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Vaughan AL, Parvizi E, Matheson P, McGaughran A, Dhami MK. Current stewardship practices in invasion biology limit the value and secondary use of genomic data. Mol Ecol Resour 2023. [PMID: 37647021 DOI: 10.1111/1755-0998.13858] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/09/2023] [Accepted: 08/14/2023] [Indexed: 09/01/2023]
Abstract
Invasive species threaten native biota, putting fragile ecosystems at risk and having a large-scale impact on primary industries. Growing trade networks and the popularity of personal travel make incursions a more frequent risk, one only compounded by global climate change. With increasing publication of whole-genome sequences lies an opportunity for cross-species assessment of invasive potential. However, the degree to which published sequences are accompanied by satisfactory spatiotemporal data is unclear. We assessed the metadata associated with 199 whole-genome assemblies of 89 invasive terrestrial invertebrate species and found that only 38% of these were derived from field-collected samples. Seventy-six assemblies (38%) reported an 'undescribed' sample origin and, while further examination of associated literature closed this gap to 23.6%, an absence of spatial data remained for 47 of the total assemblies. Of the 76 assemblies that were ultimately determined to be field-collected, associated metadata relevant for invasion studies was predominantly lacking: only 35% (27 assemblies) provided granular location data, and 33% (n = 25) lacked sufficient collection date information. Our results support recent calls for standardized metadata in genome sequencing data submissions, highlighting the impact of missing metadata on current research in invasion biology (and likely other fields). Notably, large-scale consortia tended to provide the most complete metadata submissions in our analysis-such cross-institutional collaborations can foster a culture of increased adherence to improved metadata submission standards and a standard of metadata stewardship that enables reuse of genomes in invasion science.
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Affiliation(s)
- Amy L Vaughan
- Biocontrol & Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
| | - Elahe Parvizi
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Paige Matheson
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Angela McGaughran
- Te Aka Mātuatua/School of Science, University of Waikato, Hamilton, New Zealand
| | - Manpreet K Dhami
- Biocontrol & Molecular Ecology, Manaaki Whenua Landcare Research, Lincoln, New Zealand
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Planthopper salivary sheath protein LsSP1 contributes to manipulation of rice plant defenses. Nat Commun 2023; 14:737. [PMID: 36759625 PMCID: PMC9911632 DOI: 10.1038/s41467-023-36403-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Salivary elicitors secreted by herbivorous insects can be perceived by host plants to trigger plant immunity. However, how insects secrete other salivary components to subsequently attenuate the elicitor-induced plant immunity remains poorly understood. Here, we study the small brown planthopper, Laodelphax striatellus salivary sheath protein LsSP1. Using Y2H, BiFC and LUC assays, we show that LsSP1 is secreted into host plants and binds to salivary sheath via mucin-like protein (LsMLP). Rice plants pre-infested with dsLsSP1-treated L. striatellus are less attractive to L. striatellus nymphs than those pre-infected with dsGFP-treated controls. Transgenic rice plants with LsSP1 overexpression rescue the insect feeding defects caused by a deficiency of LsSP1 secretion, consistent with the potential role of LsSP1 in manipulating plant defenses. Our results illustrate the importance of salivary sheath proteins in mediating the interactions between plants and herbivorous insects.
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Ettinger CL, Byrne FJ, de Souza Pacheco I, Brown DJ, Walling LL, Atkinson PW, Redak RA, Stajich JE. Transcriptome and population structure of glassy-winged sharpshooters (Homalodisca vitripennis) with varying insecticide resistance in southern California. BMC Genomics 2022; 23:721. [PMID: 36273137 PMCID: PMC9587601 DOI: 10.1186/s12864-022-08939-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/13/2022] [Indexed: 12/02/2022] Open
Abstract
Background Homalodisca vitripennis Germar, the glassy-winged sharpshooter, is an invasive insect in California and a critical threat to agriculture through its transmission of the plant pathogen, Xylella fastidiosa. Quarantine, broad-spectrum insecticides, and biological control have been used for population management of H. vitripennis since its invasion and subsequent proliferation throughout California. Recently wide-spread neonicotinoid resistance has been detected in populations of H. vitripennis in the southern portions of California’s Central Valley. In order to better understand potential mechanisms of H. vitripennis neonicotinoid resistance, we performed RNA sequencing on wild-caught insecticide-resistant and relatively susceptible sharpshooters to profile their transcriptome and population structure. Results We identified 81 differentially expressed genes with higher expression in resistant individuals. The significant largest differentially expressed candidate gene linked to resistance status was a cytochrome P450 gene with similarity to CYP6A9. Furthermore, we observed an over-enrichment of GO terms representing functions supportive of roles in resistance mechanisms (cytochrome P450s, M13 peptidases, and cuticle structural proteins). Finally, we saw no evidence of broad-scale population structure, perhaps due to H. vitripennis' relatively recent introduction to California or due to the relatively small geographic scale investigated here. Conclusions In this work, we characterized the transcriptome of insecticide-resistant and susceptible H. vitripennis and identified candidate genes that may be involved in resistance mechanisms for this species. Future work should seek to build on the transcriptome profiling performed here to confirm the role of the identified genes, particularly the cytochrome P450, in resistance in H. vitripennis. We hope this work helps aid future population management strategies for this and other species with growing insecticide resistance. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08939-1.
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Affiliation(s)
- Cassandra L Ettinger
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, USA.
| | - Frank J Byrne
- Department of Entomology, University of California, Riverside, Riverside, CA, USA
| | | | - Dylan J Brown
- Department of Entomology, University of California, Riverside, Riverside, CA, USA
| | - Linda L Walling
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA.,Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
| | - Peter W Atkinson
- Department of Entomology, University of California, Riverside, Riverside, CA, USA.,Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA
| | - Richard A Redak
- Department of Entomology, University of California, Riverside, Riverside, CA, USA
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, USA. .,Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA.
