Cacao Matina1-6 Genome v1.1
Details
Analysis Name | Cacao Matina1-6 Genome v1.1 |
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Software | Customized version of the Arachne2 assembler (in-house) (in-house) |
Source | Roche 454 Titanium STD reads (USDA-ARS, Stoneville) |
Date performed | 2021-03-28 |
Description | Theobroma cacao Matina1-6 v1.1 ReleaseFrom this page you can read about the genome sequence assembly statistics and annotation protocol, browse and download the whole v1.1 genome sequence; predicted gene transcripts, their locations and putative function based on homology to known genes in Arabidopsis and SwissProt. You can BLAST your sequences against the genome sequence, and the predicted gene transcripts and peptides. You can search and browse the chromosomes, contigs, markers, and genes in GBrowse and view the evidence for each prediction and feature. Genome v1.1 Statistics The resulting pseudomolecules (numbered 1-10) capture 94.6% of the assembled sequence and 98.2% of the sample EST set.
More Information
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Organisms | Theobroma cacao |
Downloads
Cacao Genome Sequence (v1.1) |
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Scaffolds (FASTA file, 97MB compressed) | Cacao_genome_v1.1_Scaffolds.fa.gz |
Scaffolds w/ masked repeats (FASTA file, 101MB compressed) | Cacao_genome_v1.1_Scaffolds_RM.fa.gz |
Scaffolds (GFF3 file, 55KB) | Cacao_genome_v1.1_Scaffolds.gff3 |
Cacao Genome Genome Annotation (v1.1) |
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Predicted gene transcripts (FASTA file, 28MB compressed) | Cacao_genome_v1.1_transcript.fa.gz |
Predicted gene peptides (FASTA file, 11MB compressed) | Cacao_genome_v1.1_peptide.fa.gz |
Predicted gene CDs (FASTA file, 17MB compressed) | Cacao_genome_v1.1_cds.gz |
Cacao predicted genes blastp vs protein databases. Best hit reports in Excel |
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UniProtKB/Swiss-Prot (5.3MB) | Cacao_genome_v1.1_vs_sprot.xlsx |
UniProtKB/TrEMBL (38.2MB) | Cacao_genome_v1.1_vs_TrEMBL.xls |
TAIR10 (arabidopsis) proteins (4.8MB) | Cacao_genome_v1.1_vs_arabidopsis.xlsx |
Prunus persica (peach) v1.0 proteins (4.5MB) | Cacao_genome_v1.1_vs_peach.xlsx |
Vitis vinifera (grape) proteins (4.3MB) | Cacao_genome_v1.1_vs_grape.xlsx |
Populus trichocarpa (poplar) v2.0 proteins (4.6MB) | Cacao_genome_v1.1_vs_poplar.xlsx |
Resources
- Genome Browser
- Search Tools
- BLAST your sequences against the cacao genome v1.1 datasets
- View the sytneny between T. cacao cv. Criollo vs T. cacao cv. Matina1-6 in GBrowse_syn
- View the cacao predicted gene KEGG Report
- View the cacao predicated gene GO Report
- CacaoCyc
- DNA Libraries