Genome sequence of the plant growth promoting endophytic yeast Rhodotorula graminis WP1

Wine is a complex beverage, comprising thousands of metabolites that are produced through the action of a plethora of yeasts and bacteria during fermentation of grape must. These microbial communities originate in the vineyard and the winery and reflect the influence of several factors including grape variety, geographical location, climate, vineyard spraying, technological practices, processing stage and season (pre-harvest, harvest, post-harvest). Vineyard and winery microbial communities have the potential to participate during fermentation and influence wine flavour and aroma. Therefore, there is an enormous interest in isolating and characterising these communities, particularly non-Saccharomyces yeast species to increase wine flavour diversity, while also exploting regional signature microbial populations to enhance regionality. In this review we describe the role and relevance of the main non-Saccharomyces yeast species found in vineyards and wineries. This includes the latest reports covering the application of these species for winemaking; and the biotechnological characteristics and potential applications of non-Saccharomyces species in other areas. In particular, we focus attention on the species for which molecular and genomic tools and resources are available for study. Copyright © 2016 John Wiley & Sons, Ltd.

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“…glutinis (Paul et al ., ), R . graminis (Firrincieli et al ., ) and R . ‬ mucilaginosa ‬ (Deligios et al ., ).…”

Section: Rhodotorula Sppmentioning

confidence: 92%

“…Genome sequences are available for R. toruloides (synonym, R. gracilis) (Kumar et al, 2012a;Morin et al, 2014), R. glutinis (Paul et al, 2014), R. graminis (Firrincieli et al, 2015) and R. mucilaginosa (Deligios et al, 2015). The genomes of the Rhodotorula spp.…”

Section: Rhodotorula Sppmentioning

confidence: 99%

Yeasts found in vineyards and wineries

Varela

Borneman

2016

Yeast

119

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“…Genomic, transcripts, and coding sequences (CDS) together with the corresponding expressed sequence tags (EST) data were downloaded from the MycoCosm website (https://genome.jgi.doe.gov/programs/fungi/index.jsf) for the following red yeast species: Rhodotorula graminis WP1 (Firrincieli et al, ), C. minutum MCA4210, Rhodotorula (= Rhodosporidium ) toruloides ATCC26217, R. glutinis , R. mucilaginosa ATCC58901, and Rhodotorula sp. J31.…”

Section: Methodsmentioning

confidence: 99%

“…Rhodotorula graminis WP1 (Firrincieli et al, 2015), C. minutum MCA4210, Rhodotorula (=Rhodosporidium) toruloides ATCC26217, R. glutinis, R. mucilaginosa ATCC58901, and Rhodotorula sp. J31.…”

Section: Sequences and Expression Datamentioning

confidence: 99%

An analysis of codon bias in six red yeast species

Camiolo

Toome‐Heller

Aime

et al. 2018

Yeast

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Red yeasts, primarily species of Rhodotorula, Sporobolomyces, and other genera of Pucciniomycotina, are traditionally considered proficient systems for lipid and terpene production, and only recently have also gained consideration for the production of a wider range of molecules of biotechnological potential. Improvements of transgene delivery protocols and regulated gene expression systems have been proposed, but a dearth of information on compositional and/or structural features of genes has prevented transgene sequence optimization efforts for high expression levels. Here, the codon compositional features of genes in six red yeast species were characterized, and the impact that evolutionary forces may have played in shaping this compositional bias was dissected by using several computational approaches. Results obtained are compatible with the hypothesis that mutational bias, although playing a significant role, cannot alone explain synonymous codon usage bias of genes. Nevertheless, several lines of evidences indicated a role for translational selection in driving the synonymous codons that allow high expression efficiency. These optimal synonymous codons are identified for each of the six species analyzed. Moreover, the presence of intragenic patterns of codon usage, which are thought to facilitate polyribosome formation, was highlighted. The information presented should be taken into consideration for transgene design for optimal expression in red yeast species.

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“…tritici (Wicker et al , 2013); Ustilago maydis (Kämper et al , 2006); Venturia pirina (Cooke et al , 2014); Venturia inaequalis (Deng et al , 2017); Cladosporium fulvum (de Wit et al , 2012); Phytophthora infestans (Haas et al , 2009); Phytophthora capsici (Lamour et al , 2012); Phytophthora sojae and Phytophthora ramorum (Tyler et al , 2006); Fusarium graminearum (Cuomo et al , 2007), Fusarium oxysporum f. sp. lycopersici and Fusarium oxysporum 47 (Ma et al , 2010); Leptosphaeria maculans (Rouxel et al , 2011); Magnaporthe oryzae (Dean et al , 2005); Zymoseptoria tritici (Goodwin et al , 2011); Verticillium dahliae (Klosterman et al , 2011); Colletotrichum higginsianum (O’Connell et al , 2012); Pythium ultimum (Levesque et al , 2010); Stagonospora nodorum (Hane et al , 2007); Botrytis cinerea and Sclerotinia sclerotiorum (Amselem et al , 2011); Rhizoctonia solani AG8 (Hane et al , 2014); Pyrenophora tritici-repentis (Manning et al , 2013); Penicillium digitatum (Marcet-Houben et al , 2012); Laccaria bicolor (Martin et al , 2008); Amanita muscaria , Hebeloma cylindrosporum , Laccaria amethystina , Paxillus involutus , Paxillus rubicundulus , Piloderma croceum , Pisolithus microcarpus , Pisolithus tinctorius , Scleroderma citrinum , Sebacina vermifera , Suillus luteus and Tulasnella calospora (Kohler et al , 2015); Aspergillus flavus (Arnaud et al , 2012); Tremella mesenterica , Coniophora puteana , Dacryopinax sp ., Fomitopsis pinicola, Gloeophyllum trabeum, Wolfiporia cocos , Dichomitus squalens, Fomitiporia mediterranea, Punctularia strigosozonata, Stereum hirsutum and Trametes versicolor (Floudas et al , 2012); Rhodotorula graminis (Firrincieli et al , 2015); Batrachochytrium dendrobatidis (https://www.broadinstitute.org/fungal-genome-initiative/batrachochytrium-genome-project); Ashbya gossypii (Gattiker et al , 2007); Taphrina deformans (Cisse et al , 2013); Pichia stipitis (Jeffries et al , 2007); Sacch aromyces cerevisiae (Goffeau et al , 1996); Hysterium pulicare (Ohm et al , 2012); Coprinus cinereus (Stajich et al , 2010); Aspergillus oryzae (Machida et al , 2005); Aspergillus niger (Andersen et al , 2011); Neurospora crassa (Galagan et al , 2003); Agaricus bisporus var bisporus (Morin et al , 2012); Rhodosporidium toruloides (Zhu et al , 2012). Secretome predictions of fungal and oomycete genomes was done using SignalP 3 (Bendtsen et al , 2004b), TMHMM (Krogh et al , 2001) and TargetP (Emanuelsson et al , 2000) as described in…”

Section: Descriptionmentioning

confidence: 99%