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Liang Y, Dikow RB, Su X, Wen J, Ren Z. Comparative genomics of the primary endosymbiont Buchnera aphidicola in aphid hosts and their coevolutionary relationships. BMC Biol 2024; 22:137. [PMID: 38902723 PMCID: PMC11188193 DOI: 10.1186/s12915-024-01934-w] [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: 05/04/2023] [Accepted: 05/28/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Coevolution between modern aphids and their primary obligate, bacterial endosymbiont, Buchnera aphidicola, has been previously reported at different classification levels based on molecular phylogenetic analyses. However, the Buchnera genome remains poorly understood within the Rhus gall aphids. RESULTS We assembled the complete genome of the endosymbiont Buchnera in 16 aphid samples, representing 13 species in all six genera of Rhus gall aphids by shotgun genome skimming method. We compared the newly assembled genomes with those from GenBank to comprehensively investigate patterns of coevolution between the bacteria Buchnera and their aphid hosts. Buchnera genomes were mostly collinear, and the pan-genome contained 684 genes, in which the core genome contained 256 genes with some lineages having large numbers of tandem gene duplications. There has been substantial gene-loss in each Buchnera lineage. We also reconstructed the phylogeny for Buchnera and their host aphids, respectively, using 72 complete genomes of Buchnera, along with the complete mitochondrial genomes and three nuclear genes of 31 corresponding host aphid accessions. The cophylogenetic test demonstrated significant coevolution between these two partner groups at individual, species, generic, and tribal levels. CONCLUSIONS Buchnera exhibits very high levels of genomic sequence divergence but relative stability in gene order. The relationship between the symbionts Buchnera and its aphid hosts shows a significant coevolutionary pattern and supports complexity of the obligate symbiotic relationship.
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Affiliation(s)
- Yukang Liang
- School of Life Science and Shanxi Key Laboratory of Nucleic Acid Biopesticides, Shanxi University, 92 Wucheng Rd, Taiyuan Shanxi, 030006, China
| | - Rebecca B Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, 600 Maryland Avenue SW, Washington, DC, 20024, USA
| | - Xu Su
- School of Geography and Life Science, Qinghai Normal University, 38 Wusixi Road, Xining, 810008, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, MRC-166, Washington, DC, 20013-7012, USA.
| | - Zhumei Ren
- School of Life Science and Shanxi Key Laboratory of Nucleic Acid Biopesticides, Shanxi University, 92 Wucheng Rd, Taiyuan Shanxi, 030006, China.
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Wang Z, Hao W, Wang H, Deng P, Li T, Wang C, Zhao J, Chen C, Ji W, Liu X. Genome-Wide Comparative Analysis of the Cytochrome P450 Monooxygenase Family in 19 Aphid Species and Their Expression Analysis in 4 Cereal Crop Aphids. Int J Mol Sci 2024; 25:6668. [PMID: 38928374 PMCID: PMC11203792 DOI: 10.3390/ijms25126668] [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: 05/09/2024] [Revised: 05/30/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Cytochrome P450 monooxygenases (CYP450s) play a variety of physiological roles, including pesticide resistance, plant allelochemical detoxification, and hormone metabolism catalysis. However, limited information is available on the classification and expression profiles of the CYP450 gene family in aphid species. This is the first study to identify the cytochrome P450 gene family in 19 aphid species at the whole genome level. A total of 1100 CYP450 genes were identified in 19 aphid species. Three hundred CYP450 genes belonged to six cereal crop aphid species, which were further classified into four subfamilies according to the phylogenetic relationship. The conserved motifs, exon-intron structures, and genomic organization of the same subfamilies were similar. Predictions of subcellular localization revealed that the endoplasmic reticulum harbored the majority of CYP450 proteins. In Sitobion avenae and Rhopalosiphum maidis, the increase in the CYP450 gene was primarily caused by segmental duplication events. However, only tandem duplication occurred in the CYP450 gene family of Diuraphis noxia, Rhopalosiphum padi, Schizaphis graminum, and Sitobion miscanthi. Synteny analysis found three continuous colinear CYP450 gene pairs among six cereal crop aphid species. Furthermore, we obtained the expression profiles of four cereal crop aphids, including R. padi, D. noxia, S. graminum, and S. avenae. Differential expression analysis provided growth stage specificity genes, tissue specificity genes, organ specificity genes and some detoxification metabolic genes among these four cereal crop aphids. Meanwhile, their expression patterns were showed. The related functions and pathways of CYP450s were revealed by GO and KEGG enrichment analysis. Above all, we picked the differentially expressed CYP450 genes from all of the differentially expressed genes (DEGs). These differentially expressed CYP450 genes provided some new potential candidates for aphid control and management. This work establishes the foundation for further investigations into the regulatory functions of the CYP450 gene family in aphid species and beyond.
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Affiliation(s)
- Zhenyu Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Xianyang 712100, China; (Z.W.); (W.H.); (H.W.); (P.D.); (T.L.); (C.W.); (J.Z.); (C.C.)
| | - Weixi Hao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Xianyang 712100, China; (Z.W.); (W.H.); (H.W.); (P.D.); (T.L.); (C.W.); (J.Z.); (C.C.)
| | - Hao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Xianyang 712100, China; (Z.W.); (W.H.); (H.W.); (P.D.); (T.L.); (C.W.); (J.Z.); (C.C.)
| | - Pingchuan Deng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Xianyang 712100, China; (Z.W.); (W.H.); (H.W.); (P.D.); (T.L.); (C.W.); (J.Z.); (C.C.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, Xianyang 712100, China
| | - Tingdong Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Xianyang 712100, China; (Z.W.); (W.H.); (H.W.); (P.D.); (T.L.); (C.W.); (J.Z.); (C.C.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, Xianyang 712100, China
| | - Changyou Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Xianyang 712100, China; (Z.W.); (W.H.); (H.W.); (P.D.); (T.L.); (C.W.); (J.Z.); (C.C.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, Xianyang 712100, China
| | - Jixin Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Xianyang 712100, China; (Z.W.); (W.H.); (H.W.); (P.D.); (T.L.); (C.W.); (J.Z.); (C.C.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, Xianyang 712100, China
| | - Chunhuan Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Xianyang 712100, China; (Z.W.); (W.H.); (H.W.); (P.D.); (T.L.); (C.W.); (J.Z.); (C.C.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, Xianyang 712100, China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Xianyang 712100, China; (Z.W.); (W.H.); (H.W.); (P.D.); (T.L.); (C.W.); (J.Z.); (C.C.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, Xianyang 712100, China
| | - Xinlun Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A & F University, Yangling, Xianyang 712100, China; (Z.W.); (W.H.); (H.W.); (P.D.); (T.L.); (C.W.); (J.Z.); (C.C.)
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling, Xianyang 712100, China
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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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Jin J, Zhan Z, Wei X, Pan Z, Zhao Y, Yu D, Zhang F. Genomic insights into the chromosomal elongation in a family of Collembola. Proc Biol Sci 2024; 291:20232937. [PMID: 38471545 DOI: 10.1098/rspb.2023.2937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/12/2024] [Indexed: 03/14/2024] Open
Abstract
Collembola is a highly diverse and abundant group of soil arthropods with chromosome numbers ranging from 5 to 11. Previous karyotype studies indicated that the Tomoceridae family possesses an exceptionally long chromosome. To better understand chromosome size evolution in Collembola, we obtained a chromosome-level genome of Yoshiicerus persimilis with a size of 334.44 Mb and BUSCO completeness of 97.0% (n = 1013). Both genomes of Y. persimilis and Tomocerus qinae (recently published) have an exceptionally large chromosome (ElChr greater than 100 Mb), accounting for nearly one-third of the genome. Comparative genomic analyses suggest that chromosomal elongation occurred independently in the two species approximately 10 million years ago, rather than in the ancestor of the Tomoceridae family. The ElChr elongation was caused by large tandem and segmental duplications, as well as transposon proliferation, with genes in these regions experiencing weaker purifying selection (higher dN/dS) than conserved regions. Moreover, inter-genomic synteny analyses indicated that chromosomal fission/fusion events played a crucial role in the evolution of chromosome numbers (ranging from 5 to 7) within Entomobryomorpha. This study provides a valuable resource for investigating the chromosome evolution of Collembola.
