ChaetoBase v1.1
ChaetoBase is the gene annotation database for a marine centric diatom
Chaetoceros gracilis – one of the leading species used for photosynthetic research
and algal biotechnology.
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ex. fucoxanthin,
FASTA Format
- Non redundant Scaffolds + Large contigs 35MB 4,199 seqs
Large Contigs has some overlap with scaffolds. This is recommended for RNA-seq. - Scaffolds 35MB 797 scaffolds
- Large contigs (Over500bp) 34MB 10,919 contigs
- All contigs 39MB 33,730 contigs
- Predicted genes by BRAKER Amino Acid sequence
IsoSeq sequences are corresponding to the additional cell culture described in the reference.
- Chloroplast genes 101KB 163 contigs
Gene annotation list
- Annotated gene list (TSV)
- Predicted genes by BRAKER2 : All predicted genes are included (GFF3)
- Former predicted genes by Augustus : Former predicted genes (IDs are old and don't match the above) (GFF3)
The current version of the genome assembly and gene annotation is ver 1.1.
The genome sequences are also available from the INSDC under the accession number BioProject: PRJDB12186.
Note that the current gene annotation is still in Beta-version and is subject to change in future revisions.
Citation
Minoru Kumazawa, Hiroyo Nishide, Ryo Nagao, Natsuko Inoue-Kashino, Jian-Ren Shen, Takeshi Nakano, Ikuo Uchiyama, Yasuhiro Kashino and Kentaro Ifuku
Molecular phylogeny of fucoxanthin-chlorophyll a/c proteins from Chaetoceros gracilis and Lhcq/Lhcf diversity
Physiologia Plantarum, e13598. doi: 10.1111/ppl.13598
Molecular phylogeny of fucoxanthin-chlorophyll a/c proteins from Chaetoceros gracilis and Lhcq/Lhcf diversity
Physiologia Plantarum, e13598. doi: 10.1111/ppl.13598
Inquiries and feedback:
Kentaro Ifuku (Kyoto Univ.) ifuku.kentaro.2m[at]kyoto-u.ac.jp
Kentaro Ifuku (Kyoto Univ.) ifuku.kentaro.2m[at]kyoto-u.ac.jp
