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 (68), 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 (68).
TABLE 1
TABLE 1 Genomic features and raw data of Tuber brumale and Tuber indicum
OrganismSourceNo. of readsDraft genome size (Mb)No. of scaffoldsN50 (bp)G+C content (%)Mean coverage (×)SRA accession no.GenBank accession no.BioProject accession no.
Tuber brumaleDNA136,348,163171.441,475336,26746.46131.63SRR12018987, SRR12018988, SRR12018989JACCEG000000000PRJNA633036
  135,457,273     SRR12018993, SRR12018994,SRR12018995  
 RNA128,865,953     SRR12018990, SRR12018991, SRR12018992  
           
Tuber indicumDNA558,521,206110.49734538,73347.41239.48SRR12104989, SRR12104990, SRR12104991JACCEH000000000PRJNA633038
 RNA86,652,466     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 (68).

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.

REFERENCES

1.
Merényi Z, Varga T, Bratek Z. 2016. Tuber brumale: a controversial tuber species, p 49–68. In Zambonelli A, Iotti M, Murat C (ed), True truffle (Tuber spp.) in the world. Springer International Publishing, Cham, Switzerland.
2.
Olivier J-M, Savignac J-C, Sourzat P. 2012. Truffe et trufficulture. FANLAC Editions, Périgueux, France.
3.
Chen J, Murat C, Oviatt P, Wang Y, Le Tacon F. 2016. The black truffles Tuber melanosporum and Tuber indicum, p 19–32. In Zambonelli A, Iotti M, Murat C (ed), True truffle (Tuber spp.) in the world. Springer International Publishing, Cham, Switzerland.
4.
Bonito G, Smith ME, Nowak M, Healy RA, Guevara G, Cázares E, Kinoshita A, Nouhra ER, Dominguez LS, Tedersoo L, Murat C, Wang Y, Moreno BA, Pfister DA, Nara K, Zambonelli A, Trappe JM, Vilgalys R. 2013. Historical biogeography and diversification of truffles in the Tuberaceae and their newly identified southern hemisphere sister lineage. PLoS One 81:e52765.
5.
Murat C. 2015. Forty years of inoculating seedlings with truffle fungi: past and future perspectives. Mycorrhiza 25:77–81.
6.
Murat C, Payen T, Noel B, Kuo A, Morin E, Chen J, Kohler A, Krizsán K, Balestrini R, Da Silva C, Montanini B, Hainaut M, Levati E, Barry KW, Belfiori B, Cichocki N, Clum A, Dockter RB, Fauchery L, Guy J, Iotti M, Le Tacon F, Lindquist EA, Lipzen A, Malagnac F, Mello A, Molinier V, Miyauchi S, Poulain J, Riccioni C, Rubini A, Sitrit Y, Splivallo R, Traeger S, Wang M, Žifčáková L, Wipf D, Zambonelli A, Paolocci F, Nowrousian M, Ottonello S, Baldrian P, Spatafora JW, Henrissat B, Nagy LG, Aury J-M, Wincker P, Grigoriev IV, Bonfante P, Martin FM. 2018. Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle. Nat Ecol Evol 2:1956–1965.
7.
Murat C, Kuo A, Barry KW, Clum A, Dockter RB, Fauchery L, Iotti M, Kohler A, LaButti K, Lindquist EA, Lipzen A, Morin E, Wang M, Grigoriev IV, Zambonelli A, Martin FM. 2018. Draft genome sequence of Tuber borchii Vittad., a whitish edible truffle. Genome Announc 6:e00537-18.
8.
Martin F, Kohler A, Murat C, Balestrini R, Coutinho PM, Jaillon O, Montanini B, Morin E, Noel B, Percudani R, Porcel B, Rubini A, Amicucci A, Amselem J, Anthouard V, Arcioni S, Artiguenave F, Aury J-M, Ballario P, Bolchi A, Brenna A, Brun A, Buée M, Cantarel B, Chevalier G, Couloux A, Da Silva C, Denoeud F, Duplessis S, Ghignone S, Hilselberger B, Iotti M, Marçais B, Mello A, Miranda M, Pacioni G, Quesneville H, Riccioni C, Ruotolo R, Splivallo R, Stocchi V, Tisserant E, Viscomi AR, Zambonelli A, Zampieri E, Henrissat B, Lebrun M-H, Paolocci F, Bonfante P, Ottonello S, et al. 2010. Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis. Nature 464:1033–1038.
9.
Kohler A, Kuo A, Nagy LG, Morin E, Barry KW, Buscot F, Canbäck B, Choi C, Cichocki N, Clum A, Colpaert J, Copeland A, Costa MD, Doré J, Floudas D, Gay G, Girlanda M, Henrissat B, Herrmann S, Hess J, Högberg N, Johansson T, Khouja H-R, LaButti K, Lahrmann U, Levasseur A, Lindquist EA, Lipzen A, Marmeisse R, Martino E, Murat C, Ngan CY, Nehls U, Plett JM, Pringle A, Ohm RA, Perotto S, Peter M, Riley R, Rineau F, Ruytinx J, Salamov A, Shah F, Sun H, Tarkka M, Tritt A, Veneault-Fourrey C, Zuccaro A, Tunlid A, Grigoriev IV, Mycorrhizal Genomics Initiative Consortium, et al. 2015. Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists. Nat Genet 47:410–415.
10.
Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120.
11.
Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Burton JN, Walker BJ, Sharpe T, Hall G, Shea TP, Sykes S, Berlin AM, Aird D, Costello M, Daza R, Williams L, Nicol R, Gnirke A, Nusbaum C, Lander ES, Jaffe DB. 2011. High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A 108:1513–1518.
12.
Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu S-M, Peng S, Xiaoqian Z, Liu G, Liao X, Li Y, Yang H, Wang J, Lam T-W, Wang J. 2012. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 1:18.
13.
Grigoriev IV, Nikitin R, Haridas S, Kuo A, Ohm R, Otillar R, Riley R, Salamov A, Zhao X, Korzeniewski F, Smirnova T, Nordberg H, Dubchak I, Shabalov I. 2014. MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res 42:D699–D704.
14.
Kuo A, Bushnell B, Grigoriev IV. 2014. Fungal genomics: sequencing and annotation, p 1–52. In Martin F (ed), Advances in botanical research: fungi, vol 70. Elsevier Academic Press, Cambridge, MA.
15.
Price AL, Jones NC, Pevzner PA. 2005. De novo identification of repeat families in large genomes. Bioinformatics 21:i351–i358.
16.
Peter M, Kohler A, Ohm RA, Kuo A, Krützmann J, Morin E, Arend M, Barry KW, Binder M, Choi C, Clum A, Copeland A, Grisel N, Haridas S, Kipfer T, LaButti K, Lindquist E, Lipzen A, Maire R, Meier B, Mihaltcheva S, Molinier V, Murat C, Pöggeler S, Quandt CA, Sperisen C, Tritt A, Tisserant E, Crous PW, Henrissat B, Nehls U, Egli S, Spatafora JW, Grigoriev IV, Martin FM. 2016. Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum. Nat Commun 7:12662.
17.
Smit AFA, Hubley R, Green P. 2015. RepeatMasker Open 4.0. http://www.repeatmasker.org.

