Draft genome sequence data of Rhodosporidium toruloides VN1, a strain capable of producing natural astaxanthin

Tran, Tuyet Nhung; Ngo, Dai Hung; Nguyen, Ngoc Tuan; Ngo, Dai‐Hung

doi:10.1016/j.dib.2019.104443

Cited by 11 publications

(8 citation statements)

References 7 publications

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“…With the availability of complete genome sequencing of R. toruloides, − several genome-scale models of R. toruloides have been constructed. , These works are used not only to understand and annotate the genome and metabolic network, but also to predict a range of cellular functions, including the ability of cells to grow on various substrates and the effects of gene knockout on a genome scale.…”

Section: Development Of Synthetic Biology Elements and Toolsmentioning

confidence: 99%

“…On the other hand, the discovery of the knowledge about their physiology and metabolic abilities is facilitating the utilization of R. toruloides as a chassis cell factory. − In this review, we discuss current achievements of engineering R. toruloides as chassis platform, including how system and synthetic biology has been used to revolutionize strain construction, followed by trends and prospects of future research directions.…”

Section: Introductionmentioning

confidence: 99%

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Development and Perspective of Rhodotorula toruloides as an Efficient Cell Factory

Shi

2023

J. Agric. Food Chem.

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Rhodotorula toruloides is receiving significant attention as a novel cell factory because of its high production of lipids and carotenoids, fast growth and high cell density, as well as the ability to utilize a wide variety of substrates. These attractive traits of R. toruloides make it possible to become a low-cost producer that can be engineered for the production of various fuels and chemicals. However, the lack of understanding and genetic engineering tools impedes its metabolic engineering applications. A number of research efforts have been devoted to filling these gaps. This review focuses on recent developments in genetic engineering tools, advances in systems biology for improved understandings, and emerging engineered strains for metabolic engineering applications. Finally, future trends and barriers in developing R. toruloides as a cell factory are also discussed.

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Section: Development Of Synthetic Biology Elements and Toolsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Development and Perspective of Rhodotorula toruloides as an Efficient Cell Factory

Shi

2023

J. Agric. Food Chem.

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“… 2016c ; Tran et al . 2019 ). More recently, two Rhodosporidium haploids with A1 and A2 mating type isolated from the same diploid strain were sequenced for comparison and sequencing data showed very close genome size (20.75 and 21.49 Mbp), GC content (62.0% and 61.8%) and protein-coding genes (7730 and 7800) (Hu and Ji 2016 ).…”

Section: Introductionmentioning

confidence: 99%

Rhodosporidium toruloides - A potential red yeast chassis for lipids and beyond

Wen

Zhang

Odoh

et al. 2020

FEMS Yeast Research

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ABSTRACT The red yeast Rhodosporidium toruloides naturally produces microbial lipids and carotenoids. In the past decade or so, many studies demonstrated R. toruloides as a promising platform for lipid production owing to its diverse substrate appetites, robust stress resistance and other favorable features. Also, significant progresses have been made in genome sequencing, multi-omic analysis and genome-scale modeling, thus illuminating the molecular basis behind its physiology, metabolism and response to environmental stresses. At the same time, genetic parts and tools are continuously being developed to manipulate this distinctive organism. Engineered R. toruloides strains are emerging for enhanced production of conventional lipids, functional lipids as well as other interesting metabolites. This review updates those progresses and highlights future directions for advanced biotechnological applications.

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“…For R. kratochvilovae , Miccoli et al (2018) have completed whole genome sequencing of the strain LS11, and several other Rhodosporidium strains have also been sequenced ( Hu and Ji, 2016 ; Zhang et al, 2016 ; Tran et al, 2019 ). In addition, multi-omics analyses of the oleaginous fungal yeast Rhodosporidium toruloides were conducted to shield lights on Pi-limitation-induced lipid accumulation ( Wang et al, 2018 ).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Transcriptional Changes of Rhodosporidium kratochvilovae at Low Temperature

Guo

Zhang

et al. 2021

Front. Microbiol.

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Rhodosporidium kratochvilovae strain YM25235 is a cold-adapted oleaginous yeast strain that can grow at 15°C. It is capable of producing polyunsaturated fatty acids. Here, we used the Nanopore Platform to first assemble the R. kratochvilovae strain YM25235 genome into a 23.71 Mb size containing 46 scaffolds and 8,472 predicted genes. To explore the molecular mechanism behind the low temperature response of R. kratochvilovae strain YM25235, we analyzed the RNA transcriptomic data from low temperature (15°C) and normal temperature (30°C) groups using the next-generation deep sequencing technology (RNA-seq). We identified 1,300 differentially expressed genes (DEGs) by comparing the cultures grown at low temperature (15°C) and normal temperature (30°C) transcriptome libraries, including 553 significantly upregulated and 747 significantly downregulated DEGs. Gene ontology and pathway enrichment analysis revealed that DEGs were primarily related to metabolic processes, cellular processes, cellular organelles, and catalytic activity, whereas the overrepresented pathways included the MAPK signaling pathway, metabolic pathways, and amino sugar and nucleotide sugar metabolism. We validated the RNA-seq results by detecting the expression of 15 DEGs using qPCR. This study provides valuable information on the low temperature response of R. kratochvilovae strain YM25235 for further research and broadens our understanding for the response of R. kratochvilovae strain YM25235 to low temperature.

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Draft genome sequence data of Rhodosporidium toruloides VN1, a strain capable of producing natural astaxanthin

Cited by 11 publications

References 7 publications

Development and Perspective of Rhodotorula toruloides as an Efficient Cell Factory

Development and Perspective of Rhodotorula toruloides as an Efficient Cell Factory

Rhodosporidium toruloides - A potential red yeast chassis for lipids and beyond

Genome-Wide Transcriptional Changes of Rhodosporidium kratochvilovae at Low Temperature

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