7824821 DOI: 10.3390/insects12010033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 11/16/2022]
Abstract
Simple Summary Toxoneuron nigriceps is an endoparasitoid of the tobacco budworm Heliothis virescens. Parasitoid strategies to survive involve different regulating factors that are injected into the host body together with the egg: the venom and the calyx fluid, containing a Polydnavirus (PDV) and Ovarian Proteins (OPs). The combination of these factors increases the success of parasitism. Although many studies have been reported on venom protein components and the knowledge on PDVs is increasing, little is known on OPs. These secretions are able to interfere early with the host cellular immune response, acting specifically on host haemocytes, cells involved in immune response. Our results show that OPs induce several alterations on haemocytes, including cellular oxidative stress condition and modifications of actin cytoskeleton, so inducing both a loss of haemocyte functionality and cell death. Overall, in synergy with PDV and venom, OPs positively contribute to the evasion of the host immune response by T. nigriceps. Abstract Toxoneuron nigriceps (Viereck) (Hymenoptera, Braconidae) is an endophagous parasitoid of the larval stages of the tobacco budworm, Heliothis virescens (Fabricius) (Lepidoptera, Noctuidae). During oviposition, T. nigriceps injects into the host body, along with the egg, the venom, the calyx fluid, which contains a Polydnavirus (T. nigriceps BracoVirus: TnBV), and the Ovarian Proteins (OPs). Although viral gene expression in the host reaches detectable levels after a few hours, a precocious disruption of the host metabolism and immune system is observed right after parasitization. This alteration appears to be induced by female secretions including TnBV venom and OPs. OPs, originating from the ovarian calyx cells, are involved in the induction of precocious symptoms in the host immune system alteration. It is known that OPs in braconid and ichneumonid wasps can interfere with the cellular immune response before Polydnavirus infects and expresses its genes in the host tissues. Here we show that T. nigriceps OPs induce several alterations on host haemocytes that trigger cell death. The OP injection induces an extensive oxidative stress and a disorganization of actin cytoskeleton and these alterations can explain the high-level of haemocyte mortality, the loss of haemocyte functionality, and so the reduction in encapsulation ability by the host.
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Affiliation(s)
- Rosanna Salvia
- Department of Sciences, University of Basilicata, Via dell’Ateneo Lucano 10, 85100 Potenza, Italy; (R.S.); (C.S.); (P.F.); (A.M.); (A.F.)
- Spinoff XFlies s.r.l, University of Basilicata, Via dell’Ateneo Lucano 10, 85100 Potenza, Italy
| | - Carmen Scieuzo
- Department of Sciences, University of Basilicata, Via dell’Ateneo Lucano 10, 85100 Potenza, Italy; (R.S.); (C.S.); (P.F.); (A.M.); (A.F.)
- Spinoff XFlies s.r.l, University of Basilicata, Via dell’Ateneo Lucano 10, 85100 Potenza, Italy
| | - Annalisa Grimaldi
- Department of Biotechnology and Life Science, University of Insubria, Via J.H. Dunant 3, 21100 Varese, Italy;
| | - Paolo Fanti
- Department of Sciences, University of Basilicata, Via dell’Ateneo Lucano 10, 85100 Potenza, Italy; (R.S.); (C.S.); (P.F.); (A.M.); (A.F.)
| | - Antonio Moretta
- Department of Sciences, University of Basilicata, Via dell’Ateneo Lucano 10, 85100 Potenza, Italy; (R.S.); (C.S.); (P.F.); (A.M.); (A.F.)
| | - Antonio Franco
- Department of Sciences, University of Basilicata, Via dell’Ateneo Lucano 10, 85100 Potenza, Italy; (R.S.); (C.S.); (P.F.); (A.M.); (A.F.)
