Moschetti R., Dimitri P., Caizzi R., Junakovic N. 2010. Genomic instability of I elements of Drosophila mela-nogaster in absence of dysgenic crosses. PLoS One. 5 (10), e13142.
Article PubMed PubMed Central Google Scholar
Coline G., Theron E., Brasset E., Vaury C. 2014. History of the discovery of a master locus producing piR-NAs: The flamenco/COM locus in Drosophila melanogaster. Front. Genet. 5, 257.
Article PubMed Central Google Scholar
Lee Y.S., Nakahara K., Pham J.W., Kim K., He Z., Sontheimer E.J., Carthew R.W. 2004. Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways. Cell. 117 (1), 69–81.
Article CAS PubMed Google Scholar
Brennecke J., Aravin A.A., Stark A., Dus M., Kellis M., Sachidanandam R., Hannon G.J. 2007. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell. 128 (6), 1089‒1103.
Article CAS PubMed Google Scholar
Aravin A.A., Hannon G.J., Brennecke J. 2007. The piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science. 318 (5851), 761–764.
Article CAS PubMed Google Scholar
Siomi H., Siomi M.C. 2009. On the road to reading the RNA-interference code. Nature. 457 (7228), 396–404.
Article CAS PubMed Google Scholar
Cox D.N., Chao A., Baker J., Chang L., Qiao D., Lin H. 1998. A novel class of evolutionarily conserved genes defined by piwi are essential for stem cell self-renewal. Genes Dev. 12 (23), 3715–3727.
Article CAS PubMed PubMed Central Google Scholar
Baumgartner L., Handler D., Platzer S. W., Yu C., Duchek P., Brennecke J. 2022. The Drosophila ZAD zinc finger protein Kipferl guides Rhino to piRNA clusters. Elife. 11, e80067.
Article CAS PubMed PubMed Central Google Scholar
Czech B., Malone C.D., Zhou R., Stark A., Schlingeheyde C., Dus M., Perrimon N., Kellis M., Wohlschlegel J.A., Sachidanandam R., Hannon G.J., Brennecke J. 2008. An endogenous small interfering RNA pathway in Drosophila. Nature. 453 (7196), 798‒802.
Article CAS PubMed PubMed Central Google Scholar
Flutre T., Duprat E., Feuillet C., Quesneville H. 2011. Considering transposable element diversification in de novo annotation approaches. PLoS One. 6 (1), e16526.
Article CAS PubMed PubMed Central Google Scholar
Benson D.A., Cavanaugh M., Clark K., Karsch-Mizrachi I., Lipman D.J., Ostell J., Sayers E.W. 2012. GenBank. Nucleic Acids Res. 41, D36–D42.
Article PubMed PubMed Central Google Scholar
Larkin A., Marygold S.J., Antonazzo G., Attrill H., dos Santos G., Garapati P.V., Goodman J.L., Gra-mates L.S., Millburn G., Strelets V.B., Tabone C.J., Thurmond J., FlyBase Consortium 2021. FlyBase: Updates to the Drosophila melanogaster knowledge base. Nucleic Acids Res. 49, D899–D907.
Rech G.E. 2021. Fasta sequences for the Drosophila melanogaster manually curated transposable elements (MCTE) library. https://www.lareferencia.info/vufind/Record/ES_a77af0688d4516b156d77549ef83f0e 4#core.
Simmons M.J., Thorp M.W., Buschette J.T., Peterson K., Cross E.W., Bjorklund E.L. 2010. Maternal impairment of transposon regulation in Drosophila melanogaster by mutations in the genes aubergine, piwi and Suppressor of variegation 205. Genet. Res. 92 (4), 261–272.
Vasil’eva L.A., Antonenko O.V., Zakharov I.K. 2011. Role of transposable elements in the genome of Drosophila melanogaster. Russ. J. Genet.: Appl. Res. 1, 463–488.
Rech G.E., Radío S., Guirao-Rico S., Aguilera L., Horvath V., Green L., Lindstadt H., Jamilloux V., Quesneville H., González J. 2022. Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila. Nat. Commun. 13 (1), 1948.
