Pan-Genome Analysis of Wolbachia, Endosymbiont of Diaphorina citri, Reveals Independent Origin in Asia and North America
Abstract
:1. Introduction
2. Results
2.1. The Genome Characteristics
2.2. Identification of Two wDi Types Based on ANI Analysis, PCoA, and Phylogenetic Analysis
2.3. wDi Possesses a Closed Pan-Genome
2.4. Core Genes Associated with Metabolism, and SNP Analysis Revealing Potential Co-Infection of wDiTW_2
2.5. The Conservation of Pathways in wDi Underlines the Wolbachia–Host Symbiotic Relationship
2.6. Comparative Genomics of NA_wDi and AS_wDi
3. Discussion
4. Materials and Methods
4.1. Genome Assembly and Annotation
4.2. Orthogroup Detection, PCoA, and ANI Analysis
4.3. Pan-Genome Analysis
4.4. Construction of Metabolic Pathways and Functional Analysis
4.5. Phylogenomic Analysis
4.6. Identification of Syntenic and Rearranged Regions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
- Kaur, R.; Shropshire, J.D.; Cross, K.L.; Leigh, B.; Mansueto, A.J.; Stewart, V.; Bordenstein, S.R.; Bordenstein, S.R. Living in the Endosymbiotic World of Wolbachia: A Centennial Review. Cell Host Microbe 2021, 29, 879–893. [Google Scholar] [CrossRef] [PubMed]
- Serbus, L.R.; Casper-Lindley, C.; Landmann, F.; Sullivan, W. The Genetics and Cell Biology of Wolbachia-Host Interactions. Annu. Rev. Genet. 2008, 42, 683–707. [Google Scholar] [CrossRef] [PubMed]
- Brownlie, J.C.; Cass, B.N.; Riegler, M.; Witsenburg, J.J.; Iturbe-Ormaetxe, I.; McGraw, E.A.; O’Neill, S.L. Evidence for Metabolic Provisioning by a Common Invertebrate Endosymbiont, Wolbachia pipientis, during Periods of Nutritional Stress. PLoS Pathog. 2009, 5, e1000368. [Google Scholar] [CrossRef] [PubMed]
- Fenn, K.; Blaxter, M. Are Filarial Nematode Wolbachia Obligate Mutualist Symbionts? Trends Ecol. Evol. 2004, 19, 163–166. [Google Scholar] [CrossRef] [PubMed]
- Foster, J.; Ganatra, M.; Kamal, I.; Ware, J.; Makarova, K.; Ivanova, N.; Bhattacharyya, A.; Kapatral, V.; Kumar, S.; Posfai, J.; et al. The Wolbachia Genome of Brugia malayi: Endosymbiont Evolution within a Human Pathogenic Nematode. PLoS. Biol. 2005, 3, e121. [Google Scholar] [CrossRef] [PubMed]
- Schultz, M.J.; Tan, A.L.; Gray, C.N.; Isern, S.; Michael, S.F.; Frydman, H.M.; Connor, J.H. Wolbachia wStri Blocks Zika Virus Growth at Two Independent Stages of Viral Replication. mBio 2018, 9, e00738-18. [Google Scholar] [CrossRef] [PubMed]
- Gong, J.-T.; Li, Y.; Li, T.-P.; Liang, Y.; Hu, L.; Zhang, D.; Zhou, C.-Y.; Yang, C.; Zhang, X.; Zha, S.-S.; et al. Stable Introduction of Plant-Virus-Inhibiting Wolbachia into Planthoppers for Rice Protection. Curr. Biol. 2020, 30, 4837–4845.e5. [Google Scholar] [CrossRef]
- Halbert, S.E.; Núñez, C.A. Distribution of the Asian Citrus Psyllid, Diaphorina citri Kuwayama (Rhynchota: Psyllidae) in the Caribbean Basin. Fla. Entomol. 2004, 87, 401–402. [Google Scholar] [CrossRef]
