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Complete genome sequence and comparative genomics of the probiotic yeast Saccharomyces boulardii

Khatri, Indu, Tomar, Rajul, Ganesan, K., Prasad, G. S., Subramanian, Srikrishna·2017·Scientific Reports
DOI 10.1038/s41598-017-00414-2PMC PMC5428479
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Abstract

The probiotic yeast, Saccharomyces boulardii (Sb) is known to be effective against many gastrointestinal disorders and antibiotic-associated diarrhea. To understand molecular basis of probiotic-properties ascribed to Sb we determined the complete genomes of two strains of Sb i.e. Biocodex and unique28 and the draft genomes for three other Sb strains that are marketed as probiotics in India. We compared these genomes with 145 strains of S. cerevisiae (Sc) to understand genome-level similarities and differences between these yeasts. A distinctive feature of Sb from other Sc is absence of Ty elements Ty1, Ty3, Ty4 and associated LTR. However, we could identify complete Ty2 and Ty5 elements in Sb. The genes for hexose transporters HXT 11 and HXT 9, and asparagine-utilization are absent in all Sb strains. We find differences in repeat periods and copy numbers of repeats in flocculin genes that are likely related to the differential adhesion of Sb as compared to Sc. Core-proteome based taxonomy places Sb strains along with wine strains of Sc. We find the introgression of five genes from Z. bailii into the chromosome IV of Sb and wine strains of Sc. Intriguingly, genes involved in conferring known probiotic properties to Sb are conserved in most Sc strains.

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Figure 1 (A) Circular representation of the Sb-biocodex and Sb-unique28 complete genome. Circles (from inside to outside): circle 1 (GC content), circle 2 (Sc S288C complete chromosomes with alternative blue and red color); circle 3 (GC skew); circle 4 (Sb-biocodex complete chromosomes); circle 5 (Sb-unique28 complete chromosomes). BRIG 0.95 was used to build the circular representation. Mapping studies were done using BLASTn with an E-value cut-off 1e-5. (B) Core orthologous proteins among all Sb proteome represented by orthology diagram depicting dispensable proteome and homologs among these strains.
Figure 1 (A) Circular representation of the Sb-biocodex and Sb-unique28 complete genome. Circles (from inside to outside): circle 1 (GC content), circle 2 (Sc S288C complete chromosomes with alternative blue and red color); circle 3 (GC skew); circle 4 (Sb-biocodex complete chromosomes); circle 5 (Sb-unique28 complete chromosomes). BRIG 0.95 was used to build the circular representation. Mapping studies were done using BLASTn with an E-value cut-off 1e-5. (B) Core orthologous proteins among all Sb proteome represented by orthology diagram depicting dispensable proteome and homologs among these strains.CC BY · PubMed Central
Figure 2 MAT Locus of Sb biocodex depicting the annotated regions. (A) MATa locus with yellow arrows depicting the MAT region divided in W, X, YA and Z1 regions with coded MATa1 and MATa2 regulatory proteins. (B) MATα locus with yellow arrows depicting the MAT region divided in W, X, Y, Z1 and Z2 regions with coded MATα1 and MATα2 regulatory proteins.
Figure 2 MAT Locus of Sb biocodex depicting the annotated regions. (A) MATa locus with yellow arrows depicting the MAT region divided in W, X, YA and Z1 regions with coded MATa1 and MATa2 regulatory proteins. (B) MATα locus with yellow arrows depicting the MAT region divided in W, X, Y, Z1 and Z2 regions with coded MATα1 and MATα2 regulatory proteins.CC BY · PubMed Central
Figure 3 Introgression of five genes in two copies from Zygosaccharomyces bailii to Chromosome IV of Sb genomes.
Figure 3 Introgression of five genes in two copies from Zygosaccharomyces bailii to Chromosome IV of Sb genomes.CC BY · PubMed Central
Figure 4 Maximum Evolution tree for 182 orthologous proteins of all strains of Sb, Sc and S. kudriavzevii as outgroup species. The taxa are shaded based on the isolation source of strains as boulardii: gold; Fruits: lightsalmon; Wine: hotpink; Tree isolate: skyblue; Brewery: lawngreen; Lab strains: palegoldenrod; Bakery: darkorange; Bioethanol: peru; Clinical: mediumseagreen; Environmental samples: cornflowerblue.
Figure 4 Maximum Evolution tree for 182 orthologous proteins of all strains of Sb, Sc and S. kudriavzevii as outgroup species. The taxa are shaded based on the isolation source of strains as boulardii: gold; Fruits: lightsalmon; Wine: hotpink; Tree isolate: skyblue; Brewery: lawngreen; Lab strains: palegoldenrod; Bakery: darkorange; Bioethanol: peru; Clinical: mediumseagreen; Environmental samples: cornflowerblue.CC BY · PubMed Central

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Authors
Khatri, I., Tomar, R., Ganesan, K., Prasad, G. S., & Subramanian, S.
ORCID
Venue
Scientific Reports
Publisher
Springer Science and Business Media LLC
Published
2017-03-23
Volume
7
Issue
1
ISSN
2045-2322
DOI
10.1038/s41598-017-00414-2
PMC
PMC5428479
Cited by
123
References
3
Language
en
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Khatri, I., Tomar, R., Ganesan, K., Prasad, G. S., & Subramanian, S. (2017). Complete genome sequence and comparative genomics of the probiotic yeast Saccharomyces boulardii. Scientific Reports. https://doi.org/10.1038/s41598-017-00414-2