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Affiliation(s)
- Jianfeng Jin
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Zhihong Zhan
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Xiping Wei
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Zhixiang Pan
- School of Life Sciences, Taizhou University, Taizhou 318000, People's Republic of China
| | - Yuxin Zhao
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Daoyuan Yu
- Soil Ecology Lab, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Feng Zhang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
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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: 0] [Impact Index Per Article: 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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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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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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Zhang Z, Pei P, Zhang M, Li F, Tang G. Chromosome-level genome assembly of Dastarcus helophoroides provides insights into CYP450 genes expression upon insecticide exposure. PEST MANAGEMENT SCIENCE 2023; 79:1467-1482. [PMID: 36502364 DOI: 10.1002/ps.7319] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 10/26/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Dastarcus helophoroides is an important natural enemy of cerambycids, and is wildly used in biological control of pests. Nevertheless, the absence of complete genomic information limits the investigation of the underlying molecular mechanisms. Here, a chromosome-level of Dastarcus helophoroides genome is assembled using a combination strategy of Illumina, PacBio, 10x™ Genomics, and Hi-C. RESULTS The final assembly is 609.09 Mb with contig N50, scaffold N50 and GC content of 5.46 Mb, 42.56 Mb and 31.50%, respectively, and 95.25% of the contigs anchor into 13 chromosomes. In total 14 890 protein-coding genes and 65.37% repeat sequences are predicted in the assembly genome. The phylogenetic analysis of single-copy gene families shared among 20 insect species indicates that Dastarcus helophoroides is placed as the sister species to clade (Nitidulidae+Curculionoidea+Chrysomeloidea) + Tenebrionoidea, and diverges from the related species ~242.9 Mya. In total 36 expanded gene families are identified in Dastarcus helophoroides genome, and are functionally related to drug metabolism and metabolism of xenobiotics by cytochrome P450. Some members of CYP4 Clade and CYP6 Clade are up-regulated in Dastarcus helophoroides adults upon insecticide exposure, of which expressions of DhCYP4Q, DhCYP6A14X1 and DhCYP4C1 are significantly up-regulated. The silencing of the three genes leads to adults more sensitive to insecticide and increased knocked-down rate, which may indicate their critical roles in stress resistance and detoxication. CONCLUSION Our study systematically integrated the chromosome-level genome, transcriptome and gene expression of Dastarcus helophoroides, which will provide valuable resources for understanding mechanisms of pesticide metabolism, growth and development, and utilization of the natural enemy in integrated control. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Zhengqing Zhang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
| | - Pei Pei
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
| | - Meng Zhang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
| | - Feifei Li
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
| | - Guanghui Tang
- Key Laboratory of National Forestry and Grassland Administration on Management of Western Forest Bio-Disaster, College of Forestry, Northwest A&F University, Yangling, P. R. China
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Boissot N. NLRs are highly relevant resistance genes for aphid pests. CURRENT OPINION IN INSECT SCIENCE 2023; 56:101008. [PMID: 36764482 DOI: 10.1016/j.cois.2023.101008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/19/2023] [Accepted: 01/25/2023] [Indexed: 05/03/2023]
Abstract
Since the 20th century, when plant resistance to aphids was available, it has been widely used by farmers and the inheritance of plant resistance has been understood for several crops. However, it is only when the plant-aphid relationship was compared with that of microbial pathogens, that aphid resistance has begun to be understood and integrated into the plant immune network. Three of the four genes identified for plant resistance to aphid encode nucleotide-binding site leucine-rich repeat receptor (NLR) proteins responsible for aphid-effector triggered immunity, and NLRs are serious candidates for aphid resistance in four other plant species. Aphids are vectors for plant viruses, and aphid-effectors triggering immunity when they pierce plant cells are expected to trigger resistance to the viruses transmitted to the plant with effectors, as has been shown for aphid resistance in melon. This dual phenotype increases the interest of NLRs in the control of aphids.
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Affiliation(s)
- Nathalie Boissot
- INRAE, Génétique et Amélioration des Fruits et Légumes, 84143 Montfavet, France.
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Liu S, Liu X, Zhang T, Bai S, He K, Zhang Y, Francis F, Wang Z. Secondary symbionts affect aphid fitness and the titer of primary symbiont. FRONTIERS IN PLANT SCIENCE 2023; 14:1096750. [PMID: 36818877 PMCID: PMC9933779 DOI: 10.3389/fpls.2023.1096750] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Bacterial symbionts associated with aphids are important for their ecological fitness. The corn leaf aphid, Rhopalosiphum maidis (Fitch), is one of the most damaging aphid pests on maize and has been reported to harbor Hamiltonella defensa and Regiella insecticola while the effects of the secondary symbionts (S-symbionts) on host ecology and primary symbiont Buchnera aphidicola remain unclear. Here, four aphid strains were established, two of which were collected from Langfang - Hebei Province, China, with similar symbiont pattern except for the presence of H. defensa. Two other aphid strains were collected from Nanning - Guangxi Province, China, with the same symbiont infection except for the presence of R. insecticola. Phylogenetic analysis and aphid genotyping indicated that the S-symbiont-infected and free aphid strains from the same location had identical genetic backgrounds. Aphid fitness measurement showed that aphid strain infected with H. defensa performed shortened developmental duration for 1st instar and total nymph stages, reduced aphid survival rate, offspring, and longevity. While the developmental duration of H-infected strains was accelerated, and the adult weight was significantly higher compared to the H-free strain. Infection with R. insecticola did not affect the aphid's entire nymph stage duration and survival rate. As the H-strain does, aphids infected with R. insecticola also underwent a drop in offspring, along with marginally lower longevity. Unlike the H-infected strain, the R-infected strain performed delayed developmental duration and lower adult weight. The B. aphidicola titers of the H-infected strains showed a steep drop during the aphid 1st to 3rd instar stages, while the augmentation of B. aphidicola titers was found in the R-infected strain during the aphid 1st to 3rd instar. Our study investigated for the first time the effect of the S-symbionts on the ecology fitness and primary symbiont in R. maidis, indicating that infection with secondary symbionts leads to the modulation of aphid primary symbiont abundance, together inducing significant fitness costs on aphids with further impact on environmental adaptation and trophic interactions.
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Affiliation(s)
- Shen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Functional and Evolutionary Entomology, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Xiaobei Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tiantao Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shuxiong Bai
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kanglai He
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongjun Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Frédéric Francis
- Functional and Evolutionary Entomology, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Zhenying Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Genetic Variation, DIMBOA Accumulation, and Candidate Gene Identification in Maize Multiple Insect-Resistance. Int J Mol Sci 2023; 24:ijms24032138. [PMID: 36768464 PMCID: PMC9916695 DOI: 10.3390/ijms24032138] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/12/2023] [Accepted: 01/15/2023] [Indexed: 01/25/2023] Open
Abstract
Maize seedlings contain high amounts of 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA), and the effect of DIMBOA is directly associated with multiple insect-resistance against insect pests such as Asian corn borer and corn leaf aphids. Although numerous genetic loci for multiple insect-resistant traits have been identified, little is known about genetic controls regarding DIMBOA content. In this study, the best linear unbiased prediction (BLUP) values of DIMBOA content in two ecological environments across 310 maize inbred lines were calculated; and their phenotypic data and BLUP values were used for marker-trait association analysis. We identified nine SSRs that were significantly associated with DIMBOA content, which explained 4.30-20.04% of the phenotypic variation. Combined with 47 original genetic loci from previous studies, we detected 19 hot loci and approximately 11 hot loci (in Bin 1.04, Bin 2.00-2.01, Bin 2.03-2.04, Bin 4.00-4.03, Bin 5.03, Bin 5.05-5.07, Bin 8.01-8.03, Bin 8.04-8.05, Bin 8.06, Bin 9.01, and Bin 10.04 regions) supported pleiotropy for their association with two or more insect-resistant traits. Within the 19 hot loci, we identified 49 candidate genes, including 12 controlling DIMBOA biosynthesis, 6 involved in sugar metabolism/homeostasis, 2 regulating peroxidases activity, 21 associated with growth and development [(auxin-upregulated RNAs (SAUR) family member and v-myb avian myeloblastosis viral oncogene homolog (MYB)], and 7 involved in several key enzyme activities (lipoxygenase, cysteine protease, restriction endonuclease, and ubiquitin-conjugating enzyme). The synergy and antagonism interactions among these genes formed the complex defense mechanisms induced by multiple insect pests. Moreover, sufficient genetic variation was reported for DIMBOA performance and SSR markers in the 310 tested maize inbred lines, and 3 highly (DIMBOA content was 402.74-528.88 μg g-1 FW) and 15 moderate (DIMBOA content was 312.92-426.56 μg g-1 FW) insect-resistant genotypes were major enriched in the Reid group. These insect-resistant inbred lines can be used as parents in maize breeding programs to develop new varieties.
