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Garrett D, Teakle G, Collier R, Bell JR, Cerezo-Medina S, Morales-Hojas R. Genome assembly and transcriptomic analysis to elucidate the ability of Nasonovia ribisnigri to break host plant resistance. INSECT MOLECULAR BIOLOGY 2024; 33:228-245. [PMID: 38348538 DOI: 10.1111/imb.12894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 01/09/2024] [Indexed: 02/27/2024]
Abstract
Aphid genomic resources enable the study of complex life history traits and provide information on vector biology, host adaption and speciation. The currant-lettuce aphid (Nasonovia ribisnigri (Hemiptera: Aphididae) (Mosley)) is a cosmopolitan pest of outdoor lettuce (Lactuca sativa (Asterales: Asteraceae) (Linnaeus)). Until recently, the use of resistant cultivars was an effective method for managing N. ribisnigri. A resistant cultivar containing a single gene (Nr-locus), introduced in the 1980s, conferred complete resistance to feeding. Overreliance of this Nr-locus in lettuce resulted in N. ribisnigri's ability to break resistance mechanism, with first reports during 2003. Our work attempts to understand which candidate gene(s) are associated with this resistance-breaking mechanism. We present two de novo draft assembles for N. ribisnigri genomes, corresponding to both avirulent (Nr-locus susceptible) and virulent (Nr-locus resistant) biotypes. Changes in gene expression of the two N. ribisnigri biotypes were investigated using transcriptomic analyses of RNA-sequencing (RNA-seq) data to understand the potential mechanisms of resistance to the Nr-locus in lettuce. The draft genome assemblies were 94.2% and 91.4% complete for the avirulent and virulent biotypes, respectively. Out of the 18,872 differentially expressed genes, a single gene/locus was identified in N. ribisnigri that was shared between two resistant-breaking biotypes. This locus was further explored and validated in Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) experiments and has predicted localisations in both the cytoplasm and nucleus. This is the first study to provide evidence that a single gene/locus is likely responsible for the ability of N. ribisnigri to overcome the Nr-locus resistance in the lettuce host.
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Affiliation(s)
- Dion Garrett
- Rothamsted Insect Survey, Rothamsted Research, Harpenden, UK
- Warwick Crop Centre, Wellesbourne Campus, University of Warwick, Warwick, UK
| | - Graham Teakle
- Warwick Crop Centre, Wellesbourne Campus, University of Warwick, Warwick, UK
| | - Rosemary Collier
- Warwick Crop Centre, Wellesbourne Campus, University of Warwick, Warwick, UK
| | - James R Bell
- Rothamsted Insect Survey, Rothamsted Research, Harpenden, UK
- Centre for Applied Entomology and Parasitology, School of Life Sciences, Keele University, Keele, UK
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2
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Wang Y, Xu S. A high-quality genome assembly of the waterlily aphid Rhopalosiphum nymphaeae. Sci Data 2024; 11:194. [PMID: 38351256 PMCID: PMC10864314 DOI: 10.1038/s41597-024-03043-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 02/03/2024] [Indexed: 02/16/2024] Open
Abstract
Waterlily aphid, Rhopalosiphum nymphaeae (Linnaeus), is a host-alternating aphid known to feed on both terrestrial and aquatic hosts. It causes damage through direct herbivory and acting as a vector for plant viruses, impacting worldwide Prunus spp. fruits and aquatic plants. Interestingly, R. nymphaeae's ability to thrive in both aquatic and terrestrial conditions sets it apart from other aphids, offering a unique perspective on adaptation. We present the first high-quality R. nymphaeae genome assembly with a size of 324.4 Mb using PacBio long-read sequencing. The resulting assembly is highly contiguous with a contig N50 reached 12.7 Mb. The BUSCO evaluation suggested a 97.5% completeness. The R. nymphaeae genome consists of 16.9% repetitive elements and 16,834 predicted protein-coding genes. Phylogenetic analysis positioned R. nymphaeae within the Aphidini tribe, showing close relations to R. maidis and R. padi. The high-quality reference genome R. nymphaeae provides a unique resource for understanding genome evolution in aphids and paves the foundation for understanding host plant adaptation mechanisms and developing pest control strategies.
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Affiliation(s)
- Yangzi Wang
- Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, 55128, Mainz, Germany
- Institute for Evolution and Biodiversity, University of Münster, 48161, Münster, Germany
| | - Shuqing Xu
- Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, 55128, Mainz, Germany.
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3
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Ahmad A, von Dohlen C, Ren Z. A chromosome-level genome assembly of the Rhus gall aphid Schlechtendalia chinensis provides insight into the endogenization of Parvovirus-like DNA sequences. BMC Genomics 2024; 25:16. [PMID: 38166596 PMCID: PMC10759679 DOI: 10.1186/s12864-023-09916-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024] Open
Abstract
The Rhus gall aphid, Schlechtendalia chinensis, feeds on its primary host plant Rhus chinensis to induce galls, which have economic importance in medicines and the food industry. Rhus gall aphids have a unique life cycle and are economically beneficial but there is huge gap in genomic information about this group of aphids. Schlechtendalia chinensis induces rich-tannin galls on its host plant and is emerging as a model organism for both commercial applications and applied research in the context of gall production by insects. Here, we generated a high-quality chromosome-level assembly for the S. chinensis genome, enabling the comparison between S. chinensis and non-galling aphids. The final genome assembly is 344.59 Mb with 91.71% of the assembled sequences anchored into 13 chromosomes. We predicted 15,013 genes, of which 14,582 (97.13%) coding genes were annotated, and 99% of the predicted genes were anchored to the 13 chromosomes. This assembly reveals the endogenization of parvovirus-related DNA sequences (PRDs) in the S. chinensis genome, which could play a role in environmental adaptations. We demonstrated the characterization and classification of cytochrome P450s in the genome assembly, which are functionally crucial for sap-feeding insects and have roles in detoxification and insecticide resistance. This genome assembly also revealed the whole genome duplication events in S. chinensis, which can be considered in comparative evolutionary analysis. Our work represents a reference genome for gall-forming aphids that could be used for comparative genomic studies between galling and non-galling aphids and provides the first insight into the endogenization of PRDs in the genome of galling aphids. It also provides novel genetic information for future research on gall-formation and insect-plant interactions.
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Affiliation(s)
- Aftab Ahmad
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China
| | - Carol von Dohlen
- Department of Biology, Utah State University, Logan, Utah, United States of America
| | - Zhumei Ren
- School of Life Science, Shanxi University, Taiyuan, Shanxi, China.
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4
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Dial DT, Weglarz KM, Brunet BMT, Havill NP, von Dohlen CD, Burke GR. Whole-genome sequence of the Cooley spruce gall adelgid, Adelges cooleyi (Hemiptera: Sternorrhyncha: Adelgidae). G3 (BETHESDA, MD.) 2023; 14:jkad224. [PMID: 37766465 PMCID: PMC10755206 DOI: 10.1093/g3journal/jkad224] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023]
Abstract
The adelgids (Adelgidae) are a small family of sap-feeding insects, which, together with true aphids (Aphididae) and phylloxerans (Phylloxeridae), make up the infraorder Aphidomorpha. Some adelgid species are highly destructive to forest ecosystems such as Adelges tsugae, Adelges piceae, Adelges laricis, Pineus pini, and Pineus boerneri. Despite this, there are no high-quality genomic resources for adelgids, hindering advanced genomic analyses within Adelgidae and among Aphidomorpha. Here, we used PacBio continuous long-read and Illumina RNA-sequencing to construct a high-quality draft genome assembly for the Cooley spruce gall adelgid, Adelges cooleyi (Gillette), a gall-forming species endemic to North America. The assembled genome is 270.2 Mb in total size and has scaffold and contig N50 statistics of 14.87 and 7.18 Mb, respectively. There are 24,967 predicted coding sequences, and the assembly completeness is estimated at 98.1 and 99.6% with core BUSCO gene sets of Arthropoda and Hemiptera, respectively. Phylogenomic analysis using the A. cooleyi genome, 3 publicly available adelgid transcriptomes, 4 phylloxera transcriptomes, the Daktulosphaira vitifoliae (grape phylloxera) genome, 4 aphid genomes, and 2 outgroup coccoid genomes fully resolves adelgids and phylloxerans as sister taxa. The mitochondrial genome is 24 kb, among the largest in insects sampled to date, with 39.4% composed of noncoding regions. This genome assembly is currently the only genome-scale, annotated assembly for adelgids and will be a valuable resource for understanding the ecology and evolution of Aphidomorpha.
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Affiliation(s)
- Dustin T Dial
- Department of Entomology, University of Georgia, Athens, GA 30602, USA
| | | | - Bryan M T Brunet
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada K1A 0C6
| | - Nathan P Havill
- USDA Forest Service, Northern Research Station, Hamden, CT 06514, USA
| | | | - Gaelen R Burke
- Department of Entomology, University of Georgia, Athens, GA 30602, USA
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Mathers TC, Wouters RHM, Mugford ST, Biello R, van Oosterhout C, Hogenhout SA. Hybridisation has shaped a recent radiation of grass-feeding aphids. BMC Biol 2023; 21:157. [PMID: 37443008 PMCID: PMC10347838 DOI: 10.1186/s12915-023-01649-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 06/13/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Aphids are common crop pests. These insects reproduce by facultative parthenogenesis involving several rounds of clonal reproduction interspersed with an occasional sexual cycle. Furthermore, clonal aphids give birth to live young that are already pregnant. These qualities enable rapid population growth and have facilitated the colonisation of crops globally. In several cases, so-called "super clones" have come to dominate agricultural systems. However, the extent to which the sexual stage of the aphid life cycle has shaped global pest populations has remained unclear, as have the origins of successful lineages. Here, we used chromosome-scale genome assemblies to disentangle the evolution of two global pests of cereals-the English (Sitobion avenae) and Indian (Sitobion miscanthi) grain aphids. RESULTS Genome-wide divergence between S. avenae and S. miscanthi is low. Moreover, comparison of haplotype-resolved assemblies revealed that the S. miscanthi isolate used for genome sequencing is likely a hybrid, with one of its diploid genome copies closely related to S. avenae (~ 0.5% divergence) and the other substantially more divergent (> 1%). Population genomics analyses of UK and China grain aphids showed that S. avenae and S. miscanthi are part of a cryptic species complex with many highly differentiated lineages that predate the origins of agriculture. The complex consists of hybrid lineages that display a tangled history of hybridisation and genetic introgression. CONCLUSIONS Our analyses reveal that hybridisation has substantially contributed to grain aphid diversity, and hence, to the evolutionary potential of this important pest species. Furthermore, we propose that aphids are particularly well placed to exploit hybridisation events via the rapid propagation of live-born "frozen hybrids" via asexual reproduction, increasing the likelihood of hybrid lineage formation.
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Affiliation(s)
- Thomas C Mathers
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK.
- Tree of Life, Welcome Sanger Institute, Hinxton, Cambridge, UK.
| | - Roland H M Wouters
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Sam T Mugford
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Roberto Biello
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Saskia A Hogenhout
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK.
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6
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Huang T, Liu Y, He K, Francis F, Wang B, Wang G. Chromosome-level genome assembly of the spotted alfalfa aphid Therioaphis trifolii. Sci Data 2023; 10:274. [PMID: 37173339 PMCID: PMC10181989 DOI: 10.1038/s41597-023-02179-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023] Open
Abstract
The spotted alfalfa aphid (SAA, Therioaphis trifolii) (Hemiptera: Aphididae) is a destructive pest of cultivated alfalfa (Medicago sativa L.) that leads to large financial losses in the livestock industry around the world. Here, we present a chromosome-scale genome assembly of T. trifolii, the first genome assembly for the aphid subfamily Calaphidinae. Using PacBio long-read sequencing, Illumina sequencing, and Hi-C scaffolding techniques, a 541.26 Mb genome was generated, with 90.01% of the assembly anchored into eight scaffolds, and the contig and scaffold N50 are 2.54 Mb and 44.77 Mb, respectively. BUSCO assessment showed a completeness score of 96.6%. A total of 13,684 protein-coding genes were predicted. The high-quality genome assembly of T. trifolii not only provides a genomic resource for the more complete analysis of aphid evolution, but also provides insights into the ecological adaptation and insecticide resistance of T. trifolii.
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Affiliation(s)
- Tianyu Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Guangdong Laboratory of Lingnan Modern Agriculture, Shenzhen; Genome Analysis Laboratory of the Ministry of Agriculture; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- Functional and Evolutionary Entomology, Gembloux Agro-Bio Tech, University of Liège, Gembloux, 5030, Belgium
| | - Yang Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Kang He
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Frédéric Francis
- Functional and Evolutionary Entomology, Gembloux Agro-Bio Tech, University of Liège, Gembloux, 5030, Belgium
| | - Bing Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Guirong Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
- Guangdong Laboratory of Lingnan Modern Agriculture, Shenzhen; Genome Analysis Laboratory of the Ministry of Agriculture; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
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7
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Jing K, Li M, Zhao H, Guo J, Yang N, Yang M, Xian X, Liu W. Estimating the Global Geographical Distribution Patterns of the Invasive Crop Pest Diuraphis noxia Kurdjumov under Current and Future Climatic Scenarios. INSECTS 2023; 14:insects14050425. [PMID: 37233053 DOI: 10.3390/insects14050425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/27/2023]
Abstract
Invasive crop pests (ICPs) are a major cause of crop losses and adversely affect global food security. Diuraphis noxia Kurdjumov is a significant ICP that feeds on the sap of crops, reducing crop yield and quality. Although estimating the geographical distribution patterns of D. noxia under climate change is critical for its management and global food security, such information remains unclear. Based on 533 global occurrence records and 9 bioclimatic variables, an optimized MaxEnt model was used to predict the potential global geographical distribution of D. noxia. The results showed that Bio1, Bio2, Bio7, and Bio12 were significant bioclimatic variables that influenced the potential geographical distribution of D. noxia. Under current climatic conditions, D. noxia was mainly distributed in west-central Asia, most of Europe, central North America, southern South America, southern and northern Africa, and southern Oceania. Under the SSP 1-2.6, SSP 2-4.5, and SSP 5-8.5 scenarios for the 2030s and 2050s, the potential suitable areas increased, and the centroid migrated to higher latitudes. The early warning of D. noxia in northwestern Asia, western Europe, and North America should be attended to further. Our results provide a theoretical basis for early monitoring and warning of D. noxia worldwide.