- Spinoff XFlies s.r.l, University of Basilicata, Via dell’Ateneo Lucano 10, 85100 Potenza, Italy
| | - Paola Varricchio
- Department of Agricultural Sciences, University of Naples “Federico II”, 80055 Portici, Italy;
| | - S. Bradleigh Vinson
- Department of Entomology, Texas A&M University, 370 Olsen Blvd, College Station, TX 77843-2475, USA;
| | - Patrizia Falabella
- Department of Sciences, University of Basilicata, Via dell’Ateneo Lucano 10, 85100 Potenza, Italy; (R.S.); (C.S.); (P.F.); (A.M.); (A.F.)
- Spinoff XFlies s.r.l, University of Basilicata, Via dell’Ateneo Lucano 10, 85100 Potenza, Italy
- Correspondence:
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13
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Zhang Q, Dou W, Song ZH, Jin TJ, Yuan GR, De Schutter K, Smagghe G, Wang JJ. Identification and profiling of Bactrocera dorsalis microRNAs and their potential roles in regulating the developmental transitions of egg hatching, molting, pupation and adult eclosion. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 127:103475. [PMID: 33059019 DOI: 10.1016/j.ibmb.2020.103475] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/28/2020] [Accepted: 09/19/2020] [Indexed: 06/11/2023]
Abstract
MicroRNAs (miRNAs) are endogenous small noncoding RNAs (18-25 nt) that are involved in many physiological processes including development, cancer, immunity, apoptosis and host-microbe interactions through post-transcriptional regulation of gene expression. In this study, we measured the profile of small RNAs over the developmental transitions of the oriental fruit fly Bactrocera dorsalis from egg hatching, molting, and pupation to adult eclosion. We identified 250 miRNAs, including 83 known and 167 novel miRNAs, and 47 isomiRNAs. In addition, we identified the miRNAs differentially expressed over the developmental transitions. Interestingly, the miR-309 cluster, the miR-2 cluster/family and the let-7 cluster were among these differentially expressed miRNAs, suggesting a role in the regulation of egg hatching, molting and pupation/adult eclosion, respectively. Moreover, a detailed analysis of the temporal expression patterns of 14 highly expressed miRNAs in the pupal stage revealed three types of expression profiles. Furthermore, injection of a miR-100 mimic in the 3rd instar larvae resulted in a significant decrease in pupation and adult eclosion rates, whereas injection of a miR-317 antagomir resulted in a significant decrease in the pupation rate and a decrease in the pupation time, indicating that miR-100 and miR-317 are involved in the process of pupation. Finally, injection of a miR-100/miR-285 mimic or antagomir in pupae resulted in a significant decrease in the eclosion rate and a significant increase in the prevalence of a partial eclosion phenotype, implying the involvement of miR-100 and miR-285 in the process of adult eclosion. This study identified critical miRNAs involved in the transitions of this important holometabolic model and pest insect B. dorsalis from egg hatching to adult eclosion, thus providing a useful resource for exploring the regulatory role of miRNAs during insect post-embryonic development.
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Affiliation(s)
- Qiang Zhang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, China; Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China; International China-Belgium Joint Laboratory on Sustainable Crop Pest Control Between Southwest University in China and Ghent University in Belgium, Chongqing, 400715, China
| | - Wei Dou
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, China; Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China; International China-Belgium Joint Laboratory on Sustainable Crop Pest Control Between Southwest University in China and Ghent University in Belgium, Chongqing, 400715, China
| | - Zhong-Hao Song
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, China; Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China; International China-Belgium Joint Laboratory on Sustainable Crop Pest Control Between Southwest University in China and Ghent University in Belgium, Chongqing, 400715, China
| | - Tong-Jun Jin
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, China; Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China; International China-Belgium Joint Laboratory on Sustainable Crop Pest Control Between Southwest University in China and Ghent University in Belgium, Chongqing, 400715, China
| | - Guo-Rui Yuan
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, China; Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China; International China-Belgium Joint Laboratory on Sustainable Crop Pest Control Between Southwest University in China and Ghent University in Belgium, Chongqing, 400715, China
| | - Kristof De Schutter
- International China-Belgium Joint Laboratory on Sustainable Crop Pest Control Between Southwest University in China and Ghent University in Belgium, Chongqing, 400715, China; Department of Plants and Crops, Ghent University, Ghent, 9000, Belgium
| | - Guy Smagghe
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, China; Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China; International China-Belgium Joint Laboratory on Sustainable Crop Pest Control Between Southwest University in China and Ghent University in Belgium, Chongqing, 400715, China; Department of Plants and Crops, Ghent University, Ghent, 9000, Belgium.