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Li Q, Cheng Y, Fan J, Chen J. Metabolic relay gene of aphid and primary symbiont as RNAi target loci for aphid control. FRONTIERS IN PLANT SCIENCE 2023; 13:1092638. [PMID: 36743566 PMCID: PMC9890070 DOI: 10.3389/fpls.2022.1092638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Aphids form a stable and mutually beneficial relationship with their primary symbiont Buchnera aphidicola, which play an important role in providing the missing nutrients to the host aphid. Based on the genome sequence of wheat aphid Siotobion miscanthi and its primary symbiont Buchnera that we obtained in our previously study, we identified a metabolic relay gene, ilvA, involved in the isoleucine synthesis pathway between aphids and Buchnera. METHOD In this study, we identified the location and sequence structure of ilvA gene in aphid genome, the expression level in different instars and tissues of aphids, and the effect of reducing ilvA expression on the growth and development of aphids by bioinformatics analysis, quantitative PCR, RNAi and bioassay experiments. RESULT Our study showed that ilvA was expressed at the highest level in the 2nd instar of the aphid, while the expression of this gene was significantly higher in the aphid bacteriocytes than in other tissues. Notably, this gene is localized on the aphid sex chromosome and remains highly conserved and collinearity across different aphid genomes. Knocking down the expression of ilvA reduced the aphid body weight and production. However, the indices of mortality decreased slightly, but were not significantly different, compared to the control. DISCUSSION The results show that the relay genes between aphids and their symbionts in the metabolism of essential nutrients have potential roles in the growth and development of aphids, meanwhile, providing target loci and new ideas for RNAi-based aphid green control strategies.
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Affiliation(s)
- Qian Li
- College of Bioscience and Resource Environment/Key Laboratory of Urban Agriculture (North China), Ministry of Agriculture and Rural Affairs of the People’s Republic of China, Beijing University of Agriculture, Beijing, China
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Cheng
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jia Fan
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Julian Chen
- The State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Ministry of Agricultural and Rural Affairs -Center of Applied Biological International (MARA-CABI) Joint Laboratory for Bio-Safety, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Pfeifer K, Frieß JL, Giese B. Insect allies-Assessment of a viral approach to plant genome editing. INTEGRATED ENVIRONMENTAL ASSESSMENT AND MANAGEMENT 2022; 18:1488-1499. [PMID: 35018716 PMCID: PMC9790436 DOI: 10.1002/ieam.4577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/02/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
The Insect Allies program of the Defense Advanced Research Projects Agency has already sparked scientific debate concerning technology assessment-related issues, among which the most prevalent is that of dual use. Apart from the issues concerning peaceful applications, the technology also provides the blueprint for a potential bioweapon. However, the combination of a virus-induced genetic modification of crop plants in the field using genetically modified insect vectors poses a greater risk than the hitherto existing use of genetically modified organisms. The technology's great depth of intervention allows a number of sources for hazard and a tendency towards high exposure, but it is also encumbered with notable deficits in knowledge. These issues call for a thorough technology assessment. This article aims to provide an initial characterization from a technology assessment perspective, focusing on potential sources of risk for this novel invasive environmental biotechnology at an early stage of research and development. Integr Environ Assess Manag 2022;18:1488-1499. © 2022 The Authors. Integrated Environmental Assessment and Management published by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC).
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Affiliation(s)
- Kevin Pfeifer
- Institute of Synthetic BioarchitecturesUniversity of Natural Resources and Life SciencesViennaAustria
| | - Johannes L. Frieß
- Institute of Safety and Risk Sciences (ISR)University of Natural Resources and Life SciencesViennaAustria
| | - Bernd Giese
- Institute of Safety and Risk Sciences (ISR)University of Natural Resources and Life SciencesViennaAustria
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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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Wang S, Tang H, Huang W, Liu X, Hou W, Cesar Piñero J, Peng X, Chen M. Octopamine receptor genes are involved in the starvation response of Rhopalosiphum padi (Hemiptera: Aphididae). INSECT MOLECULAR BIOLOGY 2022; 31:471-481. [PMID: 35312201 DOI: 10.1111/imb.12773] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/07/2022] [Accepted: 03/17/2022] [Indexed: 06/14/2023]
Abstract
Insect octopamine (OA) receptors are G-protein coupled receptors (GPCRs) that play essential roles in physiological and behavioural processes. However, there is little information about the function of OA receptors in the aphids' response to stress. From the genome sequence of Rhopalosiphum padi genome sequence, a cosmopolitan cereal pest, we identified six OA receptor genes RpOAMB, RpOctR, RpOctβ1R, RpOctβ2R, RpOctβ3R, RpOctR-like with two, one, one, four, four, seven exons, respectively. All the OA receptors contain seven transmembrane domains, which were the signature of GPCRs. Our results showed that (1) the contents of OA increased significantly after food starvation, (2) the transcription levels of RpOAMB, RpOctR, RpOctβ2R and RpOctβ3R increased after starvation and were restored after re-feeding, and (3) the expression levels of these four genes decreased significantly 48 h post-injection of dsRNA that targeted the respective genes. Knockdown of RpOctR, RpOctβ2R or RpOctβ3R genes significantly increased aphid mortality under 24 h starvation conditions. Mortality of R. padi injected with dsRpOctR or dsRpOctβ2R was significantly higher than control under 48 h starvation treatments. This is the first report on the role of OA receptors in the starvation response of aphids. The current study provides knowledge for a better understanding the physiological roles of insect OA receptors.
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Affiliation(s)
- Suji Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, China
| | - Hongcheng Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, China
| | - Wenjie Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, China
| | - Xi Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, China
| | - Wenhua Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, China
| | - Jaime Cesar Piñero
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, Massachusetts, USA
| | - Xiong Peng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, China
| | - Maohua Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, Shaanxi, China
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Dangol A, Shavit R, Yaakov B, Strickler SR, Jander G, Tzin V. Characterizing serotonin biosynthesis in Setaria viridis leaves and its effect on aphids. PLANT MOLECULAR BIOLOGY 2022; 109:533-549. [PMID: 35020104 DOI: 10.1007/s11103-021-01239-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
A combined transcriptomic and metabolic analysis of Setaria viridis leaves responding to aphid infestation was used to identify genes related to serotonin biosynthesis. Setaria viridis (green foxtail), a short life-cycle C4 plant in the Poaceae family, is the wild ancestor of Setaria italica (foxtail millet), a resilient crop that provides good yields in dry and marginal land. Although S. viridis has been studied extensively in the last decade, the molecular mechanisms of insect resistance in this species remain under-investigated. To address this issue, we performed a metabolic analysis of S. viridis and discovered that these plants accumulate the tryptophan-derived compounds tryptamine and serotonin. To elucidate the defensive functions of serotonin, Rhophalosiphum padi (bird cherry-oat aphids) were exposed to this compound, either by exogenous application to the plant medium or with artificial diet bioassays. In both cases, exposure to serotonin increased aphid mortality. To identify genes that are involved in serotonin biosynthesis, we conducted a transcriptome analysis and identified several predicted S. viridis tryptophan decarboxylase (TDC) and tryptamine 5-hydroxylase (T5H) genes. Two candidate genes were ectopically expressed in Nicotiana tabacum, where SvTDC1 (Sevir.6G066200) had tryptophan decarboxylase activity, and SvT5H1 (Sevir.8G219600) had tryptamine hydroxylase activity. Moreover, the function of the SvTDC1 gene was validated using virus-induced gene silencing in S. italica, which caused a reduction in serotonin levels. This study provides the first evidence of serotonin biosynthesis in Setaria leaves. The biosynthesis of serotonin may play an important role in defense responses and could prove to be useful for developing more pest-tolerant Setaria italica cultivars.
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Affiliation(s)
- Anuma Dangol
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Reut Shavit
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | - Beery Yaakov
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel
| | | | - Georg Jander
- Boyce Thompson Institute, 533 Tower Road, Ithaca, NY, 14853, USA
| | - Vered Tzin
- French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, 8499000, Israel.