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Affiliation(s)
- Kaiting Jing
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ming Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Haoxiang Zhao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jianyang Guo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Nianwan Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Ming Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaoqing Xian
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wanxue Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Sun Z, Chen Y, Chen Y, Lu Z, Gui F. Tracking Adaptive Pathways of Invasive Insects: Novel Insight from Genomics. Int J Mol Sci 2023; 24:ijms24098004. [PMID: 37175710 PMCID: PMC10179030 DOI: 10.3390/ijms24098004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
Despite the huge human and economic costs of invasive insects, which are the main group of invasive species, their environmental impacts through various mechanisms remain inadequately explained in databases and much of the invasion biology literature. High-throughput sequencing technology, especially whole-genome sequencing, has been used as a powerful method to study the mechanisms through which insects achieve invasion. In this study, we reviewed whole-genome sequencing-based advances in revealing several important invasion mechanisms of invasive insects, including (1) the rapid genetic variation and evolution of invasive populations, (2) invasion history and dispersal paths, (3) rapid adaptation to different host plant ranges, (4) strong environmental adaptation, (5) the development of insecticide resistance, and (6) the synergistic damage caused by invasive insects and endosymbiotic bacteria. We also discussed prevention and control technologies based on whole-genome sequencing and their prospects.
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Affiliation(s)
- Zhongxiang Sun
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China
| | - Yao Chen
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China
| | - Yaping Chen
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China
| | - Zhihui Lu
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China
| | - Furong Gui
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China
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9
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Mobilome of the Rhus Gall Aphid Schlechtendalia chinensis Provides Insight into TE Insertion-Related Inactivation of Functional Genes. Int J Mol Sci 2022; 23:ijms232415967. [PMID: 36555609 PMCID: PMC9783078 DOI: 10.3390/ijms232415967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Transposable elements (TEs) comprise a considerable proportion of insect genomic DNA; how they contribute to genome structure and organization is still poorly understood. Here, we present an analysis of the TE repertoire in the chromosome-level genome assembly of Rhus gall aphid Schlechtendalia chinensis. The TE fractions are composed of at least 32 different superfamilies and many TEs from different families were transcriptionally active in the S. chinensis genome. Furthermore, different types of transposase-derived proteins were also found in the S. chinensis genome. We also provide insight into the TEs related insertional inactivation, and exogenization of TEs in functional genes. We considered that the presence of TE fragments in the introns of functional genes could impact the activity of functional genes, and a large number of TE fragments in introns could lead to the indirect inactivation of functional genes. The present study will be beneficial in understanding the role and impact of TEs in genomic evolution of their hosts.
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Xiao KR, Wu CY, Yang L, Wang J, Song QS, Stanley D, Wei SJ, Zhu JY. Comparative genomic analysis of ABC transporter genes in Tenebrio molitor and four other tenebrionid beetles (Coleoptera: Tenebrionidea). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2022; 111:e21916. [PMID: 35584005 DOI: 10.1002/arch.21916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
ATP-binding cassette (ABC) transporters, one of the largest transmembrane protein families, transport a diverse number of substate across membranes. Details of their diverse physiological functions have not been established. Here, we identified 87 ABC transporter genes in the genomes of Tenebrio molitor along with those from Asbolus verrucosus (104), Hycleus cichorii (65), and Hycleus phaleratus (80). Combining these genes (336 in total) with genes reported in Tribolium castaneum (73), we analyzed the phylogeny of ABC transporter genes in all five Tenebrionids. They are assigned into eight subfamilies (ABCA-H). In comparison to other species, the ABCC subfamily in this group of beetles appears expanded. The expression profiles of the T. molitor genes at different life stages and in various tissues were also investigated using transcriptomic analysis. Most of them display developmental specific expression patterns, suggesting to us their possible roles in development. Most of them are highly expressed in detoxification-related tissues including gut and Malpighian tubule, from which we infer their roles in insecticide resistance. We detected specific or abundant expressions of many ABC transporter genes in various tissues such as salivary gland, ovary, testis, and antenna. This new information helps generate new hypotheses on their biological significance within tissues.
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Affiliation(s)
- Kai-Ran Xiao
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Chao-Yan Wu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Lin Yang
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Jun Wang
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Qi-Sheng Song
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri, USA
| | - David Stanley
- USDA/ARS Biological Control of Insects Research Laboratory, Columbia, Missouri, USA
| | - Shu-Jun Wei
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jia-Ying Zhu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
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11
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Wang YX, Chen HF, Yin ZY, Chen WL, Lu LT. The genetic adaptations of Toxoptera aurantii facilitated its rapid multiple plant hosts dispersal and invasion. Genomics 2022; 114:110472. [PMID: 36055573 DOI: 10.1016/j.ygeno.2022.110472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/24/2022] [Accepted: 08/27/2022] [Indexed: 01/14/2023]
Abstract
Toxoptera aurantii Boyer de Fonscolombe (Hemiptera: Aphididae) can attack many plant hosts, including tea (Camellia sinensis L.), citrus (Citrus spp.), lychee (Litchi chinensis Sonn.), banana (Musa spp.), and pineapple (Ananas comasus L.) among others. It is a widely distributed hexapod and one of the most destructive pests in tea plantations, causing enormous economic losses in tea production each year. A high-quality reference genome is important to study the phylogenetics and evolution of T. aurantii because its genome is highly heterozygous and repetitive. We obtained a de novo genome assembly of T. aurantii at the chromosome level using a combination of long Nanopore reads from sequencing with high-throughput chromosome conformation capture technology. When finally assembled, the genome was 318.95 Mb on four chromosomes with a 15.19 Mb scaffold N50. A total of 12,162 genes encoded proteins, while there were 22.01% repetitive sequences that totaled 67.73 Mb. Phylogenetic analyses revealed that T. aurantii and Aphis gossypii parted ways approximately 7.6 million years ago (Mya). We used a combination of long-read single-molecule sequencing with Hi-C-based chromatin interaction maps that resulted in a reference chromosomal level reference genome of T. aurantii that was high quality. Our results will enable the exploration of the genetics behind the special biological features of T. aurantii and also provide a source of data that should be useful to compare the compare genome among the Hemiptera.
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Affiliation(s)
- Yan-Xia Wang
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang 550025, China; College of Tea Science, Guizhou University, Guiyang 550025, China
| | - Hu-Fang Chen
- College of Tea Science, Guizhou University, Guiyang 550025, China
| | - Zheng-Yan Yin
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang 550025, China
| | - Wen-Long Chen
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang 550025, China.
| | - Li-Tang Lu
- College of Tea Science, Guizhou University, Guiyang 550025, China.
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12
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Zhao Q, Shi L, He W, Li J, You S, Chen S, Lin J, Wang Y, Zhang L, Yang G, Vasseur L, You M. Genomic Variation in the Tea Leafhopper Reveals the Basis of Adaptive Evolution. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:1092-1105. [PMID: 36041663 DOI: 10.1016/j.gpb.2022.05.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 04/27/2022] [Accepted: 05/12/2022] [Indexed: 11/21/2022]
Abstract
Tea green leafhopper (TGL), Empoasca onukii, is of biological and economic interest. Despite numerous studies, the mechanisms underlying its adaptation and evolution remain enigmatic. Here, we use previously untapped genome and population genetics approaches to examine how the pest adapted to different environmental variables and thus has expanded geographically. We complete a chromosome-level assembly and annotation of the E. onukii genome, showing notable expansions of gene families associated with adaptation to chemoreception and detoxification. Genomic signals indicating balancing selection highlight metabolic pathways involved in adaptation to a wide range of tea varieties grown across ecologically diverse regions. Patterns of genetic variations among 54 E. onukii samples unveil the population structure and evolutionary history across different tea-growing regions in China. Our results demonstrate that the genomic changes in key pathways, including those linked to metabolism, circadian rhythms, and immune system functions, may underlie the successful spread and adaptation of E. onukii. This work highlights the genetic and molecular bases underlying the evolutionary success of a species with broad economic impacts, and provides insights into insect adaptation to host plants, which will ultimately facilitate more sustainable pest management.
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Affiliation(s)
- Qian Zhao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Longqing Shi
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Institute of Rice, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China
| | - Weiyi He
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jinyu Li
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Tea Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350001, China
| | - Shijun You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shuai Chen
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jing Lin
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yibin Wang
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liwen Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Guang Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liette Vasseur
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada
| | - Minsheng You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Dalaisón-Fuentes LI, Pascual A, Gazza E, Welchen E, Rivera-Pomar R, Catalano MI. Development of efficient RNAi methods in the corn leafhopper Dalbulus maidis, a promising application for pest control. PEST MANAGEMENT SCIENCE 2022; 78:3108-3116. [PMID: 35442515 DOI: 10.1002/ps.6937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 04/13/2022] [Accepted: 04/20/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The corn leafhopper Dalbulus maidis is the main vector of important stunting pathogens that affect maize production. Currently, there are no effective methods available to manage this pest without adverse impact on the environment. In this context, genomic-based technologies such as RNA interference (RNAi) provide a more environmentally friendly pest control strategy. Therefore, we aimed to assess the application of RNAi in D. maidis and determine the function of a candidate gene related to insect reproduction and propagation. RESULTS We have characterized the core RNAi genes and evaluated the functionality of the RNAi machinery. We assessed the potential of RNAi technology in D. maidis via injection or ingestion of double-stranded RNA (dsRNA) to adult females. We chose Bicaudal C (BicC) as a target gene due to its important role during insect oogenesis. Administration of dsRNABicC caused significant reductions in the transcript levels (fold changes up to 170 times) and ovipositions. Phenotypic analysis of the ovaries revealed alterations in oocyte development, providing additional confirmation for our results and supporting the idea that Dmai-BicC is a key player of D. maidis oogenesis. CONCLUSION This is, to our knowledge, the first report of efficient RNAi in D. maidis. We believe our findings provide a starting point for future control strategies against one of the most important maize pests in the Americas. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Lucía Inés Dalaisón-Fuentes
- Centro de BioInvestigaciones (Universidad Nacional del Noroeste de la Provincia de Buenos Aires-CICBA), Pergamino, Argentina
- Centro de Investigaciones y Transferencias del Noroeste de la provincia de Buenos Aires (CITNOBA-CONICET), Pergamino, Argentina
| | - Agustina Pascual
- Centro de BioInvestigaciones (Universidad Nacional del Noroeste de la Provincia de Buenos Aires-CICBA), Pergamino, Argentina
- Centro de Investigaciones y Transferencias del Noroeste de la provincia de Buenos Aires (CITNOBA-CONICET), Pergamino, Argentina
| | - Elías Gazza
- Centro de BioInvestigaciones (Universidad Nacional del Noroeste de la Provincia de Buenos Aires-CICBA), Pergamino, Argentina
- Centro de Investigaciones y Transferencias del Noroeste de la provincia de Buenos Aires (CITNOBA-CONICET), Pergamino, Argentina
| | - Elina Welchen
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Rolando Rivera-Pomar
- Centro de BioInvestigaciones (Universidad Nacional del Noroeste de la Provincia de Buenos Aires-CICBA), Pergamino, Argentina
- Centro de Investigaciones y Transferencias del Noroeste de la provincia de Buenos Aires (CITNOBA-CONICET), Pergamino, Argentina
- Centro Regional de Estudios Genómicos (Facultad de Ciencias Exactas, Universidad Nacional de La Plata), La Plata, Argentina
| | - María Inés Catalano
- Centro de BioInvestigaciones (Universidad Nacional del Noroeste de la Provincia de Buenos Aires-CICBA), Pergamino, Argentina
- Centro de Investigaciones y Transferencias del Noroeste de la provincia de Buenos Aires (CITNOBA-CONICET), Pergamino, Argentina
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Wei H, Ye Y, Huang H, Chen M, Yang Z, Chen X, Zhang C. Chromosome‐level genome assembly for the horned‐gall aphid provides insights into interactions between gall‐making insect and its host plant. Ecol Evol 2022; 12:e8815. [PMID: 35475184 PMCID: PMC9021935 DOI: 10.1002/ece3.8815] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 11/16/2022] Open
Abstract
The aphid Schlechtendalia chinensis is an economically important insect that can induce horned galls, which are valuable for the medicinal and chemical industries. Up to now, more than twenty aphid genomes have been reported. Most of the sequenced genomes are derived from free‐living aphids. Here, we generated a high‐quality genome assembly from a galling aphid. The final genome assembly is 271.52 Mb, representing one of the smallest sequenced genomes of aphids. The genome assembly is based on contig and scaffold N50 values of the genome sequence are 3.77 Mb and 20.41 Mb, respectively. Nine‐seven percent of the assembled sequences was anchored onto 13 chromosomes. Based on BUSCO analysis, the assembly involved 96.9% of conserved arthropod and 98.5% of the conserved Hemiptera single‐copy orthologous genes. A total of 14,089 protein‐coding genes were predicted. Phylogenetic analysis revealed that S. chinensis diverged from the common ancestor of Eriosoma lanigerum approximately 57 million years ago (MYA). In addition, 35 genes encoding salivary gland proteins showed differentially when S. chinensis forms a gall, suggesting they have potential roles in gall formation and plant defense suppression. Taken together, this high‐quality S. chinensis genome assembly and annotation provide a solid genetic foundation for future research to reveal the mechanism of gall formation and to explore the interaction between aphids and their host plants.
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Affiliation(s)
- Hong‐Yuan Wei
- Key Laboratory of Breeding and Utilization of Resource Insects National Forestry and Grassland Administration Institute of Highland Forest Science Chinese Academy of Forestry Kunming China
| | - Yu‐Xuan Ye
- Institute of Insect Sciences Zhejiang University Hangzhou China
| | - Hai‐Jian Huang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province Institute of Plant Virology Ningbo University Ningbo China
| | - Ming‐Shun Chen
- Department of Entomology Kansas State University Manhattan Kansas USA
| | - Zi‐Xiang Yang
- Key Laboratory of Breeding and Utilization of Resource Insects National Forestry and Grassland Administration Institute of Highland Forest Science Chinese Academy of Forestry Kunming China
| | - Xiao‐Ming Chen
- Key Laboratory of Breeding and Utilization of Resource Insects National Forestry and Grassland Administration Institute of Highland Forest Science Chinese Academy of Forestry Kunming China
| | - Chuan‐Xi Zhang
- Institute of Insect Sciences Zhejiang University Hangzhou China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro‐products Key Laboratory of Biotechnology in Plant Protection of MOA of China and Zhejiang Province Institute of Plant Virology Ningbo University Ningbo China
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Lin R, Yang M, Yao B. The phylogenetic and evolutionary analyses of detoxification gene families in Aphidinae species. PLoS One 2022; 17:e0263462. [PMID: 35143545 PMCID: PMC8830634 DOI: 10.1371/journal.pone.0263462] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 01/19/2022] [Indexed: 11/18/2022] Open
Abstract
Detoxification enzymes play significant roles in the interactions between insects and host plants, wherein detoxification-related genes make great contributions. As herbivorous pests, aphids reproduce rapidly due to parthenogenesis. They are good biological materials for studying the mechanisms that allow insect adaptation to host plants. Insect detoxification gene families are associated with insect adaptation to host plants. The Aphidinae is the largest subfamily in the Aphididae with at least 2483 species in 256 genera in 2 tribes: the Macrosiphini (with 3/4 of the species) and the Aphidini. Most aphid pests on crops and ornamental plants are Aphidinae. Members of the Aphidinae occur in nearly every region of the world. The body shape and colour vary significantly. To research the role that detoxification gene families played in the process of aphid adaptation to host evolution, we analyzed the phylogeny and evolution of these detoxification gene families in Aphidinae. In general, the P450/GST/CCE gene families contract, whereas the ABC/UGT families are conserved in Aphidinae species compared to these families in other herbivorous insects. Genus-specific expansions of P450 CYP4, and GST Delta have occurred in the genus Acyrthosiphon. In addition, the evolutionary rates of five detoxification gene families in the evolution process of Aphidinae are different. The comparison of five detoxification gene families among nine Aphidinae species and the estimated relative evolutionary rates provided herein support an understanding of the interaction between and the co-evolution of Aphidinae and plants.
