Corchorus capsularis Assembly and Gene Annotation
About Corcorus capsularis
Corcorus capsularis (white jute) is one of the most important sources of natural fibre, along with Corcorus olitorius, covering ∼80% of global bast fibre production. The genome size is approximately 400 Mbp (n = 7). The assembly presented here is at the scaffold level, comprising 6,125 scaffolds with a scaffold N50 of 4.1 Mbp.
Whole-genome shotgun sequencing was performed using Roche/454 GS FLX and was assembled using CABOG (version 7). A total of 13.69 Gbp of sequence data was generated (~30x), consisting of 7.87 Gbp of shotgun sequences (~20x), 2.04 Gbp of 3-kbp paired-end sequences (14x physical coverage), 2.26 Gbp of 8-kbp paired-end sequences (15x physical coverage), and 1.51 Gbp of 20-kbp paired-end sequences (11x physical coverage). The resulting assembly was 338 Mbp in 6,125 scaffolds with a scaffold N50 of 4.1 Mbp. Eighty per cent of the assembly was covered with 231 scaffolds (minimum length 120 kbp) and is estimated to cover about 82% of the genome .
More than 97% of the isotigs generated from transcriptome sequencing of seedlings aligned to the genome indicating comprehensive coverage of the gene-rich regions. In addition, more than 97% of the conserved core eukaryotic genes  were present in the genome.
A total of 30,096 protein-coding genes were predicted by a combination of de novo, homology and transcriptome-based approaches .
- Comparative genomics of two jute species and insight into fibre biogenesis.
Islam MS, Saito JA, Emdad EM, Ahmed B, Islam MM, Halim A, Hossen QM, Hossain MZ, Ahmed R, Hossain MS et al. 2017. Nature plants. 3:16223.
- CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes.
Parra G, Bradnam K, Korf I. 2007. Bioinformatics. 23:1061.
Picture credit: By Luigi Chiesa (Scan by Luigi Chiesa) [GFDL (http://www.gnu.org/copyleft/fdl.html), CC-BY-SA-3.0 (http://creativecommons.org/licenses/by-sa/3.0/) or CC BY-SA 2.0 it (http://creativecommons.org/licenses/by-sa/2.0/it/deed.en)], via Wikimedia Commons
General information about this species can be found in Wikipedia.
|Assembly||CCACVL1_1.0, INSDC Assembly GCA_001974805.1, Jan 2017|
|Golden Path Length||317,178,409|
|Genebuild method||Imported from ENA|
|Data source||Bangladesh Jute Research Institute|
|Non coding genes||2,014|
|Small non coding genes||1,816|
|Long non coding genes||198|