- Kuwayama, S. Die Psylliden Japans. Trans. Sopporo Nat. Hist. Soc. 1908, 2, 149–189. [Google Scholar]
- Lima, A.D.C. Insetos do Brasil, Homopteros. Ser. Didat. 4 Esc. Nac. Agron. 1942, 3, 327. [Google Scholar]
- Halbert, S.E. Entomology Section. Triology 1998, 37, 6–7. [Google Scholar]
- French, J.V.; Kahlke, C.J. First Record of the Asian Citrus Psylla, Diaphorina citri Kuwayama (Homoptera:Psyllidae), in Texas. Subtrop. Plant Sci. 2001, 53, 14–15. [Google Scholar]
- Hummel, N.A.; Ferrin, D.M. Asian Citrus Psyllid (Hemiptera: Psyllidae) and Citrus Greening Disease in Louisiana. Southw. Entomol. 2010, 35, 467–469. [Google Scholar] [CrossRef]
- Luis, M.; Collazo, C.; Llauger, R.; Blanco, E.; Peña, I.; López, D.; González, C.; Casín, J.C.; Batista, L.; Kitajima, E.; et al. Occurrence of Citrus Huanglongbing in Cuba and Association of the Disease with Candidatus Liberibacter Asiaticus. J. Plant Pathol. 2009, 91, 709–712. [Google Scholar]
- Ren, S.-L.; Li, Y.-H.; Ou, D.; Guo, Y.-J.; Qureshi, J.A.; Stansly, P.A.; Qiu, B.-L. Localization and Dynamics of Wolbachia Infection in Asian Citrus Psyllid Diaphorina citri, the Insect Vector of the Causal Pathogens of Huanglongbing. MicrobiologyOpen 2018, 7, e00561. [Google Scholar] [CrossRef] [PubMed]
- Jiang, R.-X.; Shang, F.; Jiang, H.-B.; Dou, W.; Cernava, T.; Wang, J.-J. Candidatus Liberibacter Asiaticus: An Important Factor Affecting Bacterial Community Composition and Wolbachia Titers in Asian Citrus Psyllid. Front. Microbiol. 2023, 14, 1109803. [Google Scholar] [CrossRef] [PubMed]
- Jain, M.; Fleites, L.A.; Gabriel, D.W. A Small Wolbachia Protein Directly Represses Phage Lytic Cycle Genes in “Candidatus Liberibacter Asiaticus” within Psyllids. mSphere 2017, 2, e00171-17. [Google Scholar] [CrossRef] [PubMed]
- Lopes, S.A.; Frare, G.F.; Yamamoto, P.T.; Ayres, A.J.; Barbosa, J.C. Ineffectiveness of Pruning to Control Citrus Huanglongbing Caused by Candidatus Liberibacter Americanus. Eur. J. Plant Pathol. 2007, 119, 463–468. [Google Scholar] [CrossRef]
- Lopes, S.A.; Frare, G.F. Graft Transmission and Cultivar Reaction of Citrus to ‘Candidatus Liberibacter Americanus’. Plant Dis. 2008, 92, 21–24. [Google Scholar] [CrossRef]
- Nieberding, C.M.; Olivieri, I. Parasites: Proxies for Host Genealogy and Ecology? Trends Ecol. Evol. 2007, 22, 156–165. [Google Scholar] [CrossRef]
- Wang, Y.; Lu, J.; Beattie, G.A.; Islam, M.R.; Om, N.; Dao, H.T.; Van Nguyen, L.; Zaka, S.M.; Guo, J.; Tian, M.; et al. Phylogeography of Diaphorina citri (Hemiptera: Liviidae) and Its Primary Endosymbiont, ‘Candidatus Carsonella Ruddii’: An Evolutionary Approach to Host–Endosymbiont Interaction. Pest. Manag. Sci. 2018, 74, 2185–2194. [Google Scholar] [CrossRef] [PubMed]
