Bioscience Division, Los Alamos National Laboratory, Los Alamos 87545, NM, USA.
BMC Genomics. 2014 Mar 19;15:212. doi: 10.1186/1471-2164-15-212.
Microalgae in the genus Nannochloropsis are photosynthetic marine Eustigmatophytes of significant interest to the bioenergy and aquaculture sectors due to their ability to efficiently accumulate biomass and lipids for utilization in renewable transportation fuels, aquaculture feed, and other useful bioproducts. To better understand the genetic complement that drives the metabolic processes of these organisms, we present the assembly and comparative pangenomic analysis of the chloroplast and mitochondrial genomes from Nannochloropsis salina CCMP1776.
The chloroplast and mitochondrial genomes of N. salina are 98.4% and 97% identical to their counterparts in Nannochloropsis gaditana. Comparison of the Nannochloropsis pangenome to other algae within and outside of the same phyla revealed regions of significant genetic divergence in key genes that encode proteins needed for regulation of branched chain amino synthesis (acetohydroxyacid synthase), carbon fixation (RuBisCO activase), energy conservation (ATP synthase), protein synthesis and homeostasis (Clp protease, ribosome).
Many organellar gene modifications in Nannochloropsis are unique and deviate from conserved orthologs found across the tree of life. Implementation of secondary and tertiary structure prediction was crucial to functionally characterize many proteins and therefore should be implemented in automated annotation pipelines. The exceptional similarity of the N. salina and N. gaditana organellar genomes suggests that N. gaditana be reclassified as a strain of N. salina.
由于能够高效积累生物质和脂质，用于可再生交通燃料、水产养殖饲料和其他有用的生物制品，小球藻属（Nannochloropsis）中的微藻成为生物能源和水产养殖领域的重要研究对象。为了更好地了解推动这些生物代谢过程的遗传成分，我们对盐生小球藻（Nannochloropsis salina CCMP1776）的叶绿体和线粒体基因组进行了组装和比较全基因组分析。
盐生小球藻的叶绿体和线粒体基因组与同属的栅藻（Nannochloropsis gaditana）相比，相似度分别达到 98.4%和 97%。将小球藻的泛基因组与同一门内和门外的其他藻类进行比较，发现了在调控支链氨基酸合成（乙酰羟酸合酶）、碳固定（RuBisCO 激活酶）、能量守恒（ATP 合酶）、蛋白质合成和稳态（Clp 蛋白酶、核糖体）所需的关键基因中存在显著遗传差异的区域。
小球藻的许多细胞器基因修饰是独特的，与生命之树中发现的保守直系同源物不同。实施二级和三级结构预测对于功能表征许多蛋白质至关重要，因此应该在自动化注释管道中实施。盐生小球藻和栅藻的细胞器基因组非常相似，表明栅藻应重新归类为盐生小球藻的一个菌株。