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Li D, Li Z, Wang X, Wang L, Li Y, Liu D. Increasing risk of aphids spreading plant viruses in maize fields on both sides of China's Heihe-Tengchong line under climate change. PEST MANAGEMENT SCIENCE 2022; 78:3061-3070. [PMID: 35437931 DOI: 10.1002/ps.6932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/25/2022] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND In the coming decades, geographical distribution patterns of farmland organisms may undergo drastic changes due to climate change, with significant implications for global food security. In China, Rhopalosiphum maidis and its spread of sugarcane mosaic virus (ScMV) can become an increasingly serious threat to maize (Zea mays) production. We conducted ecological niche modeling for Z. mays, R. maidis, and ScMV under current and future (2041-2060 and 2081-2100) climate scenarios by using MaxEnt software to explore changes in this system. RESULTS The Heihe-Tengchong line (an imaginary separation line of human population density) can divide China into main (east of the line) and secondary (west of the line) habitats for the three species. With climate change, rapid expansion in suitable areas is projected for ScMV and the aphid vector R. maidis. Taking species interactions into consideration, our overlaying analyses show that most areas east of the Heihe-Tengchong line (optimal for maize and suitable for R. maidis) will become increasingly highly suitable for ScMV, suggesting that the prevention and control of this plant virus and its aphid vector in China's main maize-growing areas (e.g. northeast) will become an increasing challenge in the future. CONCLUSION Climate change will profoundly affect ScMV-vector-maize interactions, which may contribute favorably to invasion of this virus into new areas. Our comprehensive and in-depth analyses on shifts in this multi-species system under climate change provide useful and insightful information for devising strategies for the prevention and control of plant viruses and aphid vectors on maize in the future. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Dexian Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, China
- College of Plant Protection, Northwest A&F University, Yangling, China
| | - Zixin Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, China
- College of Plant Protection, Northwest A&F University, Yangling, China
| | - Xiaoxia Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, China
- College of Plant Protection, Northwest A&F University, Yangling, China
| | - Li Wang
- College of Plant Protection, Northwest A&F University, Yangling, China
| | - Yonghong Li
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, China
| | - Deguang Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, China
- College of Plant Protection, Northwest A&F University, Yangling, China
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Wang Q, Liu L, Zhang S, Wu H, Huang J. A chromosome-level genome assembly and intestinal transcriptome of Trypoxylus dichotomus (Coleoptera: Scarabaeidae) to understand its lignocellulose digestion ability. Gigascience 2022; 11:giac059. [PMID: 35764601 PMCID: PMC9239855 DOI: 10.1093/gigascience/giac059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/30/2022] [Accepted: 05/27/2022] [Indexed: 12/15/2022] Open
Abstract
Lignocellulose, as the key structural component of plant biomass, is a recalcitrant structure, difficult to degrade. The traditional management of plant waste, including landfill and incineration, usually causes serious environmental pollution and health problems. Interestingly, the xylophagous beetle, Trypoxylus dichotomus, can decompose lignocellulosic biomass. However, the genomics around the digestion mechanism of this beetle remain to be elucidated. Here, we assembled the genome of T. dichotomus, showing that the draft genome size of T. dichotomus is 636.27 Mb, with 95.37% scaffolds anchored onto 10 chromosomes. Phylogenetic results indicated that a divergent evolution between the ancestors of T. dichotomus and the closely related scarabaeid species Onthophagus taurus occurred in the early Cretaceous (120 million years ago). Through gene family evolution analysis, we found 67 rapidly evolving gene families, within which there were 2 digestive gene families (encoding Trypsin and Enoyl-(Acyl carrier protein) reductase) that have experienced significant expansion, indicating that they may contribute to the high degradation efficiency of lignocellulose in T. dichotomus. Additionally, events of chromosome breakage and rearrangement were observed by synteny analysis during the evolution of T. dichotomus due to chromosomes 6 and 8 of T. dichotomus being intersected with chromosomes 2 and 10 of Tribolium castaneum, respectively. Furthermore, the comparative transcriptome analyses of larval guts showed that the digestion-related genes were more commonly expressed in the midgut or mushroom residue group than the hindgut or sawdust group. This study reports the well-assembled and annotated genome of T. dichotomus, providing genomic and transcriptomic bases for further understanding the functional and evolutionary mechanisms of lignocellulose digestion in T. dichotomus.
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Affiliation(s)
- Qingyun Wang
- National Joint Local Engineering Laboratory for High-Efficient Preparation of Biopesticide, Zhejiang A&F University, 666 Wusu Street, Lin'an, Hangzhou, Zhejiang 311300, China
| | - Liwei Liu
- National Joint Local Engineering Laboratory for High-Efficient Preparation of Biopesticide, Zhejiang A&F University, 666 Wusu Street, Lin'an, Hangzhou, Zhejiang 311300, China
- Zhejiang Museum of Natural History, No. 6 West Lake Cultural Square, Hangzhou, Zhejiang 310014, China
| | - Sujiong Zhang
- Dapanshan Insect Institute of Zhejiang, Pan'an, Zhejiang 322300, China
| | - Hong Wu
- National Joint Local Engineering Laboratory for High-Efficient Preparation of Biopesticide, Zhejiang A&F University, 666 Wusu Street, Lin'an, Hangzhou, Zhejiang 311300, China
| | - Junhao Huang
- National Joint Local Engineering Laboratory for High-Efficient Preparation of Biopesticide, Zhejiang A&F University, 666 Wusu Street, Lin'an, Hangzhou, Zhejiang 311300, China
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Pacheco ID, Walling LL, Atkinson PW. Gene Editing and Genetic Control of Hemipteran Pests: Progress, Challenges and Perspectives. Front Bioeng Biotechnol 2022; 10:900785. [PMID: 35747496 PMCID: PMC9209771 DOI: 10.3389/fbioe.2022.900785] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/09/2022] [Indexed: 12/16/2022] Open
Abstract
The origin of the order Hemiptera can be traced to the late Permian Period more than 230 MYA, well before the origin of flowering plants 100 MY later in during the Cretaceous period. Hemipteran species consume their liquid diets using a sucking proboscis; for phytophagous hemipterans their mouthparts (stylets) are elegant structures that enable voracious feeding from plant xylem or phloem. This adaptation has resulted in some hemipteran species becoming globally significant pests of agriculture resulting in significant annual crop losses. Due to the reliance on chemical insecticides for the control of insect pests in agricultural settings, many hemipteran pests have evolved resistance to insecticides resulting in an urgent need to develop new, species-specific and environmentally friendly methods of pest control. The rapid advances in CRISPR/Cas9 technologies in model insects such as Drosophila melanogaster, Tribolium castaneum, Bombyx mori, and Aedes aegypti has spurred a new round of innovative genetic control strategies in the Diptera and Lepidoptera and an increased interest in assessing genetic control technologies for the Hemiptera. Genetic control approaches in the Hemiptera have, to date, been largely overlooked due to the problems of introducing genetic material into the germline of these insects. The high frequency of CRISPR-mediated mutagenesis in model insect species suggest that, if the delivery problem for Hemiptera could be solved, then gene editing in the Hemiptera might be quickly achieved. Significant advances in CRISPR/Cas9 editing have been realized in nine species of Hemiptera over the past 4 years. Here we review progress in the Hemiptera and discuss the challenges and opportunities for extending contemporary genetic control strategies into species in this agriculturally important insect orderr.
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Affiliation(s)
- Inaiara D. Pacheco
- Department of Entomology, University of California, Riverside, Riverside, CA, United States
| | - Linda L. Walling
- Department of Botany & Plant Sciences, University of California, Riverside, Riverside, CA, United States
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
| | - Peter W. Atkinson
- Department of Entomology, University of California, Riverside, Riverside, CA, United States
- Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, United States
- *Correspondence: Peter W. Atkinson,
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21
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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: 6] [Impact Index Per Article: 3.0] [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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22
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Villarroel CA, González-González A, Alvarez-Baca JK, Villarreal P, Ballesteros GI, Figueroa CC, Cubillos FA, Ramírez CC. Genome sequencing of a predominant clonal lineage of the grain aphid Sitobion avenae. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 143:103742. [PMID: 35183733 DOI: 10.1016/j.ibmb.2022.103742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/15/2022] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
The English grain aphid, Sitobion avenae, is a cosmopolitan pest that feeds on cereals, provoking substantial yield losses by injuring plant tissue and by vectoring plant viruses. Here we report a highly complete, de novo draft genome of the grain aphid using long-read sequencing. We generated an assembly of 2740 contigs with a N50 of 450 kb. We compared this draft genome with that of other aphid species, inspecting gene family evolution, genome-wide positive selection, and searched for horizontal gene transfer events. In addition, we described a recent copy number variant expansion of gene families involving aconitase, ABC transporter, and esterase genes that could be associated with resistance to insecticides and plant chemical defenses. This S. avenae genome obtained from a predominant invasive genotype can provide a framework for studying the spatial-temporal success of these clonal lineages in invaded agroecosystems.
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Affiliation(s)
- Carlos A Villarroel
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile; Instituto de Investigación Interdisciplinaria (I3), Universidad de Talca, Talca, Chile; Millennium Institute for Integrative Biology (iBio), Santiago, Chile.
| | | | | | - Pablo Villarreal
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile; Universidad de Santiago de Chile, Facultad de Química y Biología, Departamento de Biología, Santiago, Chile
| | - Gabriel I Ballesteros
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile; Instituto de Investigación Interdisciplinaria (I3), Universidad de Talca, Talca, Chile
| | - Christian C Figueroa
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile; Centro de Ecología Molecular y Funcional, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Francisco A Cubillos
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile; Universidad de Santiago de Chile, Facultad de Química y Biología, Departamento de Biología, Santiago, Chile
| | - Claudio C Ramírez
- Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile; Centro de Ecología Molecular y Funcional, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
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23
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Byrne S, Schughart M, Carolan JC, Gaffney M, Thorpe P, Malloch G, Wilkinson T, McNamara L. Genome sequence of the English grain aphid, Sitobion avenae and its endosymbiont Buchnera aphidicola. G3 GENES|GENOMES|GENETICS 2022; 12:6456306. [PMID: 34878113 PMCID: PMC9210274 DOI: 10.1093/g3journal/jkab418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022]
Abstract
The English grain aphid, Sitobion avenae, is a major agricultural pest of wheat, barley and oats, and one of the principal vectors of barley yellow dwarf virus leading to significant reductions in grain yield, annually. Emerging resistance to and increasing regulation of insecticides has resulted in limited options for their control. Using PacBio HiFi data, we have produced a high-quality draft assembly of the S. avenae genome; generating a primary assembly with a total assembly size of 475.7 Mb, and an alternate assembly with a total assembly size of 430.8 Mb. Our primary assembly was highly contiguous with only 326 contigs and a contig N50 of 15.95 Mb. Assembly completeness was estimated at 97.7% using BUSCO analysis and 31,007 and 29,037 protein-coding genes were predicted from the primary and alternate assemblies, respectively. This assembly, which is to our knowledge the first for an insecticide resistant clonal lineage of English grain aphid, will provide novel insight into the molecular and mechanistic determinants of resistance and will facilitate future research into mechanisms of viral transmission and aphid behavior.
