Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity

Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity
Repository accompanying "Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity" manuscript

microRNA curation
Potential miRNA clusters, generated using Shortstack (https://github.com/MikeAxtell/ShortStack), are analyzed with miRNA_curation.py. An example run of the miRNA curation can be performed by running the 'example_run/explore_all.sh' and 'example_run/refine_all.sh' scripts in order. A sample of the sRNA sequences from D. discoideum is included in the 'example/example_sizeselected_data' folder. A sample of miRNA candidates are included in 'example_run/pot-miRNAs_merged.fa' to facilitate the example run.
Prerequisites: Python 3, Biopython, RNAlib, matplotlib, numpy

microRNA analysis
Following miRNA curation, high confidence miRNAs are identified and further analysed in amoeba_miRNAevo.Rmd. The data for the analysis is located in  'data_in' and are mostly derived from the miRNA_curation.py script and other scripts located in the 'helper_scripts' folder. The plots generated in the analysis is located in the 'plots' folder. Tables and other data generated from the analysis are located in the 'data_out' folder. In order to perform the miRNA conservation search, refer to the 'helper_scripts/miRNA_conservation_search/' folder.
Access genomes/annotations
For Dictyostelium firmibasis, the genome was de-novo sequenced and is located in 'data_in/novel_assembly'. Assembly was done using Flye v2.9.1 in nano-hq mode, and two rounds of long-read polishing were done using Medaka v1.7.2. The filtered reads used for assembly can be accessed from NCBI BioProject PRJNA972620. The Acanthamoeba castellanii genome and annotation were accessed at https://www.doi.org/10.5281/zenodo.680005. The other genomes and annotations for this study were accessed from NCBI and can be downloaded using the 'get_references.sh' script located in the helper_scripts folder.