CRISPR/Cas9-mediated mutagenesis of the white-eye gene in the tephritid pest Bactrocera zonata

Albert Nazarov , Tamir Partosh , Flavia Krsticevic , Dimitris Rallis , Yael Arien , Guy Ostrovsky , Reut Madar Kramer , Eyal Halon , Alfred M. Handler , Simon W. Baxter , Yoav Gazit , Kostas D. Mathiopoulos , Gur Pines , Philippos A. Papathanos

Insect Science ›› 2026, Vol. 33 ›› Issue (2) : 476 -490.

PDF (1921KB)
Insect Science ›› 2026, Vol. 33 ›› Issue (2) :476 -490. DOI: 10.1111/1744-7917.70150
SPECIAL ISSUE ARTICLE
CRISPR/Cas9-mediated mutagenesis of the white-eye gene in the tephritid pest Bactrocera zonata
Author information +
History +
PDF (1921KB)

Abstract

Bactrocera zonata is a highly invasive agricultural pest that causes extensive damage to fruit crops. The Sterile Insect Technique (SIT), a species-specific and environmentally friendly pest control method, significantly benefits from the availability of Genetic Sexing Strains (GSSs) that enable efficient mass production of males for sterile release. However, no GSS currently exists for B. zonata limiting SIT applications targeting this important invasive pest. Here, we report two key advancements toward GSS development in this species. First, we present a high-quality, chromosome-level genome assembly from male B. zonata, identifying two scaffolds derived from the Y chromosome, which represent potential targets for future male-specific genetic engineering. Second, we demonstrate the feasibility of CRISPR/Cas9 genome editing in B. zonata by generating stable, homozygous white-eye mutants through targeted disruption of the conserved white-eye gene. This visible, recessive phenotype serves as a proof-of-concept for developing selectable markers in this species. Together, these results provide foundational genomic and genetic tools to support the development of GSSs in B. zonata, advancing the potential for sustainable, genetics-based pest control strategies.

Keywords

Bactrocera zonata / CRISPR/Cas9 / genetic sexing strain / sterile insect technique / tephritidae / white eye

Cite this article

Download citation ▾
Albert Nazarov, Tamir Partosh, Flavia Krsticevic, Dimitris Rallis, Yael Arien, Guy Ostrovsky, Reut Madar Kramer, Eyal Halon, Alfred M. Handler, Simon W. Baxter, Yoav Gazit, Kostas D. Mathiopoulos, Gur Pines, Philippos A. Papathanos. CRISPR/Cas9-mediated mutagenesis of the white-eye gene in the tephritid pest Bactrocera zonata. Insect Science, 2026, 33 (2) : 476-490 DOI:10.1111/1744-7917.70150

登录浏览全文

4963

注册一个新账户 忘记密码

References

[1]

Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. Journal of Molecular Biology, 215, 403–410.

[2]

ArimaGenomics. (2023) Arima Genomics Mapping Pipeline. Available from https://github.com/ArimaGenomics/mapping_pipeline/tree/master.

[3]

Augustinos, A.A., Targovska, A., Cancio-Martinez, E., Schorn, E., Franz, G., Cáceres, C. et al. (2017) Ceratitis capitata genetic sexing strains: laboratory evaluation of strains from mass-rearing facilities worldwide. Entomologia Experimentalis et Applicata, 164, 305–317.

[4]

Bachtrog, D. (2013) Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration. Nature Reviews Genetics, 14, 113–124.

[5]

Bayega, A., Djambazian, H., Tsoumani, K.T., Gregoriou, M.E., Sagri, E., Drosopoulou, E. et al. (2020) De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly. BMC Genomics, 21, 259.

[6]

Bourtzis, K. and Vreysen, M.J.B. (2021) Sterile insect technique (SIT) and its applications. Insects, 12, 638.

[7]

Carraretto, D., Aketarawong, N., Di Cosimo, A., Manni, M., Scolari, F., Valerio, F. et al. (2020) Transcribed sex-specific markers on the Y chromosome of the oriental fruit fly, Bactrocera dorsalis. BMC Genetics, 21, 125.

[8]

Carvalho, A.B. and Clark, A.G. (2013) Efficient identification of Y chromosome sequences in the human and Drosophila genomes. Genome Research, 23, 1894–1907.

[9]

Choo, A., Crisp, P., Saint, R., O'Keefe, L.V. and Baxter, S.W. (2018) CRISPR/Cas9-mediated mutagenesis of the white gene in the tephritid pest Bactrocera tryoni. Journal of Applied Entomology, 142, 52–58.

