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Analysis of Transcriptome of Drosophila melanogaster Strains with Disrupted Control of gypsy Retrotransposon Transposition

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Abstract

To study the causes of impaired control of the activity of mobile genetic elements in the strains with the flamenco phenotype SS (w, flamenco mutant) and MS (w, flamenco mutant, active copy of gypsy), sequencing of these transcriptomes was performed. The D32 strain was used as control (laboratory wild type strain). An algorithm was developed for the search for amino acid substitutions in high-throughput RNA sequencing data using a triplet code for analysis. With the help of this algorithm, seven nonsense mutations were detected. The allele-specific PCR method confirmed the presence of five of the seven nonsense mutations found in silico. However, the detected nonsense mutations are not associated with the flamenco phenotype. A search for mutations in 89 genes of the RNA interference system in the SS and MS strains relative to the reference BDGP6 genome and the wild type D32 strain was carried out. No deletions, insertions, nonsense codons, and other disorders that can unambiguously lead to a change in the function of the gene are detected. To identify genes with specific expression for the strains with the flamenco phenotype, the transcriptomes of the SS and MS strains were compared with the control strains D-32, OregonR, and w1118. A set of 25 genes with differential expression was identified, among which two genes, sosie and CR45822, significantly changed the expression in the SS and MS strains. Both genes, directly or indirectly, are involved in oogenesis. Thus, the expression of the sosie and CR45822 genes can be used as a marker of the flamenco phenotype in the SS and MS strains.

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Funding

This study was supported by the Russian Foundation for Basic Research (project no. 17-04-01250).

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Authors and Affiliations

  1. Moscow State University, 119234, Moscow, Russia

    I. V. Kukushkina, L. N. Nefedova, P. A. Milyaeva, I. V. Kuzmin, A. R. Lavrenov & A. I. Kim

  2. Institute for Biomedical Problems, Russian Academy of Sciences, 123007, Moscow, Russia

    P. A. Makhnovskii

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  1. I. V. Kukushkina
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Correspondence to L. N. Nefedova or A. I. Kim.

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Kukushkina, I.V., Makhnovskii, P.A., Nefedova, L.N. et al. Analysis of Transcriptome of Drosophila melanogaster Strains with Disrupted Control of gypsy Retrotransposon Transposition. Russ J Genet 56, 562–571 (2020). https://doi.org/10.1134/S1022795420050087

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