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, 400715, China; Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China; International China-Belgium Joint Laboratory on Sustainable Crop Pest Control Between Southwest University in China and Ghent University in Belgium, Chongqing, 400715, China.
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Yu K, Xiong S, Xu G, Ye X, Yao H, Wang F, Fang Q, Song Q, Ye G. Identification of Neuropeptides and Their Receptors in the Ectoparasitoid, Habrobracon hebetor. Front Physiol 2020; 11:575655. [PMID: 33178044 PMCID: PMC7596734 DOI: 10.3389/fphys.2020.575655] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/16/2020] [Indexed: 12/20/2022] Open
Abstract
Neuropeptides are a group of signal molecules that regulate many physiological and behavioral processes by binding to corresponding receptors, most of which are G-protein-coupled receptors (GPCRs). Using bioinformatic methods, we screened genomic and transcriptomic data of the ectoparasitoid wasp, Habrobracon hebetor, and annotated 34 neuropeptide candidate precursor genes and 44 neuropeptide receptor candidate genes. The candidate neuropeptide genes were found to encode all known insect neuropeptides except allatotropin, neuropeptide F, pigment dispersing factor, and CCHamides. When compared with the endoparasitic wasp Pteromalus puparum and the ectoparasitic wasp Nasonia vitripennis, trissin and FMRFamide were found only in H. hebetor. A similar result held for the neuropeptide receptor genes, for the receptors were found in H. hebetor except the receptors of CCHamides and neuroparsin. Furthermore, we compared and analyzed the differences in neuropeptides in eight Braconidae wasps and identified natalisin in H. hebetor, Diachasma alloeum, Fopius arisanus and Microplitis demolitor, but not in the other wasps. We also analyzed the transcriptome data and qRT-PCR data from different developmental stages and tissues to reveal the expression patterns of the neuropeptides and their receptors. In this study, we revealed composition of neuropeptides and neuropeptide receptors in H. hebetor, which may contribute to future neurobiological studies.
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Affiliation(s)
- Kaili Yu
- State Key Laboratory of Rice Biology and Key Laboratory of Agricultural Entomology of Ministry of Agriculture, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Shijiao Xiong
- State Key Laboratory of Rice Biology and Key Laboratory of Agricultural Entomology of Ministry of Agriculture, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Gang Xu
- State Key Laboratory of Rice Biology and Key Laboratory of Agricultural Entomology of Ministry of Agriculture, Institute of Insect Sciences, Zhejiang University, Hangzhou, China.,College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Xinhai Ye
- State Key Laboratory of Rice Biology and Key Laboratory of Agricultural Entomology of Ministry of Agriculture, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Hongwei Yao
- State Key Laboratory of Rice Biology and Key Laboratory of Agricultural Entomology of Ministry of Agriculture, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fang Wang
- State Key Laboratory of Rice Biology and Key Laboratory of Agricultural Entomology of Ministry of Agriculture, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Qi Fang
- State Key Laboratory of Rice Biology and Key Laboratory of Agricultural Entomology of Ministry of Agriculture, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Qisheng Song
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO, United States
| | - Gongyin Ye
- State Key Laboratory of Rice Biology and Key Laboratory of Agricultural Entomology of Ministry of Agriculture, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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15
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Ye X, Yan Z, Yang Y, Xiao S, Chen L, Wang J, Wang F, Xiong S, Mei Y, Wang F, Yao H, Song Q, Li F, Fang Q, Werren JH, Ye G. A chromosome-level genome assembly of the parasitoid wasp Pteromalus puparum. Mol Ecol Resour 2020; 20:1384-1402. [PMID: 32562592 DOI: 10.1111/1755-0998.13206] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 05/29/2020] [Accepted: 06/01/2020] [Indexed: 01/30/2023]
Abstract