Information & Contributors

Information

Published In

cover image Microbiology Resource Announcements
Microbiology Resource Announcements
Volume 10Number 428 January 2021
eLocator: 10.1128/mra.00799-20
Editor: Antonis Rokas, Vanderbilt University

History

Received: 5 August 2020
Accepted: 11 January 2021
Published online: 28 January 2021

Contributors

Authors

Université de Lorraine, INRAE, IAM, Nancy, France
Claude Murat
Université de Lorraine, INRAE, IAM, Nancy, France
Nicolas Cichocki
Université de Lorraine, INRAE, IAM, Nancy, France
Herminia De la Varga
Université de Lorraine, INRAE, IAM, Nancy, France
Present address: Herminia De la Varga, Fertinagro Biotech, S.L., R+D+i Department, Teruel, Spain.
Annegret Kohler
Université de Lorraine, INRAE, IAM, Nancy, France
McMaster University, Department of Biology, Hamilton, Canada
Igor V. Grigoriev
DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
Université de Lorraine, INRAE, IAM, Nancy, France

Editor

Antonis Rokas
Editor
Vanderbilt University

Notes

Address correspondence to Emmanuelle Morin, [email protected], or Francis M. Martin, [email protected].

Metrics & Citations

Metrics

Note: There is a 3- to 4-day delay in article usage, so article usage will not appear immediately after publication.

Citation counts come from the Crossref Cited by service.

Citations

If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. For an editable text file, please select Medlars format which will download as a .txt file. Simply select your manager software from the list below and click Download.

View Options

Figures and Media

Figures

Media

Tables

Share

Share

Share the article link

Share with email

Email a colleague

Share on social media

American Society for Microbiology ("ASM") is committed to maintaining your confidence and trust with respect to the information we collect from you on websites owned and operated by ASM ("ASM Web Sites") and other sources. This Privacy Policy sets forth the information we collect about you, how we use this information and the choices you have about how we use such information.
FIND OUT MORE about the privacy policy