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 th...
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doaj-03fa35e328e44c88be995901d60011c62020-11-25T02:08:41ZengBMCBMC Genomics1471-21642020-02-0121111110.1186/s12864-020-6593-1Whole genome sequencing and comparative genomic analysis of oleaginous red yeast Sporobolomyces pararoseus NGR identifies candidate genes for biotechnological potential and ballistospores-shootingChun-Ji Li0Die Zhao1Bing-Xue Li2Ning Zhang3Jian-Yu Yan4Hong-Tao Zou5College of Land and Environment, Shenyang Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityCollege of Land and Environment, Shenyang Agricultural UniversityCollege of Biological Science and Technology, Shenyang Agricultural UniversityCollege of Land and Environment, Shenyang Agricultural UniversityCollege of Land and Environment, Shenyang Agricultural UniversityAbstract 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.http://link.springer.com/article/10.1186/s12864-020-6593-1Sporobolomyces pararoseusGenome sequencingComparative genomicBiotechnological potentialBallistospores-shootingEvolutionary direction |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Chun-Ji Li Die Zhao Bing-Xue Li Ning Zhang Jian-Yu Yan Hong-Tao Zou |
spellingShingle |
Chun-Ji Li Die Zhao Bing-Xue Li Ning Zhang Jian-Yu Yan Hong-Tao Zou Whole genome sequencing and comparative genomic analysis of oleaginous red yeast Sporobolomyces pararoseus NGR identifies candidate genes for biotechnological potential and ballistospores-shooting BMC Genomics Sporobolomyces pararoseus Genome sequencing Comparative genomic Biotechnological potential Ballistospores-shooting Evolutionary direction |
author_facet |
Chun-Ji Li Die Zhao Bing-Xue Li Ning Zhang Jian-Yu Yan Hong-Tao Zou |
author_sort |
Chun-Ji Li |
title |
Whole genome sequencing and comparative genomic analysis of oleaginous red yeast Sporobolomyces pararoseus NGR identifies candidate genes for biotechnological potential and ballistospores-shooting |
title_short |
Whole genome sequencing and comparative genomic analysis of oleaginous red yeast Sporobolomyces pararoseus NGR identifies candidate genes for biotechnological potential and ballistospores-shooting |
title_full |
Whole genome sequencing and comparative genomic analysis of oleaginous red yeast Sporobolomyces pararoseus NGR identifies candidate genes for biotechnological potential and ballistospores-shooting |
title_fullStr |
Whole genome sequencing and comparative genomic analysis of oleaginous red yeast Sporobolomyces pararoseus NGR identifies candidate genes for biotechnological potential and ballistospores-shooting |
title_full_unstemmed |
Whole genome sequencing and comparative genomic analysis of oleaginous red yeast Sporobolomyces pararoseus NGR identifies candidate genes for biotechnological potential and ballistospores-shooting |
title_sort |
whole genome sequencing and comparative genomic analysis of oleaginous red yeast sporobolomyces pararoseus ngr identifies candidate genes for biotechnological potential and ballistospores-shooting |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2020-02-01 |
description |
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. |
topic |
Sporobolomyces pararoseus Genome sequencing Comparative genomic Biotechnological potential Ballistospores-shooting Evolutionary direction |
url |
http://link.springer.com/article/10.1186/s12864-020-6593-1 |
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