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Affiliation(s)
- Stephen Byrne
- Teagasc, Crop Science Department, Carlow R93 XE12, Ireland
| | - Maximilian Schughart
- Teagasc, Crop Science Department, Carlow R93 XE12, Ireland
- School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
| | - James C Carolan
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, W23 F2H6, Ireland
| | | | - Peter Thorpe
- School of Medicine, University of St Andrews, North Haugh, KY16 9TF St Andrews, UK
| | - Gaynor Malloch
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Tom Wilkinson
- School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland
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24
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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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25
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Wang Y, Zhang R, Wang M, Zhang L, Shi CM, Li J, Fan F, Geng S, Liu X, Yang D. The first chromosome-level genome assembly of a green lacewing Chrysopa pallens and its implication for biological control. Mol Ecol Resour 2021; 22:755-767. [PMID: 34549894 PMCID: PMC9292380 DOI: 10.1111/1755-0998.13503] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/04/2021] [Accepted: 09/09/2021] [Indexed: 12/13/2022]
Abstract
Many lacewing species (Insecta: Neuroptera) are important predators of pests with great potential in biological control. So far, there is no chromosome‐level published genome available for Neuroptera. Here we report a high‐quality chromosome‐level reference genome for a green lacewing species Chrysopa pallens (Neuroptera: Chrysopidae), which is one of the most important insect natural enemies used in pest biocontrol. The genome was sequenced using a combination of PacBio and Hi‐C technologies and assembled into seven chromosomes with a total size of 517.21 Mb, occupying 96.07% of the genome sequence. A total of 12,840 protein‐coding genes were identified and approximately 206.21 Mb of repeated sequences were annotated. Phylogenetic analyses indicated that C. pallens diverged from its common ancestor with Tribolium castaneum (Coleoptera) approximately 300 million years ago. The gene families involved in digestion, detoxification, chemoreception, carbohydrate metabolism, immunity, nerves and development were significantly expanded, revealing the potential genomic basis for the polyphagia of C. pallens and its role as an excellent biocontrol agent. This high‐quality genome of C. pallens will provide an important genomic resource for future population genetics, evolutionary and phylogenetic investigations of Chrysopidae as well as comparative genomic studies of Neuropterida and other insects.
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Affiliation(s)
- Yuyu Wang
- College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Ruyue Zhang
- College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Mengqing Wang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lisheng Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cheng-Min Shi
- College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Jing Li
- College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Fan Fan
- College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Shuo Geng
- College of Plant Protection, Hebei Agricultural University, Baoding, China
| | - Xingyue Liu
- Department of Entomology, China Agricultural University, Beijing, China
| | - Ding Yang
- Department of Entomology, China Agricultural University, Beijing, China
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26
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Chung SH, Jander G. Inhibition of Rhopalosiphum maidis (Corn Leaf Aphid) Growth on Maize by Virus-Induced Gene Silencing with Sugarcane Mosaic Virus. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2360:139-153. [PMID: 34495513 DOI: 10.1007/978-1-0716-1633-8_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The corn leaf aphid (Rhopalosiphum maidis), a damaging pest of maize (Zea mays), is not controlled by the insecticidal proteins in commercially available transgenic crop varieties. One promising approach is to reduce aphid growth and fecundity by targeting the expression of essential genes using plant-mediated RNA interference (RNAi). Here we describe a method whereby Sugarcane Mosaic Virus (SCMV), a positive-strand RNA virus in the Potyviridae family, is used for virus-induced gene silencing (VIGS) of gene expression in R. maidis. A segment of the R. maidis target gene is cloned into SCMV, maize plants are infected with the transgenic virus, aphids are placed on the virus-infected plants and, after a few days of feeding, decreases in target gene expression and aphid reproduction are assessed. This VIGS method can be used for rapid screening of suitable RNAi targets for aphid pest control, as well as to study the in vivo function of specific aphid genes.
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27
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Chung SH, Bigham M, Lappe RR, Chan B, Nagalakshmi U, Whitham SA, Dinesh‐Kumar SP, Jander G. A sugarcane mosaic virus vector for rapid in planta screening of proteins that inhibit the growth of insect herbivores. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1713-1724. [PMID: 33763921 PMCID: PMC8428830 DOI: 10.1111/pbi.13585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/07/2021] [Accepted: 03/16/2021] [Indexed: 05/03/2023]
Abstract
Spodoptera frugiperda (fall armyworm) is a notorious pest that threatens maize production worldwide. Current control measures involve the use of chemical insecticides and transgenic maize expressing Bacillus thuringiensis (Bt) toxins. Although additional transgenes have confirmed insecticidal activity, limited research has been conducted in maize, at least partially due to the technical difficulty of maize transformation. Here, we describe implementation of a sugarcane mosaic virus (SCMV) vector for rapidly testing the efficacy of both endogenous maize genes and heterologous genes from other organisms for the control of S. frugiperda in maize. Four categories of proteins were tested using the SCMV vector: (i) maize defence signalling proteins: peptide elicitors (Pep1 and Pep3) and jasmonate acid conjugating enzymes (JAR1a and JAR1b); (ii) maize defensive proteins: the previously identified ribosome-inactivating protein (RIP2) and maize proteinase inhibitor (MPI), and two proteins with predicted but unconfirmed anti-insect activities, an antimicrobial peptide (AMP) and a lectin (JAC1); (iii) lectins from other plant species: Allium cepa agglutinin (ACA) and Galanthus nivalis agglutinin (GNA); and (iv) scorpion and spider toxins: peptides from Urodacus yaschenkoi (UyCT3 and UyCT5) and Hadronyche versuta (Hvt). In most cases, S. frugiperda larval growth was reduced by transient SCMV-mediated overexpression of genes encoding these proteins. Additionally, experiments with a subset of the SCMV-expressed genes showed effectiveness against two aphid species, Rhopalosiphum maidis (corn leaf aphid) and Myzus persicae (green peach aphid). Together, these results demonstrate that SCMV vectors are a rapid screening method for testing the efficacy and insecticidal activity of candidate genes in maize.
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Affiliation(s)
| | | | - Ryan R. Lappe
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Barry Chan
- Department of Plant Biology and The Genome CenterCollege of Biological SciencesUniversity of CaliforniaDavisCAUSA
| | - Ugrappa Nagalakshmi
- Department of Plant Biology and The Genome CenterCollege of Biological SciencesUniversity of CaliforniaDavisCAUSA
| | - Steven A. Whitham
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIAUSA
| | - Savithramma P. Dinesh‐Kumar
- Department of Plant Biology and The Genome CenterCollege of Biological SciencesUniversity of CaliforniaDavisCAUSA
| | - Georg Jander
- Boyce Thompson Institute for Plant ResearchIthacaNYUSA
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28
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Singh KS, Cordeiro EMG, Troczka BJ, Pym A, Mackisack J, Mathers TC, Duarte A, Legeai F, Robin S, Bielza P, Burrack HJ, Charaabi K, Denholm I, Figueroa CC, ffrench-Constant RH, Jander G, Margaritopoulos JT, Mazzoni E, Nauen R, Ramírez CC, Ren G, Stepanyan I, Umina PA, Voronova NV, Vontas J, Williamson MS, Wilson ACC, Xi-Wu G, Youn YN, Zimmer CT, Simon JC, Hayward A, Bass C. Global patterns in genomic diversity underpinning the evolution of insecticide resistance in the aphid crop pest Myzus persicae. Commun Biol 2021; 4:847. [PMID: 34234279 PMCID: PMC8263593 DOI: 10.1038/s42003-021-02373-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 06/17/2021] [Indexed: 02/06/2023] Open
Abstract
The aphid Myzus persicae is a destructive agricultural pest that displays an exceptional ability to develop resistance to both natural and synthetic insecticides. To investigate the evolution of resistance in this species we generated a chromosome-scale genome assembly and living panel of >110 fully sequenced globally sampled clonal lines. Our analyses reveal a remarkable diversity of resistance mutations segregating in global populations of M. persicae. We show that the emergence and spread of these mechanisms is influenced by host-plant associations, uncovering the widespread co-option of a host-plant adaptation that also offers resistance against synthetic insecticides. We identify both the repeated evolution of independent resistance mutations at the same locus, and multiple instances of the evolution of novel resistance mechanisms against key insecticides. Our findings provide fundamental insights into the genomic responses of global insect populations to strong selective forces, and hold practical relevance for the control of pests and parasites.
