Vol. 63 No. 1 (2024)
Articles

Complete genome assemblies of several Xylella fastidiosa subspecies multiplex strains reveals high phage content and novel plasmids

PDF
  • María Pilar VELASCO-AMO ,
  • Luis F. ARIAS-GIRALDO ,
  • Blanca B. LANDA
María Pilar VELASCO-AMO
Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas (CSIC), Córdoba
Bio
Luis F. ARIAS-GIRALDO
Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas (CSIC), Córdoba
Bio
Blanca B. LANDA
Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas (CSIC), Córdoba, Spain
DOI: https://doi.org/10.36253/phyto-14931

Published 2024-02-17

Keywords

  • quarantine phytopathogens,
  • prophages,
  • hybrid assembly

How to Cite

[1]
M. P. VELASCO-AMO, L. F. ARIAS-GIRALDO, and B. B. LANDA, “Complete genome assemblies of several Xylella fastidiosa subspecies multiplex strains reveals high phage content and novel plasmids”, Phytopathol. Mediterr., vol. 63, no. 1, pp. 15–23, Feb. 2024.

Copyright (c) 2024 María Pilar VELASCO-AMO , Luis F. ARIAS-GIRALDO , Blanca B. LANDA

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.

Crossref
Scopus
Google Scholar
Europe PMC

Abstract

The Gram-negative bacterium Xylella fastidiosa (Xf) was originally found in the Americas, but has now been identified in more than 20 countries across America, Asia, and Europe. This plant pathogen is currently listed as a priority pest in Europe due to its socio-economic and ecological impacts. Within the three Xf subspecies fastidiosa, multiplex and pauca, subsp. multiplex displays a notably wider range of host plants than the other two subspecies. Comparative genomics may allow determination of how Xf subsp. multiplex adapts to new and diverse hosts and environments, so it is important that more genomes of this subspecies are defined. Twelve complete closed genomes sequences of Xf subsp. multiplex were obtained using a hybrid assembly approach combining Illumina and Oxford Nanopore technologies. The combined use of Canu and Unicycler assemblers enabled identification and closure of several plasmid sequences with high similarity to other plasmids described in strains of Xf subsp. fastidiosa and subsp. pauca. The analysis also revealed prophage sequences and contigs outside the chromosomes, annotated as phages. These new genomes, in conjunction with those existing in GenBank, will facilitate exploration of the evolutionary dynamics of Xf subsp. multiplex, its host adaptation mechanisms, and the potential emergence of novel strains of this important plant pathogen.

PDF

Downloads

Download data is not yet available.

Metrics

Metrics Loading ...

