Open access
Announcement
21 June 2018

Draft Genome Sequence of the Yeast Nadsonia starkeyi-henricii UCD142, Isolated from Forest Soil in Ireland

ABSTRACT

We report a draft genome sequence of a strain of the nonfermentative yeast Nadsonia starkeyi-henricii, isolated from soil in a forest in Ireland. Comparison to Nadsonia fulvescens shows few rearrangements and a level of divergence similar to that of Saccharomyces cerevisiae versus Saccharomyces paradoxus. Its mitochondrial genome lacks NAD genes.

GENOME ANNOUNCEMENT

Nadsonia starkeyi-henricii (1) is a little-studied yeast. It is one of the four accepted species and varieties in the genus Nadsonia and was formerly called Schizoblastosporion starkeyi-henricii (24). It is unable to ferment sugars and is only able to grow by respiration (4).
Nadsonia species have lower maximum temperatures for growth than most other yeasts, which may have caused them to be overlooked in previous surveys of yeast diversity. Most previous isolates of N. starkeyi-henricii were found in soils from forests or bogs, mainly in Northern Europe (2, 3, 5). It will not grow at temperatures above 25 to 30°C, and it dies at 35°C (6). Nadsonia species are characterized by their unusual mode of mitotic cell division, with buds forming alternately from opposite poles of the cell. Sporulation has never been observed in N. starkeyi-henricii, unlike the other members of this genus. Phylogenetically, Nadsonia is in the Yarrowia clade, distantly related to Saccharomyces cerevisiae (7, 8). One genome sequence has been published from this genus, Nadsonia fulvescens var. elongata (7).
Strain UCD142 was isolated from soil in a coniferous forest in Dublin, Ireland (global positioning satellite [GPS] coordinates N53.241645, W6.294017). It was cultured at room temperature on yeast extract-peptone-dextrose (YPD) agar plates containing chloramphenicol (3% wt/vol) and carbenicillin (10% wt/vol). Genome sequencing (6.6 million paired-end reads of 150 bp) was performed by BGI Tech Solutions (China) with an Illumina HiSeq 4000. The genome was assembled into 318 contigs (60× coverage, >1 kb) using SPAdes v 3.11.1 (9).
The N. starkeyi-henricii genome assembly is 14.6 Mb, similar to Nadsonia fulvescens (13.7 Mb; reference 7). Half the data are present in the 40 scaffolds (L50) that are larger than 120 kb (N50), and the largest scaffold is 404 kb. BWA and SAMtools (10, 11) identified only 2,337 single nucleotide polymorphisms (SNPs), and the genome appears to be haploid. Annotation using YGAP (12) predicted 5,216 protein-coding genes, which compares to 5,657 in N. fulvescens (7). tRNAscan-SE (13) predicted 607 tRNA genes in the nuclear genome, an unusually high number for a yeast. Similar to N. fulvescens, the 5S rRNA genes are not located within the repeating 18S-5.8S-26S array but instead are dispersed at approximately 115 locations (7).
Comparison of the 10 largest N. starkeyi-henricii scaffolds to N. fulvescens by BLAST and dot-matrix plots showed that the genomes are mostly collinear. Protein sequence divergence between the two Nadsonia species is approximately equal to that between S. cerevisiae and S. paradoxus (e.g., 89% amino acid sequence identity in MDN1, the largest gene in the genome).
The mitochondrial genome is a 22,069-bp circle containing 8 protein-coding genes with no introns. It does not contain any NAD genes for NADH dehydrogenase subunits, in contrast to Yarrowia lipolytica (14), indicating an absence of mitochondrial respiratory complex I. Complex I is present in most yeasts but has been lost in three clades centered on Saccharomyces, Schizosaccharomyces, and Nadsonia (7).

Accession number(s).

This whole-genome shotgun project has been deposited in DDBJ/ENA/GenBank under accession no. QBLK00000000. The version described in this paper is the first version, QBLK01000000.