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Affiliation(s)
- Kumar Saurabh Singh
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK
| | - Erick M. G. Cordeiro
- grid.11899.380000 0004 1937 0722Departamento de Entomologia e Acarologia, Escola Superior de Agricultura “Luiz de Queiroz,”, Universidade de São Paulo, Piracicaba, Brazil
| | - Bartlomiej J. Troczka
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK
| | - Adam Pym
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK
| | - Joanna Mackisack
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK
| | - Thomas C. Mathers
- grid.14830.3e0000 0001 2175 7246Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Ana Duarte
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK
| | | | | | - Pablo Bielza
- grid.218430.c0000 0001 2153 2602Departamento de Producción Vegetal, Universidad Politécnica de Cartagena, Cartagena, Spain
| | - Hannah J. Burrack
- grid.40803.3f0000 0001 2173 6074Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC USA
| | - Kamel Charaabi
- Laboratory of Biotechnology and Nuclear Technologies, National Center of Nuclear Sciences and Technologies, Biotechpole of Sidi Thabet, Sidi Thabet, Ariana Tunisia
| | - Ian Denholm
- grid.5846.f0000 0001 2161 9644Department of Biological and Environmental Sciences, University of Hertfordshire, Hatfield, UK
| | - Christian C. Figueroa
- grid.10999.380000 0001 0036 2536Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Richard H. ffrench-Constant
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK
| | - Georg Jander
- grid.5386.8000000041936877XBoyce Thompson Institute, Ithaca, NY USA
| | - John T. Margaritopoulos
- Department of Plant Protection at Volos, Institute of Industrial and Fodder Crops, Hellenic Agricultural Organization ‘DEMETER’, Volos, Greece
| | - Emanuele Mazzoni
- grid.8142.f0000 0001 0941 3192Department of Sustainable Crop Production, Section Sustainable Crop and Food Protection, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Ralf Nauen
- grid.420044.60000 0004 0374 4101Bayer AG, Crop Science Division, R&D, Monheim, Germany
| | - Claudio C. Ramírez
- grid.10999.380000 0001 0036 2536Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Guangwei Ren
- grid.410727.70000 0001 0526 1937Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Ilona Stepanyan
- grid.418094.00000 0001 1146 7878Scientific Center of Zoology and Hydroecology, National Academy of Science, Republic of Armenia, Yerevan, Armenia
| | - Paul A. Umina
- Cesar, Parkville, Victoria Australia ,grid.1008.90000 0001 2179 088XSchool of BioSciences, The University of Melbourne, Parkville, Victoria Australia
| | - Nina V. Voronova
- grid.17678.3f0000 0001 1092 255XThe Department of General Ecology and Methods of Biology Teaching, Belarusian State University, Minsk, Republic of Belarus
| | - John Vontas
- grid.4834.b0000 0004 0635 685XInstitute of Molecular Biology & Biotechnology, Foundation for Research & Technology Hellas, Crete, Greece ,grid.10985.350000 0001 0794 1186Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Martin S. Williamson
- grid.418374.d0000 0001 2227 9389Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK
| | - Alex C. C. Wilson
- grid.26790.3a0000 0004 1936 8606Department of Biology, University of Miami, Coral Gables, FL USA
| | - Gao Xi-Wu
- grid.22935.3f0000 0004 0530 8290Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Young-Nam Youn
- grid.254230.20000 0001 0722 6377Department of Applied Biology, College of Agricultural and Life Science, Chungnam National University, Daejeon, Korea
| | - Christoph T. Zimmer
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK ,grid.420222.40000 0001 0669 0426Present Address: Syngenta Crop Protection, Werk Stein, Schaffhauserstrasse, Stein, Switzerland
| | | | - Alex Hayward
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK
| | - Chris Bass
- grid.8391.30000 0004 1936 8024College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, Cornwall UK
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29
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Li Y, Zhang B, Moran NA. The Aphid X Chromosome Is a Dangerous Place for Functionally Important Genes: Diverse Evolution of Hemipteran Genomes Based on Chromosome-Level Assemblies. Mol Biol Evol 2021; 37:2357-2368. [PMID: 32289166 PMCID: PMC7403619 DOI: 10.1093/molbev/msaa095] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Different evolutionary forces shape gene content and sequence evolution on autosomes versus sex chromosomes. Location on a sex chromosome can favor male-beneficial or female-beneficial mutations depending on the sex determination system and selective pressure on different sexual morphs. An X0 sex determination can lead to autosomal enrichment of male-biased genes, as observed in some hemipteran insect species. Aphids share X0 sex determination; however, models predict the opposite pattern, due to their unusual life cycles, which alternate between all-female asexual generations and a single sexual generation. Predictions include enrichment of female-biased genes on autosomes and of male-biased genes on the X, in contrast to expectations for obligately sexual species. Robust tests of these models require chromosome-level genome assemblies for aphids and related hemipterans with X0 sex determination and obligate sexual reproduction. In this study, we built the first chromosome-level assembly of a psyllid, an aphid relative with X0 sex determination and obligate sexuality, and compared it with recently resolved chromosome-level assemblies of aphid genomes. Aphid and psyllid X chromosomes differ strikingly. In aphids, female-biased genes are strongly enriched on autosomes and male-biased genes are enriched on the X. In psyllids, male-biased genes are enriched on autosomes. Furthermore, functionally important gene categories of aphids are enriched on autosomes. Aphid X-linked genes and male-biased genes are under relaxed purifying selection, but gene content and order on the X is highly conserved, possibly reflecting constraints imposed by unique chromosomal mechanisms associated with the unusual aphid life cycle.
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Affiliation(s)
- Yiyuan Li
- Department of Integrative Biology, University of Texas at Austin, Austin, TX
| | - Bo Zhang
- Department of Integrative Biology, University of Texas at Austin, Austin, TX.,Laboratory of Predatory Mites, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, People's Republic of China
| | - Nancy A Moran
- Department of Integrative Biology, University of Texas at Austin, Austin, TX
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Chung SH, Feng H, Jander G. Engineering pest tolerance through plant-mediated RNA interference. CURRENT OPINION IN PLANT BIOLOGY 2021; 60:102029. [PMID: 33639339 DOI: 10.1016/j.pbi.2021.102029] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 02/04/2021] [Accepted: 02/07/2021] [Indexed: 05/18/2023]
Abstract
Expression of insect-targeted RNA interference (RNAi) constructs in transgenic plants is a promising approach for agricultural pest control. Compared to conventional chemical insecticides, RNAi target specificity is high and the potential for negative environmental effects is low. However, although numerous laboratory studies show insect growth inhibition by double stranded RNA or artificial microRNA, few of these constructs have been moved into commercial application as genetically engineered plants. Variation in RNA degradation, uptake, processing, and systemic transport in insects can influence interspecific and intraspecific differences in RNAi efficacy and the development of resistance to RNAi in agricultural settings. Further research is needed, both to identify optimal gene targets for efficient RNAi in pest species and to reduce the potential for off-target effects in beneficial species.
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Affiliation(s)
- Seung Ho Chung
- Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14853, USA
| | - Honglin Feng
- Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14853, USA
| | - Georg Jander
- Boyce Thompson Institute, 533 Tower Road, Ithaca, NY 14853, USA.
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Peng X, Qu MJ, Wang SJ, Huang YX, Chen C, Chen MH. Chemosensory proteins participate in insecticide susceptibility in Rhopalosiphum padi, a serious pest on wheat crops. INSECT MOLECULAR BIOLOGY 2021; 30:138-151. [PMID: 33188557 DOI: 10.1111/imb.12683] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/27/2020] [Accepted: 11/06/2020] [Indexed: 06/11/2023]
Abstract
Rhopalosiphum padi is a worldwide agricultural pest. Chemosensory proteins (CSPs) are considered to be a type of transporters which can bind chemicals from external environments. Previous research showed that the expression of some insect CSPs were significantly increased after exposure to insecticides, and CSPs were involved in insecticide resistance or susceptibility. However, the role of CSPs in the susceptibility and response of R. padi to insecticides is still unknown. In this study, we identified eight CSP (RpCSP) from R. padi by genome-wide investigation. Seven RpCSP genes had two exons, while RpCSP7 had three exons. qPCR analyses showed that the mRNA levels of the eight RpCSP genes were significantly affected by imidacloprid and beta-cypermethrin in different post-treatment periods. Molecular docking predicted that there were hydrogen bonding sites which played key roles in binding of RpCSP4, RpCSP5, RpCSP6, RpCSP7 and RpCSP10 with imidacloprid and beta-cypermethrin. Knockdown of RpCSP4, RpCSP5, RpCSP6 and RpCSP10 by RNA interference significantly increased the aphid mortality under two sublethal concentrations of imidacloprid. Mortalities under two sublethal concentrations of beta-cypermethrin conditions were significantly higher after injection of R. padi with dsCSP4 and dsCSP6. The results indicate that some RpCSP genes are involved in the insecticide susceptibility of R. padi.