Parasitoid wasps represent a large proportion of hymenopteran species. They have complex evolutionary histories and are important biocontrol agents. To advance parasitoid research, a combination of Illumina short-read, PacBio long-read and Hi-C scaffolding technologies was used to develop a high-quality chromosome-level genome assembly for Pteromalus puparum, which is an important pupal endoparasitoid of caterpillar pests. The chromosome-level assembly has aided in studies of venom and detoxification genes. The assembled genome size is 338 Mb with a contig N50 of 38.7 kb and a scaffold N50 of 1.16 Mb. Hi-C analysis assembled scaffolds onto five chromosomes and raised the scaffold N50 to 65.8 Mb, with more than 96% of assembled bases located on chromosomes. Gene annotation was assisted by RNA sequencing for the two sexes and four different life stages. Analysis detected 98% of the BUSCO (Benchmarking Universal Single-Copy Orthologs) gene set, supporting a high-quality assembly and annotation. In total, 40.1% (135.6 Mb) of the assembly is composed of repetitive sequences, and 14,946 protein-coding genes were identified. Although venom genes play important roles in parasitoid biology, their spatial distribution on chromosomes was poorly understood. Mapping has revealed venom gene tandem arrays for serine proteases, pancreatic lipase-related proteins and kynurenine-oxoglutarate transaminases, which have amplified in the P. puparum lineage after divergence from its common ancestor with Nasonia vitripennis. In addition, there is a large expansion of P450 genes in P. puparum. These examples illustrate how chromosome-level genome assembly can provide a valuable resource for molecular, evolutionary and biocontrol studies of parasitoid wasps.
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Affiliation(s)
- Xinhai Ye
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China.,Department of Biology, University of Rochester, Rochester, NY, USA
| | - Zhichao Yan
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yi Yang
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Shan Xiao
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Longfei Chen
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Jiale Wang
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fei Wang
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Shijiao Xiong
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Yang Mei
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fang Wang
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Hongwei Yao
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Qisheng Song
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO, USA
| | - Fei Li
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Qi Fang
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Gongyin Ye
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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Du J, Lin Z, Volovych O, Lu Z, Zou Z. A RhoGAP venom protein from Microplitis mediator suppresses the cellular response of its host Helicoverpa armigera. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 108:103675. [PMID: 32173445 DOI: 10.1016/j.dci.2020.103675] [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] [Received: 10/10/2019] [Revised: 03/09/2020] [Accepted: 03/09/2020] [Indexed: 06/10/2023]
Abstract
Female parasitoid wasps normally inject virulence factors together with eggs into their host to counter host immunity defenses. A newly identified RhoGAP protein in the venom of Microplitis mediator compromises the cellular immunity of its host, Helicoverpa armigera. RhoGAP1 proteins entered H. armigera hemocytes, and the host cellular cytoskeleton was disrupted. Depletion of MmGAP1 by injection of dsRNA or antibody increased the wasp egg encapsulation rate. An immunoprecipitation assay of overexpressed MmGAP1 protein in a Helicoverpa cell line showed that MmGAP1 interacts with many cellular cytoskeleton associated proteins as well as Rho GTPases. A yeast two-hybrid and a pull-down assay demonstrated that MmGAP1 interacts with H. armigera RhoA and Cdc42. These results show that the RhoGAP protein in M. mediator can destroy the H. armigera hemocyte cellular cytoskeleton, restrain host cellular immune defense, and increase the probability of successful parasitism.
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Affiliation(s)
- Jie Du
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhe Lin
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Olga Volovych
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiqiang Lu
- Department of Entomology, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhen Zou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China; Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, Huzhou University, Huzhou, 311300, China.