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Li Z, Li Y, Xue AZ, Dang V, Renee Holmes V, Spencer Johnston J, Barrick JE, Moran NA. The genomic basis of evolutionary novelties in a leafhopper. Mol Biol Evol 2022; 39:6677381. [PMID: 36026509 PMCID: PMC9450646 DOI: 10.1093/molbev/msac184] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Evolutionary innovations generate phenotypic and species diversity. Elucidating the genomic processes underlying such innovations is central to understanding biodiversity. In this study, we addressed the genomic basis of evolutionary novelties in the glassy-winged sharpshooter (Homalodisca vitripennis, GWSS), an agricultural pest. Prominent evolutionary innovations in leafhoppers include brochosomes, proteinaceous structures that are excreted and used to coat the body, and obligate symbiotic associations with two bacterial types that reside within cytoplasm of distinctive cell types. Using PacBio long-read sequencing and Dovetail Omni-C technology, we generated a chromosome-level genome assembly for the GWSS and then validated the assembly using flow cytometry and karyotyping. Additional transcriptomic and proteomic data were used to identify novel genes that underlie brochosome production. We found that brochosome-associated genes include novel gene families that have diversified through tandem duplications. We also identified the locations of genes involved in interactions with bacterial symbionts. Ancestors of the GWSS acquired bacterial genes through horizontal gene transfer (HGT), and these genes appear to contribute to symbiont support. Using a phylogenomics approach, we inferred HGT sources and timing. We found that some HGT events date to the common ancestor of the hemipteran suborder Auchenorrhyncha, representing some of the oldest known examples of HGT in animals. Overall, we show that evolutionary novelties in leafhoppers are generated by the combination of acquiring novel genes, produced both de novo and through tandem duplication, acquiring new symbiotic associations that enable use of novel diets and niches, and recruiting foreign genes to support symbionts and enhance herbivory.
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Affiliation(s)
- Zheng Li
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Yiyuan Li
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA.,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 Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo, Zhejiang, China
| | - Allen Z Xue
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
| | - Vy Dang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - V Renee Holmes
- Department of Entomology, Texas A&M University, College Station, TX,USA
| | | | - Jeffrey E Barrick
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Nancy A Moran
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX, USA
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Metagenome-Assembled Genomes of Bacterial Symbionts Associated with Insecticide-Resistant and -Susceptible Individuals of the Glassy-Winged Sharpshooter (Homalodisca vitripennis). Microbiol Resour Announc 2022; 11:e0050622. [PMID: 35708345 PMCID: PMC9302190 DOI: 10.1128/mra.00506-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The role of microbes in insecticide resistance is an emerging question. Here, we describe six metagenome-assembled genomes (MAGs) associated with the glassy-winged sharpshooter (Homalodisca vitripennis [Germar, 1821]) (Hemiptera, Cicadellidae). MAGs representing the obligate symbionts Candidatus Sulcia muelleri and Candidatus Baumannia cicadellinicola and the facultative symbiont Wolbachia were obtained from imidacloprid-resistant and imidacloprid-susceptible sharpshooters.
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de Souza Pacheco I, Doss ALA, Vindiola BG, Brown DJ, Ettinger CL, Stajich JE, Redak RA, Walling LL, Atkinson PW. Efficient CRISPR/Cas9-mediated genome modification of the glassy-winged sharpshooter Homalodisca vitripennis (Germar). Sci Rep 2022; 12:6428. [PMID: 35440677 PMCID: PMC9018754 DOI: 10.1038/s41598-022-09990-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/28/2022] [Indexed: 12/26/2022] Open
Abstract
CRISPR/Cas9 technology enables the extension of genetic techniques into insect pests previously refractory to genetic analysis. We report the establishment of genetic analysis in the glassy-winged sharpshooter (GWSS), Homalodisca vitripennis, which is a significant leafhopper pest of agriculture in California. We use a novel and simple approach of embryo microinjection in situ on the host plant and obtain high frequency mutagenesis, in excess of 55%, of the cinnabar and white eye pigmentation loci. Through pair matings, we obtained 100% transmission of w and cn alleles to the G3 generation and also established that both genes are located on autosomes. Our analysis of wing phenotype revealed an unexpected discovery of the participation of pteridine pigments in wing and wing-vein coloration, indicating a role for these pigments beyond eye color. We used amplicon sequencing to examine the extent of off-target mutagenesis in adults arising from injected eggs, which was found to be negligible or non-existent. Our data show that GWSS can be easily developed as a genetic model system for the Hemiptera, enabling the study of traits that contribute to the success of invasive pests and vectors of plant pathogens. This will facilitate novel genetic control strategies.
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Affiliation(s)
| | - Anna-Louise A Doss
- Department of Entomology, University of California, Riverside, CA, 92521, USA
| | - Beatriz G Vindiola
- Department of Entomology, University of California, Riverside, CA, 92521, USA
| | - Dylan J Brown
- Department of Entomology, University of California, Riverside, CA, 92521, USA
| | - Cassandra L Ettinger
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA, 92521, USA
| | - Jason E Stajich
- Department of Microbiology & Plant Pathology, University of California, Riverside, CA, 92521, USA.,Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Richard A Redak
- Department of Entomology, University of California, Riverside, CA, 92521, USA
| | - Linda L Walling
- Department of Botany & Plant Sciences, University of California, Riverside, CA, 92521, USA. .,Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
| | - Peter W Atkinson
- Department of Entomology, University of California, Riverside, CA, 92521, USA. .,Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
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