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Affiliation(s)
- Rongmei Lin
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
- CAS Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- * E-mail: (RL); (BY)
| | - Mengquan Yang
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Bowen Yao
- School of Science, Beijing University of Chemical Technology, Chaoyang District, Beijing, China
- * E-mail: (RL); (BY)
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Bailey E, Field L, Rawlings C, King R, Mohareb F, Pak KH, Hughes D, Williamson M, Ganko E, Buer B, Nauen R. A scaffold-level genome assembly of a minute pirate bug, Orius laevigatus (Hemiptera: Anthocoridae), and a comparative analysis of insecticide resistance-related gene families with hemipteran crop pests. BMC Genomics 2022; 23:45. [PMID: 35012450 PMCID: PMC8751118 DOI: 10.1186/s12864-021-08249-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Orius laevigatus, a minute pirate bug, is a highly effective beneficial predator of crop pests including aphids, spider mites and thrips in integrated pest management (IPM) programmes. No genomic information is currently available for O. laevigatus, as is the case for the majority of beneficial predators which feed on crop pests. In contrast, genomic information for crop pests is far more readily available. The lack of publicly available genomes for beneficial predators to date has limited our ability to perform comparative analyses of genes encoding potential insecticide resistance mechanisms between crop pests and their predators. These mechanisms include several gene/protein families including cytochrome P450s (P450s), ATP binding cassette transporters (ABCs), glutathione S-transferases (GSTs), UDP-glucosyltransferases (UGTs) and carboxyl/cholinesterases (CCEs). METHODS AND FINDINGS In this study, a high-quality scaffold level de novo genome assembly for O. laevigatus has been generated using a hybrid approach with PacBio long-read and Illumina short-read data. The final assembly achieved a scaffold N50 of 125,649 bp and a total genome size of 150.98 Mb. The genome assembly achieved a level of completeness of 93.6% using a set of 1658 core insect genes present as full-length genes. Genome annotation identified 15,102 protein-coding genes - 87% of which were assigned a putative function. Comparative analyses revealed gene expansions of sigma class GSTs and CYP3 P450s. Conversely the UGT gene family showed limited expansion. Differences were seen in the distributions of resistance-associated gene families at the subfamily level between O. laevigatus and some of its targeted crop pests. A target site mutation in ryanodine receptors (I4790M, PxRyR) which has strong links to diamide resistance in crop pests and had previously only been identified in lepidopteran species was found to also be present in hemipteran species, including O. laevigatus. CONCLUSION AND SIGNIFICANCE This assembly is the first published genome for the Anthocoridae family and will serve as a useful resource for further research into target-site selectivity issues and potential resistance mechanisms in beneficial predators. Furthermore, the expansion of gene families often linked to insecticide resistance may be an indicator of the capacity of this predator to detoxify selective insecticides. These findings could be exploited by targeted pesticide screens and functional studies to increase effectiveness of IPM strategies, which aim to increase crop yields by sustainably, environmentally-friendly and effectively control pests without impacting beneficial predator populations.
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Affiliation(s)
- Emma Bailey
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK.
- Department of Computational and Analytical Sciences, Rothamsted Research, Harpenden, UK.
- The Bioinformatics Group, Cranfield Soil and Agrifood Institute, Cranfield University, Cranfield, UK.
| | - Linda Field
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Christopher Rawlings
- Department of Computational and Analytical Sciences, Rothamsted Research, Harpenden, UK
| | - Rob King
- Department of Computational and Analytical Sciences, Rothamsted Research, Harpenden, UK
| | - Fady Mohareb
- The Bioinformatics Group, Cranfield Soil and Agrifood Institute, Cranfield University, Cranfield, UK
| | - Keywan-Hassani Pak
- Department of Computational and Analytical Sciences, Rothamsted Research, Harpenden, UK
| | - David Hughes
- Department of Computational and Analytical Sciences, Rothamsted Research, Harpenden, UK
| | - Martin Williamson
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Eric Ganko
- Syngenta Biotechnology Inc, Research Triangle Park, NC, USA
| | - Benjamin Buer
- Bayer AG, Crop Science Division, R&D, Monheim, Germany
| | - Ralf Nauen
- Bayer AG, Crop Science Division, R&D, Monheim, Germany
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Chertemps T, Le Goff G, Maïbèche M, Hilliou F. Detoxification gene families in Phylloxera: Endogenous functions and roles in response to the environment. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2021; 40:100867. [PMID: 34246923 DOI: 10.1016/j.cbd.2021.100867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 06/08/2021] [Accepted: 06/08/2021] [Indexed: 10/21/2022]
Abstract
Phylloxera, Daktulosphaira vitifoliae, is an agronomic pest that feeds monophagously on grapevine, Vitis spp. host plants. Phylloxera manipulates primary and secondary plant metabolism to establish either leaf or root galls. We manually annotated 198 detoxification genes potentially involved in plant host manipulation, including cytochrome P450 (66 CYPs), carboxylesterase (20 CCEs), glutathione-S-transferase (10 GSTs), uridine diphosphate-glycosyltransferase (35 UGTs) and ABC transporter (67 ABCs) families. Transcriptomic expression patterns of these detoxification genes were analyzed for root and leaf galls. In addition to these transcriptomic analyses, we reanalyzed recent data from L1 and L2-3 stages feeding on tolerant and resistant rootstock. Data from two agricultural pest aphids, the generalist Myzus persicae and the Fabaceae specialist Acyrthosiphon pisum, and from the true bug vector of Chagas disease, Rhodnius prolixus, were used to perform phylogenetic analyses for each detoxification gene family. We found expansions of several gene sub-families in the genome of D. vitifoliae. Phylogenetically close genes were found to be organized in clusters in the same genomic position and orientation suggesting recent successive duplications. These results highlight the roles of the phylloxera detoxification gene repertoire in insect physiology and in adaptation to plant secondary metabolites, and provide gene candidates for further functional analyses.
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Affiliation(s)
- Thomas Chertemps
- Sorbonne Université, UPEC, Université Paris 7, INRAE, CNRS, IRD, Institute of Ecology and Environmental Sciences, Paris, France
| | - Gaëlle Le Goff
- Université Côte d'Azur, INRAE, CNRS, ISA, 400 Route des Chappes, 06903 Sophia Antipolis, France
| | - Martine Maïbèche
- Sorbonne Université, UPEC, Université Paris 7, INRAE, CNRS, IRD, Institute of Ecology and Environmental Sciences, Paris, France
| | - Frédérique Hilliou
- Université Côte d'Azur, INRAE, CNRS, ISA, 400 Route des Chappes, 06903 Sophia Antipolis, France.
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Zhang S, Gao X, Wang L, Jiang W, Su H, Jing T, Cui J, Zhang L, Yang Y. Chromosome-level genome assemblies of two cotton-melon aphid Aphis gossypii biotypes unveil mechanisms of host adaption. Mol Ecol Resour 2021; 22:1120-1134. [PMID: 34601821 DOI: 10.1111/1755-0998.13521] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 11/30/2022]
Abstract
The cotton-melon aphid Aphis gossypii is a sap-sucking insect that is considered a serious global pest. The species is distributed over a large geographical range and uses a wide variety of hosts, with some populations being specialized to attack different plant species. Here, we provide de novo chromosome-level genome assemblies of a cotton specialist population (Hap1) and a cucurbit specialist population (Hap3). We achieved this by using a combination of third-generation sequencing platforms, namely Illumina and Hi-C sequencing technologies. We were able to anchor a total of 334.89 Mb (scaffold N50 of 89.13 Mb) and 359.95 Mb (scaffold N50 of 68.88 Mb) to four chromosomes for Hap1 and Hap3, respectively. Moreover, our results showed that the X-chromosome of Hap3 (113.01 Mb) was significantly longer than that of Hap1 (100.26 Mb), with a high level of sequence conservation between the aphid species. We also report variation in the number of protein-coding genes and repeat sequences between Hap1 and Hap3. In particular, olfactory and gustatory receptor genes underwent a high level of gene duplication and expansion events in A. gossypii, including between Hap1 and Hap3. Moreover, we identified two glutathione S-transferase genes which underwent single gene duplications in Hap3, and tandem duplication and inversion events affecting the cytochrome P450 monooxygenase between Hap1 and Hap3, all of which include the CYP3 family. Our results illustrate the variance in the genomic composition of two specialized A. gossypii populations and provide a helpful resource for the study of aphid population evolution, host adaption and insecticide resistance.
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Affiliation(s)
- Shuai Zhang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Xueke Gao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Li Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Weili Jiang
- Basic Experimental Teaching Center of Life Sciences, Yangzhou University, Yangzhou, China
| | - Honghua Su
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Tianxing Jing
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Jinjie Cui
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Lijuan Zhang
- Department of Entomology, College of Plant Protection, Henan Agricultural University, Zhengzhou, China
| | - Yizhong Yang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
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Kattupalli D, Barbadikar KM, Balija V, Ballichatla S, R A, Padmakumari AP, Saxena S, Gaikwad K, Yerram S, Kokku P, Madhav MS. The Draft Genome of Yellow Stem Borer, an Agriculturally Important Pest, Provides Molecular Insights into Its Biology, Development and Specificity Towards Rice for Infestation. INSECTS 2021; 12:insects12060563. [PMID: 34205299 PMCID: PMC8234988 DOI: 10.3390/insects12060563] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/20/2021] [Accepted: 05/23/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary Yellow stem borer (YSB), is the most destructive and widely occurring pest that attacks rice throughout the growing season. Rice (Oryza sativa L.) is a major staple cereal worldwide, providing essential caloric requirements for more than half of the world’s population. Annual losses to rice borers are approximately 5–10%, but losses in individual fields may reach up to 50–60%. The use of traditional pest management strategies in controlling YSB is somewhat challenging due to its unique internal feeding habit. Genome sequence information of economically important crop pests is important for designing or developing pest-resistant rice varieties. In an approach to achieve this, we present our first-ever study on the draft genome sequence of YSB. The information provided from our current study might be useful in developing genome-based approaches for the management of pest species. Abstract Yellow stem borer (YSB), Scirpophaga incertulas (Walker) (Lepidoptera: Crambidae), a major monophagous insect pest of rice, causes significant yield losses. The rice–YSB interaction is very dynamic, making it difficult for management. The development of resistant lines has been unsuccessful as there are no effective resistant sources in the germplasm. Genome information is necessary for a better understanding of interaction with rice in terms of its recognition, response, and infestation mechanism. The draft genome of YSB is predicted to have 46,057 genes with an estimated size of 308 Mb, being correlated with the flow cytometry analysis. The existence of complex metabolic mechanisms and genes related to specific behavior was identified, being conditioned by a higher level of regulation. We deciphered the possible visual, olfactory, and gustatory mechanisms responsible for its evolution as a monophagous pest. Comparative genomic analysis revealed that YSB is unique in the way it has evolved. The obvious presence of high-immunity-related genes, well-developed RNAi machinery, and diverse effectors provides a means for developing genomic tools for its management. The identified 21,696 SSR markers can be utilized for diversity analysis of populations across the rice-growing regions. We present the first draft genome of YSB. The information emanated paves a way for biologists to design novel pest management strategies as well as for the industry to design new classes of safer and specific insecticide molecules.
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Affiliation(s)
- Divya Kattupalli
- Biotechnology Section, Division of Crop Improvement, ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (D.K.); (K.M.B.); (V.B.); (S.B.)
| | - Kalyani M. Barbadikar
- Biotechnology Section, Division of Crop Improvement, ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (D.K.); (K.M.B.); (V.B.); (S.B.)
| | - Vishalakshi Balija
- Biotechnology Section, Division of Crop Improvement, ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (D.K.); (K.M.B.); (V.B.); (S.B.)
| | - Suneel Ballichatla
- Biotechnology Section, Division of Crop Improvement, ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (D.K.); (K.M.B.); (V.B.); (S.B.)
| | - Athulya R
- Entomology Section, Division of Crop Protection, ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (A.R.); (A.P.P.); (S.Y.)
| | - Ayyagari Phani Padmakumari
- Entomology Section, Division of Crop Protection, ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (A.R.); (A.P.P.); (S.Y.)
| | - Swati Saxena
- Genomics Lab, ICAR-National Institute of Plant Biotechnology, New Delhi 110012, India; (S.S.); (K.G.)
| | - Kishor Gaikwad
- Genomics Lab, ICAR-National Institute of Plant Biotechnology, New Delhi 110012, India; (S.S.); (K.G.)
| | - Sridhar Yerram
- Entomology Section, Division of Crop Protection, ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (A.R.); (A.P.P.); (S.Y.)
| | - Premalatha Kokku
- Department of Chemistry, Osmania University, Hyderabad 500007, India;
| | - Maganti Sheshu Madhav
- Biotechnology Section, Division of Crop Improvement, ICAR-Indian Institute of Rice Research, Hyderabad 500030, India; (D.K.); (K.M.B.); (V.B.); (S.B.)
- Correspondence:
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Botha AM. Fast developing Russian wheat aphid biotypes remains an unsolved enigma. CURRENT OPINION IN INSECT SCIENCE 2021; 45:42-52. [PMID: 33359167 DOI: 10.1016/j.cois.2020.12.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/05/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
Diuraphis noxia, commonly known as the Russian wheat aphid, is an economically important cereal pest species, highly invasive and reproduces mostly asexually. Remarkably, many new virulent populations continue to develop, despite the lack of genetic diversity in the aphid. Russian wheat aphid is a phloem feeder and is therefore engaged in a continuous arms battle with its cereal host, with the acquisition of virulence central to the breakdown of host resistance. In the review, most attention is given to recent topics about mechanisms and strategies whereby the aphid acquires virulence against its host, with special reference given to the role of noncoding RNA elements, bacteria, and the epigenetic pathway in possibly directing virulence.
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Affiliation(s)
- Anna-Maria Botha
- Genetics Department, Stellenbosch University, Private Bag X1, Matieland, Stellenbosch 7601, South Africa.