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17
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Brivio MF, Mastore M. When Appearance Misleads: The Role of the Entomopathogen Surface in the Relationship with Its Host. INSECTS 2020; 11:E387. [PMID: 32585858 PMCID: PMC7348879 DOI: 10.3390/insects11060387] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/18/2020] [Accepted: 06/20/2020] [Indexed: 12/14/2022]
Abstract
Currently, potentially harmful insects are controlled mainly by chemical synthetic insecticides, but environmental emergencies strongly require less invasive control techniques. The use of biological insecticides in the form of entomopathogenic organisms is undoubtedly a fundamental resource for the biological control of insect pests in the future. These infectious agents and endogenous parasites generally act by profoundly altering the host's physiology to death, but their success is closely related to the neutralization of the target insect's immune response. In general, entomopathogen parasites, entomopathogenic bacteria, and fungi can counteract immune processes through the effects of secretion/excretion products that interfere with and damage the cells and molecules typical of innate immunity. However, these effects are observed in the later stages of infection, whereas the risk of being recognized and neutralized occurs very early after penetration and involves the pathogen surface components and molecular architecture; therefore, their role becomes crucial, particularly in the earliest pathogenesis. In this review, we analyze the evasion/interference strategies that entomopathogens such as the bacterium Bacillus thuringiensis, fungi, nematocomplexes, and wasps implement in the initial stages of infection, i.e., the phases during which body or cell surfaces play a key role in the interaction with the host receptors responsible for the immunological discrimination between self and non-self. In this regard, these organisms demonstrate evasive abilities ascribed to their body surface and cell wall; it appears that the key process of these mechanisms is the capability to modify the surface, converting it into an immunocompatible structure, or interaction that is more or less specific to host factors.
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Affiliation(s)
- Maurizio Francesco Brivio
- Laboratory of Comparative Immunology and Parasitology, Department of Theoretical and Applied Sciences, University of Insubria, 21100 Varese, Italy;
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Wang C, Jin F, De Mandal S, Zeng L, Zhang Y, Hua Y, Hong Y, Zhao C, Li J, Li D, Xu X. Insights into the venom protein components of the egg parasitoid Anastatus japonicus (Hymenoptera: Eupelmidae). PEST MANAGEMENT SCIENCE 2020; 76:2113-2126. [PMID: 31951096 DOI: 10.1002/ps.5750] [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] [Received: 10/04/2019] [Revised: 01/08/2020] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Parasitoid venom is composed of a complex mixture of various active substances with different biological functions and is injected in the host during the parasitoid oviposition. Anastatus japonicus (Hymenoptera: Eupelmidae) is an egg parasite of Tessaratoma papillosa (Hemiptera: Tessaratomidae). Although the venom of this egg parasitoid plays an important role in the parasitic process, relatively little work has been done to address the mechanism. RESULTS In the present study, proteomic analysis was performed to identify the proteins that play an important role in the parasitic process of A. japonicus. A total of 2084 proteins were identified, including 81 putative venom proteins, most of which were identified as Hexamerin, Chitinase 2, Calreticulin, Heat shock protein 83-like, Serine protease, Arginine kinase, Phosphoserine aminotransferase and Actin protein. Together the before (Be) and after (Af) parasitization venom contains 1628 proteins, including 212 DEPs with 181 and 31 significantly up-regulated and down-regulated respectively. In addition, 10 differentially expressed proteins (DEPs) with fold change ≥8.71 were subjected to RT-qPCR to validate the proteomic data. The differential expression analysis revealed that nine proteins were specifically present in the pre-parasitic venom, whereas 26 proteins were specific to the post-parasitic treatments. Results of RT-qPCR analysis showed high expression of the selected DEPs which further validated our proteomics data. CONCLUSION These new proteomic data greatly enrich our current knowledge about key venom proteins associated with parasitic process in A. japonicus and contribute to better understanding of the parasitic mechanisms leading to the development of new biological control strategies. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Chengxing Wang
