Info • Tuber indicum v1.0

Status

[June 2020] The genome sequence of Tuber indicum was not determined by the JGI.

 

The genome sequence was assembled with ALLPATHS-LG by Claude Murat (INRA Nancy - France).

The genome was provided by INRA on September 2016. The annotation was done by Emmanuelle Morin of INRA using the JGI Annotation Pipeline.

This copy of the genome include the mitochondrial chromosome or genes.

Summary statistics for the Tuber indicum v1.0 release are below.
Genome Assembly
Genome Assembly size (Mbp) 110.49
Sequencing read coverage depth 240x
# of contigs 3049
# of scaffolds 734
# of scaffolds >= 2Kbp 562
Scaffold N50 60
Scaffold L50 (Mbp) 0.54
# of gaps 2315
% of scaffold length in gaps 3.9%
Three largest Scaffolds (Mbp) 2.09, 1.91, 1.83


ESTs Data set # sequences total # mapped to genome % mapped to genome
Ests est.fasta 173188488 170841558 98.6%
Other Tubin1_RNA_contigs 43410 36175 83.3%


Gene Models FilteredModels1
length (bp) of: average median
gene 1559 1294
transcript 1345 1086
exon 391 246
intron 89 65
description:
protein length (aa) 391 300
exons per gene 3.44 3
# of gene models 11872


Genome Reference(s)

Please cite the following publication(s) if you use the data from this genome in your research:

Morin E, Murat C, Cichocki N, De la Varga H, Kohler A, Xu J, Grigoriev IV, Martin FM
Draft Genome Sequences of the Black Truffles Tuber brumale Vittad. and Tuber indicum Cook & Massee.
Microbiol Resour Announc. 2021 Jan 28;10(4):. doi: 10.1128/MRA.00799-20

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.