- Saha, S.; Hunter, W.B.; Reese, J.; Morgan, J.K.; Marutani-Hert, M.; Huang, H.; Lindeberg, M. Survey of Endosymbionts in the Diaphorina citri Metagenome and Assembly of a Wolbachia wDi Draft Genome. PLoS ONE 2012, 7, e50067. [Google Scholar] [CrossRef] [PubMed]
- Jolley, K.A.; Bray, J.E.; Maiden, M.C.J. Open-Access Bacterial Population Genomics: BIGSdb Software, the PubMLST.Org Website and Their Applications. Wellcome Open Res. 2018, 3, 124. [Google Scholar] [CrossRef] [PubMed]
- Chu, C.-C.; Hoffmann, M.; Braswell, W.E.; Pelz-Stelinski, K.S. Genetic Variation and Potential Coinfection of Wolbachia among Widespread Asian Citrus Psyllid (Diaphorina citri Kuwayama) Populations. Insect Sci. 2019, 26, 671–682. [Google Scholar] [CrossRef] [PubMed]
- Jain, C.; Rodriguez-R, L.M.; Phillippy, A.M.; Konstantinidis, K.T.; Aluru, S. High Throughput ANI Analysis of 90K Prokaryotic Genomes Reveals Clear Species Boundaries. Nat. Commun. 2018, 9, 5114. [Google Scholar] [CrossRef] [PubMed]
- Emms, D.M.; Kelly, S. OrthoFinder: Phylogenetic Orthology Inference for Comparative Genomics. Genome Biol. 2019, 20, 238. [Google Scholar] [CrossRef] [PubMed]
- Kolde, R. Pheatmap: Pretty Heatmaps. R Package Version 1.0.12. 2019. Available online: https://cran.r-project.org/web/packages/pheatmap/index.html (accessed on 15 March 2024).
- Oksanen, J.; Simpson, G.L.; Blanchet, F.G.; Kindt, R.; Legendre, P.; Minchin, P.R.; O’Hara, R.B.; Solymos, P.; Stevens, M.H.H.; Szoecs, E.; et al. Vegan: Community Ecology Package. R Package Version 2.6-4. 2022. Available online: https://cran.r-project.org/web/packages/vegan/index.html (accessed on 15 March 2024).
- Paradis, E.; Claude, J.; Strimmer, K. APE: Analyses of Phylogenetics and Evolution in R Language. Bioinformatics 2004, 20, 289–290. [Google Scholar] [CrossRef] [PubMed]
- Minh, B.Q.; Schmidt, H.A.; Chernomor, O.; Schrempf, D.; Woodhams, M.D.; von Haeseler, A.; Lanfear, R. IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era. Mol. Biol. Evol. 2020, 37, 1530–1534. [Google Scholar] [CrossRef] [PubMed]
- Cantalapiedra, C.P.; Hernández-Plaza, A.; Letunic, I.; Bork, P.; Huerta-Cepas, J. eggNOG-Mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale. Mol. Biol. Evol. 2021, 38, 5825–5829. [Google Scholar] [CrossRef]
- Huerta-Cepas, J.; Szklarczyk, D.; Heller, D.; Hernández-Plaza, A.; Forslund, S.K.; Cook, H.; Mende, D.R.; Letunic, I.; Rattei, T.; Jensen, L.J.; et al. eggNOG 5.0: A Hierarchical, Functionally and Phylogenetically Annotated Orthology Resource Based on 5090 Organisms and 2502 Viruses. Nucleic Acids Res. 2019, 47, D309–D314. [Google Scholar] [CrossRef]
- Seemann, T. Snippy: Rapid Haploid Variant Calling and Core Genome Alignment. Available online: https://github.com/tseemann/snippy (accessed on 15 March 2024).