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, China
- Plant Protection Research Institute, , Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, China
| | - Fengliang Jin
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Surajit De Mandal
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Lu Zeng
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Yuxin Zhang
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Yanyan Hua
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Yingying Hong
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Can Zhao
- Plant Protection Research Institute, , Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, China
| | - Junzhai Li
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, China
- Plant Protection Research Institute, , Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, China
| | - Dunsong Li
- Plant Protection Research Institute, , Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, China
| | - Xiaoxia Xu
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, Department of Entomology, College of Agriculture, South China Agricultural University, Guangzhou, China
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Dennis AB, Ballesteros GI, Robin S, Schrader L, Bast J, Berghöfer J, Beukeboom LW, Belghazi M, Bretaudeau A, Buellesbach J, Cash E, Colinet D, Dumas Z, Errbii M, Falabella P, Gatti JL, Geuverink E, Gibson JD, Hertaeg C, Hartmann S, Jacquin-Joly E, Lammers M, Lavandero BI, Lindenbaum I, Massardier-Galata L, Meslin C, Montagné N, Pak N, Poirié M, Salvia R, Smith CR, Tagu D, Tares S, Vogel H, Schwander T, Simon JC, Figueroa CC, Vorburger C, Legeai F, Gadau J. Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum. BMC Genomics 2020; 21:376. [PMID: 32471448 PMCID: PMC7257214 DOI: 10.1186/s12864-020-6764-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/30/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Parasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biological control. Their success depends on adapting to develop inside aphids and overcoming both host aphid defenses and their protective endosymbionts. RESULTS We present the de novo genome assemblies, detailed annotation, and comparative analysis of two closely related parasitoid wasps that target pest aphids: Aphidius ervi and Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae). The genomes are small (139 and 141 Mbp) and the most AT-rich reported thus far for any arthropod (GC content: 25.8 and 23.8%). This nucleotide bias is accompanied by skewed codon usage and is stronger in genes with adult-biased expression. AT-richness may be the consequence of reduced genome size, a near absence of DNA methylation, and energy efficiency. We identify missing desaturase genes, whose absence may underlie mimicry in the cuticular hydrocarbon profile of L. fabarum. We highlight key gene groups including those underlying venom composition, chemosensory perception, and sex determination, as well as potential losses in immune pathway genes. CONCLUSIONS These findings are of fundamental interest for insect evolution and biological control applications. They provide a strong foundation for further functional studies into coevolution between parasitoids and their hosts. Both genomes are available at https://bipaa.genouest.org.
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Affiliation(s)
- Alice B Dennis
- Department of Aquatic Ecology, Eawag, 8600, Dübendorf, Switzerland.
- Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland.
- Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.
| | - Gabriel I Ballesteros
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centre for Molecular and Functional Ecology in Agroecosystems, Universidad de Talca, Talca, Chile
- Laboratorio de Control Biológico, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Stéphanie Robin
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
- Université de Rennes 1, INRIA, CNRS, IRISA, 35000, Rennes, France
| | - Lukas Schrader
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Jens Bast
- Department of Ecology and Evolution, Université de Lausanne, 1015, Lausanne, Switzerland
- Institute of Zoology, Universität zu Köln, 50674, Köln, Germany
| | - Jan Berghöfer
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Leo W Beukeboom
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Maya Belghazi
- Aix-Marseille Univ, CNRS, INP, Inst Neurophysiopathol, PINT, PFNT, Marseille, France
| | - Anthony Bretaudeau
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
- Université de Rennes 1, INRIA, CNRS, IRISA, 35000, Rennes, France
| | - Jan Buellesbach
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Elizabeth Cash
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, CA, 94720, USA
| | | | - Zoé Dumas
- Department of Ecology and Evolution, Université de Lausanne, 1015, Lausanne, Switzerland
