Info • Minidiscus variabilis CCMP495 v1.0


(August 2016) The Minidiscus trioculatus CCMP495 genome was sequenced with PacBio, assembled with Falcon, and annotated with the JGI Annotation Pipeline. The transcriptome was sequenced with Illumina and assemblied with Trinity. The mitochondrial and plastid genomes were sequenced with PacBio technology and assembled with Celera.

Minidiscus trioculatus CCMP495 is likely a polymorphic diploid, and this is reflected in an assembly and annotation with significant separation of alleles. 394 of the 584 scaffolds are very similar to larger scaffolds and are predicted to constitute an alternate or secondary haplotype. To represent these primary and secondary haplotypes in the Portal, we have created 'primary alleles' and 'secondary alleles' gene model tracks, comprising the models found on each haplotype. The goal of the GeneCatalog (GC) is to produce a non-redundant set of models which captures the full functional repertiore of the genome, and so the few secondary alleles that are unique were included in the GC, while all others were not.

Summary statistics for the Minidiscus trioculatus CCMP495 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 76.19
Sequencing read coverage depth
# of contigs 584
# of scaffolds 584
# of scaffolds >= 2Kbp 570
Scaffold N50 59
Scaffold L50 (Mbp) 0.36
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 1.57, 1.49, 1.27

ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests est.fasta 180601291 177637111 98.4%
Other JGI_RNA_contigs 59496 54787 92.1%

Gene Models FilteredModels1
length (bp) of: average median
gene 1619 1334
transcript 1466 1206
exon 632 424
intron 118 91
protein length (aa) 436 347
exons per gene 2.32 2
# of gene models 25179


The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.