Download

 Name                               Size  Description
 RefBeet.variants.1302.gff3.gz      119M  Variants on RefBeet-1.1
 RefBeet.unfiltered_genes.1302.gff3 104M  Positions of all coding genes predicted
 RefBeet.repeats.1302.gff3          132M  Positions of Beta vulgaris repeats
 RefBeet.ncgenes.1302.gff3          323K  Positions of non-coding genes
 RefBeet.ncgenes.1302.fa            481K  Sequences of non-coding genes
 RefBeet.genes.1302.pep.fa           12M  Protein sequences
 RefBeet.genes.1302.mrna.fa          47M  Transcript sequences (incl. UTR)
 RefBeet.genes.1302.cds.fa           32M  CDS sequences
 RefBeet.funct_anno.1302.txt        1.2M  Functional annotation
 RefBeet-1.1.masked.fna.gz           74M  Masked genome sequence
 RefBeet-1.1.fna.gz                 137M  Genome sequence
 README.txt                         1.8K  README

Data sets available for RefBeet-1.1, annotations as of February 2013
====================================================================

Assembly
--------
- RefBeet-1.1.fna: The genome assembly of reference genotype KWS2320 (Beta 
vulgaris ssp. vulgaris) integrated with genetic and physical maps
- RefBeet-1.1.masked.fna: Masked genome assembly, repeats determined by 
RepeatModeler based on RefBeet-1.1, masked by RepeatMasker

Protein coding genes
--------------------
- RefBeet.genes.1302.cds.fa: CDS of 27,421 predicted gene models supported 
by mRNA evidence and filtered for transposable elements
- RefBeet.genes.1302.mrna.fa: mRNA sequences of these genes
- RefBeet.genes.1302.pep.fa: Translated protein sequences of these genes
- RefBeet.funct_anno.1302.txt: List of functional annotations for these 
genes. The longest protein sequence per gene was used for sequence 
similarity searches.
- RefBeet.unfiltered_genes.1302.gff3: Positions of all protein coding genes 
predicted including genes which are not supported by mRNA evidence

Non-coding RNA genes
--------------------
- RefBeet.ncgenes.1302.fa: Sequences of predicted non-coding RNA genes
- RefBeet.ncgenes.1302.gff3: Positions of predicted non-coding RNA genes

Repeats
-------
- RefBeet.repeats.1302.gff3: Positions and annotation of repeats determined 
by RepeatModeler based on RefBeet-1.1, repeat classification was manually 
revised

Variants
--------
- RefBeet.variants.1302.gff3: All variant positions of RefBeet-1.1 after
comparison with double haploid sugar beet accessions KDHBv, UMSBv, YMoBv, 
YTiBv, as well as sea beet (DeKBm). Differences between RefBeet-1.1 and 
RefBv (same genotype) may represent errors in the reference assembly. 
Variants were determined by read mapping and by scaffold alignment. Variants 
of sea beet (DeKBm) were determined by read mapping only.