- Moriyama, M.; Nikoh, N.; Hosokawa, T.; Fukatsu, T. Riboflavin Provisioning Underlies Wolbachia’s Fitness Contribution to Its Insect Host. mBio 2015, 6, e01732-15. [Google Scholar] [CrossRef]
- Darby, A.C.; Armstrong, S.D.; Bah, G.S.; Kaur, G.; Hughes, M.A.; Kay, S.M.; Koldkjær, P.; Rainbow, L.; Radford, A.D.; Blaxter, M.L.; et al. Analysis of Gene Expression from the Wolbachia Genome of a Filarial Nematode Supports Both Metabolic and Defensive Roles within the Symbiosis. Genome Res. 2012, 22, 2467–2477. [Google Scholar] [CrossRef]
- Lefoulon, E.; Clark, T.; Guerrero, R.; Cañizales, I.; Cardenas-Callirgos, J.M.; Junker, K.; Vallarino-Lhermitte, N.; Makepeace, B.L.; Darby, A.C.; Foster, J.M.; et al. Diminutive, Degraded but Dissimilar: Wolbachia Genomes from Filarial Nematodes Do Not Conform to a Single Paradigm. Microb. Genomics 2020, 6, mgen000487. [Google Scholar] [CrossRef] [PubMed]
- Gu, Z. Complex Heatmap Visualization. iMeta 2022, 1, e43. [Google Scholar] [CrossRef]
- Marçais, G.; Delcher, A.L.; Phillippy, A.M.; Coston, R.; Salzberg, S.L.; Zimin, A. MUMmer4: A Fast and Versatile Genome Alignment System. PLoS Comput. Biol. 2018, 14, e1005944. [Google Scholar] [CrossRef] [PubMed]
- Goel, M.; Sun, H.; Jiao, W.-B.; Schneeberger, K. SyRI: Finding Genomic Rearrangements and Local Sequence Differences from Whole-Genome Assemblies. Genome Biol. 2019, 20, 277. [Google Scholar] [CrossRef]
- Goel, M.; Schneeberger, K. Plotsr: Visualizing Structural Similarities and Rearrangements between Multiple Genomes. Bioinformatics 2022, 38, 2922–2926. [Google Scholar] [CrossRef] [PubMed]
- Carlson, C.R.; ter Horst, A.M.; Johnston, J.S.; Henry, E.; Falk, B.W.; Kuo, Y.-W. High-Quality, Chromosome-Scale Genome Assemblies: Comparisons of Three Diaphorina citri (Asian Citrus Psyllid) Geographic Populations. DNA Res. 2022, 29, dsac027. [Google Scholar] [CrossRef] [PubMed]
- Ju, J.-F.; Bing, X.-L.; Zhao, D.-S.; Guo, Y.; Xi, Z.; Hoffmann, A.A.; Zhang, K.-J.; Huang, H.-J.; Gong, J.-T.; Zhang, X.; et al. Wolbachia Supplement Biotin and Riboflavin to Enhance Reproduction in Planthoppers. ISME J. 2020, 14, 676–687. [Google Scholar] [CrossRef]
- Nikoh, N.; Hosokawa, T.; Moriyama, M.; Oshima, K.; Hattori, M.; Fukatsu, T. Evolutionary Origin of Insect–Wolbachia Nutritional Mutualism. Proc. Natl. Acad. Sci. USA 2014, 111, 10257–10262. [Google Scholar] [CrossRef]
- Green, E.R.; Mecsas, J. Bacterial Secretion Systems: An Overview. In Virulence Mechanisms of Bacterial Pathogens; Kudva, I.T., Cornick, N.A., Plummer, P.J., Zhang, Q., Nicholson, T.L., Bannantine, J.P., Bellaire, B.H., Eds.; ASM Press: Washington, DC, USA, 2016; pp. 213–239. ISBN 978-1-68367-071-1. [Google Scholar]
- Rancès, E.; Voronin, D.; Tran-Van, V.; Mavingui, P. Genetic and Functional Characterization of the Type IV Secretion System in Wolbachia. J. Bacteriol. 2008, 190, 5020–5030. [Google Scholar] [CrossRef]
- Cordaux, R.; Pichon, S.; Ling, A.; Pérez, P.; Delaunay, C.; Vavre, F.; Bouchon, D.; Grève, P. Intense Transpositional Activity of Insertion Sequences in an Ancient Obligate Endosymbiont. Mol. Biol. Evol. 2008, 25, 1889–1896. [Google Scholar] [CrossRef]