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Affiliation(s)
- X Peng
- Northwest A&F University, State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, China
| | - M J Qu
- Shandong Academy of Agricultural Sciences, Shandong Peanut Research Institute, Qingdao, China
| | - S J Wang
- Northwest A&F University, State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, China
| | - Y X Huang
- Northwest A&F University, State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, China
| | - C Chen
- Northwest A&F University, State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, China
| | - M H Chen
- Northwest A&F University, State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling, China
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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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Yan T, Xu W, Lin J, Duan L, Gao P, Zhang C, Lv X. Combining Multi-Dimensional Convolutional Neural Network (CNN) With Visualization Method for Detection of Aphis gossypii Glover Infection in Cotton Leaves Using Hyperspectral Imaging. FRONTIERS IN PLANT SCIENCE 2021; 12:604510. [PMID: 33659014 PMCID: PMC7917247 DOI: 10.3389/fpls.2021.604510] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/11/2021] [Indexed: 05/08/2023]
Abstract
Cotton is a significant economic crop. It is vulnerable to aphids (Aphis gossypii Glovers) during the growth period. Rapid and early detection has become an important means to deal with aphids in cotton. In this study, the visible/near-infrared (Vis/NIR) hyperspectral imaging system (376-1044 nm) and machine learning methods were used to identify aphid infection in cotton leaves. Both tall and short cotton plants (Lumianyan 24) were inoculated with aphids, and the corresponding plants without aphids were used as control. The hyperspectral images (HSIs) were acquired five times at an interval of 5 days. The healthy and infected leaves were used to establish the datasets, with each leaf as a sample. The spectra and RGB images of each cotton leaf were extracted from the hyperspectral images for one-dimensional (1D) and two-dimensional (2D) analysis. The hyperspectral images of each leaf were used for three-dimensional (3D) analysis. Convolutional Neural Networks (CNNs) were used for identification and compared with conventional machine learning methods. For the extracted spectra, 1D CNN had a fine classification performance, and the classification accuracy could reach 98%. For RGB images, 2D CNN had a better classification performance. For HSIs, 3D CNN performed moderately and performed better than 2D CNN. On the whole, CNN performed relatively better than conventional machine learning methods. In the process of 1D, 2D, and 3D CNN visualization, the important wavelength ranges were analyzed in 1D and 3D CNN visualization, and the importance of wavelength ranges and spatial regions were analyzed in 2D and 3D CNN visualization. The overall results in this study illustrated the feasibility of using hyperspectral imaging combined with multi-dimensional CNN to detect aphid infection in cotton leaves, providing a new alternative for pest infection detection in plants.
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Affiliation(s)
- Tianying Yan
- College of Information Science and Technology, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Ecology Agriculture, Shihezi University, Shihezi, China
| | - Wei Xu
- College of Agriculture, Shihezi University, Shihezi, China
- Xinjiang Production and Construction Corps Key Laboratory of Special Fruits and Vegetables Cultivation Physiology and Germplasm Resources Utilization, Shihezi, China
| | - Jiao Lin
- College of Agriculture, Shihezi University, Shihezi, China
| | - Long Duan
- College of Information Science and Technology, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Ecology Agriculture, Shihezi University, Shihezi, China
| | - Pan Gao
- College of Information Science and Technology, Shihezi University, Shihezi, China
- Key Laboratory of Oasis Ecology Agriculture, Shihezi University, Shihezi, China
| | - Chu Zhang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
- Key Laboratory of Spectroscopy Sensing, Ministry of Agriculture and Rural Affairs, Hangzhou, China
- School of Information Engineering, Huzhou University, Huzhou, China
| | - Xin Lv
- Key Laboratory of Oasis Ecology Agriculture, Shihezi University, Shihezi, China
- College of Agriculture, Shihezi University, Shihezi, China
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Peng X, Wang S, Huang L, Su S, Chen M. Characterization of Rhopalosiphum padi takeout-like genes and their role in insecticide susceptibility. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2021; 171:104725. [PMID: 33357548 DOI: 10.1016/j.pestbp.2020.104725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/23/2020] [Accepted: 10/10/2020] [Indexed: 06/12/2023]
Abstract
Due to the extensive use of chemical insecticides, the field populations of Rhopalosiphum padi, a serious wheat pest worldwide, have developed resistance to insecticides. Therefore, deep understanding of the mechanisms of the aphid's physiological response to insecticides would be of importance for the management of insecticide resistance in pests. Takeout belongs to a protein superfamily found exclusively in insects. Previous research showed that the takeout gene had various functions in insect physiology and behavior. However, few studies have explored the functions of takeout in insect insecticide susceptibility. The susceptibility of R. padi to imidacloprid and beta-cypermethrin was tested. Thirteen takeout-like genes were identified based on the genome database of R. padi. The number of exons was variable in these takeout-like genes, and nine highly conserved amino acids (two Cysteine, two Proline, four Glycine and one Aspartic acid) were identified. Expression levels of takeout-like-2, takeout-like-3, takeout-like-5, takeout-like-8, takeout-like-10 and takeout-like-11 were significantly increased after imidacloprid treatment; seven genes (takeout-like-1, takeout-like-2, takeout-like-5, takeout-like-6, takeout-like-7, takeout-like-8 and takeout-like-11) tended to be upregulated after beta-cypermethrin treatment. RNA interference results showed that the mortalities of R. padi injected with dsTOL-2, dsTOL-5, dsTOL-8, dsTOL-10 and dsTOL-11 were significantly increased after exposure to imidacloprid in comparison with control (injection of dsGFP). Under two sublethal concentrations of beta-cypermethrin, the silencing of takeout-like-2, takeout-like-5 and takeout-like-11 significantly increased the mortalities of R. padi. These results provide evidence for the involvement of takeout-like genes in insecticide susceptibility of R. padi, which improves our understanding the determinant of insecticide susceptibility.
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Affiliation(s)
- Xiong Peng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Suji Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Lei Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Sha Su
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Maohua Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture and Rural Affairs, Northwest A&F University, Yangling 712100, Shaanxi, China.
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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: 11] [Impact Index Per Article: 2.8] [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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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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Dommel M, Oh J, Huguet-Tapia JC, Guy E, Boulain H, Sugio A, Murugan M, Legeai F, Heck M, Smith CM, White FF. Big Genes, Small Effectors: Pea Aphid Cassette Effector Families Composed From Miniature Exons. FRONTIERS IN PLANT SCIENCE 2020; 11:1230. [PMID: 33013944 PMCID: PMC7495047 DOI: 10.3389/fpls.2020.01230] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 07/27/2020] [Indexed: 05/25/2023]
Abstract
Aphids secrete proteins from their stylets that evidence indicates function similar to pathogen effectors for virulence. Here, we describe two small candidate effector gene families of the pea aphid, Acyrthosiphon pisum, that share highly conserved secretory signal peptide coding regions and divergent non-secretory coding sequences derived from miniature exons. The KQY candidate effector family contains eleven members with additional isoforms, generated by alternative splicing. Pairwise comparisons indicate possible four unique KQY families based on coding regions without the secretory signal region. KQY1a, a representative of the family, is encoded by a 968 bp mRNA and a gene that spans 45.7 kbp of the genome. The locus consists of 37 exons, 33 of which are 15 bp or smaller. Additional KQY members, as well as members of the KHI family, share similar features. Differential expression analyses indicate that the genes are expressed preferentially in salivary glands. Proteomic analysis on salivary glands and saliva revealed 11 KQY members in salivary proteins, and KQY1a was detected in an artificial diet solution after aphid feeding. A single KQY locus and two KHI loci were identified in Myzus persicae, the peach aphid. Of the genes that can be anchored to chromosomes, loci are mostly scattered throughout the genome, except a two-gene region (KQY4/KQY6). We propose that the KQY family expanded in A. pisum through combinatorial assemblies of a common secretory signal cassette and novel coding regions, followed by classical gene duplication and divergence.