References

  1. Almeida R.P.P., Nunney L., 2015. How do plant diseases caused by Xylella fastidiosa emerge? Plant Disease 99: 1457–1467. https://doi.org/10.1094/PDIS-02-15-0159-FE DOI: https://doi.org/10.1094/PDIS-02-15-0159-FE
  2. Alonge M., Lebeigle L., Kirsche M., Jenike K., Ou S., … Soyk S., 2022. Automated assembly scaffolding using RagTag elevates a new tomato system for high-throughput genome editing. Genome Biology 23: 258. https://doi.org/10.1186/s13059-022-02823-7 DOI: https://doi.org/10.1186/s13059-022-02823-7
  3. Aziz R.K., Bartels D., Best A.A., DeJongh M., Disz T., … Zagnitko O., 2008. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics 9: 75. https://doi.org/10.1186/1471-2164-9-75 DOI: https://doi.org/10.1186/1471-2164-9-75
  4. Burbank L.P., Van Horn C.R., 2017. Conjugative plasmid transfer in Xylella fastidiosa is dependent on tra and trb Operon Functions. Journal of Bacteriology 199: e00388-17. https://doi.org/10.1128/JB.00388-17 DOI: https://doi.org/10.1128/JB.00388-17
  5. Castillo A.I., Almeida R.P.P., 2023. The multifaceted role of homologous recombination in a fastidious bacterial plant pathogen. Applied and Environmental Microbiology 89: e00439-23. https://doi.org/10.1128/aem.00439-23 DOI: https://doi.org/10.1128/aem.00439-23
  6. Chen J., Civerolo E.L., 2008. Morphological evidence for phages in Xylella fastidiosa. Virology Journal 5: 75. https://doi.org/10.1186/1743-422X-5-75 DOI: https://doi.org/10.1186/1743-422X-5-75
  7. Chen, Zhou Y., Chen Y., Gu J., 2018. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34: i884–i890. https://doi.org/10.1093/bioinformatics/bty560 DOI: https://doi.org/10.1093/bioinformatics/bty560
  8. Darriba D., Posada D., Kozlov A.M., Stamatakis A., Morel B., Flouri T., 2020. ModelTest-NG: A new and scalable tool for the selection of DNA and protein evolutionary models. Molecular Biology and Evolution 37: 291–294. https://doi.org/10.1093/molbev/msz189 DOI: https://doi.org/10.1093/molbev/msz189
  9. Denancé N., Legendre B., Briand M., Olivier V., Boisseson C. de, … Jacques M.-A., 2017. Several subspecies and sequence types are associated with the emergence of Xylella fastidiosa in natural settings in France. Plant Pathology 66: 1054–1064. https://doi.org/10.1111/ppa.12695 DOI: https://doi.org/10.1111/ppa.12695
  10. Denancé N., Briand M., Gaborieau R., Gaillard S., Jacques M.-A., 2019. Identification of genetic relationships and subspecies signatures in Xylella fastidiosa. BMC Genomics 20: 239. https://doi.org/10.1186/s12864-019-5565-9 DOI: https://doi.org/10.1186/s12864-019-5565-9
  11. Desprez-Loustau M.-L., Balci Y., Cornara D., Gonthier P., Robin C., Jacques M.-A., 2021. Is Xylella fastidiosa a serious threat to European forests? Forestry: An International Journal of Forest Research 94: 1–17. https://doi.org/10.1093/forestry/cpaa029 DOI: https://doi.org/10.1093/forestry/cpaa029
  12. Dupas E., Durand K., Rieux A., Briand M., Pruvost O., … Jacques M.-A., 2023. Suspicions of two bridgehead invasions of Xylella fastidiosa subsp. multiplex in France. Communications Biology 6: 1–13. https://doi.org/10.1038/s42003-023-04499-6 DOI: https://doi.org/10.1038/s42003-023-04499-6
  13. EFSA E.F.S., Gibin D., Pasinato L., Delbianco A., 2023. Update of the Xylella spp. host plant database – systematic literature search up to 31 December 2022. EFSA Journal 21: e08061. https://doi.org/10.2903/j.efsa.2023.8061 DOI: https://doi.org/10.2903/j.efsa.2023.8061
  14. EPPO, 2023. PM 7/24 (5) Xylella fastidiosa. EPPO Bulletin 53: 205–276. https://doi.org/10.1111/epp.12923. DOI: https://doi.org/10.1111/epp.12923
  15. Guilhabert M.R., Stewart V.J., Kirkpatrick B.C., 2006. Characterization of putative rolling-circle plasmids from the Gram-negative bacterium Xylella fastidiosa and their use as shuttle vectors. Plasmid 55: 70–80. https://doi.org/10.1016/j.plasmid.2005.06.004 DOI: https://doi.org/10.1016/j.plasmid.2005.06.004
  16. Harris J.L., Di Bello P.L., Lear M., Balci Y., 2014. Bacterial Leaf Scorch in the district of Columbia: Distribution, host range, and presence of Xylella fastidiosa among urban trees. Plant Disease 98: 1611–1618. https://doi.org/10.1094/PDIS-02-14-0158-SR DOI: https://doi.org/10.1094/PDIS-02-14-0158-SR
  17. Johnson J., Soehnlen M., Blankenship H.M., 2023. Long read genome assemblers struggle with small plasmids. Microbial Genomics 9. https://doi.org/10.1099/mgen.0.001024 DOI: https://doi.org/10.1099/mgen.0.001024