Article CAS PubMed PubMed Central Google Scholar
Mohamed M., Dang N.T., Ogyama Y., Burlet N., Mugat B., Boulesteix M., Mérel V, Veber P., Salces-Ortiz J., Severac D., Pélisson A., Vieira C., Sabot F., Fablet M., Chambeyron S. 2020. A transposon story: From TE content to TE dynamic invasion of Drosophila genomes using the single-molecule sequencing technology from Oxford nanopore. Cells. 9 (8), 1776.
Article CAS PubMed PubMed Central Google Scholar
Rang F.J., Kloosterman W.P., de Ridder J. 2018. From squiggle to basepair: Computational approaches for improving nanopore sequencing read accuracy. Genome Biol. 19 (1), 90.
Article PubMed PubMed Central Google Scholar
Li H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint arXiv:1303.3997.
Li H. 2018. Minimap2: Pairwise alignment for nucleotide sequences. Bioinformatics. 34 (18), 3094–3100.
Article CAS PubMed PubMed Central Google Scholar
Sedlazeck F.J., Rescheneder P., Smolka M., Fang H., Nattestad M., von Haeseler A., Schatz M.C. 2018. Accurate detection of complex structural variations using single-molecule sequencing. Nat. Methods. 15 (6), 461–468.
Article CAS PubMed PubMed Central Google Scholar
Kiełbasa S.M., Wan R., Sato K., Horton P., Frith M.C. 2011. Adaptive seeds tame genomic sequence comparison. Genome Res. 21 (3), 487–493.
Article PubMed PubMed Central Google Scholar
Chaisson M.J., Tesler G. 2012. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): Application and theory. BMC Bioinf. 13 (1), 238.
Xiao C.L., Chen Y., Xie S.Q., Chen K.N., Wang Y., Han Y., Luo F., Xie Z. 2017. MECAT: Fast mapping, error correction, and de novo assembly for single-molecule sequencing reads. Nat. Methods. 14 (11), 1072–1074.
Article CAS PubMed Google Scholar
Lavrenov A.R., Nefedova L.N., Romanova N.I., Kim A.I. 2014. Expression of hp1 family genes and their plausible role in formation of flamenco phenotype in D. melanogaster. Biochemistry (Moscow). 79 (11), 1267‒1272.
Kukushkina I.V., Makhnovskii P.A., Nefedova L.N., Balakireva E.A., Romanova N.I., Kuzmin I.V., Lavrenov A.R., Kim A.I. 2020. A study of the fertility of a Drosophila melanogaster MS strain with impaired transposition control of the gypsy mobile element. Mol. Biol. (Moscow). 54 (3), 361‒373.
Kim A.I., Lyubomirskaya N.V., Belyaeva E.S., Shostack N.G., Ilyin Y.V. 1994. The introduction of a transpositionally active copy of retrotransposon GYPSY into the stable strain of Drosophila melanogaster causes genetic instability. Mol. Gen. Genet. 242 (4), 472–477.
Article CAS PubMed Google Scholar
Kukushkina I.V., Makhnovskii P.A., Nefedova L.N., Milyaeva P.A., Kuzmin I.V., Lavrenov A.R., Kim A.I. 2020. Analysis of transcriptome of Drosophila melanogaster strains with disrupted control of gypsy retrotransposon transposition. Russ. J. Genet. 56 (5), 562‒571.
Andrews S., Krueger F., Segonds-Pichon A., Biggins L., Krueger C., Wingett S. 2010. FastQC. A quality control tool for high throughput sequence data. 370.
Bolger A.M., Lohse M., Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 30 (15), 2114‒2120.
Article CAS PubMed PubMed Central Google Scholar
Kim D., Pertea G., Trapnell C., Pimentel H., Kelley R., Salzberg S.L. 2013. TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14 (4), 1‒13.
Anders S., Pyl P.T., Huber W. 2015. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics. 31 (2), 166‒169.
Article CAS PubMed Google Scholar
Anders S., Huber W. 2012. Differential expression of RNA-Seq data at the gene level–the DESeq package. Eur. Mol. Biol. Lab. (Heidelberg). 10, f1000research.
Koren S., Walenz B.P., Berlin K., Miller J.R., Bergman N.H., Phillippy A.M. 2017. Canu: Scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27 (5), 722–736.
留言 (0)