File description:
sc.mlc.cns.sgl.utg.scga7.importdb.fa.gz* - Genome assembly
sc.mlc.cns.sgl.utg.scga7.CDS.codingseq.fasta.gz* - CDS nucleotide sequences
sc.mlc.cns.sgl.utg.scga7.predicted_protein.fasta.gz* - Coding genes translated sequences

sc.mlc.cns.sgl.utg_scga7.sort.gff3* - Coding genes annotation
sc.mlc.cns.sgl.utg_scga7_transposable_elements.sort.gff3.gz* - Transposable Elements annotation

RNASeqTranscriptomeAssembly.fa.gz* - Genome guided transcriptome assembly

full_table_SUGARCANE_merge.txt - BUSCO output
sc.mlc.cegma.gff.id.loci.complete.txt - CEGMA output

SNV_annotation.vcf.gz* - SNP annotation

PAL_clustalW.meg - PAL gene family alignment
PAL_tree_ML.nwk - PAL phylogenetic tree newick format
PAL_tree_ML.mtsx - PAL phylogenetic tree - MEGA software

SuSy_clustalW.meg - SuSy gene family alignment
SuSy_ML.nwk - SuSy phylogenetic tree newick format
SuSy_tree_ML.mtsx - SuSy phylogenetic tree - MEGA software 

proteins_SP803280_X_R570_Cluters_MCA_top_hit_query_coverage_90.txt - Protein correspondence table SP80-3280 X R570 for circos plot
proteins_SP803280_X_Spont_Cluters_MCA_top_hit_query_coverage_90.txt - Protein correspondence table SP80-3280 X S.spontaneum for circos plot

co_expression_analysis.tar.gz - Directory with data and scripts for co-expression analysis - readme included
rna-seq_gene_expression_levels.tar.gz - Directory with rna-seq expression levels from all libraries - readme included
scripts.tar.gz - Directory with scripts used in different analysis - readme included