Info • Macrocystis pyrifera CI_03 v1.0


[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
protein length (aa) 373 270
exons per gene 5.90 4
# of gene models 25919




This project was not sequenced at the JGI.