[10]

Congrains, C., Sim, S.B., Paulo, D.F., Corpuz, R.L., Kauwe, A.N., Simmonds, T.J. et al. (2024) Chromosome-scale genome of the polyphagous pest Anastrepha ludens (Diptera: Tephritidae) provides insights on sex chromosome evolution in Anastrepha. G3-Genes Genomes Genetics, 14, jkae239.

[11]

De Meyer, M., Mohamed, S. and White, I.M. (2023) Invasive fruit fly pests in Africa. Available from https://www.africamuseum.be/fruitfly/AfroAsia.htm.

[12]

Deschepper, P., Vanbergen, S., Esselens, L., Terblanche, J.S., Karsten, M., Snyman, M. et al. (2024) A new genome sequence resource for five invasive fruit flies of agricultural concern: Ceratitis capitata, C. quilicii, C. rosa, Zeugodacus cucurbitae and Bactrocera zonata (Diptera, Tephritidae). F1000Research, 13, 1492.

[13]

Den Dunnen, J.T., Dalgleish, R., Maglott, D.R., Hart, R.K., Greenblatt, M.S., McGowan-Jordan, J. et al. (2016) HGVS recommendations for the description of sequence variants: 2016 update. Human Mutation, 37, 564–569.

[14]

El-Gendy, I. (2022) Bactrocera zonata (peach fruit fly). CABI Compendium. https://doi.org/10.1079/cabicompendium.17694.

[15]

Ewart, G.D. and Howells, J. (1998) ABC transporters involved in transport of eye pigment precursors in Drosophila melanogaster. Methods in Enzymology, 292, 213–224.

[16]

Falk, S., Crowley, L.M. and Medd, N.C. (2024) The genome sequence of a tephritid fruit fly, Merzomyia westermanni Meigen 1826. Wellcome Open Research, 9, 480.

[17]

Fan, Z.Z., Ma, Q., Ma, S.Y., Zhao, Y.X., Liu, J.F. and Zheng, Y.Z. (2023) Maleness-on-the-Y (MoY) orthologue is a key regulator of male sex determination in Zeugodacus cucurbitae (Diptera: Tephritidae). Journal of Integrative Agriculture, 22, 505–513.

[18]

Flynn, J.M., Hubley, R., Goubert, C., Rosen, J., Clark, A.G., Feschotte, C. et al. (2020) RepeatModeler2 for automated genomic discovery of transposable element families. Proceedings of the National Academy of Sciences USA, 117, 9451–9457.

[19]

Franz, G., Bourtzis, K. and Cáceres, C. (2021) Practical and operational genetic sexing systems based on classical genetic approaches in fruit flies, an example for other species amenable to large-scale rearing for the sterile insect technique. In Sterile Insect Technique (eds. V.A. Dyck, J. Hendrichs & A.S. Robinson), pp. 575–604. CRC Press, Boca Raton, Florida, USA.

[20]

Gazit, Y. and Akiva, R. (2017) Toxicity of malathion and spinosad to Bactrocera zonata and Ceratitis capitata (Diptera: Tephritidae). Florida Entomologist, 100, 385–389.

[21]

Gel, B. and Serra, E. (2017) karyoploteR: An R/Bioconductor package to plot customizable genomes displaying arbitrary data. Bioinformatics, 33, 3088–3090.

[22]

Guan, D., McCarthy, S.A., Wood, J., Howe, K., Wang, Y. and Durbin, R. (2020) Identifying and removing haplotypic duplication in primary genome assemblies. Bioinformatics, 36, 2896–2898.

[23]

Guo, S., Liu, B., He, J., Zhao, Z., Zhang, R. and Li, Z. (2023) Chromosome-level genome assembly of an important wolfberry fruit fly (Neoceratitis asiatica Becker). Scientific Data, 10, 675.

[24]

Hall, A.B., Qi, Y., Timoshevskiy, V., Sharakhova, M.V., Sharakhov, I.V. and Tu, Z. (2013) Six novel Y chromosome genes in Anopheles mosquitoes discovered by independently sequencing males and females. BMC Genomics, 14, 273.

[25]

Jiang, F., Liang, L., Wang, J. and Zhu, S. (2022) Chromosome-level genome assembly of Bactrocera dorsalis reveals its adaptation and invasion mechanisms. Communications Biology, 5, 25.

