# Genome Sequence of the Yeast Clavispora lusitaniae Type Strain CBS 6936

Pascal Durrens, Christophe C. Kropp, Nicolas Biteau, Valérie Fitton-Ouhabi, Karine Dementhon, Isabelle Accoceberry, David J. Sherman, Thierry Noël

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Pascal Durrens, Christophe C. Kropp, Nicolas Biteau, Valérie Fitton-Ouhabi, Karine Dementhon, et al. Genome Sequence of the Yeast Clavispora lusitaniae Type Strain CBS 6936. Genome Announcements, 2017, 5 (31), pp.e00724-17. 10.1128/genomeA.00724-17. hal-01583349

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1 The genome of the yeast *Clavispora lusitaniae* type strain CBS 6936

2

3 Pascal Durrens<sup>#abc</sup>, Christophe Klopp<sup>e</sup>, Nicolas Biteau<sup>bd</sup>, Valérie Fitton-Ouhabi<sup>bd</sup>,

4 Karine Dementhon<sup>bd</sup>, Isabelle Accoceberry<sup>bd</sup>, David J. Sherman<sup>cab</sup>, Thierry Noël<sup>bd</sup>

5

6 Laboratoire Bordelais de Recherche en Informatique (LaBRI), UMR-CNRS 5800,

7 Talence, France<sup>a</sup>; Université de Bordeaux, Bordeaux, France<sup>b</sup>; INRIA joint project

8 team PLEIADE<sup>c</sup>; Laboratoire de Microbiologie Fondamentale et Pathogénicité UMR-

9 CNRS 5234, Bordeaux, France<sup>d</sup>; Genotoul Bioinfo, MIAT, INRA Toulouse, Castanet-

10 Tolosan, France<sup>e</sup>

11

12

13 Running Head: Genome of *C. lusitaniae* type strain CBS 6936

14

15 #Address correspondence to Pascal Durrens, pascal.durrens@labri.fr

16
17 Abstract

18

19 *Clavispora lusitaniae*, an environmental saprophytic yeast belonging to the CTG clade
20 of *Candida*, can behave occasionally as an opportunistic pathogen in humans. We
21 report the genome sequence of the type strain CBS 6936. Comparison with sequences
22 of strain ATCC 42720 indicates conservation of chromosomal structure but significant
23 nucleotide divergence.

24
25 *Clavispora lusitaniae*, teleomorph of *Candida lusitaniae*, is an ubiquist environmental
26 ascomycetous yeast, with no known specific ecological niche. It can be isolated from
27 different substrates, such as soils, waters, plants, and gastrointestinal tracts of many
28 animals including birds, mammals and humans. In immunocompromised hosts, C.
29 *lusitaniae* can be pathogenic and is responsible for about 1% of invasive candidiasis,
30 particularly in pediatric and onco-haematology patients (1).
31

31
32 So far, two strains have had their genomes sequenced : ATCC 42720, isolated from the
33 blood of a patient with myeloid leukemia (2), and MTCC 1001, a self-fertile strain
34 isolated from citrus (3). We report here the genome sequencing and assembly of the C.
35 lusitaniae type strain CBS 6936 (4), isolated from citrus peel juice. Genomic DNA was
36 isolated from a 50 ml YPD yeast culture, after sphaeroplast osmotic lysis and glass rod
37 purification of ethanol-precipitated nucleic acids. The DNA library was prepared from
38 1 µg according to the NEBNext DNA Library Prep Master Mix Set for Illumina
39 (E6040) protocol with an insert size of 368±122nt generated with an ultrasonicator
40 Covaris.
41

41
42 The library was sequenced on a MiSeq Illumina v1.18.54 producing circa 1.5 million
43 paired end reads, representing a 28X coverage. A de novo assembly of the reads was
44 performed with the aim to compare the contigs to those of the ATCC 42720 strain. We
45 used SPAdes v3.9.0 with default parameters (5) to perform the assembly. Only the 53
46 scaffolds longer than 1kb were retained as the GC % of many shorter ones deviated
47 from the average.
48

48
The scaffolds represent an overall length of 12.0Mb which is close to the 12.11Mb of the ATCC 42720 genome. The GC% amounts to 44.5% which is identical to that of ATCC 42720 strain. The alignment of CBS 6936 scaffolds against ATCC 42720 contigs by Nucmer (6) shows almost co-linearity between the two sets, apart from a 66kb long inversion. The number of SNPs between CBS 6936 and ATCC 42720 amounts to 132141 SNPs with Phred quality higher than 30, according to BWA (7) alignment of reads and Freebayes detection (8). This SNP density of 1 SNP per 90bp is twice the level observed between the strains SC5314 and WO-1 of *Candida albicans*, members of different subgroups in the species and qualified as relatively recent divergent (9).

Genes for 4 rRNA, 197 tRNA and 5539 proteins were predicted by alignment, TRNAscan-SE and a combination of Augustus (10), Snap (11) and Genmark-ES (12), respectively. The average identity of proteins between the two strains amounts to 89.9% ± 23.2, based on BLASTp (13) best hit alignments.

Altogether, these results indicate that, in spite of a conserved genome structure, the sequences are different, meaning that the strains underwent a significant divergence.

**Accession numbers.** This whole genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession numbers SRP075809 for reads and LYUB00000000 for scaffolds. The second version of the assembly of CBS 6936 is version LYUB02000000 and is described here.

71
72 Acknowledgements

73

74 The library and nucleotide sequencing were performed at the Genomic and Transcrip-
tomic Facility of Bordeaux (grants from the Conseil Regional d'Aquitaine
75 n°20030304002FA and 20040305003FA and from the European Union, FEDER
76 n°2003227 and from Investissements d'avenir, Convention attributive d'aide N°ANR-
77 10-EQPX-16-01). We would like to thank Christophe Hubert for its expertise and tech-
78 nical assistance.
79

79

80 The development of the bioinformatic pipeline was carried out using the PLAFRIM
81 experimental testbed, being developed under the Inria PlaFRIM development action
82 with support from Bordeaux INP, LABRI and IMB and other entities: Conseil
83 Régional d'Aquitaine, Université de Bordeaux and CNRS (and ANR in accordance to
84 the programme d'investissements d'Avenir (see https://plafrim.fr/).

81

82

83

84

85
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