| | - Mohammed Errbii
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | | | - Jean-Luc Gatti
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Elzemiek Geuverink
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Joshua D Gibson
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, CA, 94720, USA
- Department of Biology, Georgia Southern University, Statesboro, GA, 30460, USA
| | - Corinne Hertaeg
- Department of Aquatic Ecology, Eawag, 8600, Dübendorf, Switzerland
- Department of Environmental Systems Sciences, D-USYS, ETH Zürich, Zürich, Switzerland
| | - Stefanie Hartmann
- Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Emmanuelle Jacquin-Joly
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université Paris Diderot, Institute of Ecology and Environmental Sciences of Paris, iEES-Paris, F-78000, Versailles, France
| | - Mark Lammers
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | - Blas I Lavandero
- Laboratorio de Control Biológico, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Ina Lindenbaum
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany
| | | | - Camille Meslin
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université Paris Diderot, Institute of Ecology and Environmental Sciences of Paris, iEES-Paris, F-78000, Versailles, France
| | - Nicolas Montagné
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université Paris Diderot, Institute of Ecology and Environmental Sciences of Paris, iEES-Paris, F-78000, Versailles, France
| | - Nina Pak
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Marylène Poirié
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Rosanna Salvia
- Department of Sciences, University of Basilicata, 85100, Potenza, Italy
| | - Chris R Smith
- Department of Biology, Earlham College, Richmond, IN, 47374, USA
| | - Denis Tagu
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
| | - Sophie Tares
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Tanja Schwander
- Department of Ecology and Evolution, Université de Lausanne, 1015, Lausanne, Switzerland
| | | | - Christian C Figueroa
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
- Centre for Molecular and Functional Ecology in Agroecosystems, Universidad de Talca, Talca, Chile
| | - Christoph Vorburger
- Department of Aquatic Ecology, Eawag, 8600, Dübendorf, Switzerland
- Institute of Integrative Biology, ETH Zürich, 8092, Zürich, Switzerland
| | - Fabrice Legeai
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes, 35650, Le Rheu, France
- Université de Rennes 1, INRIA, CNRS, IRISA, 35000, Rennes, France
| | - Jürgen Gadau
- Institute for Evolution and Biodiversity, Universität Münster, Münster, Germany.
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Zhang L, Li S, Luo J, Du P, Wu L, Li Y, Zhu X, Wang L, Zhang S, Cui J. Chromosome‐level genome assembly of the predatorPropylea japonicato understand its tolerance to insecticides and high temperatures. Mol Ecol Resour 2019; 20:292-307. [DOI: 10.1111/1755-0998.13100] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/19/2019] [Accepted: 10/07/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Lijuan Zhang
- Zhengzhou Research Base State Key Laboratory of Cotton Biology Zhengzhou University Zhengzhou China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Sciences Anyang China
| | - Song Li
- Biomarker Technologies Corporation Beijing China
| | - Junyu Luo
- Zhengzhou Research Base State Key Laboratory of Cotton Biology Zhengzhou University Zhengzhou China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Sciences Anyang China
| | - Pei Du
- Industrial Crops Research Institute Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang‐Huai‐Hai Plains Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement Zhengzhou China
| | - Linke Wu
- Zhengzhou Research Base State Key Laboratory of Cotton Biology Zhengzhou University Zhengzhou China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Sciences Anyang China
| | - Yarong Li
- Zhengzhou Research Base State Key Laboratory of Cotton Biology Zhengzhou University Zhengzhou China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Sciences Anyang China
| | - Xiangzhen Zhu
- Zhengzhou Research Base State Key Laboratory of Cotton Biology Zhengzhou University Zhengzhou China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Sciences Anyang China
| | - Li Wang
- Zhengzhou Research Base State Key Laboratory of Cotton Biology Zhengzhou University Zhengzhou China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Sciences Anyang China
| | - Shuai Zhang
- Zhengzhou Research Base State Key Laboratory of Cotton Biology Zhengzhou University Zhengzhou China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Sciences Anyang China
| | - Jinjie Cui