[26]

Kaiser, V.B. and Bachtrog, D. (2010) Evolution of sex chromosomes in insects. Annual Review of Genetics, 44, 91–112.

[27]

Kolmogorov, M., Yuan, J., Lin, Y. and Pevzner, P.A. (2019) Assembly of long, error-prone reads using repeat graphs. Nature Biotechnology, 37, 540–546.

[28]

Koskinioti, P., Augustinos, A.A., Carvalho, D.O., Misbah-ul-Haq, M., Pillwax, G., de la Fuente, L.D. et al. (2021) Genetic sexing strains for the population suppression of the mosquito vector Aedes aegypti. Philosophical Transactions of the Royal Society B-Biological Sciences, 376, 20190808.

[29]

Langmead, B., Trapnell, C., Pop, M. and Salzberg, S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology, 10, R25.

[30]

Li, H. (2018) Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34, 3094–3100.

[31]

Li, H. and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754–1760.

[32]

Liu, P., Zheng, W., Qiao, J., Li, Z., Deng, Z., Yuan, Y. et al. (2022) Early embryonic transcriptomes of Zeugodacus tau provide insight into sex determination and differentiation genes. Insect Science, 29, 915–931.

[33]

Mak, Q.X.C., Wick, R.R., Holt, J.M. and Wang, J.R. (2023) Polishing de novo nanopore assemblies of bacteria and eukaryotes with FMLRC2. Molecular Biology and Evolution, 40, msad048.

[34]

Meccariello, A., Monti, S.M., Romanelli, A., Colonna, R., Primo, P., Inghilterra, M.G. et al. (2017) Highly efficient DNA-free gene disruption in the agricultural pest Ceratitis capitata by CRISPR-Cas9 ribonucleoprotein complexes. Scientific Reports, 7, 10061.

[35]

Meccariello, A., Salvemini, M., Primo, P., Hall, B., Koskinioti, P., Dalíková, M. et al. (2019) Maleness-on-the-Y (MoY) orchestrates male sex determination in major agricultural fruit fly pests. Science, 365, 1457–1460.

[36]

Meccariello, A., Tsoumani, K.T., Gravina, A., Primo, P., Buonanno, M., Mathiopoulos, K.D. et al. (2020) Targeted somatic mutagenesis through CRISPR/Cas9 ribonucleoprotein complexes in the olive fruit fly, Bactrocera oleae. Archives of Insect Biochemistry and Physiology, 104, e21667.

[37]

Musapa, M., Kumwenda, T., Mkulama, M., Chishimba, S., Norris, D.E., Thuma, P.E. et al. (2013) A simple Chelex protocol for DNA extraction from Anopheles spp. Journal of Visualized Experiments, 71, e3281.

[38]

Ni, W.L., Li, Z.H., Chen, H.J., Wan, F.H., Qu, W.W., Zhang, Z. et al. (2012) Including climate change in pest risk assessment: the peach fruit fly, Bactrocera zonata (Diptera: Tephritidae). Bulletin of Entomological Research, 102, 173–183.

[39]

NPPO of France. (2023) New incursions of Bactrocera dorsalis and B. zonata in France. EPPO Reporting Service, 2023/038. Available from https://gd.eppo.int/reporting/article-7520.

[40]

Palmer, J.M. and Stajich, J. (2020) Funannotate v1.8.1: Eukaryotic Genome Annotation. Zenodo, https://doi.org/10.5281/ZENODO.1134477.

[41]

Paulo, D.F., Cha, A.Y., Kauwe, A.N., Curbelo, K., Corpuz, R.L., Simmonds, T.J. et al. (2022) A unified protocol for CRISPR/Cas9-mediated gene knockout in tephritid fruit flies led to the recreation of white eye and white puparium phenotypes in the melon fly. Journal of Economic Entomology, 115, 2110–2115.

[42]

Perez, G., Barber, G.P., Benet-Pages, A., Casper, J., Clawson, H., Diekhans, M. et al. (2025) The UCSC Genome Browser database: 2025 update. Nucleic Acids Research, 53, D1243–D1249.

[43]

Quinlan, A.R. and Hall, I.M. (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841–842.

[44]

Rallis, D., Tsoumani, K.T., Krsticevic, F., Papathanos, P.A., Mathiopoulos, K.D. and Papanicolaou, A. (2023) Revisiting Y-chromosome detection methods: R-CQ and KAMY efficiently identify Y chromosome sequences in Tephritidae insect pests. BioRxiv, https://doi.org/10.1101/2023.10.27.564325.

