Molecular characteristics of five genomes of Buchnera aphidicola – an obligate symbiontof aphids in the fauna of Belarus

Authors

  • Yana P. Kananovich Belarusian State University
  • Raman S. Shulinski Belarusian State University
  • Uladislav Yu. Bandarenka Belarusian State University
  • Dmitrii G. Zhorov Belarusian State University
  • Nina Vladimirovna Voronova-Barte Belarusian State University

Keywords:

aphid symbiont, Buchnera aphidicola, genome assembly, ortholog analysis, bioinformatics

Abstract

This paper presents the results of genome assembly and annotation of the obligate symbiotic bacteria Buchnera aphidicola associated with five aphid species, namely Acyrthosiphon caraganae, Aphis craccivora, Brevicoryne brassicae, Macrosiphum albifrons and Myzus persicae, common in Belarus. These aphid species are pests of food and industrial agricultural plants, and plants that perform an ornamental function, which determines the relevance of studying the bacteria that ensure the viability of insects. The aim of the study was to obtain whole-genome sequences of bacteria and conduct comparative analysis to identify the structural features, degree of genome preservation, and functional deviations that can affect the symbiotic relationship between B. aphidicola and the aphid host. The analysis revealed that the studied B. aphidicola strains have a typical "complete" genome, however, despite the general conservation of genomes, the analysis of orthologs revealed differences in the composition and integrity of a number of genes between the strains. In addition, it was shown that the trpE gene of the B. aphidicola tryptophan plasmid from M. persicae and trpG in the plasmid of the strain from A. craccivora have disturbances in the reading frame, which requires further careful study, since tryptophan synthesis is one of the most important functions of B. aphidicola as an aphid symbiont. In the presence of such a violation, it can be assumed that this function is taken over by one of the secondary symbionts, which is possible given the complementary action of secondary and primary symbionts in the aphid species B. aphidicola, which has a "small" genome. Thus, the study expands the existing understanding of the genomic variability and adaptations of B. aphidicola in various aphid species and emphasizes the importance of an integrated approach to the study of symbiotic systems, including not only genome annotation but also the analysis of potential functional interactions between microbial symbionts, which in the future will allow us to identify the mechanisms of resistance and adaptation of phytophages to various environmental conditions.

Author Biographies

  • Yana P. Kananovich, Belarusian State University

    assistant of junior researcher at the laboratory of bioinformatics and molecular evolution of animals, faculty of biology

  • Raman S. Shulinski, Belarusian State University

    postgraduate student at the department of general ecology and methods of teaching biology, faculty of biology

  • Uladislav Yu. Bandarenka, Belarusian State University

    junior researcher; senior lecturer at the department of cell biology and plant bioengineering, faculty of biology

  • Dmitrii G. Zhorov, Belarusian State University

    docent of the department of zoology, faculty of biology

  • Nina Vladimirovna Voronova-Barte, Belarusian State University

    PhD (biology), docent; head of the laboratory of bioinformatics and molecular evolution of animals, faculty of biology

