Tuber brumale and Tuber indicum (Pezizomycetes) are two edible black truffles establishing ectomycorrhizal symbiosis with trees and shrubs. T. brumale is ubiquitous in Europe, and T. indicum is mainly found in China. Here, we present the draft genome sequences of T. brumale and T. indicum.
ABSTRACT
Tuber brumale and Tuber indicum (Pezizomycetes) are two edible black truffles establishing ectomycorrhizal symbiosis with trees and shrubs. T. brumale is ubiquitous in Europe, and T. indicum is mainly found in China. Here, we present the draft genome sequences of T. brumale and T. indicum.
ANNOUNCEMENT
The black truffles Tuber brumale Vittadini and Tuber indicum Cook & Massee are ectomycorrhizal ascomycetes. T. brumale is widespread in Europe, except in the boreal and Arctic regions (1). This species often competes with the Périgord black truffle (Tuber melanosporum) in truffle orchards (2). T. indicum is found mainly in the Chinese provinces of Yunnan and Sichuan (3). The two species belong to the Melanosporum phylogenetic clade (4) and have morphological features similar to those of T. melanosporum, making their distinctions sometimes difficult (5). Together with the published genome sequences of T. aestivum, T. borchii, T. magnatum, and T. melanosporum (6–8), these newly sequenced genomes will allow a better understanding of the evolution, biology, and ecology of truffles.
For genome and RNA sequencing, a T. brumale fruiting body was harvested in Lozère (Occitanie, France) in March 2014, and a T. indicum fruiting body was purchased at a French market in 2013. For both species, genomic DNA (gDNA) was extracted from 2 g of fruiting body by using a modified cetyl trimethylammonium bromide (CTAB) protocol (9). Total RNA was extracted using the RNeasy plant minikit (Qiagen) as described earlier (6). The gDNA and the Illumina TruSeq Nano kit were used to construct paired-end libraries (2 × 100 bp for both and 2 × 125 bp for T. brumale) as well as mate pair libraries (with insert sizes of 3 and 8 kbp) using the Illumina Nextera mate pair kit. In addition, paired-end libraries (2 × 100 bp and 2 × 125 bp) were generated from total RNA using the Illumina TruSeq stranded mRNA kit. Sequencing was performed at the GeT-PlaGe sequencing facility (Toulouse, France) using the Illumina HiSeq 2500 platform. The raw Illumina reads were trimmed of adapter sequences and low-quality bases using Trimmomatic v.0.32 (10) with the following parameters: TRAILING:20, LEADING:20, SLIDINGWINDOW:4:20, and MINLEN:70. Assembly of the genomes was carried out using ALLPATHS-LG v.46154 (11) and GapCloser v.1.12.6 (12). The genome assemblies were then annotated using the Joint Genome Institute (JGI) annotation pipeline (13, 14).
The sequencing data statistics are shown in Table 1. The genome sizes of T. brumale and T. indicum are in the range of other truffle species, from 97.18 to 192 Mb (6–8).
TABLE 1.
Genomic features and raw data of Tuber brumale and Tuber indicum
| Organism | Source | No. of reads | Draft genome size (Mb) | No. of scaffolds | N50 (bp) | G+C content (%) | Mean coverage (×) | SRA accession no. | GenBank accession no. | BioProject accession no. |
|---|---|---|---|---|---|---|---|---|---|---|
| Tuber brumale | DNA | 136,348,163 | 171.44 | 1,475 | 336,267 | 46.46 | 131.63 | SRR12018987, SRR12018988, SRR12018989 | JACCEG000000000 | PRJNA633036 |
| 135,457,273 | SRR12018993, SRR12018994,SRR12018995 | |||||||||
| RNA | 128,865,953 | SRR12018990, SRR12018991, SRR12018992 | ||||||||
| Tuber indicum | DNA | 558,521,206 | 110.49 | 734 | 538,733 | 47.41 | 239.48 | SRR12104989, SRR12104990, SRR12104991 | JACCEH000000000 | PRJNA633038 |
| RNA | 86,652,466 | SRR12104986, SRR12104987, SRR12104988 |
RepeatScout v.1.0.5 (15) was used to identify de novo repetitive DNA in the genome assemblies as reported by Peter et al. (16). RepeatMasker v.4.0.9 (17) was used to estimate the repeat element coverage in the genomes. Transposable elements constitute 61.5% and 47.1% of the T. brumale and T. indicum genomes, respectively. Default parameters were used for all software except where otherwise noted.
A total of 12,380 protein-coding genes for T. brumale and 11,870 protein-coding genes for T. indicum were predicted. The number of protein-coding genes is also in the range of other truffle species, from 9,344 to 12,346 protein-coding genes (6–8).
Data availability.
The draft whole-genome shotgun projects were deposited in DDBJ/ENA/GenBank. The SRA and GenBank accession numbers for T. brumale and T. indicum are listed in Table 1. The genome assemblies and annotations are also available at the JGI-DOE Mycocosm portal (13) (https://mycocosm.jgi.doe.gov/Tubbr1_1 and https://mycocosm.jgi.doe.gov/Tubin1_1).
ACKNOWLEDGMENTS
This research was supported by the Laboratory of Excellence ARBRE (ANR-11-LABX-0002-01), the Region Lorraine, and the European Regional Development Fund. The project was also funded by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, and supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231 within the framework of the Mycorrhizal Genomics Initiative (CSP no. 305), Metatranscriptomics of Forest Soil Ecosystems project (CSP no. 570), and the 1000 Fungal Genomes Project (CSP no. 1974).
We are grateful to Jean-Yves Magaud for providing the T. brumale ascocarp and to François Le Tacon for purchasing the T. indicum ascocarps. We thank Alan Kuo, Sajeet Haridas, and Stephen Mondo from JGI for their advice on gene annotation.
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Data Availability Statement
The draft whole-genome shotgun projects were deposited in DDBJ/ENA/GenBank. The SRA and GenBank accession numbers for T. brumale and T. indicum are listed in Table 1. The genome assemblies and annotations are also available at the JGI-DOE Mycocosm portal (13) (https://mycocosm.jgi.doe.gov/Tubbr1_1 and https://mycocosm.jgi.doe.gov/Tubin1_1).