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21
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Mathers TC, Wouters RHM, Mugford ST, Swarbreck D, van Oosterhout C, Hogenhout SA. Chromosome-Scale Genome Assemblies of Aphids Reveal Extensively Rearranged Autosomes and Long-Term Conservation of the X Chromosome. Mol Biol Evol 2021; 38:856-875. [PMID: 32966576 PMCID: PMC7947777 DOI: 10.1093/molbev/msaa246] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Chromosome rearrangements are arguably the most dramatic type of mutations, often leading to rapid evolution and speciation. However, chromosome dynamics have only been studied at the sequence level in a small number of model systems. In insects, Diptera and Lepidoptera have conserved genome structure at the scale of whole chromosomes or chromosome arms. Whether this reflects the diversity of insect genome evolution is questionable given that many species exhibit rapid karyotype evolution. Here, we investigate chromosome evolution in aphids-an important group of hemipteran plant pests-using newly generated chromosome-scale genome assemblies of the green peach aphid (Myzus persicae) and the pea aphid (Acyrthosiphon pisum), and a previously published assembly of the corn-leaf aphid (Rhopalosiphum maidis). We find that aphid autosomes have undergone dramatic reorganization over the last 30 My, to the extent that chromosome homology cannot be determined between aphids from the tribes Macrosiphini (Myzus persicae and Acyrthosiphon pisum) and Aphidini (Rhopalosiphum maidis). In contrast, gene content of the aphid sex (X) chromosome remained unchanged despite rapid sequence evolution, low gene expression, and high transposable element load. To test whether rapid evolution of genome structure is a hallmark of Hemiptera, we compared our aphid assemblies with chromosome-scale assemblies of two blood-feeding Hemiptera (Rhodnius prolixus and Triatoma rubrofasciata). Despite being more diverged, the blood-feeding hemipterans have conserved synteny. The exceptional rate of structural evolution of aphid autosomes renders them an important emerging model system for studying the role of large-scale genome rearrangements in evolution.
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Affiliation(s)
- Thomas C Mathers
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Roland H M Wouters
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Sam T Mugford
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - David Swarbreck
- Earlham Institute, Norwich Research Park, Norwich, United Kingdom
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich, United Kingdom
| | - Saskia A Hogenhout
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
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22
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Genome Sequence of the Banana Aphid, Pentalonia nigronervosa Coquerel (Hemiptera: Aphididae) and Its Symbionts. G3-GENES GENOMES GENETICS 2020; 10:4315-4321. [PMID: 33004433 PMCID: PMC7718742 DOI: 10.1534/g3.120.401358] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The banana aphid, Pentalonia nigronervosa Coquerel (Hemiptera: Aphididae), is a major pest of cultivated bananas (Musa spp., order Zingiberales), primarily due to its role as a vector of Banana bunchy top virus (BBTV), the most severe viral disease of banana worldwide. Here, we generated a highly complete genome assembly of P. nigronervosa using a single PCR-free Illumina sequencing library. Using the same sequence data, we also generated complete genome assemblies of the P. nigronervosa symbiotic bacteria Buchnera aphidicola and Wolbachia. To improve our initial assembly of P. nigronervosa we developed a k-mer based deduplication pipeline to remove genomic scaffolds derived from the assembly of haplotigs (allelic variants assembled as separate scaffolds). To demonstrate the usefulness of this pipeline, we applied it to the recently generated assembly of the aphid Myzus cerasi, reducing the duplication of conserved BUSCO genes by 25%. Phylogenomic analysis of P. nigronervosa, our improved M. cerasi assembly, and seven previously published aphid genomes, spanning three aphid tribes and two subfamilies, reveals that P. nigronervosa falls within the tribe Macrosiphini, but is an outgroup to other Macrosiphini sequenced so far. As such, the genomic resources reported here will be useful for understanding both the evolution of Macrosphini and for the study of P. nigronervosa. Furthermore, our approach using low cost, high-quality, Illumina short-reads to generate complete genome assemblies of understudied aphid species will help to fill in genomic black spots in the diverse aphid tree of life.
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23
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Hong F, Mo SH, Lin XY, Niu J, Yin J, Wei D. The PacBio Full-Length Transcriptome of the Tea Aphid as a Reference Resource. Front Genet 2020; 11:558394. [PMID: 33304379 PMCID: PMC7693467 DOI: 10.3389/fgene.2020.558394] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 10/09/2020] [Indexed: 12/30/2022] Open
Abstract
The tea aphid, Aphis aurantii, has become one of the destructive pests in tea plantations in the tropics and subtropics. Very few functional studies have so far focused on the developmental and reproductive biology at a molecular level, because of the lack of comprehensive genetic information. Full-length transcriptomes represent a very highly efficient approach to obtain reference gene sequences in non-model insects. In the present study, the transcriptome of A. aurantii was comprehensively sequenced using PacBio Iso-Seq technology. A total of 46.8 Gb nucleotides and 15,938 non-redundant full-length transcripts were obtained, 13,498 (84.69%) of which were annotated into seven databases. Of these transcripts, 2,029 alternative splicing events and 15,223 simple sequence repeats were detected. Among these transcripts, 4,571 (28.68%) and 11,367 (71.32%) were long non-coding RNAs (lncRNAs) and protein-coding genes, respectively. Five hundred and ninety transcription factors were detected. The first full-length transcriptome represents a significant increase in the known genetic information of A. aurantii. It will assist the future functional study of genes involved in its development and reproduction.
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Affiliation(s)
- Feng Hong
- College of Agriculture, Xinyang Agriculture and Forestry University, Xinyang, China
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Si-Hua Mo
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
| | - Xing-Yu Lin
- College of Agriculture, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Jinzhi Niu
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jian Yin
- College of Agriculture, Xinyang Agriculture and Forestry University, Xinyang, China
| | - Dong Wei
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Academy of Agricultural Sciences, Southwest University, Chongqing, China
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24
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Rotenberg D, Baumann AA, Ben-Mahmoud S, Christiaens O, Dermauw W, Ioannidis P, Jacobs CGC, Vargas Jentzsch IM, Oliver JE, Poelchau MF, Rajarapu SP, Schneweis DJ, Snoeck S, Taning CNT, Wei D, Widana Gamage SMK, Hughes DST, Murali SC, Bailey ST, Bejerman NE, Holmes CJ, Jennings EC, Rosendale AJ, Rosselot A, Hervey K, Schneweis BA, Cheng S, Childers C, Simão FA, Dietzgen RG, Chao H, Dinh H, Doddapaneni HV, Dugan S, Han Y, Lee SL, Muzny DM, Qu J, Worley KC, Benoit JB, Friedrich M, Jones JW, Panfilio KA, Park Y, Robertson HM, Smagghe G, Ullman DE, van der Zee M, Van Leeuwen T, Veenstra JA, Waterhouse RM, Weirauch MT, Werren JH, Whitfield AE, Zdobnov EM, Gibbs RA, Richards S. Genome-enabled insights into the biology of thrips as crop pests. BMC Biol 2020; 18:142. [PMID: 33070780 PMCID: PMC7570057 DOI: 10.1186/s12915-020-00862-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 09/02/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide resistance are largely unknown. To address this gap, we present the F. occidentalis draft genome assembly and official gene set. RESULTS We report on the first genome sequence for any member of the insect order Thysanoptera. Benchmarking Universal Single-Copy Ortholog (BUSCO) assessments of the genome assembly (size = 415.8 Mb, scaffold N50 = 948.9 kb) revealed a relatively complete and well-annotated assembly in comparison to other insect genomes. The genome is unusually GC-rich (50%) compared to other insect genomes to date. The official gene set (OGS v1.0) contains 16,859 genes, of which ~ 10% were manually verified and corrected by our consortium. We focused on manual annotation, phylogenetic, and expression evidence analyses for gene sets centered on primary themes in the life histories and activities of plant-colonizing insects. Highlights include the following: (1) divergent clades and large expansions in genes associated with environmental sensing (chemosensory receptors) and detoxification (CYP4, CYP6, and CCE enzymes) of substances encountered in agricultural environments; (2) a comprehensive set of salivary gland genes supported by enriched expression; (3) apparent absence of members of the IMD innate immune defense pathway; and (4) developmental- and sex-specific expression analyses of genes associated with progression from larvae to adulthood through neometaboly, a distinct form of maturation differing from either incomplete or complete metamorphosis in the Insecta. CONCLUSIONS Analysis of the F. occidentalis genome offers insights into the polyphagous behavior of this insect pest that finds, colonizes, and survives on a widely diverse array of plants. The genomic resources presented here enable a more complete analysis of insect evolution and biology, providing a missing taxon for contemporary insect genomics-based analyses. Our study also offers a genomic benchmark for molecular and evolutionary investigations of other Thysanoptera species.
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Affiliation(s)
- Dorith Rotenberg
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA.
| | - Aaron A Baumann
- Virology Section, College of Veterinary Medicine, University of Tennessee, A239 VTH, 2407 River Drive, Knoxville, TN, 37996, USA
| | - Sulley Ben-Mahmoud
- Department of Entomology and Nematology, University of California Davis, Davis, CA, 95616, USA
| | - Olivier Christiaens
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Wannes Dermauw
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Panagiotis Ioannidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Vassilika Vouton, 70013, Heraklion, Greece
- Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Chris G C Jacobs
- Institute of Biology, Leiden University, 2333 BE, Leiden, The Netherlands
| | - Iris M Vargas Jentzsch
- Institute for Zoology: Developmental Biology, University of Cologne, 50674, Cologne, Germany
| | - Jonathan E Oliver
- Department of Plant Pathology, University of Georgia - Tifton Campus, Tifton, GA, 31793-5737, USA
| | | | - Swapna Priya Rajarapu
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Derek J Schneweis
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Simon Snoeck
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
- Department of Biology, University of Washington, Seattle, WA, 98105, USA
| | - Clauvis N T Taning
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Dong Wei
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China and Ghent University, Ghent, Belgium
| | | | - Daniel S T Hughes
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shwetha C Murali
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Samuel T Bailey
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | | | - Christopher J Holmes
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Emily C Jennings
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Andrew J Rosendale
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
- Department of Biology, Mount St. Joseph University, Cincinnati, OH, 45233, USA
| | - Andrew Rosselot
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Kaylee Hervey
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Brandi A Schneweis
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Sammy Cheng
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | | | - Felipe A Simão
- Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Ralf G Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4072, Australia
| | - Hsu Chao
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Huyen Dinh
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Harsha Vardhan Doddapaneni
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Shannon Dugan
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Yi Han
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Sandra L Lee
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Joshua B Benoit
- Department of Biological Sciences, University of Cincinnati, Cincinnati, OH, 45221, USA
| | - Markus Friedrich
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Jeffery W Jones
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Kristen A Panfilio
- Institute for Zoology: Developmental Biology, University of Cologne, 50674, Cologne, Germany
- School of Life Sciences, University of Warwick, Gibbet Hill Campus, Coventry, CV4 7AL, UK
| | - Yoonseong Park
- Department of Entomology, Kansas State University, Manhattan, KS, 66506, USA
| | - Hugh M Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
- Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory of China-Belgium on Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China and Ghent University, Ghent, Belgium
| | - Diane E Ullman
- Department of Entomology and Nematology, University of California Davis, Davis, CA, 95616, USA
| | | | - Thomas Van Leeuwen
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Jan A Veenstra
- INCIA UMR 5287 CNRS, University of Bordeaux, Pessac, France
| | - Robert M Waterhouse
- Department of Ecology and Evolution, Swiss Institute of Bioinformatics, University of Lausanne, 1015, Lausanne, Switzerland
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology, Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- Department of Pediatrics, University of Cincinnati, College of Medicine, Cincinnati, OH, 45229, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Anna E Whitfield
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Evgeny M Zdobnov
- Department of Genetic Medicine and Development, University of Geneva Medical School, and Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Human and Molecular Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA
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25
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Biello R, Singh A, Godfrey CJ, Fernández FF, Mugford ST, Powell G, Hogenhout SA, Mathers TC. A chromosome-level genome assembly of the woolly apple aphid, Eriosoma lanigerum Hausmann (Hemiptera: Aphididae). Mol Ecol Resour 2020; 21:316-326. [PMID: 32985768 DOI: 10.1111/1755-0998.13258] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 08/21/2020] [Accepted: 09/07/2020] [Indexed: 01/18/2023]
Abstract
Woolly apple aphid (WAA, Eriosoma lanigerum Hausmann) (Hemiptera: Aphididae) is a major pest of apple trees (Malus domestica, order Rosales) and is critical to the economics of the apple industry in most parts of the world. Here, we generated a chromosome-level genome assembly of WAA-representing the first genome sequence from the aphid subfamily Eriosomatinae-using a combination of 10X Genomics linked-reads and in vivo Hi-C data. The final genome assembly is 327 Mb, with 91% of the assembled sequences anchored into six chromosomes. The contig and scaffold N50 values are 158 kb and 71 Mb, respectively, and we predicted a total of 28,186 protein-coding genes. The assembly is highly complete, including 97% of conserved arthropod single-copy orthologues based on Benchmarking Universal Single-Copy Orthologs (busco) analysis. Phylogenomic analysis of WAA and nine previously published aphid genomes, spanning four aphid tribes and three subfamilies, reveals that the tribe Eriosomatini (represented by WAA) is recovered as a sister group to Aphidini + Macrosiphini (subfamily Aphidinae). We identified syntenic blocks of genes between our WAA assembly and the genomes of other aphid species and find that two WAA chromosomes (El5 and El6) map to the conserved Macrosiphini and Aphidini X chromosome. Our high-quality WAA genome assembly and annotation provides a valuable resource for research in a broad range of areas such as comparative and population genomics, insect-plant interactions and pest resistance management.
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Affiliation(s)
- Roberto Biello
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Archana Singh
- Earlham Institute, John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | - Sam T Mugford
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Saskia A Hogenhout
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Thomas C Mathers
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
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26
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Jain RG, Robinson KE, Fletcher SJ, Mitter N. RNAi-Based Functional Genomics in Hemiptera. INSECTS 2020; 11:E557. [PMID: 32825516 PMCID: PMC7564473 DOI: 10.3390/insects11090557] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 08/17/2020] [Accepted: 08/17/2020] [Indexed: 01/05/2023]
Abstract
RNA interference (RNAi) is a powerful approach for sequence-specific gene silencing, displaying tremendous potential for functional genomics studies in hemipteran insects. Exploiting RNAi allows the biological roles of critical genes to be defined and aids the development of RNAi-based biopesticides. In this review, we provide context to the rapidly expanding field of RNAi-based functional genomics studies in hemipteran insects. We highlight the most widely used RNAi delivery strategies, including microinjection, oral ingestion and topical application. Additionally, we discuss the key variables affecting RNAi efficacy in hemipteran insects, including insect life-stage, gene selection, the presence of nucleases, and the role of core RNAi machinery. In conclusion, we summarise the application of RNAi in functional genomics studies in Hemiptera, focusing on genes involved in reproduction, behaviour, metabolism, immunity and chemical resistance across 33 species belonging to 14 families.
