ABSTRACT

Taphrina betulina is the ascomycete yeast that causes the formation of witches’ brooms in birch trees. Here, we report the first draft genome sequence of T. betulina, from strain UCD315, isolated from soil in Ireland. The genome is haploid and 12.5 Mb long.

ANNOUNCEMENT

Taphrina species are plant pathogens in the subphylum Taphrinomycotina of the phylum Ascomycota (1). Taphrina species cause plant deformity diseases in a diversity of tree species, including Prunus (edible fruit trees and shrubs), Cerasus (sour cherry), and Populus (poplar) (2). Taphrina betulina was first described in Norway in 1883 (3). It infects Betula pubescens (downy birch), Betula nana (dwarf birch), crosses between the two species (Betula intermedia), and Betula pendula (silver birch) (1, 4). Infection results in host tissue deformities, such as nest-like tumors called “witches’ broom” (5). Ultimately, infection affects the diameter, height, and life span of the tree (4).
T. betulina UCD315 was isolated from soil near Lough Corrib, County Galway, Ireland (global positioning system coordinates, 53.4344816, –9.1534624). The yeast was cultured at room temperature on yeast extract-peptone-dextrose (YPD) medium with chloramphenicol (3% [wt/vol]) and ampicillin (10% [wt/vol]). The species was identified by sequencing the internal transcribed spacer (ITS) of the ribosomal DNA (rDNA) gene locus (GenBank accession number MN540705). Genomic DNA was extracted and purified using Qiagen’s QIAamp DNA minikit. Libraries with an insert size of 800 bp were made from genomic DNA and sequenced by BGI Tech Solutions using an Illumina HiSeq 4000 instrument with 150-bp paired-end reads (9.5 million spots). All parameters used for sequence assembly and analysis are available at https://www.doi.org/10.6084/m9.figshare.9775517.
Low-quality reads (1.69 million) were trimmed using Skewer v0.2.2 (6). The genome was assembled from all reads using SPAdes v3.11.1 with the “careful” parameter (7). Based on coverage-versus-length analysis (8), contigs below 72× coverage or 1-kb length were removed. The results were then analyzed using QUAST v4.6.1 (9). The genome size was 12.5 Mb with an N50 value of 321 kb, an L50 value of 16, an average coverage of 101×, and a GC content of 49.8%. The largest contig is 682,403 bp. This is similar in size and contiguity to other sequenced Taphrina genomes, which range from 11.9 to 15.7 Mb (2). Using BUSCO v3.0.1 (10), genome completeness was estimated at 91.5% (compared to the Ascomycota lineage data set). This is similar to the other eight Taphrina genomes (2, 11), which have an average completeness of 91.95% (ranging from 89.6% to 93.1%). The mitochondrial genome was assembled as a 42.9-kb contig (GenBank accession number VWSI01000053).
Analyses using SAMtools v1.1.19 (12), Burrows-Wheeler Aligner MEM (BWA-MEM) v0.7.12-r1039 (13), and Genome Analysis Toolkit (GATK) v4.0.1.2 (14) with default settings identified very small numbers of putative heterozygous single-nucleotide polymorphisms (1,385) and insertion/deletions (181), suggesting that the genome is haploid.

Data availability.

This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under the accession number VWSI00000000 and the raw reads under SRA number SRX6812536. These data are also available under BioProject number PRJNA564291. The ITS sequence is available at accession number MN540705, and the mitochondrial genome is available under accession number VWSI01000053.

ACKNOWLEDGMENTS

This work was supported by undergraduate teaching resources from University College Dublin and Science Foundation Ireland (13/IA/1910). The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
We thank James Mooney for collecting the soil sample.

REFERENCES

1.
Rodrigues MG, Fonseca A. 2003. Molecular systematics of the dimorphic ascomycete genus Taphrina. Int J Syst Evol Microbiol 53:607–616.
2.
Tsai IJ, Tanaka E, Masuya H, Tanaka R, Hirooka Y, Endoh R, Sahashi N, Kikuchi T. 2014. Comparative genomics of Taphrina fungi causing varying degrees of tumorous deformity in plants. Genome Biol Evol 6:861–872.
3.
Rostrup FGE. 1883. Fortsatte Underogolser over Snyltesvampes Angreb paa Skovtraeorne. Tidsskr Skogbruk 6:199–300.
4.
Spanos YA, Woodward S. 1994. The effects of Taphrina betulina infection on growth of Betula pubescens. Forest Pathol 24:277–286.
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Jump BA, Woodward S. 1994. Histology of witches’ brooms on Betula pubescens. Forest Pathol 24:229–237.
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Jiang H, Lei R, Ding S-W, Zhu S. 2014. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics 15:182.
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Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477.
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Douglass AP, O’Brien CE, Offei B, Coughlan AY, Ortiz-Merino RA, Butler G, Byrne KP, Wolfe KH. 2019. Coverage-versus-length plots, a simple quality control step for de novo yeast genome sequence assemblies. G3 (Bethesda) 9:879–887.
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Gurevich A, Saveliev V, Vyahhi N, Tesler G. 2013. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075.
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Waterhouse RM, Seppey M, Simão FA, Manni M, Ioannidis P, Klioutchnikov G, Kriventseva EV, Zdobnov EM. 2018. BUSCO applications from quality assessments to gene prediction and phylogenomics. Mol Biol Evol 35:543–548.
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Cissé OH, Almeida JMGCF, Fonseca A, Kumar AA, Salojärvi J, Overmyer K, Hauser PM, Pagni M. 2013. Genome sequencing of the plant pathogen Taphrina deformans, the causal agent of peach leaf curl. mBio 4:e00055.
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Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078–2079.
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Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1760.
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McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. 2010. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303.

Information & Contributors

Information

Published In

cover image Microbiology Resource Announcements
Microbiology Resource Announcements
Volume 8Number 4827 November 2019
eLocator: 10.1128/mra.01255-19
Editor: Antonis Rokas, Vanderbilt University

History

Received: 4 October 2019
Accepted: 1 November 2019
Published online: 27 November 2019

Contributors

Authors

Padraic Heneghan
School of Biomedical and Biomolecular Sciences, Conway Institute, University College Dublin, Dublin, Ireland
Adam P. Ryan
School of Biomedical and Biomolecular Sciences, Conway Institute, University College Dublin, Dublin, Ireland
Darragh Nimmo
School of Biomedical and Biomolecular Sciences, Conway Institute, University College Dublin, Dublin, Ireland
Claudine Duggan
School of Biomedical and Biomolecular Sciences, Conway Institute, University College Dublin, Dublin, Ireland
Paurush Kumar
School of Biomedical and Biomolecular Sciences, Conway Institute, University College Dublin, Dublin, Ireland
Peadar O’Gaora
School of Biomedical and Biomolecular Sciences, Conway Institute, University College Dublin, Dublin, Ireland
Eoin Ó.'Cinnéide
School of Medicine, Conway Institute, University College Dublin, Dublin, Ireland
Kevin P. Byrne
School of Medicine, Conway Institute, University College Dublin, Dublin, Ireland
Kenneth H. Wolfe
School of Medicine, Conway Institute, University College Dublin, Dublin, Ireland
Caoimhe E. O’Brien
School of Biomedical and Biomolecular Sciences, Conway Institute, University College Dublin, Dublin, Ireland
School of Biomedical and Biomolecular Sciences, Conway Institute, University College Dublin, Dublin, Ireland

Editor

Antonis Rokas
Editor
Vanderbilt University

Notes

Address correspondence to Geraldine Butler, [email protected].

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