Genome Browser (instructions)

Genome Annotation (high-quality genes)

Genome Overview 
(Genes vs. TEs - idiogram map)

Red: TEs - Blue: Genes

Annotation Features and Functional Results

PASA

Program to Assemble Spliced Alignments Web Portal.  Summary report of the annotation (EVidence Modeler).

Go!

PlantiSMASH

Pre-computed plantiSMASH providing the annotation and analysis of secondary metabolite biosynthesis gene clusters.

GO!

Functional Annotation

Functional Annotation Plots: 
EC numbers, GOs, Transposable elements and others

GO!

Dowload genomic and annotation data

Genome Sequence (fasta) | ptDNA (gbk) | mtDNA (gbk) 
Annotation (gene models and functional annotation) (gff3 file)
Genes (fasta) | Proteins (fasta) | CDS (fasta)
Transposable Elements Annotation (gff3 file) | (FASTA)
PASA Assemblies (gff3) | (fasta)
RNAseq aligned data (short-reads) (bam)

The data is also avaliable at GenBank

PRJNA239715

Genome Browser Content and Instructions

jBrowser2 is a platform for visualizing genomic data. The  A. Sellowiana  genome browser contains the following tracks:  a) the gene models accompanied by annotation integrated in InterProScan visualization of each coding region; b) Transposable Elements and Repeats Annotation; c) PASA assemblies; d) tRNA and rRNA annotation and e) Aligned  RNAseq data, and other annotation features.
Use the "open track selector" to navigate into the different and avaliable tracks.

About

Theobroma cacao , is a member of the Malvaceae family, and one of the most popular species in the Brazilian Amazon.​​ Its seeds, cocoa beans, are used to make chocolate liquor, cocoa solids, cocoa butter and chocolate. The largest producer of cocoa beans in 2018 was Ivory Coast, 2.2 million tons (see more on on wikipedia ).

Genome Facts

- Genome Size:  341,709,215 bp;
- Number of chromosomes: 10;
- Number of genes: 28,896(47,828 CDS);
- Gene vs. TEs content:  31.8% of genome is covered by genes and 56.12% is covered by TEs.
- BUSCO score genome: 99.3%[S:98.3%,D:1.0%],F:0.1%,M:0.6%,n:1614 (​embryophyta_odb10).
- BUSCO score annotation:​​  C:99.5%[S:66.4%,D:33.1%],F:0.2%,M:0.3%,n:1614 (​embryophyta_odb10)

Reference:  Motamayor JC, Mockaitis K, Schmutz J, et al. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biol. 2013;14(6):r53.