Status
The Lentinula novae-zelandiae ICMP 18003A genome sequence and gene models were not determined by the Joint Genome Institute (JGI), but were provided by Christopher Alan Smith on Jul 8, 2020. In order to ensure this genome is comparable to those sequenced by the JGI, we applied filters to remove if present: 1) transposable elements, 2) pseudogenes, 3) alternative transcripts and overlapping models, 4) alleles on secondary scaffolds and 5) unsupported short models. This resulted in the removal of 678 models from L. novae-zelandiae and the generation of the FilteredModels1 gene track. All provided models are available in the ExternalModels track. Please note that this copy of the genome is not maintained by the author and is therefore not automatically updated. In order to allow comparative analyses with other fungal genomes sequenced by the JGI, a copy of this genome is incorporated into MycoCosm. The JGI Annotation Pipeline was used to add functional annotation to this genome.
Genome Assembly | |
Genome Assembly size (Mbp) | 48.94 |
Sequencing read coverage depth | 264x |
# of contigs | 19 |
# of scaffolds | 17 |
# of scaffolds >= 2Kbp | 17 |
Scaffold N50 | 4 |
Scaffold L50 (Mbp) | 4.83 |
# of gaps | 2 |
% of scaffold length in gaps | 0.1% |
Three largest Scaffolds (Mbp) | 8.12, 7.58, 5.70 |
Gene Models | FilteredModels1 | |
length (bp) of: | average | median |
gene | 1685 | 1370 |
transcript | 1391 | 1122 |
exon | 251 | 150 |
intron | 67 | 57 |
description: | ||
protein length (aa) | 464 | 374 |
exons per gene | 5.55 | 4 |
# of gene models | 11421 |
Collaborators
- Christopher Alan Smith, Manaaki Whenua – Landcare Research
Genome Reference(s)
Smith CA
Macrosynteny analysis between Lentinula edodes and Lentinula novae-zelandiae reveals signals of domestication in Lentinula edodes.
Sci Rep. 2021 May 10;11(1):9845. doi: 10.1038/s41598-021-89146-y
Links
- JGI PhyloGroup Portals: Fungi Dikarya Basidiomycota Agaricomycotina Agaricomycetes Agaricales Lentinula