- Kaur, R.; Siozios, S.; Miller, W.J.; Rota-Stabelli, O. Insertion Sequence Polymorphism and Genomic Rearrangements Uncover Hidden Wolbachia Diversity in Drosophila suzukii and D. Subpulchrella. Sci. Rep. 2017, 7, 14815. [Google Scholar] [CrossRef]
- Masui, S.; Kuroiwa, H.; Sasaki, T.; Inui, M.; Kuroiwa, T.; Ishikawa, H. Bacteriophage WO and Virus-like Particles in Wolbachia, an Endosymbiont of Arthropods. Biochem. Biophys. Res. Commun. 2001, 283, 1099–1104. [Google Scholar] [CrossRef]
- Bordenstein, S.R. Bacteriophage Flux in Endosymbionts (Wolbachia): Infection Frequency, Lateral Transfer, and Recombination Rates. Mol. Biol. Evol. 2004, 21, 1981–1991. [Google Scholar] [CrossRef]
- Leclercq, S.; Giraud, I.; Cordaux, R. Remarkable Abundance and Evolution of Mobile Group II Introns in Wolbachia Bacterial Endosymbionts. Mol. Biol. Evol. 2011, 28, 685–697. [Google Scholar] [CrossRef]
- Siozios, S.; Ioannidis, P.; Klasson, L.; Andersson, S.G.E.; Braig, H.R.; Bourtzis, K. The Diversity and Evolution of Wolbachia Ankyrin Repeat Domain Genes. PLoS ONE 2013, 8, e55390. [Google Scholar] [CrossRef]
- Li, D.; Liu, C.-M.; Luo, R.; Sadakane, K.; Lam, T.-W. MEGAHIT: An Ultra-Fast Single-Node Solution for Large and Complex Metagenomics Assembly via Succinct de Bruijn Graph. Bioinformatics 2015, 31, 1674–1676. [Google Scholar] [CrossRef]
- Feng, X.; Cheng, H.; Portik, D.; Li, H. Metagenome Assembly of High-Fidelity Long Reads with Hifiasm-Meta. Nat. Methods 2022, 19, 671–674. [Google Scholar] [CrossRef] [PubMed]
- Seemann, T. Prokka: Rapid Prokaryotic Genome Annotation. Bioinformatics 2014, 30, 2068–2069. [Google Scholar] [CrossRef] [PubMed]
- Mistry, J.; Bateman, A.; Finn, R.D. Predicting Active Site Residue Annotations in the Pfam Database. BMC Bioinform. 2007, 8, 298. [Google Scholar] [CrossRef] [PubMed]
- Mistry, J.; Chuguransky, S.; Williams, L.; Qureshi, M.; Salazar, G.A.; Sonnhammer, E.L.L.; Tosatto, S.C.E.; Paladin, L.; Raj, S.; Richardson, L.J.; et al. Pfam: The Protein Families Database in 2021. Nucleic Acids Res. 2021, 49, D412–D419. [Google Scholar] [CrossRef] [PubMed]
- HMMER: Biosequence Analysis Using Profile Hidden Markov Models. Available online: http://hmmer.org/ (accessed on 28 October 2023).
- Wickham, H.; Chang, W.; Henry, L.; Pedersen, T.L.; Takahashi, K.; Wilke, C.; Woo, K.; Yutani, H.; Dunnington, D.; Posit; et al. Ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics. R Packages Version 3.4.2. 2023. Available online: https://cran.r-project.org/web/packages/ggplot2/index.html (accessed on 15 March 2024).
- Elzhov, T.V.; Mullen, K.M.; Spiess, A.-N.; Bolker, B. Minpack.Lm: R Interface to the Levenberg-Marquardt Nonlinear Least-Squares Algorithm Found in MINPACK, Plus Support for Bounds. R Packages Version 1.2-4. 2023. Available online: https://cran.r-project.org/web/packages/minpack.lm/index.html (accessed on 15 March 2024).
- Mendiburu, F. de Agricolae: Statistical Procedures for Agricultural Research. R Packages Version 1.3-7. 2023. Available online: https://cran.r-project.org/web/packages/agricolae/index.html (accessed on 15 March 2024).
