Overview

For whole-genome sequencing, the monokaryotic strain G. frondosa 9006-11 (KCTC 46451) was used. The genomic DNA was extracted from the vegetative mycelia using a plant genomic MagExtractorTM kit (TOYOBO NPK-501) as manufacturer’s instructions and sequenced in the PacBio single molecule real-time (SMRT) sequencing platform. From the four SMRT cells, we obtained 601,168 raw subreads with a total length of 4 Gb. The low-quality reads were filtered to produce 314,541 high-quality subreads with an average length of 12,229 bp for genome assembly. De novo assembly was performed using the Falcon assembly tool kit 0.2 and SMRT analysis 2.3.0. We prepared the cDNA library for RNA-seq from the mycelia of monokaryote 9006-11. The library was sequenced by Illumina HiSeq 2500 with the TruSeq stranded mRNA prep kit and generated 46 million reads. The low quality bases (<20 Q-score) and short reads (<20 bp in length) were trimmed and excluded. The genes were predicted using Augustus 3.2.1, Braker 1.8 (http://exon.gatech.edu/genemark/braker1.html), and Maker 2.31.8. The resulting genome was 39.3 Mbp in length and annotated with 15,039 gene models.

Statistics

Genome

Approximately 39.3Mb arranged in 127 scaffolds

Scaffold N50 (L50) = 8 (1.8 Mbp)

45 scaffolds larger than 50 Kbp, with 98.18% of the genome in scaffolds larger than 50 Kbp

Assembly

De novo assembly was performed using the Falcon assembly tool kit 0.2 and SMRT analysis 2.3.0. We prepared the cDNA library for RNA-seq from the mycelia of monokaryote 9006-11.

NCBI GenBank Records

Release Date: 12/7/2016        BioProject: PRJNA314283        Accession ID: LUGG01000000

Is it complete?

Genome completeness was calculated using BUSCO v3.0 at the gene level. The genome has 91.31% completeness where 1005 of 1335 BUSCO entries are complete and single-copy.

Is it accurate?

Also, 98.50% of predicted genes are complete, implying accurate genome assembly without sequencing or assembly error.

What about polyploidy?

It's haploid genome.

Gene prediction

The genes were predicted using Augustus 3.2.1 (Stanke et al., 2006), Braker 1.8 (http://exon.gatech.edu/genemark/braker1.html), and Maker 2.31.8 (Holt and Yandell, 2011).

References:

Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W435-9.

Holt C1, Yandell M. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. BMC Bioinformatics. 2011 Dec 22;12:491. doi: 10.1186/1471-2105-12-491.

Contacts

igchoi@korea.ac.kr

Reference Publication(s)