REFERENCES
Altschul, S. (1997). Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Research , 25(17), 3389-3402. https://doi.org/10.1093/nar/25.17.3389
Bao, W., Kojima, K.K., & Kohany, O. (2015). Repbase Update, a database of repetitive elements in eukaryotic genomes. Mobile DNA . 6(11), 1-6. https://doi.org/10.1186/s13100-015-0041-9
Bellinger, P. F., Christiansen, K. A. & Janssens, F. 1996-2021. Checklist of the Collembola of the World. http://www.collembola.org
Blanc G., & Wolfe K. H. (2004). Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes.The Plant Cell , 16(7), 1667-1678. https://doi.org/10.1105/tpc.021345
Broehan, G., Kroeger, T., Lorenzen, M., & Merzendorfer H. (2013). Functional analysis of the ATP-binding cassette (ABC) transporter gene family of Tribolium castaneum . BMC Genomics , 14, 6. https://doi.org/10.1186/1471-2164-14-6
Brůna, T., Lomsadze, A., & Borodovsky, M. (2020). GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins. NAR Genomics and Bioinformatics , 2(2), lqaa026. https://doi.org/10.1093/nargab/lqaa026
Brůna, T., Hoff, K. J., Lomsadze, A., Stanke, M., & Borodovsky, M. (2021). BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. NAR Genomics and Bioinformatics , 3(1), lqaa108. https://doi.org/10.1093/nargab/lqaa108
Buchfink, B., Reuter, K., & Drost, H. G. (2021). Sensitive protein alignments at tree-of-life scale using DIAMOND. Nature Methods , 18, 366-368. https://doi.org/10.1038/s41592-021-01101-x
Bushnell, B. (2014). BBTools software package. https://sourceforge.net/projects/bbmap
Carvunis, A. R., Rolland, T., Wapinski, I., Calderwood, M.A., Yildirim, M. A., Simonis, N., … Vidal, M. (2012). Proto-genes and de novo gene birth. Nature, 487(7407), 370-374. https://doi.org/10.1038/nature11184
Capella-Gutiérrez, S., Silla-Martínez, J. M., & Gabaldón, T. (2009). trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics , 25(15), 1972-1973. https://doi.org/10.1093/bioinformatics/btp348
Chalopin, D., Naville, M., Plard, F., Galiana, D., & Volff, J. N. (2015). Comparative analysis of transposable elements highlights mobilome diversity and evolution in vertebrates. Genome Biology and Evolution , 7(2), 567-580. https://doi.org/10.1093/gbe/evv005
Chan, P. P., & Lowe, T. M. (2019). tRNAscan-SE: searching for tRNA genes in genomic sequences. Methods in Molecular Biology , 1962, 1-14. https://doi.org/10.1007/978-1-4939-9173-0_1
Chen, C., Chen, H., Zhang, Y., Thomas, H. R., Frank, M. H., He, Y., & Xia, R. (2020). TBtools: An integrative toolkit developed for interactive analyses of big biological data. Molecular Plant , 13(8), 1194-1202. https://doi.org/10.1016/j.molp.2020.06.009
Criscuolo, A., & Gribaldo, S. (2010). BMGE (Block Mapping and Gathering with Entropy): selection of phylogenetic informative regions from multiple sequence alignments. BMC Evolutionary Biology , 10(1), 210. https://doi.org/10.1186/1471-2148-10-210
Danecek, P., Bonfield, J. K., Liddle, J., Marshall, J., Ohan, V., Pollard, M. O., Whitwham, A., Keane, T., McCarthy, S. A., Davies, R. M., & Li, H. (2021). Twelve years of SAMtools and BCFtools.GigaScience , 10(2), giab008. https://doi.org/10.1093/gigascience/giab008
Dean, M., Rzhetsky, A., & Allikmets R. (2001). The human ATP-binding cassette (ABC) transporter superfamily. Genome Research , 11(7), 1156-1166. https://doi.org/10.1101/gr.184901
Dermauw, W., & Van Leeuwen, T. (2014). The ABC gene family in arthropods: comparative genomics and role in insecticide transport and resistance. Insect Biochemistry and Molecular Biology , 45, 89-110. https://doi.org/10.1016/j.ibmb.2013.11.001
Dermauw, W., Van Leeuwen, T., & Feyereisen, R. (2020). Diversity and evolution of the P450 family in arthropods. Insect Biochemistry and Molecular Biology , 127, 103490. https://doi.org/10.1016/j.ibmb.2020.103490
Diehl, A. G., Ouyang, N., & Boyle, A. P. (2020). Transposable elements contribute to cell and species-specific chromatin looping and gene regulation in mammalian genomes. Nature Communication , 11, 1796. https://doi.org/10.1038/s41467-020-15520-5
Dierckxsens, N., Mardulyn, P., & Smits, G. (2017). NOVOPlasty: de novo assembly of organelle genomes from whole genome data. Nucleic Acids Research , 45(4), e18. https://doi.org/10.1093/nar/gkw955
Donath, A., Jühling, F., Al-Arab, M., Bernhart, S.H., Reinhardt, F., Stadler, P.F., Middendorf, M., & Bernt, M. (2019). Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes. Nucleic Acids Research, 47(20), 10543-10552.