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Affiliation(s)
| | - Karl E. Robinson
- Queensland Alliance for Agriculture and Food Innovation, Centre for Horticultural Sciences, The University of Queensland, Brisbane 4072, Queensland, Australia; (R.G.J.); (S.J.F.); (N.M.)
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27
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Wenger JA, Cassone BJ, Legeai F, Johnston JS, Bansal R, Yates AD, Coates BS, Pavinato VAC, Michel A. Whole genome sequence of the soybean aphid, Aphis glycines. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 123:102917. [PMID: 28119199 DOI: 10.1016/j.ibmb.2017.01.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 01/03/2017] [Accepted: 01/14/2017] [Indexed: 05/09/2023]
Abstract
Aphids are emerging as model organisms for both basic and applied research. Of the 5,000 estimated species, only three aphids have published whole genome sequences: the pea aphid Acyrthosiphon pisum, the Russian wheat aphid, Diuraphis noxia, and the green peach aphid, Myzus persicae. We present the whole genome sequence of a fourth aphid, the soybean aphid (Aphis glycines), which is an extreme specialist and an important invasive pest of soybean (Glycine max). The availability of genomic resources is important to establish effective and sustainable pest control, as well as to expand our understanding of aphid evolution. We generated a 302.9 Mbp draft genome assembly for Ap. glycines using a hybrid sequencing approach. This assembly shows high completeness with 19,182 predicted genes, 92% of known Ap. glycines transcripts mapping to contigs, and substantial continuity with a scaffold N50 of 174,505 bp. The assembly represents 95.5% of the predicted genome size of 317.1 Mbp based on flow cytometry. Ap. glycines contains the smallest known aphid genome to date, based on updated genome sizes for 19 aphid species. The repetitive DNA content of the Ap. glycines genome assembly (81.6 Mbp or 26.94% of the 302.9 Mbp assembly) shows a reduction in the number of classified transposable elements compared to Ac. pisum, and likely contributes to the small estimated genome size. We include comparative analyses of gene families related to host-specificity (cytochrome P450's and effectors), which may be important in Ap. glycines evolution. This Ap. glycines draft genome sequence will provide a resource for the study of aphid genome evolution, their interaction with host plants, and candidate genes for novel insect control methods.
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Affiliation(s)
- Jacob A Wenger
- Department of Entomology, Ohio Agricultural Research and Development Center, The Ohio State University, USA; Center for Applied Plant Sciences, The Ohio State University, Wooster, OH, USA
| | - Bryan J Cassone
- Department of Entomology, Ohio Agricultural Research and Development Center, The Ohio State University, USA; Center for Applied Plant Sciences, The Ohio State University, Wooster, OH, USA
| | - Fabrice Legeai
- Ecology and Genetics of Insects & INRIA/IRISA, Genscale, Campus Beaulieu, Rennes, INRA, UMR IGEPP 1349, France
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - Raman Bansal
- Department of Entomology, Ohio Agricultural Research and Development Center, The Ohio State University, USA
| | - Ashley D Yates
- Department of Entomology, Ohio Agricultural Research and Development Center, The Ohio State University, USA; Center for Applied Plant Sciences, The Ohio State University, Wooster, OH, USA
| | - Brad S Coates
- USDA-ARS, Corn Insects & Crop Genetics Research Unit, Ames, IA, USA
| | - Vitor A C Pavinato
- Department of Entomology, Ohio Agricultural Research and Development Center, The Ohio State University, USA
| | - Andy Michel
- Department of Entomology, Ohio Agricultural Research and Development Center, The Ohio State University, USA; Center for Applied Plant Sciences, The Ohio State University, Wooster, OH, USA.
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28
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Zogli P, Pingault L, Grover S, Louis J. Ento(o)mics: the intersection of 'omic' approaches to decipher plant defense against sap-sucking insect pests. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:153-161. [PMID: 32721874 DOI: 10.1016/j.pbi.2020.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 05/15/2020] [Accepted: 06/07/2020] [Indexed: 05/27/2023]
Abstract
Plants are constantly challenged by insect pests that can dramatically decrease yields. Insects with piercing-sucking mouthparts, for example, aphids, whiteflies, and leaf hoppers, seemingly cause less physical damage to tissues, however, they feed on the plant's sap by piercing plant tissue and extracting plant fluids, thereby transmitting several plant-pathogenic viruses as well. As a counter-defense, plants activate an array of dynamic defense machineries against insect pests including the rapid reprogramming of the host cell processes. For a holistic understanding of plant-sap-sucking insect interactions, there is a need to call for techniques with the capacity to concomitantly capture these dynamic changes. Recent progress with various 'omic' technologies possess this capacity. In this review, we will provide a concise summary of application of 'omic' technologies and their utilization in plant and sap-sucking insect interaction studies. Finally, we will provide a perspective on the integration of 'omics' data in uncovering novel plant defense mechanisms against sap-sucking insect pests.
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Affiliation(s)
- Prince Zogli
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Lise Pingault
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Sajjan Grover
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Joe Louis
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68583, USA.
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29
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Rispe C, Legeai F, Nabity PD, Fernández R, Arora AK, Baa-Puyoulet P, Banfill CR, Bao L, Barberà M, Bouallègue M, Bretaudeau A, Brisson JA, Calevro F, Capy P, Catrice O, Chertemps T, Couture C, Delière L, Douglas AE, Dufault-Thompson K, Escuer P, Feng H, Forneck A, Gabaldón T, Guigó R, Hilliou F, Hinojosa-Alvarez S, Hsiao YM, Hudaverdian S, Jacquin-Joly E, James EB, Johnston S, Joubard B, Le Goff G, Le Trionnaire G, Librado P, Liu S, Lombaert E, Lu HL, Maïbèche M, Makni M, Marcet-Houben M, Martínez-Torres D, Meslin C, Montagné N, Moran NA, Papura D, Parisot N, Rahbé Y, Lopes MR, Ripoll-Cladellas A, Robin S, Roques C, Roux P, Rozas J, Sánchez-Gracia A, Sánchez-Herrero JF, Santesmasses D, Scatoni I, Serre RF, Tang M, Tian W, Umina PA, van Munster M, Vincent-Monégat C, Wemmer J, Wilson ACC, Zhang Y, Zhao C, Zhao J, Zhao S, Zhou X, Delmotte F, Tagu D. The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest. BMC Biol 2020; 18:90. [PMID: 32698880 PMCID: PMC7376646 DOI: 10.1186/s12915-020-00820-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 06/22/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Although native to North America, the invasion of the aphid-like grape phylloxera Daktulosphaira vitifoliae across the globe altered the course of grape cultivation. For the past 150 years, viticulture relied on grafting-resistant North American Vitis species as rootstocks, thereby limiting genetic stocks tolerant to other stressors such as pathogens and climate change. Limited understanding of the insect genetics resulted in successive outbreaks across the globe when rootstocks failed. Here we report the 294-Mb genome of D. vitifoliae as a basic tool to understand host plant manipulation, nutritional endosymbiosis, and enhance global viticulture. RESULTS Using a combination of genome, RNA, and population resequencing, we found grape phylloxera showed high duplication rates since its common ancestor with aphids, but similarity in most metabolic genes, despite lacking obligate nutritional symbioses and feeding from parenchyma. Similarly, no enrichment occurred in development genes in relation to viviparity. However, phylloxera evolved > 2700 unique genes that resemble putative effectors and are active during feeding. Population sequencing revealed the global invasion began from the upper Mississippi River in North America, spread to Europe and from there to the rest of the world. CONCLUSIONS The grape phylloxera genome reveals genetic architecture relative to the evolution of nutritional endosymbiosis, viviparity, and herbivory. The extraordinary expansion in effector genes also suggests novel adaptations to plant feeding and how insects induce complex plant phenotypes, for instance galls. Finally, our understanding of the origin of this invasive species and its genome provide genetics resources to alleviate rootstock bottlenecks restricting the advancement of viticulture.
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Affiliation(s)
| | - Fabrice Legeai
- BIPAA, IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
| | - Paul D. Nabity
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Rosa Fernández
- Bioinformatics and Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003 Barcelona, Spain
- Present address: Institute of Evolutionary Biology (CSIC-UPF), Passeig marítim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - Arinder K. Arora
- Department of Entomology, Cornell University, Ithaca, NY 14853 USA
| | | | | | | | - Miquel Barberà
- Institut de Biologia Integrativa de Sistemes, Parc Cientific Universitat de Valencia, C/ Catedrático José Beltrán n° 2, 46980 Paterna, València Spain
| | - Maryem Bouallègue
- Université de Tunis El Manar, Faculté des Sciences de Tunis, LR01ES05 Biochimie et Biotechnologie, 2092 Tunis, Tunisia
| | - Anthony Bretaudeau
- BIPAA, IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
| | | | - Federica Calevro
- Univ Lyon, INSA-Lyon, INRAE, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Pierre Capy
- Laboratoire Evolution, Génomes, Comportement, Ecologie CNRS, Univ. Paris-Sud, IRD, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Olivier Catrice
- LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Thomas Chertemps
- Sorbonne Université, UPEC, Université Paris 7, INRAE, CNRS, IRD, Institute of Ecology and Environmental Sciences, Paris, France
| | - Carole Couture
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d’Ornon, France
| | - Laurent Delière
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d’Ornon, France
| | - Angela E. Douglas
- Department of Entomology, Cornell University, Ithaca, NY 14853 USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853 USA
| | - Keith Dufault-Thompson
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI USA
| | - Paula Escuer
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Honglin Feng
- Department of Biology, University of Miami, Coral Gables, USA
- Current affiliation: Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, USA
| | | | - Toni Gabaldón
- Bioinformatics and Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Frédérique Hilliou
- Université Côte d’Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Silvia Hinojosa-Alvarez
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Yi-min Hsiao
- Institute of Biotechnology and Department of Entomology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
- Present affiliation: Bone and Joint Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Sylvie Hudaverdian
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
| | | | - Edward B. James
- Department of Biology, University of Miami, Coral Gables, FL 33146 USA
| | - Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX 77843 USA
| | | | - Gaëlle Le Goff
- Université Côte d’Azur, INRAE, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Gaël Le Trionnaire
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
| | - Pablo Librado
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Shanlin Liu
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083 Guangdong Province People’s Republic of China
- BGI-Shenzhen, Shenzhen, 518083 Guangdong Province People’s Republic of China
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Eric Lombaert
- Université Côte d’Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Hsiao-ling Lu
- Department of Post-Modern Agriculture, MingDao University, Changhua, Taiwan
| | - Martine Maïbèche
- Sorbonne Université, UPEC, Université Paris 7, INRAE, CNRS, IRD, Institute of Ecology and Environmental Sciences, Paris, France
| | - Mohamed Makni
- Université de Tunis El Manar, Faculté des Sciences de Tunis, LR01ES05 Biochimie et Biotechnologie, 2092 Tunis, Tunisia
| | - Marina Marcet-Houben
- Bioinformatics and Genomics Unit, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Dr. Aiguader, 88, 08003 Barcelona, Spain
| | - David Martínez-Torres
- Institut de Biologia Integrativa de Sistemes, Parc Cientific Universitat de Valencia, C/ Catedrático José Beltrán n° 2, 46980 Paterna, València Spain
| | - Camille Meslin
- INRAE, Institute of Ecology and Environmental Sciences, Versailles, France
| | - Nicolas Montagné
- Sorbonne Université, Institute of Ecology and Environmental Sciences, Paris, France
| | - Nancy A. Moran
- Department of Integrative Biology, University of Texas at Austin, Austin, USA
| | - Daciana Papura
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d’Ornon, France
| | - Nicolas Parisot
- Univ Lyon, INSA-Lyon, INRAE, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Yvan Rahbé
- Univ Lyon, INRAE, INSA-Lyon, CNRS, UCBL, UMR5240 MAP, F-69622 Villeurbanne, France
| | | | - Aida Ripoll-Cladellas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Stéphanie Robin
- BIPAA IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
| | - Céline Roques
- Plateforme Génomique GeT-PlaGe, Centre INRAE de Toulouse Midi-Pyrénées, 24 Chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Pascale Roux
- SAVE, INRAE, Bordeaux Sciences Agro, Villenave d’Ornon, France
| | - Julio Rozas
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Alejandro Sánchez-Gracia
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Jose F. Sánchez-Herrero
- Departament de Genètica, Microbiologia i Estadística and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Didac Santesmasses
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115 USA
| | | | - Rémy-Félix Serre
- Plateforme Génomique GeT-PlaGe, Centre INRAE de Toulouse Midi-Pyrénées, 24 Chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan Cedex, France
| | - Ming Tang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Wenhua Tian
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Paul A. Umina
- School of BioSciences, The University of Melbourne, Parkville, VIC Australia
| | - Manuella van Munster
- BGPI, Université Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | | | - Joshua Wemmer
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Alex C. C. Wilson
- Department of Biology, University of Miami, Coral Gables, FL 33146 USA
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI USA
| | - Chaoyang Zhao
- Department of Botany and Plant Sciences, University of California, Riverside, USA
| | - Jing Zhao
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen, 518083 Guangdong Province People’s Republic of China
- BGI-Shenzhen, Shenzhen, 518083 Guangdong Province People’s Republic of China
| | - Serena Zhao
- Department of Integrative Biology, University of Texas at Austin, Austin, USA
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193 People’s Republic of China
| | | | - Denis Tagu
- IGEPP, Agrocampus Ouest, INRAE, Université de Rennes 1, 35650 Le Rheu, France
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Guo S, Cao L, Song W, Shi P, Gao Y, Gong Y, Chen J, Hoffmann AA, Wei S. Chromosome‐level assembly of the melon thrips genome yields insights into evolution of a sap‐sucking lifestyle and pesticide resistance. Mol Ecol Resour 2020; 20:1110-1125. [DOI: 10.1111/1755-0998.13189] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/28/2020] [Accepted: 05/11/2020] [Indexed: 12/21/2022]
Affiliation(s)
- Shao‐Kun Guo
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences Beijing China
| | - Li‐Jun Cao
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences Beijing China
| | - Wei Song
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences Beijing China
| | - Pan Shi
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences Beijing China
| | - Yong‐Fu Gao
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences Beijing China
| | - Ya‐Jun Gong
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences Beijing China
| | - Jin‐Cui Chen
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences Beijing China
| | - Ary Anthony Hoffmann
- School of BioSciences Bio21 Molecular Science & Biotechnology Institute University of Melbourne Parkville Vic. Australia
| | - Shu‐Jun Wei
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences Beijing China
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31
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Rojas LA, Scully E, Enders L, Timm A, Sinha D, Smith CM. Comparative transcriptomics of Diuraphis noxia and Schizaphis graminum fed wheat plants containing different aphid-resistance genes. PLoS One 2020; 15:e0233077. [PMID: 32442185 PMCID: PMC7313535 DOI: 10.1371/journal.pone.0233077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 04/26/2020] [Indexed: 01/08/2023] Open
Abstract
The molecular bases of aphid virulence to aphid crop plant resistance genes are
poorly understood. The Russian wheat aphid, Diuraphis noxia,
(Kurdjumov), and the greenbug, Schizaphis graminum (Rondani),
are global pest of cereal crops. Each species damages barley, oat, rye and
wheat, but S. graminum includes fescue, maize,
rice and sorghum in its host range. This study was conducted to compare and
contrast the transcriptomes of S. graminum
biotype I and D. noxia biotype 1 when each
ingested phloem from leaves of varieties of bread wheat, Triticum
aestivum L., containing no aphid resistance (Dn0),
resistance to D. noxia biotype 1
(Dn4), or resistance to both D.
noxia biotype 1 and S.
graminum biotype I (Dn7, wheat genotype
94M370). Gene ontology enrichments, k-means analysis and KEGG pathway analysis
indicated that 94M370 plants containing the Dn7 D.
noxia resistance gene from rye had stronger effects on the
global transcriptional profiles of S. graminum
and D. noxia relative to those fed
Dn4 plants. S. graminum
responds to ingestion of phloem sap from 94M370 plants by expression of unigenes
coding for proteins involved in DNA and RNA repair, and delayed tissue and
structural development. In contrast, D. noxia
displays a completely different transcriptome after ingesting phloem sap from
Dn4 or 94M370 plants, consisting of unigenes involved
primarily in detoxification, nutrient acquisition and structural development.
