Gan Han Ming, Thomas Bolaji N, Cavanaugh Nicole T, Morales Grace H, Mayers Ashley N, Savka Michael A, Hudson André O
Centre for Integrative Ecology-School of Life and Environmental Sciences, Deakin University, Victoria, Australia.
Genomics Facility, Monash University, Selangor, Malaysia.
PeerJ. 2017 Nov 14;5:e4030. doi: 10.7717/peerj.4030. eCollection 2017.
In industry, the yeast is commonly used for the production of carotenoids. The production of carotenoids is important because they are used as natural colorants in food and some carotenoids are precursors of retinol (vitamin A). However, the identification and molecular characterization of the carotenoid pathway/s in species belonging to the genus is scarce due to the lack of genomic information thus potentially impeding effective metabolic engineering of these yeast strains for improved carotenoid production. In this study, we report the isolation, identification, characterization and the whole nuclear genome and mitogenome sequence of the endophyte RIT389 isolated from a plant known for its anti-fungal and antibacterial properties and commonly used as chewing sticks. The assembled genome of RIT389 is 19 Mbp in length with an estimated genomic heterozygosity of 9.29%. Whole genome phylogeny supports the species designation of strain RIT389 within the genus in addition to supporting the monophyly of the currently sequenced species. Further, we report for the first time, the recovery of the complete mitochondrial genome of using the genome skimming approach. The assembled mitogenome is at least 7,000 bases larger than that of which is largely attributed to the presence of large intronic regions containing open reading frames coding for homing endonuclease from the LAGLIDADG and GIY-YIG families. Furthermore, genomic regions containing the key genes for carotenoid production were identified in RIT389, revealing differences in gene synteny that may play a role in the regulation of the biotechnologically important carotenoid synthesis pathways in yeasts.
在工业上，酵母通常用于生产类胡萝卜素。类胡萝卜素的生产很重要，因为它们被用作食品中的天然色素，并且一些类胡萝卜素是视黄醇（维生素A）的前体。然而，由于缺乏基因组信息，属于该属的物种中类胡萝卜素途径的鉴定和分子特征研究较少，这可能会阻碍对这些酵母菌株进行有效的代谢工程改造以提高类胡萝卜素产量。在本研究中，我们报告了从一种以其抗真菌和抗菌特性而闻名且常用作咀嚼棒的植物中分离出的内生菌RIT389的分离、鉴定、特征分析以及全核基因组和线粒体基因组序列。RIT389的组装基因组长度为19 Mbp，估计基因组杂合度为9.29%。全基因组系统发育分析支持菌株RIT389在该属内的物种指定，同时也支持目前已测序的该属物种的单系性。此外，我们首次报告了使用基因组鸟枪法测序方法获得的该属完整线粒体基因组。组装后的线粒体基因组比该属的线粒体基因组至少大7000个碱基，这主要归因于存在包含来自LAGLIDADG和GIY - YIG家族的编码归巢内切酶的开放阅读框的大内含子区域。此外，在RIT389中鉴定出了包含类胡萝卜素生产关键基因的基因组区域，揭示了基因共线性的差异，这些差异可能在酵母中具有重要生物技术意义的类胡萝卜素合成途径的调控中发挥作用。
