Durand et al. 2019
The turnover of ribosome-associated transcripts from de novo ORFs produces gene-like characteristics available for de novo gene emergence in wild yeast populations. 
#########################################################################
# Description of Supplemental_Data folder
#########################################################################
This folder contains de novo assemblies and annotations (Genes and iORFs) of 24 HC S. paradoxus strains + the wild type S. cerevisiae strain YPS128 (See Methods)
S. paradoxus strains were sequenced in Leducq et al. 2016 study. 
Each file is named with the library id and the correspondance between the library id and the strain name is indicated in infos_lib.txt 

#FASTA files 
#========================================================================
- fasta_genomes/
	 De novo genome assemblies 
	- The assembly was performed with IDBA
	- The scaffolds were aligned along the S. paradoxus CBS432 reference 
	for S. paradoxus strains, or the reference S288C for YPS128 strain, 
	and assembled into pseudomolecules with ABACAS 
	
	- Unused scaffold in the pseudomolecule have been kept in the fasta
	 file  

# ANNOTATION files 
#========================================================================
- gff_genes/1_gff_genes_coord/
	Genomic coordinates of annotated genes
	The annotation was performed with augustus and Synchro
	If synteny is conserved among all strains: conserved =TRUE and gene name and id are indicated
	if conserved = FALSE: sequence CDS similarities with known genes in ref S288C are indicated 		(CDS_similarities) 
	augustus_id : augusus output name
	This folder contains only gene positions 
	
- gff_genes/2_gff_genesCDS/ 
	Idem with intron/CDS annotations 

-/01genomes/02annotations/03_gff/: 
	
	Genomic coordinates of intergenic ORFs 
	ORFs coordinates of all annotated iORFs (with no minimum size) or the homologous coordinate if the iORF is absent (see stat=1 : ORF presence, stat = 0 : ORF absence)
	
	
