29.11.2021:
All assemblies you can find in this subfolder were already published previously.
We used them to investigate the evolution of piRNA clusters and share them here for the sake of completeness.
Dmel:
Iso1: The release 6 of the reference strain Iso-1 was obtained from flybase but can be found on NCBI (GenBank assembly accession: GCA_000001215.4) as well. Hoskins RA, Carlson JW, Wan KH, et al. The Release 6 reference sequence of the Drosophila melanogaster genome. Genome Res. 2015;25(3):445-458. doi:10.1101/gr.185579.114
Canton-S: GenBank assembly accession: GCA_015832445.1 Wierzbicki, F., Schwarz, F., Cannalonga, O., & Kofler, R. (2021). Novel quality metrics allow identifying and generating high-quality assemblies of piRNA clusters. Molecular Ecology Resources, 00:1-20. https://doi.org/10.1111/1755-0998.13455
A4: GenBank assembly accession: GCA_003401745.1 Chakraborty, M., Emerson, J.J., Macdonald, S.J. et al. Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits. Nat Commun 10, 4872 (2019). https://doi.org/10.1038/s41467-019-12884-1
Dsim:
wXD1: GenBank assembly accession: GCA_004382185.1 Chakraborty M, Chang CH, Khost DE, et al. Evolution of genome structure in the Drosophila simulans species complex. Genome Res. 2021;31(3):380-396. doi:10.1101/gr.263442.120
m252v2: Was obtained from https://figshare.com/projects/Long-read_based_assembly_and_annotation_of_a_Drosophila_simulans_genome/62174 [last access on Nov 29 2021] Nouhaud P, Long-read based assembly and annotation of a Drosophila simulans genome. bioRxiv 2018; https://doi.org/10.1101/425710
Dmau:
mau12: GenBank assembly accession: GCA_004382145.1 Chakraborty M, Chang CH, Khost DE, et al. Evolution of genome structure in the Drosophila simulans species complex. Genome Res. 2021;31(3):380-396. doi:10.1101/gr.263442.120
Dsech:
sech25: GenBank assembly accession: GCA_004382195.1 Chakraborty M, Chang CH, Khost DE, et al. Evolution of genome structure in the Drosophila simulans species complex. Genome Res. 2021;31(3):380-396. doi:10.1101/gr.263442.120