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Affiliation(s)
- Matthew Dommel
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
| | - Jonghee Oh
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | | | - Endrick Guy
- INRAE, UMR Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Hélène Boulain
- INRAE, UMR Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Akiko Sugio
- INRAE, UMR Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Marimuthu Murugan
- Department of Entomology, Kansas State University, Manhattan, KS, United States
| | - Fabrice Legeai
- INRAE, UMR Institute of Genetics, Environment and Plant Protection, Le Rheu, France
| | - Michelle Heck
- USDA-ARS, Cornell University, Ithaca, NY, United States
| | - C. Michael Smith
- Department of Entomology, Kansas State University, Manhattan, KS, United States
| | - Frank F. White
- Department of Plant Pathology, University of Florida, Gainesville, FL, United States
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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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Silva-Sanzana C, Estevez JM, Blanco-Herrera F. Influence of cell wall polymers and their modifying enzymes during plant-aphid interactions. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3854-3864. [PMID: 31828324 PMCID: PMC7316967 DOI: 10.1093/jxb/erz550] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 12/11/2019] [Indexed: 05/05/2023]
Abstract
Aphids are a major issue for commercial crops. These pests drain phloem nutrients and transmit ~50% of the known insect-borne viral diseases. During aphid feeding, trophic structures called stylets advance toward the phloem intercellularly, disrupting cell wall polymers. It is thought that cell wall-modifying enzymes (CWMEs) present in aphid saliva facilitate stylet penetration through this intercellular polymer network. Additionally, different studies have demonstrated that host settling preference, feeding behavior, and colony performance of aphids are influenced by modulating the CWME expression levels in host plants. CWMEs have been described as critical defensive elements for plants, but also as a key virulence factor for plant pathogens. However, whether CWMEs are elements of the plant defense mechanisms or the aphid infestation process remains unclear. Therefore, in order to better consider the function of CWMEs and cell wall-derived damage-associated molecular patterns (DAMPs) during plant-aphid interactions, the present review integrates different hypotheses, perspectives, and experimental evidence in the field of plant-aphid interactions and discusses similarities to other well-characterized models such as the fungi-plant pathosystems from the host and the attacker perspectives.
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Affiliation(s)
- Christian Silva-Sanzana
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - José M Estevez
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina
| | - Francisca Blanco-Herrera
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Millennium Institute for Integrative Biology (IBio), Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES),Chile
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Züst T, Strickler SR, Powell AF, Mabry ME, An H, Mirzaei M, York T, Holland CK, Kumar P, Erb M, Petschenka G, Gómez JM, Perfectti F, Müller C, Pires JC, Mueller LA, Jander G. Independent evolution of ancestral and novel defenses in a genus of toxic plants ( Erysimum, Brassicaceae). eLife 2020; 9:51712. [PMID: 32252891 PMCID: PMC7180059 DOI: 10.7554/elife.51712] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 03/24/2020] [Indexed: 11/13/2022] Open
Abstract
Phytochemical diversity is thought to result from coevolutionary cycles as specialization in herbivores imposes diversifying selection on plant chemical defenses. Plants in the speciose genus Erysimum (Brassicaceae) produce both ancestral glucosinolates and evolutionarily novel cardenolides as defenses. Here we test macroevolutionary hypotheses on co-expression, co-regulation, and diversification of these potentially redundant defenses across this genus. We sequenced and assembled the genome of E. cheiranthoides and foliar transcriptomes of 47 additional Erysimum species to construct a phylogeny from 9868 orthologous genes, revealing several geographic clades but also high levels of gene discordance. Concentrations, inducibility, and diversity of the two defenses varied independently among species, with no evidence for trade-offs. Closely related, geographically co-occurring species shared similar cardenolide traits, but not glucosinolate traits, likely as a result of specific selective pressures acting on each defense. Ancestral and novel chemical defenses in Erysimum thus appear to provide complementary rather than redundant functions. Plants are often attacked by insects and other herbivores. As a result, they have evolved to defend themselves by producing many different chemicals that are toxic to these pests. As producing each chemical costs energy, individual plants often only produce one type of chemical that is targeted towards their main herbivore. Related species of plants often use the same type of chemical defense so, if a particular herbivore gains the ability to cope with this chemical, it may rapidly become an important pest for the whole plant family. To escape this threat, some plants have gained the ability to produce more than one type of chemical defense. Wallflowers, for example, are a group of plants in the mustard family that produce two types of toxic chemicals: mustard oils, which are common in most plants in this family; and cardenolides, which are an innovation of the wallflowers, and which are otherwise found only in distantly related plants such as foxglove and milkweed. The combination of these two chemical defenses within the same plant may have allowed the wallflowers to escape attacks from their main herbivores and may explain why the number of wallflower species rapidly increased within the last two million years. Züst et al. have now studied the diversity of mustard oils and cardenolides present in many different species of wallflower. This analysis revealed that almost all of the tested wallflower species produced high amounts of both chemical defenses, while only one species lacked the ability to produce cardenolides. The levels of mustard oils had no relation to the levels of cardenolides in the tested species, which suggests that the regulation of these two defenses is not linked. Furthermore, Züst et al. found that closely related wallflower species produced more similar cardenolides, but less similar mustard oils, to each other. This suggests that mustard oils and cardenolides have evolved independently in wallflowers and have distinct roles in the defense against different herbivores. The evolution of insect resistance to pesticides and other toxins is an important concern for agriculture. Applying multiple toxins to crops at the same time is an important strategy to slow the evolution of resistance in the pests. The findings of Züst et al. describe a system in which plants have naturally evolved an equivalent strategy to escape their main herbivores. Understanding how plants produce multiple chemical defenses, and the costs involved, may help efforts to breed crop species that are more resistant to herbivores and require fewer applications of pesticides.
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Affiliation(s)
- Tobias Züst
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | | | | | - Makenzie E Mabry
- Division of Biological Sciences, University of Missouri, Columbia, United States
| | - Hong An
- Division of Biological Sciences, University of Missouri, Columbia, United States
| | | | - Thomas York
- Boyce Thompson Institute, Ithaca, United States
| | | | - Pavan Kumar
- Boyce Thompson Institute, Ithaca, United States
| | - Matthias Erb
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Georg Petschenka
- Institut für Insektenbiotechnologie, Justus-Liebig-Universität Giessen, Giessen, Germany
| | - José-María Gómez
- Department of Functional and Evolutionary Ecology, Estación Experimental de Zonas Áridas (EEZA-CSIC), Almería, Spain
| | - Francisco Perfectti
- Research Unit Modeling Nature, Department of Genetics, University of Granada, Granada, Spain
| | - Caroline Müller
- Department of Chemical Ecology, Bielefeld University, Bielefeld, Germany
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, United States
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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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Chen W, Shakir S, Bigham M, Richter A, Fei Z, Jander G. Genome sequence of the corn leaf aphid (Rhopalosiphum maidis Fitch). Gigascience 2019; 8:5429686. [PMID: 30953568 PMCID: PMC6451198 DOI: 10.1093/gigascience/giz033] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [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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Jiang X, Zhang Q, Qin Y, Yin H, Zhang S, Li Q, Zhang Y, Fan J, Chen J. A chromosome-level draft genome of the grain aphid Sitobion miscanthi. Gigascience 2019; 8:giz101. [PMID: 31430367 PMCID: PMC6701489 DOI: 10.1093/gigascience/giz101] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/24/2019] [Accepted: 07/30/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Sitobion miscanthi is an ideal model for studying host plant specificity, parthenogenesis-based phenotypic plasticity, and interactions between insects and other species of various trophic levels, such as viruses, bacteria, plants, and natural enemies. However, the genome information for this species has not yet to be sequenced and published. Here, we analyzed the entire genome of a parthenogenetic female aphid colony using Pacific Biosciences long-read sequencing and Hi-C data to generate chromosome-length scaffolds and a highly contiguous genome assembly. RESULTS The final draft genome assembly from 33.88 Gb of raw data was ∼397.90 Mb in size, with a 2.05 Mb contig N50. Nine chromosomes were further assembled based on Hi-C data to a 377.19 Mb final size with a 36.26 Mb scaffold N50. The identified repeat sequences accounted for 26.41% of the genome, and 16,006 protein-coding genes were annotated. According to the phylogenetic analysis, S. miscanthi is closely related to Acyrthosiphon pisum, with S. miscanthi diverging from their common ancestor ∼25.0-44.9 million years ago. CONCLUSIONS We generated a high-quality draft of the S. miscanthi genome. This genome assembly should help promote research on the lifestyle and feeding specificity of aphids and their interactions with each other and species at other trophic levels. It can serve as a resource for accelerating genome-assisted improvements in insecticide-resistant management and environmentally safe aphid management.
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Affiliation(s)
- Xin Jiang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
| | - Qian Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
| | - Yaoguo Qin
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
| | - Hang Yin
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
| | - Siyu Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
| | - Qian Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
| | - Yong Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
| | - Jia Fan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
| | - Julian Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China
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