Info • Piptocephalis tieghemiana RSA 1565 v1.0

Status

[July 2018] The Piptocephalis tieghemiana RSA 1565 genome was sequenced with illumina and extracted computationally from co-culture with Umbelopsis sp. nov. AD052. Briefly, metagenomic scaffold sequences were first binned into two groups by metabat (v2.12.1), then split into two separate datasets using bbsplit.sh (bbtools) and assembled using AllPathsLG version R49403. Resulting scaffolds were then filtered by homology to closely related genomes and scaffolds matching neither lineage were discarded. This assembly was then annotated using the JGI Annotation Pipeline. Annotations can be further improved upon receipt of transcriptomic data. Mitochondrial genome was assembled separately and is available in the downloads section.

Summary statistics for the Piptocephalis tieghemiana RSA 1565 v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 18.55
Sequencing read coverage depth 145.4x
# of contigs 264
# of scaffolds 214
# of scaffolds >= 2Kbp 214
Scaffold N50 48
Scaffold L50 (Mbp) 0.13
# of gaps 50
% of scaffold length in gaps 0.1%
Three largest Scaffolds (Mbp) 0.39, 0.34, 0.30


Gene Models FilteredModels1
length (bp) of: average median
gene 1626 1305
transcript 1344 1071
exon 430 221
intron 135 108
description:
protein length (aa) 448 357
exons per gene 3.13 2
# of gene models 5811


Collaborators

Joey Spatafora, Oregon State, OR, USA

Jason Stajich, UC Riverside, CA, USA

Matthew Smith, University of Florida, FL, USA

Funding

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.