The Pepper genome database (Release 2.0):
 \Genome assembly
    directory with the genome assembly files of Capsicum annuum L. (Zunla-1) and its wild progenitor Capsicum annuum var. glabriusculum (Chiltepin).
\CDS
    directory with the CDS files of Capsicum annuum L. (Zunla-1) and its wild progenitor Capsicum annuum var. glabriusculum (Chiltepin).
\Protein Sequence
    directory with the protein files of Capsicum annuum L. (Zunla-1) and its wild progenitor Capsicum annuum var. glabriusculum (Chiltepin).
\Gene
    directory with the gene model annotation files of Capsicum annuum L. (Zunla-1) and its wild progenitor Capsicum annuum var. glabriusculum (Chiltepin).
\miRNA
   directory with high confidence miRNA genes and their putative precursors in Zunla-1.
\Repeat
   directory with the repeats datasets of Capsicum annuum L. (Zunla-1) and its wild progenitor Capsicum annuum var. glabriusculum (Chiltepin).
\Transcript
   directory with the UTR information in genes of Capsicum annuum L. (Zunla-1)

Currently there are genome assembly  and  annotations for Capsicum annuum L. (Zunla-1) and 
   its wild progenitor Capsicum annuum var. glabriusculum (Chiltepin), respectively.
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About genome assembly:
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Capsicum.annuum.L_Zunla-1_v2.0, assembly made by with 1 Illumina HiSeq2000 run: 
   4 lanes of PE-170bp, 
   2 lanes of PE-500bp, 
   1 lane of PE-800bp, 
   4 lanes of MP-2Kb,
   3 lanes of MP-5Kb,
   2 lanes of MP-10Kb,
   4 lanes of MP-20Kb, and
   1 lane of MP-40Kb,
   using SOAPdenovo as assembler (Kmer 45).
Capsicum.annuum.var.glabriusculum_Chiltepin_v2.0, assembly made by with 1 Illumina HiSeq2000 run: 
   2 lanes of PE-170bp, 
   2 lanes of PE-500bp, 
   1 lanes of PE-800bp, 
   1 lane of MP-2Kb,
   1 lane of MP-5Kb,
   2 lanes of MP-10Kb, and
   2 lanes of MP-20Kb,
  using SOAPdenovo as assembler (Kmer 45).

About sequence IDs and assembly files. There are two assembly
files for Zunla-1 and Chiltepin.
 Capsicum.annuum.L_Zunla-1_Release_2.0.fasta.gz,
    with all the chromosomes (Chr00 is not real chromosone). 
 Capsicum.annuum.var.glabriusculum_Chiltepin_v2.0.fasta.gz,
    with all the chromosomes (Chr00 is not real chromosone). 

ID for scaffolds: ChrXX where XX is the chromosome number.
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About the genome annotation:
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The current version was performed over the assembly version 
Capsicum.annuum.L_Zunla-1_Release_2.0 and  Capsicum.annuum.var.glabriusculum_Chiltepin_v2.0
using Genewise (Birney E., et al. 2004) and RNAseq data supplied by Dr. Cheng Qin. 

ID for Gene models of Zunla-1 and Chiltepin: the nomenclature of Zunla-1 and Chiltepin for genes are Capana**g###### 
   and Capang**g######, respectively, in which ¡®Capana¡¯ is the short name of Capsicum annuum var. annuum and 
   ¡®Capang¡¯ is the short name of Capsicum annuum var. glabriusculum. ¡®**¡¯ represents the number of chromosomes; 
   ¡®g¡¯ represents genome; ¡°######¡¯ is the identifier for a gene that is anchored to a certain chromosome. For example,
   Capana00g002624 is the unique identifier for Isopropylmalate dehydrogenase (IPMDH) gene in the Zunla-1 genome; 
   Capang01g000810 is the unique identifier for Isopropylmalate dehydrogenase (IPMDH) gene in the Chiltepin genome.

See README file in the annotation folder for more 
information
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 For any question, please contact with Dr. Cheng Qin
 (qincheng1001@163.com)


                                 Zunyi City, Guizhou Province, January. 19th. 2014