- Wu, T.; Hu, E.; Xu, S.; Chen, M.; Guo, P.; Dai, Z.; Feng, T.; Zhou, L.; Tang, W.; Zhan, L.; et al. clusterProfiler 4.0: A Universal Enrichment Tool for Interpreting Omics Data. Innovation 2021, 2, 100141. [Google Scholar] [CrossRef] [PubMed]
- Edgar, R.C. MUSCLE: Multiple Sequence Alignment with High Accuracy and High Throughput. Nucleic Acids Res. 2004, 32, 1792–1797. [Google Scholar] [CrossRef] [PubMed]
- Capella-Gutiérrez, S.; Silla-Martínez, J.M.; Gabaldón, T. trimAl: A Tool for Automated Alignment Trimming in Large-Scale Phylogenetic Analyses. Bioinformatics 2009, 25, 1972–1973. [Google Scholar] [CrossRef] [PubMed]
- Letunic, I.; Bork, P. Interactive Tree Of Life (iTOL) v5: An Online Tool for Phylogenetic Tree Display and Annotation. Nucleic Acids Res. 2021, 49, W293–W296. [Google Scholar] [CrossRef]
- Neupane, S.; Bonilla, S.I.; Manalo, A.M.; Pelz-Stelinski, K.S. Complete de Novo Assembly of Wolbachia Endosymbiont of Diaphorina citri Kuwayama (Hemiptera: Liviidae) Using Long-Read Genome Sequencing. Sci. Rep. 2022, 12, 125. [Google Scholar] [CrossRef]
- Li, H. Aligning Sequence Reads, Clone Sequences and Assembly Contigs with BWA-MEM. arXiv 2013, arXiv:1303.3997. [Google Scholar]
- Garrison, E.; Marth, G. Haplotype-Based Variant Detection from Short-Read Sequencing. arXiv 2012, arXiv:1207.3907. [Google Scholar]
- Croucher, N.J.; Page, A.J.; Connor, T.R.; Delaney, A.J.; Keane, J.A.; Bentley, S.D.; Parkhill, J.; Harris, S.R. Rapid Phylogenetic Analysis of Large Samples of Recombinant Bacterial Whole Genome Sequences Using Gubbins. Nucleic Acids Res. 2015, 43, e15. [Google Scholar] [CrossRef]
- Cingolani, P.; Platts, A.; Wang, L.L.; Coon, M.; Nguyen, T.; Wang, L.; Land, S.J.; Lu, X.; Ruden, D.M. A Program for Annotating and Predicting the Effects of Single Nucleotide Polymorphisms, SnpEff: SNPs in the Genome of Drosophila Melanogaster Strain W1118; Iso-2; Iso-3. Fly 2012, 6, 80–92. [Google Scholar] [CrossRef] [PubMed]
- Yang, H.; Wang, K. Genomic Variant Annotation and Prioritization with ANNOVAR and wANNOVAR. Nat. Protoc. 2015, 10, 1556–1566. [Google Scholar] [CrossRef] [PubMed]
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Zhang, J.; Liu, Q.; Dai, L.; Zhang, Z.; Wang, Y. Pan-Genome Analysis of Wolbachia, Endosymbiont of Diaphorina citri, Reveals Independent Origin in Asia and North America. Int. J. Mol. Sci. 2024, 25, 4851. https://doi.org/10.3390/ijms25094851
Zhang J, Liu Q, Dai L, Zhang Z, Wang Y. Pan-Genome Analysis of Wolbachia, Endosymbiont of Diaphorina citri, Reveals Independent Origin in Asia and North America. International Journal of Molecular Sciences. 2024; 25(9):4851. https://doi.org/10.3390/ijms25094851
Chicago/Turabian StyleZhang, Jiahui, Qian Liu, Liangying Dai, Zhijun Zhang, and Yunsheng Wang. 2024. "Pan-Genome Analysis of Wolbachia, Endosymbiont of Diaphorina citri, Reveals Independent Origin in Asia and North America" International Journal of Molecular Sciences 25, no. 9: 4851. https://doi.org/10.3390/ijms25094851