Whole genome sequencing and comparative genomic analysis of oleaginous red yeast Sporobolomyces pararoseus NGR identifies candidate genes for biotechnological potential and ballistospores-shooting

Abstract

Background: Sporobolomyces pararoseus is regarded as an oleaginous red yeast, which synthesizes numerous valuable compounds with wide industrial usages. This species hold biotechnological interests in biodiesel, food and cosmetics industries. Moreover, the ballistospores-shooting promotes the colonizing of S. pararoseus in most terrestrial and marine ecosystems. However, very little is known about the basic genomic features of S. pararoseus. To assess the biotechnological potential and ballistospores-shooting mechanism of S. pararoseus on genome-scale, the whole genome sequencing was performed by next-generation sequencing technology. Results: Here, we used Illumina Hiseq platform to firstly assemble S. pararoseus genome into 20.9 Mb containing 54 scaffolds and 5963 predicted genes with a N50 length of 2,038,020 bp and GC content of 47.59%. Genome completeness (BUSCO alignment: 95.4%) and RNA-seq analysis (expressed genes: 98.68%) indicated the high-quality features of the current genome. Through the annotation information of the genome, we screened many key genes involved in carotenoids, lipids, carbohydrate metabolism and signal transduction pathways. A phylogenetic assessment suggested that the evolutionary trajectory of the order Sporidiobolales species was evolved from genus Sporobolomyces to Rhodotorula through the mediator Rhodosporidiobolus. Compared to the lacking ballistospores Rhodotorula toruloides and Saccharomyces cerevisiae, we found genes enriched for spore germination and sugar metabolism. These genes might be responsible for the ballistospores-shooting in S. pararoseus NGR. Conclusion: These results greatly advance our understanding of S. pararoseus NGR in biotechnological potential and ballistospores-shooting, which help further research of genetic manipulation, metabolic engineering as well as its evolutionary direction.

Genomics and lipidomics analysis of the biotechnologically important oleaginous red yeast Rhodotorula glutinis ZHK provides new insights into its lipid and carotenoid metabolism

“…The substitution rates Ka/Ks (the number of nonsynonymous substitutions per nonsynonymous site to the number of synonymous substitutions per synonymous site) were averaged for all of the pairwise comparisons of each single-copy orthologous gene, using the free ratio Model of the software KaKs_Calculator Toolbox (version 2.0) with default parameters [ 75 , 76 ]. These genes showed a higher Ka/Ks value (Ka/Ks > 1 or 0.5 and p -value < 0.05) were suggested to be the positively selected genes [ 77 ].…”

Advances in production of high-value lipids by oleaginous yeasts

“…As it could be seen, the use of oleaginous yeasts as a lipid factory is a field with promising potential for future exploration, which can bring significant benefits not only to the environment but also in expanding the range of high-value lipids with new lipogenic compounds. In addition, genomes of novel oleaginous yeast species, including Trichosporon fermentans, Saitozyma podzolica and Sporobolomyces pararoseus, have recently been sequenced [172][173][174][175]. This, together with the growing number of genetic engineering tools available for their transformation, such as in the case of Candida hispaniensis, Blastobotrys adeninivorans or B. raffinosifermentans [176,177]…”

Isolation and Molecular Characterization of the Romaine Lettuce Phylloplane Mycobiome

“…These pigments, although poorly understood, seem to protect them against UV radiation and some provide antimicrobial, anticancer and antiaging activity [ 120 , 121 ]. Because of these characteristics, red-pigmented yeasts have gained interest from the pharmaceutical, cosmetics and biotechnology industries [ 122 , 123 , 124 ].…”