Status
[October 2022] The genome and transcriptome sequences of Macrocystis pyrifera CI_03 were not determined by the Joint Genome Institute (JGI). The genome was sequenced with PacBio, and then assembled by Sergey Nuzhdin's lab at the University of Southern California. Published RNAseq datasets from NCBI (Accession numbers: SRR5026366, SRR5026588, SRR5026590, SRR5026591, SRR5026593, SRR5026594, SRR3544557, SRR3615022) were assembled with Trinity. In addition, a second RNAseq dataset of the gametophyte development stages was provided by Filipe Alberto's lab and assembled with Trinity. Subsequently, the JGI Annotation Pipeline was used to generate structural and functional annotations.
| Genome Assembly | |
| Genome Assembly size (Mbp) | 537.45 |
| Sequencing read coverage depth | |
| # of contigs | 223 |
| # of scaffolds | 223 |
| # of scaffolds >= 2Kbp | 223 |
| Scaffold N50 | 16 |
| Scaffold L50 (Mbp) | 13.67 |
| # of gaps | 0 |
| % of scaffold length in gaps | 0.0% |
| Three largest Scaffolds (Mbp) | 26.51, 22.01, 19.99 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Ests | est.fasta | 297160289 | 277485892 | 93.4% |
| Other | NCBI_RNA_contigs | 219806 | 106137 | 48.3% |
| Other | UWM_RNA_contigs | 674137 | 404086 | 59.9% |
- Please note: Using BLAST, unmapped RNA contigs were found to hit Proteobacteria and Homo sapiens, suggesting that the RNA library was contaminated.
| Gene Models | FilteredModels3 | |
| length (bp) of: | average | median |
| gene | 8707 | 5765 |
| transcript | 1560 | 1203 |
| exon | 264 | 147 |
| intron | 1460 | 902 |
| description: | ||
| protein length (aa) | 373 | 270 |
| exons per gene | 5.90 | 4 |
| # of gene models | 25919 |
Collaborators
- Sergey Nuzhdin at University of Southern California, CA
- Filipe Alberto at University of Wisconsin Milwaukee, WI
Links
- JGI PhyloGroup Portals: Heterokonta Ochrophyta Phaeophyta
- JGI EcoGroup Portals: Algae Seaweeds
Funding
This project was not sequenced at the JGI.
