A unique life-strategy of an endophytic yeast Rhodotorula mucilaginosa JGTA-S1—a comparative genomics viewpoint

Abstract

Endophytic yeasts of genus Rhodotorula are gaining importance for their ability to improve plant growth. The nature of their interaction with plants, however, remains unknown. Rhodotorula mucilaginosa JGTA-S1 was isolated as an endophyte of Typha angustifolia and promoted growth in the host. To investigate the life-strategy of the yeast from a genomics perspective, we used Illumina and Oxford Nanopore reads to generate a high-quality annotated draft assembly of JGTA-S1 and compared its genome to three other Rhodotorula yeasts and the close relative Rhodosporidium toruloides . JGTA-S1 is a haploid yeast possessing several genes potentially facilitating its endophytic lifestyle such as those responsible for solubilizing phosphate and producing phytohormones. An intact mating-locus in JGTA-S1 raised the possibility of a yet unknown sexual reproductive cycle in Rhodotorula yeasts. Additionally, JGTA-S1 had functional anti-freezing genes and was also unique in lacking a functional nitrate-assimilation pathway—a feature that is associated with obligate biotrophs. Nitrogen-fixing endobacteria were found within JGTA-S1 that may circumvent this defective N-metabolism. JGTA-S1 genome data coupled with experimental evidence give us an insight into the nature of its beneficial interaction with plants.

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

“…Up to now, except for our R. glutinis ZHK, there are eleven whole genome sequences of Rhodotorula species have been sequenced. In general, the genome size of these Rhodotorula species is ~20 Mb, which represents a smaller grade when compared to other classes in order Pucciniomycotina [ 37 ]. The phenomenon of the decrease in genome size is considered as a shared feature in class Microbotryomycetes.…”

Mycobiota in the Carposphere of Sour and Sweet Cherries and Antagonistic Features of Potential Biocontrol Yeasts

“…are ubiquitous yeasts that can be recovered from many environmental sources, including fruits. Some Rhodotorula species, such as R. graminis , R. mucilaginosa , and R. babjevae award growth benefits to plants, enrich their biochemical properties [ 58 , 59 , 60 ]. Rhodotorula yeasts exhibit strong biocontrol activity against fungal and bacterial pathogens, especially towards B. cinerea and P. expansum [ 59 ].…”

Uncovering the hidden bacterial ghost communities of yeast and experimental evidences demonstrates yeast as thriving hub for bacteria

“…6 a). The recent finding on interactions between the yeast Rhodotorula mucilaginosa harbouring N 2 -fixing P. stutzeri and rice plants highlights the role of endosymbiotic bacteria in the nitrogen needs of plants 18 . This example parallels the role of endobacteria of plant-associated filamentous fungi 19 .…”

“…Yeast-bacterial interactions, particularly the endobacteria phenomenon was speculated as potentially important to nectar research, where both these microorganisms play a key role in the ecology and biochemistry of flower nectar 5 . Similarly, the yeast Rhodotorula mucilaginosa was shown to harbor endosymbiotic Pseudomonas stutzeri 18 . This yeast-endobacteria system has been implicated in interactions with rice plant that hosts the yeast, wherein these microorganisms collectively aid in nitrogen fixation 19 .…”