These variations in transcriptional responses of D.
noxia and S. graminum
suggest that the underlying evolutionary mechanism(s) of virulence in these
aphids are likely species specific, even in cases of cross resistance.
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Affiliation(s)
- Lina Aguirre Rojas
- Department of Entomology, Kansas State University, Manhattan, KS, United
States of America
| | - Erin Scully
- Stored Product Insect and Engineering Unit, USDA-ARS Centerfor Grain and
Animal Health Research, Manhattan, KS, United States of
America
| | - Laramy Enders
- Department of Entomology, Purdue University, West Lafayette, IN, United
States of America
| | - Alicia Timm
- Department of Bioagricultural Sciences and Pest Management, Colorado
State University, Fort Collins, CO, United States of America
| | - Deepak Sinha
- Department of Entomology, Kansas State University, Manhattan, KS, United
States of America
- SAGE University, Indore, India
| | - Charles Michael Smith
- Department of Entomology, Kansas State University, Manhattan, KS, United
States of America
- * E-mail:
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MacWilliams JR, Dingwall S, Chesnais Q, Sugio A, Kaloshian I. AcDCXR Is a Cowpea Aphid Effector With Putative Roles in Altering Host Immunity and Physiology. FRONTIERS IN PLANT SCIENCE 2020; 11:605. [PMID: 32499809 PMCID: PMC7243947 DOI: 10.3389/fpls.2020.00605] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 04/21/2020] [Indexed: 06/01/2023]
Abstract
Cowpea, Vigna unguiculata, is a crop that is essential to semiarid areas of the world like Sub-Sahara Africa. Cowpea is highly susceptible to cowpea aphid, Aphis craccivora, infestation that can lead to major yield losses. Aphids feed on their host plant by inserting their hypodermal needlelike flexible stylets into the plant to reach the phloem sap. During feeding, aphids secrete saliva, containing effector proteins, into the plant to disrupt plant immune responses and alter the physiology of the plant to their own advantage. Liquid chromatography tandem mass spectrometry (LC-MS/MS) was used to identify the salivary proteome of the cowpea aphid. About 150 candidate proteins were identified including diacetyl/L-xylulose reductase (DCXR), a novel enzyme previously unidentified in aphid saliva. DCXR is a member of short-chain dehydrogenases/reductases with dual enzymatic functions in carbohydrate and dicarbonyl metabolism. To assess whether cowpea aphid DCXR (AcDCXR) has similar functions, recombinant AcDCXR was purified and assayed enzymatically. For carbohydrate metabolism, the oxidation of xylitol to xylulose was tested. The dicarbonyl reaction involved the reduction of methylglyoxal, an α-β-dicarbonyl ketoaldehyde, known as an abiotic and biotic stress response molecule causing cytotoxicity at high concentrations. To assess whether cowpea aphids induce methylglyoxal in plants, we measured methylglyoxal levels in both cowpea and pea (Pisum sativum) plants and found them elevated transiently after aphid infestation. Agrobacterium-mediated transient overexpression of AcDCXR in pea resulted in an increase of cowpea aphid fecundity. Taken together, our results indicate that AcDCXR is an effector with a putative ability to generate additional sources of energy to the aphid and to alter plant defense responses. In addition, this work identified methylglyoxal as a potential novel aphid defense metabolite adding to the known repertoire of plant defenses against aphid pests.
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Affiliation(s)
- Jacob R. MacWilliams
- Graduate Program in Biochemistry and Molecular Biology, University of California, Riverside, Riverside, CA, United States
| | - Stephanie Dingwall
- Department of Biochemistry, University of California, Riverside, Riverside, CA, United States
| | | | - Akiko Sugio
- INRAE, UMR1349, Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Isgouhi Kaloshian
- Graduate Program in Biochemistry and Molecular Biology, University of California, Riverside, Riverside, CA, United States
- Department of Nematology, University of California Riverside, Riverside, CA, United States
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
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Giordano R, Donthu RK, Zimin AV, Julca Chavez IC, Gabaldon T, van Munster M, Hon L, Hall R, Badger JH, Nguyen M, Flores A, Potter B, Giray T, Soto-Adames FN, Weber E, Marcelino JAP, Fields CJ, Voegtlin DJ, Hill CB, Hartman GL. Soybean aphid biotype 1 genome: Insights into the invasive biology and adaptive evolution of a major agricultural pest. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 120:103334. [PMID: 32109587 DOI: 10.1016/j.ibmb.2020.103334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/07/2020] [Accepted: 02/10/2020] [Indexed: 05/12/2023]
Abstract
The soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae) is a serious pest of the soybean plant, Glycine max, a major world-wide agricultural crop. We assembled a de novo genome sequence of Ap. glycines Biotype 1, from a culture established shortly after this species invaded North America. 20.4% of the Ap. glycines proteome is duplicated. These in-paralogs are enriched with Gene Ontology (GO) categories mostly related to apoptosis, a possible adaptation to plant chemistry and other environmental stressors. Approximately one-third of these genes show parallel duplication in other aphids. But Ap. gossypii, its closest related species, has the lowest number of these duplicated genes. An Illumina GoldenGate assay of 2380 SNPs was used to determine the world-wide population structure of Ap. Glycines. China and South Korean aphids are the closest to those in North America. China is the likely origin of other Asian aphid populations. The most distantly related aphids to those in North America are from Australia. The diversity of Ap. glycines in North America has decreased over time since its arrival. The genetic diversity of Ap. glycines North American population sampled shortly after its first detection in 2001 up to 2012 does not appear to correlate with geography. However, aphids collected on soybean Rag experimental varieties in Minnesota (MN), Iowa (IA), and Wisconsin (WI), closer to high density Rhamnus cathartica stands, appear to have higher capacity to colonize resistant soybean plants than aphids sampled in Ohio (OH), North Dakota (ND), and South Dakota (SD). Samples from the former states have SNP alleles with high FST values and frequencies, that overlap with genes involved in iron metabolism, a crucial metabolic pathway that may be affected by the Rag-associated soybean plant response. The Ap. glycines Biotype 1 genome will provide needed information for future analyses of mechanisms of aphid virulence and pesticide resistance as well as facilitate comparative analyses between aphids with differing natural history and host plant range.
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Affiliation(s)
- Rosanna Giordano
- Puerto Rico Science, Technology and Research Trust, San Juan, PR, USA; Know Your Bee, Inc. San Juan, PR, USA.
| | - Ravi Kiran Donthu
- Puerto Rico Science, Technology and Research Trust, San Juan, PR, USA; Know Your Bee, Inc. San Juan, PR, USA.
| | - Aleksey V Zimin
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Irene Consuelo Julca Chavez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain; Institute for Research in Biomedicine, Barcelona, Spain
| | - Toni Gabaldon
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain; Institute for Research in Biomedicine, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Manuella van Munster
- CIRAD-INRA-Montpellier SupAgro, TA A54/K, Campus International de Baillarguet, Montpellier, France
| | | | | | - Jonathan H Badger
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institute of Health, DHHS, Bethesda, MD, USA
| | - Minh Nguyen
- Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Alejandra Flores
- College of Liberal Arts and Sciences, School of Molecular and Cellular Biology, University of Illinois, Urbana, IL, USA
| | - Bruce Potter
- University of Minnesota, Southwest Research and Outreach Center, Lamberton, MN, USA
| | - Tugrul Giray
- Department of Biology, University of Puerto Rico, San Juan, PR, USA
| | - Felipe N Soto-Adames
- Florida Department of Agriculture and Consumer Services, Division of Plant Industry, Entomology, Gainesville, FL, USA
| | | | - Jose A P Marcelino
- Puerto Rico Science, Technology and Research Trust, San Juan, PR, USA; Know Your Bee, Inc. San Juan, PR, USA; Department of Entomology and Nematology, University of Florida, Gainesville, FL, USA
| | - Christopher J Fields
- HPCBio, Roy J. Carver Biotechnology Center, University of Illinois, Urbana, IL, USA
| | - David J Voegtlin
- Illinois Natural History Survey, University of Illinois, Urbana, IL, USA
| | | | - Glen L Hartman
- USDA-ARS and Department of Crop Sciences, University of Illinois, Urbana, IL, USA
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Deshoux M, Masson V, Arafah K, Voisin S, Guschinskaya N, van Munster M, Cayrol B, Webster CG, Rahbé Y, Blanc S, Bulet P, Uzest M. Cuticular Structure Proteomics in the Pea Aphid Acyrthosiphon pisum Reveals New Plant Virus Receptor Candidates at the Tip of Maxillary Stylets. J Proteome Res 2020; 19:1319-1337. [PMID: 31991085 PMCID: PMC7063574 DOI: 10.1021/acs.jproteome.9b00851] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Indexed: 12/21/2022]
Abstract
Aphids are phloem-feeding insects known as major pests in agriculture that are able to transmit hundreds of plant viruses. The majority of these viruses, classified as noncirculative, are retained and transported on the inner surface of the cuticle of the needle-like mouthparts while the aphids move from plant to plant. Identification of receptors of viruses within insect vectors is a key challenge because they are promising targets for alternative control strategies. The acrostyle, an organ discovered earlier within the common food/salivary canal at the tip of aphid maxillary stylets, displays proteins at the cuticle-fluid interface, some of which are receptors of noncirculative viruses. To assess the presence of stylet- and acrostyle-specific proteins and identify putative receptors, we have developed a comprehensive comparative analysis of the proteomes of four cuticular anatomical structures of the pea aphid, stylets, antennae, legs, and wings. In addition, we performed systematic immunolabeling detection of the cuticular proteins identified by mass spectrometry in dissected stylets. We thereby establish the first proteome of stylets of an insect and determine the minimal repertoire of the cuticular proteins composing the acrostyle. Most importantly, we propose a short list of plant virus receptor candidates, among which RR-1 proteins are remarkably predominant. The data are available via ProteomeXchange (PXD016517).
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Affiliation(s)
- Maëlle Deshoux
- BGPI, University of Montpellier, INRAE, CIRAD, Montpellier SupAgro, 34000 Montpellier, France
| | - Victor Masson
- Plateforme
BioPark d’Archamps, 74160 Archamps, France
- CR
University of Grenoble-Alpes, Institute
for Advances Biosciences, Inserm U1209, CNRS UMR 5309, 38058 Grenoble, France
| | - Karim Arafah
- Plateforme
BioPark d’Archamps, 74160 Archamps, France
| | | | | | - Manuella van Munster
- BGPI, University of Montpellier, INRAE, CIRAD, Montpellier SupAgro, 34000 Montpellier, France
| | - Bastien Cayrol
- BGPI, University of Montpellier, INRAE, CIRAD, Montpellier SupAgro, 34000 Montpellier, France
| | - Craig G. Webster
- BGPI, University of Montpellier, INRAE, CIRAD, Montpellier SupAgro, 34000 Montpellier, France
| | - Yvan Rahbé
- BGPI, University of Montpellier, INRAE, CIRAD, Montpellier SupAgro, 34000 Montpellier, France
- INRAE,
INSA Lyon, UMR5240 MAP CNRS-UCBL, 69622 Villeurbanne, France
- University
of Lyon, 69007 Lyon, France
| | - Stéphane Blanc
- BGPI, University of Montpellier, INRAE, CIRAD, Montpellier SupAgro, 34000 Montpellier, France
| | - Philippe Bulet
- Plateforme
BioPark d’Archamps, 74160 Archamps, France
- CR
University of Grenoble-Alpes, Institute
for Advances Biosciences, Inserm U1209, CNRS UMR 5309, 38058 Grenoble, France
| | - Marilyne Uzest
- BGPI, University of Montpellier, INRAE, CIRAD, Montpellier SupAgro, 34000 Montpellier, France
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Mathers TC. Improved Genome Assembly and Annotation of the Soybean Aphid ( Aphis glycines Matsumura). G3 (BETHESDA, MD.) 2020; 10:899-906. [PMID: 31969427 PMCID: PMC7056979 DOI: 10.1534/g3.119.400954] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Aphids are an economically important insect group due to their role as plant disease vectors. Despite this economic impact, genomic resources have only been generated for a small number of aphid species. The soybean aphid (Aphis glycines Matsumura) was the third aphid species to have its genome sequenced and the first to use long-read sequence data. However, version 1 of the soybean aphid genome assembly has low contiguity (contig N50 = 57 Kb, scaffold N50 = 174 Kb), poor representation of conserved genes and the presence of genomic scaffolds likely derived from parasitoid wasp contamination. Here, I use recently developed methods to reassemble the soybean aphid genome. The version 2 genome assembly is highly contiguous, containing half of the genome in only 40 scaffolds (contig N50 = 2.00 Mb, scaffold N50 = 2.51 Mb) and contains 11% more conserved single-copy arthropod genes than version 1. To demonstrate the utility of this improved assembly, I identify a region of conserved synteny between aphids and Drosophila containing members of the Osiris gene family that was split over multiple scaffolds in the original assembly. The improved genome assembly and annotation of A. glycines demonstrates the benefit of applying new methods to old data sets and will provide a useful resource for future comparative genome analysis of aphids.