References

  1. Provorov NA, Onishchuk OP. Microbial symbionts of insects: genetic organization, adaptive role, and evolution. Microbiology. 2018;87(2):151–163. DOI: 10.1134/s002626171802011x.
  2. Douglas AE. Nutritional interactions in insect-microbial symbioses: aphids and their symbiotic bacteria Buchnera. Annual Review of Entomology. 1998;43(1):17–37. DOI: 10.1146/annurev.ento.43.1.17.
  3. Zytynska SE, Weisser WW. The natural occurrence of secondary bacterial symbionts in aphids. Ecological Entomology. 2016;41(1):13–26. DOI: 10.1111/een.12281.
  4. Singh KS, Troczka BJ, Duarte A, et al. The genetic architecture of a host shift: an adaptive walk protected an aphid and its endosymbiont from plant chemical defenses. Science Advances. 2020;6(19):eaba1070. DOI: 10.1126/sciadv.aba1070.
  5. Guo SK, Gong YJ, Chen JC, et al. Increased density of endosymbiotic Buchnera related to pesticide resistance in yellow morph of melon aphid. Journal of Pest Science. 2020;93(4):1281–1294. DOI: 10.1007/s10340-020-01248-0.
  6. Tougeron K, Iltis C. Impact of heat stress on the fitness outcomes of symbiotic infection in aphids: a meta-analysis. Proceedings of the Royal Society B: Biological Sciences. 2022;289:2660. DOI: 10.1098/rspb.2021.2660.
  7. Gao Y, Ren Y, Chen J, et al. Effects of fungicides on fitness and Buchnera endosymbiont density in Aphis gossypii. Pest Management Science. 2023;79(11):4282–4289. DOI: 10.1002/ps.7625.
  8. Zhang YC, Cao WJ, Zhong LR, Godfray HCJ, Liu XD. Host plant determines the population size of an obligate symbiont (Buchnera aphidicola) in aphids. Applied and Environmental Microbiology. 2016;82(8):2336–2346. DOI: 10.1128/aem.04131-15.
  9. Gómez-Valero L, Silva FJ, Christophe Simon J, Latorre A. Genome reduction of the aphid endosymbiont Buchnera aphidicola in a recent evolutionary time scale. Gene. 2007;389(1):87–95. DOI: 10.1016/j.gene.2006.10.001.
  10. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012;9(4):357–359. DOI: 10.1038/ nmeth.1923.
  11. Prjibelski A, Antipov D, Meleshko D, Lapidus A, Korobeynikov A. Using SPAdes de novo assembler. Current Protocols in Bioinformatics. 2020;70(1):e102. DOI: 10.1002/cpbi.102.
  12. Aziz RK, Bartels D, Best AA, et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics. 2008;9(1):75. DOI: 10.1186/1471-2164-9-75.
  13. Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30(14):2068–2069. DOI: 10.1093/ bioinformatics/btu153.
  14. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Research. 2000;28(1):33–36. DOI: 10.1093/nar/28.1.33.
  15. Xu L, Dong Z, Fang L, et al. OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species. Nucleic Acids Research. 2019;47(W1):W52–W58. DOI: 10.1093/nar/gkz333.
  16. Grant JR, Enns E, Marinier E, et al. Proksee: in-depth characterization and visualization of bacterial genomes. Nucleic Acids Research. 2023;51(W1):W484–W492. DOI: 10.1093/nar/gkad326.
  17. Okonechnikov K, Golosova O, Fursov M. Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics. 2012;28(8):1166–1167. DOI: 10.1093/bioinformatics/bts091.
  18. Lu C, Zou T, Liu Q, Huang X. Twenty-nine newly sequenced genomes and a comprehensive genome dataset for the insect endosymbiont Buchnera. Scientific Data. 2024;11(1):673. DOI: 10.1038/s41597-024-03537-0.
  19. Van Ham RCHJ, Kamerbeek J, Palacios C, et al. A. reductive genome evolution in Buchnera aphidicola. Proceedings of the National Academy of Sciences. 2003;100(2):581–586. DOI: 10.1073/pnas.0235981100.
  20. Parvathy ST, Udayasuriyan V, Bhadana V. Codon usage bias. Molecular Biology Reports. 2022;49(1):539–565. DOI: 10.1007/ s11033-021-06749-4.
  21. Iriarte A, Lamolle G, Musto H. Codon usage bias: an endless tale. Journal of Molecular Evolution. 2021;89(9–10):589–593. DOI: 10.1007/s00239-021-10027-z.
  22. Chong RA, Park H, Moran NA. Genome evolution of the obligate endosymbiont Buchnera aphidicola. Molecular Biology and Evolution. 2019;36(7):1481–1489. DOI: 10.1093/molbev/msz082.
  23. Latorre A, Gil R, Silva FJ, Moya A. Chromosomal stasis versus plasmid plasticity in aphid endosymbiont Buchnera aphidicola. Heredity. 2005;95(5):339–347. DOI: 10.1038/sj.hdy.6800716.

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Published

2025-10-06

Issue

No. 3 (2025): Journal of the Belarusian State University. Ecology

Section

The Study and Rehabilitation of Ecosystems

How to Cite

[1]
Kananovich, Y. et al. 2025. Molecular characteristics of five genomes of Buchnera aphidicola – an obligate symbiontof aphids in the fauna of Belarus. Journal of the Belarusian State University. Ecology. 3 (Oct. 2025), 34–41.