Pepper genome assembly
=====================

You can download all data and if you have any problems or questions, please give us feedback (ksi2204 at gmail.com).

Version 1.5 genome assembly was used in pepper genome paper and registered NCBI. 
We additionally anchored more v1.5 scaffolds to v1.5 pseudomolecules and new pseudomolecule is version 1.55.
In case of v1.55 gene annotation, v1.5 gene sequences were not changed but gene IDs are changed because of changes for orders of genes on 12 chromosomes.
In addition, 4 genes were masked and total number of genes is 34,899 in v1.55 gene annotation.



Information of files
====================
Pepper_1.55.gene_models.gff3 :		gff3 with version 1.55 annotation and valid sequence ontology terms. seq IDs correspond to Pepper_1.55.fasta.
Pepper_1.55.fasta :	     		fasta file of version 1.55 assembly. sequence IDs correspond to Pepper_1.55.gene_models.gff3.
Pepper_1.55.assembly.gff3 :  		gff3 with ultracontigs for version 1.55 assembly. 


Pepper.v.1.5.Assigned.Chr.gff3 : 	gff3 for gene information on v1.5 12 chromosomes.
Pepper.v.1.5.CDS.fa : 			version 1.5 of CDS sequences.
Pepper.v.1.5.Chr0.list : 		unassigned v1.5 scaffolds for v1.5 12 chromosomes.
Pepper.v.1.5.contig.fa : 		version 1.5 of contig sequences.
Pepper.v.1.5.PEP.fa : 			version 1.5 of protein sequences.
Pepper.v.1.5.scaffold.fa : 		version 1.5 of scaffold sequences.
Pepper.v.1.5.total.chr.fasta : 		version 1.5 of 12 chromosome sequences.
Pepper.v.1.5.total.gff3 : 		version 1.5 gff3 of gene information for v1.5 scaffolds.
Pepper.v.1.55.ChrList :			new version of anchored information for 12 chromosomes with order except for chr 0.
Pepper.v.1.55.Assigned.Info :		new version of gene information for 12 chromosomes with changed gene IDs.
Pepper.v.1.55.total.chr :		additionally anchored scaffolds for 12 chromosomes.
Pepper.v.1.55.total.gff3 :		new version of gff3 for changed gene IDs 
Pepper.v.1.55.CDS.fa :			new version of CDS sequences.
Pepper.v.1.55.PEP.fa :			new version of protein sequences.
Chinense.v0.5.fasta :			draft genome assembly of Capsicum chinense PI159236.




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