  18. Jolley K.A., Bray J.E., Maiden M.C.J., 2018. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Research 3: 124. https://doi.org/10.12688/wellcomeopenres.14826.1 DOI: https://doi.org/10.12688/wellcomeopenres.14826.1
  19. Kant P., Brohier N., Mann R., Rigano L., Taylor R., … Constable F., 2023. High-quality full genome assembly of historic Xylella fastidiosa strains from ICMP collection using a hybrid sequencing approach. Microbiology Resource Announcements 12: e00536-23. https://doi.org/10.1128/MRA.00536-23 DOI: https://doi.org/10.1128/MRA.00536-23
  20. Katoh K., Standley D.M., 2013. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in performance and usability. Molecular Biology and Evolution 30: 772–780. https://doi.org/10.1093/molbev/mst010 DOI: https://doi.org/10.1093/molbev/mst010
  21. Landa B.B., Castillo A.I., Giampetruzzi A., Kahn A., Román-Écija M., … Almeida R.P.P., 2019. Emergence of a plant pathogen in Europe associated with multiple intercontinental introductions. Applied and Environmental Microbiology 86: e01521-19, /aem/86/3/AEM.01521-19.atom. https://doi.org/10.1128/AEM.01521-19 DOI: https://doi.org/10.1128/AEM.01521-19
  22. Moralejo E., Gomila M., Montesinos M., Borràs D., Pascual A., … Olmo D., 2020. Phylogenetic inference enables reconstruction of a long-overlooked outbreak of almond leaf scorch disease (Xylella fastidiosa) in Europe. Communications Biology 3: 1–13. https://doi.org/10.1038/s42003-020-01284-7 DOI: https://doi.org/10.1038/s42003-020-01284-7
  23. Nguyen L.-T., Schmidt H.A., von Haeseler A., Minh B.Q., 2015. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution 32: 268–274. https://doi.org/10.1093/molbev/msu300 DOI: https://doi.org/10.1093/molbev/msu300
  24. Nunney L., Elfekih S., Stouthamer R., 2012. The importance of multilocus sequence typing: cautionary tales from the bacterium Xylella fastidiosa. Phytopathology 102: 456–460. https://doi.org/10.1094/PHYTO-10-11-0298 DOI: https://doi.org/10.1094/PHYTO-10-11-0298
  25. O’Leary M.L., Arias-Giraldo L.F., Burbank L.P., De La Fuente L., Landa B.B., 2022. Complete genome resources for Xylella fastidiosa strains AlmaEM3 and BB08-1 reveal prophage-associated structural variation among blueberry-infecting strains. Phytopathology®, Scientific Societies 112: 732–736. https://doi.org/10.1094/PHYTO-08-21-0317-A DOI: https://doi.org/10.1094/PHYTO-08-21-0317-A
  26. O’Leary M.L., Burbank L.P., 2023. Natural recombination among type I restriction-modification systems creates diverse genomic methylation patterns among Xylella fastidiosa strains. Applied and Environmental Microbiology 89: e01873-22. https://doi.org/10.1128/aem.01873-22. DOI: https://doi.org/10.1128/aem.01873-22
  27. Parks D.H., Imelfort M., Skennerton C.T., Hugenholtz P., Tyson G.W., 2015. CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research 25: 1043–1055. https://doi.org/10.1101/gr.186072.114 DOI: https://doi.org/10.1101/gr.186072.114
  28. Pierry P.M., Uceda-Campos G., Feitosa-Junior O.R., Martins-Junior J., de Santana W.O., … da-Silva A.M., 2020. Genetic Diversity of Xylella fastidiosa plasmids assessed by comparative genomics. Tropical Plant Pathology 45: 342–360. https://doi.org/10.1007/s40858-020-00359-4 DOI: https://doi.org/10.1007/s40858-020-00359-4
  29. Potnis N., Kandel P.P., Merfa M.V., Retchless A.C., Parker J.K., … De La Fuente L., 2019. Patterns of inter- and intrasubspecific homologous recombination inform eco-evolutionary dynamics of Xylella fastidiosa. The ISME Journal 13: 2319–2333. https://doi.org/10.1038/s41396-019-0423-y. DOI: https://doi.org/10.1038/s41396-019-0423-y
  30. Rogers E.E., Stenger D.C., 2012. A conjugative 38 kb plasmid is present in multiple subspecies of Xylella fastidiosa. PLoS ONE 7. https://doi.org/10.1371/journal.pone.0052131 DOI: https://doi.org/10.1371/journal.pone.0052131
  31. Sabot F., 2022. On the importance of metadata when sharing and opening data. BMC Genomic Data 23: 79. https://doi.org/10.1186/s12863-022-01095-1 DOI: https://doi.org/10.1186/s12863-022-01095-1
  32. Sánchez B., Barreiro-Hurle J., Soto Embodas I., Rodriguez-Cerezo E., 2019. The impact Indicator for Priority Pests (I2P2) – A tool for ranking pests according to Regulation (EU) 2016/2031. Publications Office of the European Union.