[45]

Rathore, S., Hassert, J., Clark-Hachtel, C.M., Stahl, A., Tomoyasu, Y. and Buschbeck, E.K. (2020) RNA interference in aquatic beetles as a powerful tool for manipulating gene expression at specific developmental time points. Journal of Visualized Experiments, 159, e61477.

[46]

Rossler, Y. and Rosenthal, H. (1992) Genetics of the Mediterranean fruit fly (Diptera: Tephritidae): morphological mutants on chromosome five. Annals of the Entomological Society of America, 85, 525–531.

[47]

Simão, F.A., Waterhouse, R.M., Ioannidis, P., Kriventseva, E.V. and Zdobnov, E.M. (2015) BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics, 31, 3210–3212.

[48]

Sim, S.B., Congrains, C., Velasco-Cuervo, S.M., Corpuz, R.L., Kauwe, A.N., Scheffler, B. et al. (2024) Genome report: chromosome-scale genome assembly of the West Indian fruit fly Anastrepha obliqua (Diptera: Tephritidae). G3-Genes Genomes Genetics, 14, jkae024.

[49]

Sim, S.B. and Geib, S.M. (2017) A chromosome-scale assembly of the Bactrocera cucurbitae genome provides insight to the genetic basis of white pupae. G3-Genes Genomes Genetics, 7, 1927–1940.

[50]

Tarailo-Graovac, M. and Chen, N. (2009) Using RepeatMasker to identify repetitive elements in genomic sequences. Current Protocols in Bioinformatics, 4, 4.10.1–4.10.14.

[51]

Torti, C., Malacrida, A., Yannopoulos, G., Louis, C. and Gasperi, G. (1994) Hybrid dysgenesis-like phenomena in the medfly, Ceratitis capitata (Diptera, Tephritidae). Journal of Heredity, 85, 92–99.

[52]

Venkat, B. and Carl, G. (2020) Interactive exploration of genomic conservation. In Graphics Interface Conference 2020 28−29 May. Available from https://graphicsinterface.org/proceedings/gi2020/gi2020-9/.

[53]

Walker, B.J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S. et al. (2014) Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE, 9, e112963.

[54]

Wang, Y.T., Cao, L.J., Chen, J.C., Song, W., Ma, W.H., Yang, J.F. et al. (2023) Chromosome-level genome assembly of an agricultural pest Zeugodacus tau (Diptera: Tephritidae). Scientific Data, 10, 848.

[55]

Weinberg, E. (2007) A device to hold zebrafish embryos during microinjection. In The Zebrafish Book (ed. M. Westerfield), pp. 1–5, 5th edn. University of Oregon Press, Eugene.

[56]

White, I.M. and Elson-Harris, M.M. (1992) Fruit Flies of Economic Significance: Their Identification and Bionomics. CAB International, Wallingford.

[57]

Wu, S., Wu, J., Lei, Q., He, D., Jiang, X., Ye, C. et al. (2024) The assembly of Y chromosome reveals amplification of genes regulating male fertility in Bactrocera dorsalis. BioRxiv, https://doi.org/10.1101/2024.08.01.606120.

[58]

Yesmin, F., Uddin, M., Rahman, G. and Hasanuzzaman, M. (2019) Identification of larval salivary gland polytene chromosomes of the peach fruit fly, Bactrocera zonata (Saunders) (Diptera: Tephritidae). Journal of Biological Control, 33, 295–302.

[59]

Zhao, S., Xing, Z., Liu, Z., Liu, Y., Liu, X., Chen, Z. et al. (2019) Efficient somatic and germline genome engineering of Bactrocera dorsalis by the CRISPR/Cas9 system. Pest Management Science, 75, 1921–1932.

[60]

Zhou, C., McCarthy, S.A. and Durbin, R. (2023) YaHS: yet another Hi-C scaffolding tool. Bioinformatics, 39, btac808.

[61]

Zingore, K.M., Sithole, G., Abdel-Rahman, E.M., Mohamed, S.M., Ekesi, S., Tanga, C.M. et al. (2020) Global risk of invasion by Bactrocera zonata: Implications on horticultural crop production under changing climatic conditions. PLoS ONE, 15, e0243047.

RIGHTS & PERMISSIONS

2025 The Author(s). Insect Science published by John Wiley & Sons Australia, Ltd on behalf of Institute of Zoology, Chinese Academy of Sciences.

PDF (1921KB)

0

Accesses

0

Citation

Detail

Sections
Recommended

/