Info • Piromyces sp. UH3-1 v2.0


[June 2020] Chromatin capture data (Hi-C) was generated by Phase genomics for the sequencing of the Piromyces sp. UH3-1 genome. The draft assembly of Piromyces sp. UH3-1 generated using PacBio (Piromy1), was then used along with PacBio read data to purify haplotypes using FALCON-Phase (Kronenberg et al., 2019). Phase Genomics' Hi-C genome scaffolding platform was then used to create chromosome-scale scaffolds (generated by Kyle Langford at Phase Genomics), followed by error correction using Juicebox (Neva et al., 2016, Suhas et al., 2014). The final scaffolds included 12 chromosomes for Piromyces sp. UH3-1 (spanning 83.4 Mbp) with an N50 of 7.3 Mbp. While most of the assembly is contained within these 12 scaffolds, unplaced scaffolds were additionally included here for annotation using the JGI annotation pipeline.

Summary statistics for the Piromyces sp. UH3-1 v2.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 84.10
Sequencing read coverage depth 33.02x
# of contigs 84
# of scaffolds 84
# of scaffolds >= 2Kbp 77
Scaffold N50 5
Scaffold L50 (Mbp) 7.30
# of gaps 0
% of scaffold length in gaps 0.0%
Three largest Scaffolds (Mbp) 11.05, 10.90, 8.33

ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests est.fasta 81793148 81234292 99.3%
Other Trinity_assembled_Illumina_transcriptome 46137 40693 88.2%

Gene Models FilteredModels1
length (bp) of: average median
gene 2415 1899
transcript 1816 1410
exon 393 159
intron 168 120
protein length (aa) 544 400
exons per gene 4.62 3
# of gene models 16867




This project was not sequenced at the JGI.