- Zhengzhou Research Base State Key Laboratory of Cotton Biology Zhengzhou University Zhengzhou China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research Chinese Academy of Agricultural Sciences Anyang China
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Zhang Q, Dou W, Pan D, Chen EH, Niu JZ, Smagghe G, Wang JJ. Genome-Wide Analysis of MicroRNAs in Relation to Pupariation in Oriental Fruit Fly. Front Physiol 2019; 10:301. [PMID: 30967796 PMCID: PMC6439999 DOI: 10.3389/fphys.2019.00301] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 03/07/2019] [Indexed: 12/15/2022] Open
Abstract
Insect metamorphosis is a complex process involving drastic morphological and physiological changes. microRNAs (miRNAs) are a class of endogenous small non-coding RNAs that play key roles in regulating various biological processes, including metamorphosis, by post-transcriptional repression of mRNAs. The oriental fruit fly, Bactrocera dorsalis, is one of the most destructive insect pests in many Asian countries and the Pacific Islands. The regulatory role of miRNAs in B. dorsalis metamorphosis is unclear. To better understand the molecular regulatory mechanisms of miRNAs in pupariation, Illumina sequencing of the wandering stage (WS), the late WS and the white puparium stage of B. dorsalis were performed. Two hundred forty-nine miRNAs, including 184 known miRNAs and 65 novel miRNAs, were obtained. Among these miRNAs, 19 miRNAs were differentially expressed in pupariation, and eight miRNAs showed relative high expression levels (>50 TPM), of which five differentially expressed miRNAs (DEMs) had target differentially expressed genes (DEGs) predicted by the expected miRNA-mRNA negative regulation pattern using the Illumina HiSeq data. Four sets of DEMs and their predicted target DEGs were confirmed by qPCR. Of the four miRNAs, two miRNAs were down-regulated: miR-981, which may target pdpc, and Bdo-novel-mir-55, which potentially regulates spsX1, psB/C, and chit3. The other two miRNAs were up-regulated: let-7a-3p, which possibly controls lap, and Bdo-novel-mir-24, which may regulate ipc and sp1/2. This study provides a useful resource to elucidate the regulatory role of miRNAs and understand the molecular mechanisms of metamorphosis.
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Affiliation(s)
- Qiang Zhang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China.,Academy of Agricultural Sciences, Southwest University, Chongqing, China.,International China-Belgium Joint Laboratory on Sustainable Crop Pest Control Between Southwest University in China and Ghent University in Belgium, Chongqing, China.,Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Wei Dou
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China.,Academy of Agricultural Sciences, Southwest University, Chongqing, China.,International China-Belgium Joint Laboratory on Sustainable Crop Pest Control Between Southwest University in China and Ghent University in Belgium, Chongqing, China.,Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Deng Pan
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China.,Academy of Agricultural Sciences, Southwest University, Chongqing, China.,International China-Belgium Joint Laboratory on Sustainable Crop Pest Control Between Southwest University in China and Ghent University in Belgium, Chongqing, China.,Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Er-Hu Chen
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China.,Academy of Agricultural Sciences, Southwest University, Chongqing, China.,International China-Belgium Joint Laboratory on Sustainable Crop Pest Control Between Southwest University in China and Ghent University in Belgium, Chongqing, China.,Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Jin-Zhi Niu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China.,Academy of Agricultural Sciences, Southwest University, Chongqing, China.,International China-Belgium Joint Laboratory on Sustainable Crop Pest Control Between Southwest University in China and Ghent University in Belgium, Chongqing, China.,Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Guy Smagghe
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China.,Academy of Agricultural Sciences, Southwest University, Chongqing, China.,International China-Belgium Joint Laboratory on Sustainable Crop Pest Control Between Southwest University in China and Ghent University in Belgium, Chongqing, China.,Department of Plants and Crops, Ghent University, Ghent, Belgium
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China.,Academy of Agricultural Sciences, Southwest University, Chongqing, China.,International China-Belgium Joint Laboratory on Sustainable Crop Pest Control Between Southwest University in China and Ghent University in Belgium, Chongqing, China.,Department of Plants and Crops, Ghent University, Ghent, Belgium
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