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Affiliation(s)
- Thomas C Mathers
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK
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Julca I, Marcet-Houben M, Cruz F, Vargas-Chavez C, Johnston JS, Gómez-Garrido J, Frias L, Corvelo A, Loska D, Cámara F, Gut M, Alioto T, Latorre A, Gabaldón T. Phylogenomics Identifies an Ancestral Burst of Gene Duplications Predating the Diversification of Aphidomorpha. Mol Biol Evol 2020; 37:730-756. [PMID: 31702774 PMCID: PMC7038657 DOI: 10.1093/molbev/msz261] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aphids (Aphidoidea) are a diverse group of hemipteran insects that feed on plant phloem sap. A common finding in studies of aphid genomes is the presence of a large number of duplicated genes. However, when these duplications occurred remains unclear, partly due to the high relatedness of sequenced species. To better understand the origin of aphid duplications we sequenced and assembled the genome of Cinara cedri, an early branching lineage (Lachninae) of the Aphididae family. We performed a phylogenomic comparison of this genome with 20 other sequenced genomes, including the available genomes of five other aphids, along with the transcriptomes of two species belonging to Adelgidae (a closely related clade to the aphids) and Coccoidea. We found that gene duplication has been pervasive throughout the evolution of aphids, including many parallel waves of recent, species-specific duplications. Most notably, we identified a consistent set of very ancestral duplications, originating from a large-scale gene duplication predating the diversification of Aphidomorpha (comprising aphids, phylloxerids, and adelgids). Genes duplicated in this ancestral wave are enriched in functions related to traits shared by Aphidomorpha, such as association with endosymbionts, and adaptation to plant defenses and phloem-sap-based diet. The ancestral nature of this duplication wave (106-227 Ma) and the lack of sufficiently conserved synteny make it difficult to conclude whether it originated from a whole-genome duplication event or, alternatively, from a burst of large-scale segmental duplications. Genome sequencing of other aphid species belonging to different Aphidomorpha and related lineages may clarify these findings.
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Affiliation(s)
- Irene Julca
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marina Marcet-Houben
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Fernando Cruz
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Carlos Vargas-Chavez
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and CSIC, Valencia, Spain
| | | | - Jèssica Gómez-Garrido
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Leonor Frias
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - André Corvelo
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- New York Genome Center, New York, NY
| | - Damian Loska
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Francisco Cámara
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Department of Experimental and Health Sciences, Barcelona, Spain
| | - Tyler Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Department of Experimental and Health Sciences, Barcelona, Spain
| | - Amparo Latorre
- Institute for Integrative Systems Biology (I2SysBio), University of Valencia and CSIC, Valencia, Spain
- Joint Unit in Genomics and Health, Foundation for the Promotion of Sanitary and Biomedical Research (FISABIO) and University of Valencia, Valencia, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Department of Experimental and Health Sciences, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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Paula DP, Menger J, Andow DA, Koch RL. Diverse patterns of constitutive and inducible overexpression of detoxifying enzyme genes among resistant Aphis glycines populations. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2020; 164:100-114. [PMID: 32284115 DOI: 10.1016/j.pestbp.2019.12.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/21/2019] [Accepted: 12/30/2019] [Indexed: 06/11/2023]
Abstract
Understanding the mechanisms of pyrethroid resistance is essential to the effective management of pesticide resistance in Aphis glycines Matsumura (Hemiptera: Aphididae). We mined putative detoxifying enzyme genes in the draft genome sequence of A. glycines for cytochrome oxidase P450 (CYP), glutathione-S-transferase (GST) and esterases (E4 and carboxylesterases-CES). Aphids from clonal populations resistant to pyrethroids from three sites in Minnesota, USA, were screened against a diagnostic LC99 concentration of either λ-cyhalothrin or bifenthrin and detoxifying enzyme genes expression in survivors was analyzed by qPCR. Their expression profiles were compared relative to a susceptible clonal population. We found 61 CYP (40 full-length), seven GST (all full-length), seven E4 (five full-length) and three CES (two full-length) genes, including 24 possible pseudogenes. The detoxifying enzymes had different expression profiles across resistant aphid populations, possibly reflecting differences in the genetic background and pyrethroid selection pressures as the number of constitutively overexpressed detoxifying enzyme genes was correlated with the level of resistance. Our findings will strengthen the understanding of the pyrethroid resistance mechanisms in A. glycines.
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Affiliation(s)
- Débora Pires Paula
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, W5 Norte, P.O. Box 02372, Brasília, DF 70770-917, Brazil.
| | - James Menger
- Department of Entomology, University of Minnesota, 219 Hodson Hall, 1980 Folwell Ave., St. Paul, MN 55108, USA
| | - David A Andow
- Department of Entomology, University of Minnesota, 219 Hodson Hall, 1980 Folwell Ave., St. Paul, MN 55108, USA
| | - Robert L Koch
- Department of Entomology, University of Minnesota, 219 Hodson Hall, 1980 Folwell Ave., St. Paul, MN 55108, USA
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Loxdale HD, Balog A, Biron DG. Aphids in focus: unravelling their complex ecology and evolution using genetic and molecular approaches. Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blz194] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Aphids are renowned plant parasites of agriculture, horticulture and forestry, causing direct physical damage by sucking phloem and especially by transmission of plant pathogenic viruses. The huge yield loss they cause amounts to hundreds of millions of dollars globally, and because of this damage and the intense efforts expended on control, some 20 species are now resistant to pesticides worldwide. Aphids represent an ancient, mainly northern temperate group, although some species occur in the tropics, often as obligate asexual lineages or even asexual ‘species’. However, besides their notoriety as enemies of plant growers, aphids are also extremely interesting scientifically, especially at the molecular and genetic levels. They reproduce mainly asexually, one female producing 10–90 offspring in 7–10 days and therefore, theoretically, could produce billions of offspring in one growing season in the absence of mortality factors (i.e. climate/weather and antagonists). In this overview, we provide examples of what molecular and genetic studies of aphids have revealed concerning a range of topics, especially fine-grained ecological processes. Aphids, despite their apparently limited behavioural repertoire, are in fact masters (or, perhaps more accurately, mistresses) of adaptation and evolutionary flexibility and continue to flourish in a variety of ecosystems, including the agro-ecosystem, regardless of our best efforts to combat them.
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Affiliation(s)
- Hugh D Loxdale
- School of Biosciences, Cardiff University, the Sir Martin Evans Building, Cardiff, UK
| | - Adalbert Balog
- Department of Horticulture, Faculty of Technical and Human Science, Sapientia Hungarian University of Transylvania, Tirgu-Mureș/Corunca, Romania
| | - David G Biron
- Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, UMR CNRS, Campus Universitaire des Cézeaux, Aubiere Cedex, France
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Sibisi P, Venter E. Wheat Argonaute 5 Functions in Aphid-Plant Interaction. FRONTIERS IN PLANT SCIENCE 2020; 11:641. [PMID: 32528501 PMCID: PMC7266077 DOI: 10.3389/fpls.2020.00641] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 04/24/2020] [Indexed: 05/21/2023]
Abstract
Aphids feeding on plants experience similar responses to pathogens due to the prolonged and intimate contact with the plant. Diuraphis noxia is an economically important aphid pest on wheat that exhibits such an interaction. Studies on small RNA (sRNA) that regulate genes imparting resistance to wheat against D. noxia have predicted an Argonaute 5 (TaAGO5) gene as possible role player in the resistance response. Functional characterization revealed that TaAGO5 is crucial in regulating the response to infestation by D. noxia. Knockdown of TaAGO5 by 22% in D. noxia resistant wheat resulted in a completely susceptible phenotype. The fecundity and stress levels of D. noxia feeding on these silenced plants were similar to aphids feeding on the susceptible controls. Thus, TaAGO5 is crucial in the defense response by wheat plants during aphid feeding and this is similar to Nicotiana benthaminia plants experiencing arthropod herbivory. Additionally, TaAGO5 was differentially regulated by the Barley mosaic virus (BMV) used in the functional characterization. This provides evidence that TaAGO5 could play a role during virus infection of wheat. The role of AGO5 proteins in plant responses to arthropod herbivory and virus infection is known for dicotyledonous plants. Here, we present data that indicate that this role of TaAGO5 is conserved in wheat and possibly for monocotyledonous plants. These observations extend our knowledge on the roles of AGO proteins in plant resistance.
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40
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Li F, Zhao X, Li M, He K, Huang C, Zhou Y, Li Z, Walters JR. Insect genomes: progress and challenges. INSECT MOLECULAR BIOLOGY 2019; 28:739-758. [PMID: 31120160 DOI: 10.1111/imb.12599] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/22/2019] [Accepted: 05/14/2019] [Indexed: 05/24/2023]
Abstract
In the wake of constant improvements in sequencing technologies, numerous insect genomes have been sequenced. Currently, 1219 insect genome-sequencing projects have been registered with the National Center for Biotechnology Information, including 401 that have genome assemblies and 155 with an official gene set of annotated protein-coding genes. Comparative genomics analysis showed that the expansion or contraction of gene families was associated with well-studied physiological traits such as immune system, metabolic detoxification, parasitism and polyphagy in insects. Here, we summarize the progress of insect genome sequencing, with an emphasis on how this impacts research on pest control. We begin with a brief introduction to the basic concepts of genome assembly, annotation and metrics for evaluating the quality of draft assemblies. We then provide an overview of genome information for numerous insect species, highlighting examples from prominent model organisms, agricultural pests and disease vectors. We also introduce the major insect genome databases. The increasing availability of insect genomic resources is beneficial for developing alternative pest control methods. However, many opportunities remain for developing data-mining tools that make maximal use of the available insect genome resources. Although rapid progress has been achieved, many challenges remain in the field of insect genomics.
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Affiliation(s)
- F Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - X Zhao
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - M Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - K He
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - C Huang
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Y Zhou
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - Z Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
| | - J R Walters
- Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, USA
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Niu J, Yang WJ, Tian Y, Fan JY, Ye C, Shang F, Ding BY, Zhang J, An X, Yang L, Chang TY, Christiaens O, Smagghe G, Wang JJ. Topical dsRNA delivery induces gene silencing and mortality in the pea aphid. PEST MANAGEMENT SCIENCE 2019; 75:2873-2881. [PMID: 31038279 DOI: 10.1002/ps.5457] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 04/16/2019] [Accepted: 04/30/2019] [Indexed: 05/10/2023]
Abstract
BACKGROUND With the growing number of available aphid genomes and transcriptomes, an efficient and easy-to-adapt tool for gene function study is urgently required. RNA interference (RNAi), as a post-transcriptional gene silencing mechanism, is important as a research tool for determining gene functions and has potential as a novel insect control strategy. However, these applications have been hampered by the lack of effective dsRNA delivery approaches in aphids. RESULTS Here, we developed a convenient and efficient dsRNA delivery method, topical RNAi, in aphids. An investigation of its dose and time-dependent RNAi efficiencies revealed that with as little as 60 ng dsRNA per adult pea aphid (Acyrthosiphon pisum), the indicator gene, Aphunchback, could be significantly silenced within 2 h of exposure. The method was further validated by successfully silencing other different genes, and it was also efficient toward two other aphid species, Aphis citricidus and Myzus persicae. Furthermore, a noticeable mortality was also observed in pea aphids using topical RNAi-mediated gene silencing, within 4 days post-dsRNA application for four out of seven tested genes. CONCLUSION Compared with the currently used dsRNA delivery methods in aphids, microinjection and ingestion, topical RNAi is time- and cost-effective, which could greatly influence RNAi-based gene functional studies and potential candidate gene selection for developing RNAi-based aphid control strategies in the future. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Jinzhi Niu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Wan-Jun Yang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Yuan Tian
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jia-Yao Fan
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Chao Ye
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Feng Shang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Bi-Yue Ding
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Jun Zhang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Xin An
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Li Yang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Teng-Yu Chang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
| | - Olivier Christiaens
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Guy Smagghe
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
- International Joint Laboratory on China-Belgium Sustainable Crop Pest Control, Academy of Agricultural Sciences, Southwest University, Chongqing, China
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Comparative Analysis of Intra- and Inter-Specific Genomic Variability in the Peach Potato Aphid, Myzus persicae. INSECTS 2019; 10:insects10100368. [PMID: 31652640 PMCID: PMC6835256 DOI: 10.3390/insects10100368] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/09/2019] [Accepted: 10/17/2019] [Indexed: 12/20/2022]
Abstract
The availability of genomic data in the last decade relating to different aphid species has allowed the analysis of the genomic variability occurring among such species, whereas intra-specific variability has hitherto very largely been neglected. In order to analyse the intra-genomic variability in the peach potato aphid, Myzus persicae, comparative analyses were performed revealing several clone-specific gene duplications, together with numerous deletions/rearrangements. Our comparative approach also allowed us to evaluate the synteny existing between the two M. persicae clones tested and between the peach potato aphid and the pea aphid, Acyrthosiphon pisum. Even if part of the observed rearrangements are related to a low quality of some assembled contigs and/or to the high number of contigs present in these aphid genomes, our evidence reveals that aphid clones are genetically more different than expected. These results suggest that the choice of performing genomes sequencing combining different biotypes/populations, as revealed in the case of the soybean aphid, Aphis glycines, is unlikely to be very informative in aphids. Interestingly, it is possible that the holocentric nature of aphid chromosomes favours genome rearrangements that can be successively inherited transgenerationally via the aphid's apomictic (parthenogenetic) mode of reproduction. Lastly, we evaluated the structure of the cluster of genes coding for the five histones (H1, H2A, H2B, H3 and H4) in order to better understand the quality of the two M. persicae genomes and thereby to improve our knowledge of this functionally important gene family.
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Mandrioli M, Melchiori G, Panini M, Chiesa O, Giordano R, Mazzoni E, Manicardi GC. Analysis of the extent of synteny and conservation in the gene order in aphids: A first glimpse from the Aphis glycines genome. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 113:103228. [PMID: 31446034 DOI: 10.1016/j.ibmb.2019.103228] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 07/03/2019] [Accepted: 08/21/2019] [Indexed: 06/10/2023]
Abstract
In the last decade several insect genomes have been sequenced, but for most the chromosomal mapping of the identified scaffolds/annotated genes is not available. The lack of this information makes it difficult to analyse various genetic aspects, including the presence of genome rearrangements and the extent of synteny within and across species. We mapped five multigenic DNA families (major and minor rDNAs, histone gene cluster, esterases and carotenoid desaturases) and seven scaffolds corresponding to 9 Mb of the soybean aphid, Aphis glycines, genome and identified loci spanning the four soybean aphid chromosomes. A comparative analysis of the localization of the annotated A. glycines genes with respect to the peach potato aphid, Myzus persicae, and the fly, Drosophila melanogaster, evidenced a lower degree of synteny between the two aphid species than in the aphid-fly comparison. Only 1.4 genes per syntenic block were observed in aphids in contrast to 2.3 genes per block in flies. This higher chromosomal rearrangement rate in aphids could be explained considering that they possess holocentric chromosomes that can favour the stabilization and inheritance of chromosomal rearrangements. Lastly, our experiments did not detect the presence of chimeric assemblies in the newly available A. glycines biotype 1 genome, differently from what reported in assembled genome of other aphid species, suggesting that chromosomal mapping can be used to ascertain the quality of assembled genomes.