  33. Schaad N.W., Postnikova E., Lacy G., Fatmi M., Chang C.-J., 2004. Xylella fastidiosa subspecies: X. fastidiosa subsp. fastidiosa subsp. nov., X. fastidiosa subsp. multiplex subsp. nov., and X. fastidiosa subsp. pauca subsp. nov. Systematic and Applied Microbiology 27: 290–300. https://doi.org/10.1078/0723-2020-00263 DOI: https://doi.org/10.1078/0723-2020-00263
  34. Schuenzel E.L., Scally M., Stouthamer R., Nunney L., 2005. A multigene phylogenetic study of clonal diversity and divergence in north American strains of the plant pathogen Xylella fastidiosa. Applied and Environmental Microbiology 71: 3832–3839. https://doi.org/10.1128/AEM.71.7.3832-3839.2005 DOI: https://doi.org/10.1128/AEM.71.7.3832-3839.2005
  35. Seemann T., 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics (Oxford, England) 30: 2068–2069. https://doi.org/10.1093/bioinformatics/btu153 DOI: https://doi.org/10.1093/bioinformatics/btu153
  36. Sherald J.L., Wells J.M., Hurtt S.S., Kostka S.J., 1987. Association of fastidious, xylem-inhabiting bacteria with leaf scorch in red maple. Plant Disease 71: 930–933. DOI: https://doi.org/10.1094/PD-71-0930
  37. Tatusova T., DiCuccio M., Badretdin A., Chetvernin V., Nawrocki E.P., … Ostell J., 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Research 44: 6614–6624. https://doi.org/10.1093/nar/gkw569 DOI: https://doi.org/10.1093/nar/gkw569
  38. Vanhove M., Retchless A.C., Sicard A., Rieux A., Coletta-Filho H.D., … Almeida R.P., 2019. Genomic Diversity and Recombination among Xylella fastidiosa Subspecies. Applied and Environmental Microbiology 85: e02972-18. https://doi.org/10.1128/AEM.02972-18 DOI: https://doi.org/10.1128/AEM.02972-18
  39. Varani A., Souza R.C., Nakaya H.I., Lima W.C. de, Almeida L.G.P. de, … Sluys M.-A.V., 2008. Origins of the Xylella fastidiosa prophage-like regions and their impact in genome differentiation. PLOS ONE 3: e4059. https://doi.org/10.1371/journal.pone.0004059 DOI: https://doi.org/10.1371/journal.pone.0004059
  40. Varani A., Monteiro-Vitorello C.B., Nakaya H.I., Van Sluys M.-A., 2013. The role of prophage in plant-pathogenic bacteria. Annual Review of Phytopathology 51: 429–451. https://doi.org/10.1146/annurev-phyto-081211-173010 DOI: https://doi.org/10.1146/annurev-phyto-081211-173010
  41. Velasco-Amo M.P., Vicent A., Zarco-Tejada P.J., Navas-Cortés J.A., Landa B.B., 2022. Recent research accomplishments on early detection of Xylella fastidiosa outbreaks in the Mediterranean Basin. Phytopathologia Mediterranea 61: 549–561. https://doi.org/10.36253/phyto-14171 DOI: https://doi.org/10.36253/phyto-14171
  42. Wick R.R., Holt K.E., 2022. Polypolish: Short-read polishing of long-read bacterial genome assemblies. PLOS Computational Biology 18: e1009802. https://doi.org/10.1371/journal.pcbi.1009802 DOI: https://doi.org/10.1371/journal.pcbi.1009802
  43. Wick R.R., Judd L.M., Gorrie C.L., Holt K.E., 2017. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLOS Computational Biology 13: e1005595. https://doi.org/10.1371/journal.pcbi.1005595 DOI: https://doi.org/10.1371/journal.pcbi.1005595
  44. Wood D.E., Lu J., Langmead B., 2019. Improved metagenomic analysis with Kraken 2. Genome Biology 20: 257. https://doi.org/10.1186/s13059-019-1891-0 DOI: https://doi.org/10.1186/s13059-019-1891-0
  45. Xu M., Guo L., Gu S., Wang O., Zhang R., … Zhang Y., 2020. TGS-GapCloser: A fast and accurate gap closer for large genomes with low coverage of error-prone long reads. GigaScience 9: giaa094. https://doi.org/10.1093/gigascience/giaa094 DOI: https://doi.org/10.1093/gigascience/giaa094
  46. Yu G., Smith D.K., Zhu H., Guan Y., Lam T.T.-Y., 2017. ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 8: 28–36. https://doi.org/10.1111/2041-210X.12628 DOI: https://doi.org/10.1111/2041-210X.12628
  47. Yuan X., Morano L., Bromley R., Spring-Pearson S., Stouthamer R., Nunney L., 2010. Multilocus Sequence Typing of Xylella fastidiosa causing Pierce’s Disease and Oleander Leaf Scorch in the United States. Phytopathology 100: 601–611. https://doi.org/10.1094/PHYTO-100-6-0601 DOI: https://doi.org/10.1094/PHYTO-100-6-0601
  48. Zimin A.V., Salzberg S.L., 2020. The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies. PLOS Computational Biology 16: e1007981. https://doi.org/10.1371/journal.pcbi.1007981 DOI: https://doi.org/10.1371/journal.pcbi.1007981