ACKNOWLEDGMENTS

This work was supported by an undergraduate teaching award from University College Dublin. The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

REFERENCES

1.
Starkey RL, Henrici AT. 1927. The occurrence of yeasts in soil. Soil Science 23:33–46.
2.
Smith MT. 2011. Nadsonia Sydow (1912), p 629–632. In Kurtzman CP, Fell JW, Boekhout T (ed), The yeasts, a taxonomic study. Elsevier, Amsterdam, The Netherlands.
3.
Smith MT. 2011. Schizoblastosporion Ciferri (1930), p 1329–1330. In Kurtzman CP, Fell JW, Boekhout T (ed), The yeasts, a taxonomic study. Elsevier, Amsterdam, The Netherlands.
4.
Ciferri R. 1930. Contribuzioni alla sistematica delle torulopsidaceae. II-XIV. Arch Protistenkd 71:405–452.
5.
di Menna ME. 1965. Schizoblastosporion starkeyi-henricii Ciferri. Mycopathol Mycol Appl 25:205–212.
6.
Lund A. 1954. Studies on the ecology of yeasts. Munksgaard, Copenhagen, Denmark.
7.
Riley R, Haridas S, Wolfe KH, Lopes MR, Hittinger CT, Göker M, Salamov AA, Wisecaver JH, Long TM, Calvey CH, Aerts AL, Barry KW, Choi C, Clum A, Coughlan AY, Deshpande S, Douglass AP, Hanson SJ, Klenk H-P, LaButti KM, Lapidus A, Lindquist EA, Lipzen AM, Meier-Kolthoff JP, Ohm RA, Otillar RP, Pangilinan JL, Peng Y, Rokas A, Rosa CA, Scheuner C, Sibirny AA, Slot JC, Stielow JB, Sun H, Kurtzman CP, Blackwell M, Grigoriev IV, Jeffries TW. 2016. Comparative genomics of biotechnologically important yeasts. Proc Natl Acad Sci U S A 113:9882–9887.
8.
Shen X-X, Zhou X, Kominek J, Kurtzman CP, Hittinger CT, Rokas A. 2016. Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data. G3 6:3927–3939.
9.
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.
10.
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760.
11.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Genome Project Data Processing S. 2009. The Sequence Alignment/Map Format and SAMtools. Bioinformatics 25:2078–2079.
12.
Proux-Wéra E, Armisén D, Byrne KP, Wolfe KH. 2012. A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach. BMC Bioinformatics 13:237.
13.
Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964.
14.
Kerscher S, Durstewitz G, Casaregola S, Gaillardin C, Brandt U. 2001. The complete mitochondrial genome of Yarrowia lipolytica. Comp Funct Genomics 2:80–90.

Information & Contributors

Information

Published In

cover image Genome Announcements
Genome Announcements
Volume 6Number 2521 June 2018
eLocator: 10.1128/genomea.00549-18

History

Received: 14 May 2018
Accepted: 15 May 2018
Published online: 21 June 2018

Contributors

Authors

Sinéad O’Boyle
School of Biomedical and Biomolecular Sciences, Conway Institute, University College Dublin, Dublin, Ireland
Sean A. Bergin
School of Biomedical and Biomolecular Sciences, Conway Institute, University College Dublin, Dublin, Ireland
Éabha E. Hussey
School of Biomedical and Biomolecular Sciences, Conway Institute, University College Dublin, Dublin, Ireland
Aaron D. McLaughlin
School of Biomedical and Biomolecular Sciences, Conway Institute, University College Dublin, Dublin, Ireland
Luan R. Riddell
School of Biomedical and Biomolecular Sciences, 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

Notes

Address correspondence to Geraldine Butler, [email protected].

Metrics & Citations

Metrics

Note:

  • For recently published articles, the TOTAL download count will appear as zero until a new month starts.
  • 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