Improved Reference Genome for Cyclotella cryptica CCMP332, a Model for Cell Wall Morphogenesis, Salinity Adaptation, and Lipid Production in Diatoms (Bacillariophyta)
Improved Reference Genome for Cyclotella cryptica CCMP332, a Model for Cell Wall Morphogenesis, Salinity Adaptation, and Lipid Production in Diatoms (Bacillariophyta)
复制标题
DOI：
10.1534/g3.120.401408
复制
发表时间：
2020-05
期刊：
影响因子：
--
通讯作者：
Wade R. Roberts;K. Downey;Elizabeth C. Ruck;Jesse Traller;Andrew J. Alverson
中科院分区：
文献类型：
--
作者：
Wade R. Roberts;K. Downey;Elizabeth C. Ruck;Jesse Traller;Andrew J. Alverson
硅藻，Cyclotella cryptica，是一个完善的实验模型，用于生理学研究，最近，硅藻的生物技术应用。为了进一步促进其作为模式硅藻物种的使用，我们报告了一个改进的参考基因组组装和注释的C。菌株CCMP 332。我们使用长读和短读测序的组合来组装高质量和无污染的基因组。基因组大小为171 Mb，由662个支架组成，支架N50为494 kb。这表示与先前的组装相比，支架数量减少176倍，支架N50增加41倍。该基因组包含21，250个预测基因，其中75%被分配了推定功能。重复DNA占基因组的59%，重复元件的改进分类表明，历史上稳定积累的转座元件有助于C. cryptica基因组高质量的C. cryptica基因组将为硅藻的生态学、遗传学和生物技术研究提供有价值的参考。数据来自NCBI BioProjects PRJNA 628076和PRJNA 589195
The diatom, Cyclotella cryptica, is a well-established experimental model for physiological studies and, more recently, biotechnology applications of diatoms. To further facilitate its use as a model diatom species, we report an improved reference genome assembly and annotation for C. cryptica strain CCMP332. We used a combination of long- and short-read sequencing to assemble a high-quality and contaminant-free genome. The genome is 171 Mb in size and consists of 662 scaffolds with a scaffold N50 of 494 kb. This represents a 176-fold decrease in scaffold number and 41-fold increase in scaffold N50 compared to the previous assembly. The genome contains 21,250 predicted genes, 75% of which were assigned putative functions. Repetitive DNA comprises 59% of the genome, and an improved classification of repetitive elements indicated that a historically steady accumulation of transposable elements has contributed to the relatively large size of the C. cryptica genome. The high-quality C. cryptica genome will serve as a valuable reference for ecological, genetic, and biotechnology studies of diatoms. Data available from NCBI BioProjects PRJNA628076 and PRJNA589195