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Affiliation(s)
- Mauro Mandrioli
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Via Campi 213/D, 41125, Modena, Italy.
| | - Giulia Melchiori
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Via Campi 213/D, 41125, Modena, Italy
| | - Michela Panini
- Dipartimento di Scienze delle produzioni vegetali sostenibili, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Olga Chiesa
- Dipartimento di Scienze delle produzioni vegetali sostenibili, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Rosanna Giordano
- Puerto Rico Science, Technology & Research Trust, San Juan, PR, USA; Know Your Bee, Inc., San Juan, PR, USA
| | - Emanuele Mazzoni
- Dipartimento di Scienze delle produzioni vegetali sostenibili, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Gian Carlo Manicardi
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Via Campi 213/D, 41125, Modena, Italy
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Neupane S, Purintun JM, Mathew FM, Varenhorst AJ, Nepal MP. Molecular Basis of Soybean Resistance to Soybean Aphids and Soybean Cyst Nematodes. PLANTS 2019; 8:plants8100374. [PMID: 31561499 PMCID: PMC6843664 DOI: 10.3390/plants8100374] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/05/2019] [Accepted: 09/17/2019] [Indexed: 01/25/2023]
Abstract
Soybean aphid (SBA; Aphis glycines Matsumura) and soybean cyst nematode (SCN; Heterodera glycines Ichninohe) are major pests of the soybean (Glycine max [L.] Merr.). Substantial progress has been made in identifying the genetic basis of limiting these pests in both model and non-model plant systems. Classical linkage mapping and genome-wide association studies (GWAS) have identified major and minor quantitative trait loci (QTLs) in soybean. Studies on interactions of SBA and SCN effectors with host proteins have identified molecular cues in various signaling pathways, including those involved in plant disease resistance and phytohormone regulations. In this paper, we review the molecular basis of soybean resistance to SBA and SCN, and we provide a synthesis of recent studies of soybean QTLs/genes that could mitigate the effects of virulent SBA and SCN populations. We also review relevant studies of aphid–nematode interactions, particularly in the soybean–SBA–SCN system.
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Affiliation(s)
- Surendra Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Jordan M Purintun
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Febina M Mathew
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007, USA.
| | - Adam J Varenhorst
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007, USA.
| | - Madhav P Nepal
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
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Mathers TC, Mugford ST, Percival-Alwyn L, Chen Y, Kaithakottil G, Swarbreck D, Hogenhout SA, van Oosterhout C. Sex-specific changes in the aphid DNA methylation landscape. Mol Ecol 2019; 28:4228-4241. [PMID: 31472081 PMCID: PMC6857007 DOI: 10.1111/mec.15216] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 07/22/2019] [Indexed: 12/15/2022]
Abstract
Aphids present an ideal system to study epigenetics as they can produce diverse, but genetically identical, morphs in response to environmental stimuli. Here, using whole genome bisulphite sequencing and transcriptome sequencing of the green peach aphid (Myzus persicae), we present the first detailed analysis of cytosine methylation in an aphid and investigate differences in the methylation and transcriptional landscapes of male and asexual female morphs. We found that methylation primarily occurs in a CG dinucleotide (CpG) context and that exons are highly enriched for methylated CpGs, particularly at the 3' end of genes. Methylation is positively associated with gene expression, and methylated genes are more stably expressed than unmethylated genes. Male and asexual female morphs have distinct methylation profiles. Strikingly, these profiles are divergent between the sex chromosome and the autosomes; autosomal genes are hypomethylated in males compared to asexual females, whereas genes belonging to the sex chromosome, which is haploid in males, are hypermethylated. Overall, we found correlated changes in methylation and gene expression between males and asexual females, and this correlation was particularly strong for genes located on the sex chromosome. Our results suggest that differential methylation of sex-biased genes plays a role in aphid sexual differentiation.
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Affiliation(s)
- Thomas C Mathers
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Sam T Mugford
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Yazhou Chen
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | - Saskia A Hogenhout
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
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Schmidt L, Wielsch N, Wang D, Boland W, Burse A. Tissue-specific profiling of membrane proteins in the salicin sequestering juveniles of the herbivorous leaf beetle, Chrysomela populi. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 109:81-91. [PMID: 30922827 DOI: 10.1016/j.ibmb.2019.03.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/21/2019] [Accepted: 03/21/2019] [Indexed: 06/09/2023]
Abstract
Sequestration of plant secondary metabolites is a detoxification strategy widespread in herbivorous insects including not only storage, but also usage of these metabolites for the insects' own benefit. Larvae of the poplar leaf beetle Chrysomela populi sequester plant-derived salicin to produce the deterrent salicylaldehyde in specialized exocrine glands. To identify putative transporters involved in the sequestration process we investigated integral membrane proteins of several tissues from juvenile C. populi by using a proteomics approach. Computational analyses led to the identification of 122 transport proteins in the gut, 105 in the Malpighian tubules, 94 in the fat body and 27 in the defensive glands. Among these, primary active transporters as well as electrochemical potential-driven transporters were most abundant in all tissues, including ABC transporters (especially subfamilies B, C and G) and sugar porters as most interesting families facilitating the sequestration of plant glycosides. Whereas ABC transporters are predominantly expressed simultaneously in several tissues, sugar porters are often expressed in only one tissue, suggesting that sugar porters govern more distinct functions than members of the ABC family. The inventory of transporters presented in this study provides the base for further functional characterizations on transport processes of sequestered glycosides in insects.
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Affiliation(s)
- Lydia Schmidt
- Max Planck Institute for Chemical Ecology, Department of Bioorganic Chemistry, Hans-Knöll-Str. 8, D-07745, Jena, Germany
| | - Natalie Wielsch
- Max Planck Institute for Chemical Ecology, Research Group Mass Spectrometry/ Proteomics, Hans-Knöll-Str. 8, D-07745, Jena, Germany
| | - Ding Wang
- Max Planck Institute for Chemical Ecology, Department of Bioorganic Chemistry, Hans-Knöll-Str. 8, D-07745, Jena, Germany
| | - Wilhelm Boland
- Max Planck Institute for Chemical Ecology, Department of Bioorganic Chemistry, Hans-Knöll-Str. 8, D-07745, Jena, Germany
| | - Antje Burse
- Max Planck Institute for Chemical Ecology, Department of Bioorganic Chemistry, Hans-Knöll-Str. 8, D-07745, Jena, Germany.
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Chen W, Shakir S, Bigham M, Richter A, Fei Z, Jander G. Genome sequence of the corn leaf aphid (Rhopalosiphum maidis Fitch). Gigascience 2019; 8:giz033. [PMID: 30953568 PMCID: PMC6451198 DOI: 10.1093/gigascience/giz033] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 01/14/2019] [Accepted: 03/08/2019] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND The corn leaf aphid (Rhopalosiphum maidis Fitch) is the most economically damaging aphid pest on maize (Zea mays), one of the world's most important grain crops. In addition to causing direct damage by removing photoassimilates, R. maidis transmits several destructive maize viruses, including maize yellow dwarf virus, barley yellow dwarf virus, sugarcane mosaic virus, and cucumber mosaic virus. FINDINGS The genome of a parthenogenetically reproducing R. maidis clone was assembled with a combination of Pacific Biosciences (207-fold coverage) and Illumina (83-fold coverage) sequencing. The 689 assembled contigs, which have an N50 size of 9.0 megabases (Mb) and a low level of heterozygosity, were clustered using Phase Genomics Hi-C interaction maps. Consistent with the commonly observed 2n = 8 karyotype of R. maidis, most of the contigs (473 spanning 321 Mb) were successfully oriented into 4 scaffolds. The genome assembly captured the full length of 95.8% of the core eukaryotic genes, indicating that it is highly complete. Repetitive sequences accounted for 21.2% of the assembly, and a total of 17,629 protein-coding genes were predicted with integrated evidence from ab initio and homology-based gene predictions and transcriptome sequences generated with both Pacific Biosciences and Illumina. An analysis of likely horizontally transferred genes identified 2 from bacteria, 7 from fungi, 2 from protozoa, and 9 from algae. Repeat elements, transposons, and genes encoding likely detoxification enzymes (cytochrome P450s, glutathione S-transferases, carboxylesterases, uridine diphosphate-glucosyltransferases, and ABC transporters) were identified in the genome sequence. Other than Buchnera aphidicola (642,929 base pairs, 602 genes), no endosymbiont bacteria were found in R. maidis. CONCLUSIONS A high-quality R. maidis genome was assembled at the chromosome level. This genome sequence will enable further research related to ecological interactions, virus transmission, pesticide resistance, and other aspects of R. maidis biology. It also serves as a valuable resource for comparative investigation of other aphid species.
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Affiliation(s)
- Wenbo Chen
- Boyce Thompson Institute, 533 Tower Rd, Ithaca, NY 14853, USA
| | - Sara Shakir
- Boyce Thompson Institute, 533 Tower Rd, Ithaca, NY 14853, USA
| | - Mahdiyeh Bigham
- Boyce Thompson Institute, 533 Tower Rd, Ithaca, NY 14853, USA
| | - Annett Richter
- Boyce Thompson Institute, 533 Tower Rd, Ithaca, NY 14853, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, 533 Tower Rd, Ithaca, NY 14853, USA
- US Department of Agriculture–Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, 538 Tower Rd, Ithaca, NY 14853, USA
| | - Georg Jander
- Boyce Thompson Institute, 533 Tower Rd, Ithaca, NY 14853, USA
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Nardelli A, Vecchi M, Mandrioli M, Manicardi GC. The Evolutionary History and Functional Divergence of Trehalase ( treh) Genes in Insects. Front Physiol 2019; 10:62. [PMID: 30828300 PMCID: PMC6384254 DOI: 10.3389/fphys.2019.00062] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 01/21/2019] [Indexed: 01/04/2023] Open
Abstract
Trehalases (treh) have been found in different organisms, such as bacteria, fungi, yeast, nematodes, insects, vertebrates, and plants. Their biochemical properties are extremely variable and not yet fully understood. Gene expression patterns have shown differences among insect species suggesting a potential functional diversification of trehalase enzymes during their evolution. A second gene family encoding for enzymes with hypothetical trehalase activity has been repeatedly annotated in insect genome as acid trehalases/acid trehalase-like (ath), but its functional role is still not clear. The currently available large amount of genomic data from many insect species may enable a better understanding of the evolutionary history, phylogenetic relationships and possible roles of trehalase encoding genes in this taxon. The aim of the present study is to infer the evolutionary history of trehalases and acid trehalase genes in insects and analyze the trehalase functional divergence during their evolution, combining phylogenetic and genomic synteny/colinearity analyses.
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Affiliation(s)
- Andrea Nardelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Matteo Vecchi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Mauro Mandrioli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
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Avila GA, Davidson M, van Helden M, Fagan L. The potential distribution of the Russian wheat aphid (Diuraphis noxia): an updated distribution model including irrigation improves model fit for predicting potential spread. BULLETIN OF ENTOMOLOGICAL RESEARCH 2019; 109:90-101. [PMID: 29665868 DOI: 10.1017/s0007485318000226] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Diuraphis noxia (Kurdjumov), Russian wheat aphid, is one of the world's most invasive and economically important agricultural pests of wheat and barley. In May 2016, it was found for the first time in Australia, with further sampling confirming it was widespread throughout south-eastern regions. Russian wheat aphid is not yet present in New Zealand. The impacts of this pest if it establishes in New Zealand, could result in serious control problems in wheat- and barley-growing regions. To evaluate whether D. noxia could establish populations in New Zealand we used the climate modelling software CLIMEX to locate where potential viable populations might occur. We re-parameterised the existing CLIMEX model by Hughes and Maywald (1990) by improving the model fit using currently known distribution records of D. noxia, and we also considered the role of irrigation into the potential spread of this invasive insect. The updated model now fits the current known distribution better than the previous Hughes and Maywald CLIMEX model, particularly in temperate and Mediterranean areas in Australia and Europe; and in more semi-arid areas in north-western China and Middle Eastern countries. Our model also highlights new climatically suitable areas for the establishment of D. noxia, not previously reported, including parts of France, the UK and New Zealand. Our results suggest that, when suitable host plants are present, Russian wheat aphid could establish in these regions. The new CLIMEX projections in the present study are useful tools to inform risk assessments and target surveillance and monitoring efforts for identifying susceptible areas to invasion by Russian wheat aphid.
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Affiliation(s)
- G A Avila
- The New Zealand Institute for Plant & Food Research Limited, Mt Albert Research Centre,Private Bag 92169, Mt Albert, Auckland 1142,New Zealand
| | - M Davidson
- The New Zealand Institute for Plant & Food Research Limited, Christchurch Mail Centre,Christchurch 8140, Private Bag 4704,New Zealand
| | - M van Helden
- South Australian Research and Development Institute,Waite Campus, Adelaide, SA,Australia
| | - L Fagan
- Department of Primary Industries and Regional Development,3 Baron-Hay Court, South Perth, WA 6151,Australia
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50
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Tvedte ES, Logsdon JM, Forbes AA. Sex loss in insects: causes of asexuality and consequences for genomes. CURRENT OPINION IN INSECT SCIENCE 2019; 31:77-83. [PMID: 31109677 DOI: 10.1016/j.cois.2018.11.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/03/2018] [Accepted: 11/20/2018] [Indexed: 06/09/2023]
Abstract
Boasting a staggering diversity of reproductive strategies, insects provide attractive models for the comparative study of the causes and consequences of transitions to asexuality. We provide an overview of some contemporary studies of reproductive systems in insects and compile an initial database of asexual insect genome resources. Insect systems have already yielded some important insights into various mechanisms by which sex is lost, including genetic, endosymbiont-mediated, and hybridization. Studies of mutation and substitution after loss of sex provide the strongest empirical support for hypothesized effects of asexuality, whereas there is mixed evidence for ecological hypotheses such as increased parasite load and altered niche breadth in asexuals. Most hypotheses have been explored in a select few taxa (e.g. stick insects, aphids), such that much of the great taxonomic breadth of insects remain understudied. Given the variation in the proximate causes of asexuality in insects, we argue for expanding the taxonomic breadth of study systems. Despite some challenges for investigating sex in insects, the increasing cost-effectiveness of genomic sequencing makes data generation for closely-related asexual and sexual lineages increasingly feasible.
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Affiliation(s)
- Eric S Tvedte
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, United States.
| | - John M Logsdon
- Department of Biology, University of Iowa, Iowa City, IA, United States
| | - Andrew A Forbes
- Department of Biology, University of Iowa, Iowa City, IA, United States
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