State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
Enzyme Technology Laboratory, National Center for Genetic Engineering and Biotechnology, Pathum Thani, 12120, Thailand.
BMC Genomics. 2020 Oct 27;21(1):743. doi: 10.1186/s12864-020-07142-4.
Scenedesmus obliquus belongs to green microalgae and is widely used in aquaculture as feed, which is also explored for lipid production and bioremediation. However, genomic studies of this microalga have been very limited. Cell self-flocculation of microalgal cells can be used as a simple and economic method for harvesting biomass, and it is of great importance to perform genome-scale studies for the self-flocculating S. obliquus strains to promote their biotechnological applications.
We employed the Pacific Biosciences sequencing platform for sequencing the genome of the self-flocculating microalga S. obliquus AS-6-11, and used the MECAT software for de novo genome assembly. The estimated genome size of S. obliquus AS-6-11 is 172.3 Mbp with an N50 of 94,410 bp, and 31,964 protein-coding genes were identified. Gene Ontology (GO) and KEGG pathway analyses revealed 65 GO terms and 428 biosynthetic pathways. Comparing to the genome sequences of the well-studied green microalgae Chlamydomonas reinhardtii, Chlorella variabilis, Volvox carteri and Micractinium conductrix, the genome of S. obliquus AS-6-11 encodes more unique proteins, including one gene that encodes D-mannose binding lectin. Genes encoding the glycosylphosphatidylinositol (GPI)-anchored cell wall proteins, and proteins with fasciclin domains that are commonly found in cell wall proteins might be responsible for the self-flocculating phenotype, and were analyzed in detail. Four genes encoding both GPI-anchored cell wall proteins and fasciclin domain proteins are the most interesting targets for further studies.
The genome sequence of the self-flocculating microalgal S. obliquus AS-6-11 was annotated and analyzed. To our best knowledge, this is the first report on the in-depth annotation of the S. obliquus genome, and the results will facilitate functional genomic studies and metabolic engineering of this important microalga. The comparative genomic analysis here also provides new insights into the evolution of green microalgae. Furthermore, identification of the potential genes encoding self-flocculating proteins will benefit studies on the molecular mechanism underlying this phenotype for its better control and biotechnological applications as well.
斜生栅藻属于绿色微藻，广泛应用于水产养殖作为饲料，也被用于脂质生产和生物修复。然而，对这种微藻的基因组研究非常有限。微藻细胞的自絮凝可以作为一种简单经济的收获生物质的方法，对于进行自絮凝斜生栅藻菌株的基因组规模研究以促进其生物技术应用具有重要意义。
我们使用太平洋生物科学测序平台对自絮凝微藻斜生栅藻 AS-6-11 进行了测序，并使用 MECAT 软件进行从头基因组组装。斜生栅藻 AS-6-11 的估计基因组大小为 172.3 Mbp，N50 为 94,410 bp，鉴定出 31,964 个蛋白质编码基因。基因本体论 (GO) 和 KEGG 途径分析显示 65 个 GO 术语和 428 个生物合成途径。与研究较好的绿藻莱茵衣藻、栅藻、衣藻和conductrix 相比，斜生栅藻 AS-6-11 的基因组编码更多独特的蛋白质，包括一个编码 D-甘露糖结合凝集素的基因。编码糖基磷脂酰肌醇 (GPI)-锚定细胞壁蛋白的基因和在细胞壁蛋白中常见的具有 fasciclin 结构域的蛋白可能是自絮凝表型的原因，并进行了详细分析。编码 GPI-锚定细胞壁蛋白和 fasciclin 结构域蛋白的四个基因是进一步研究的最有趣的目标。
对自絮凝微藻斜生栅藻 AS-6-11 的基因组序列进行了注释和分析。据我们所知，这是斜生栅藻基因组的首次深度注释报告，结果将有助于该重要微藻的功能基因组研究和代谢工程。这里的比较基因组分析也为绿藻的进化提供了新的见解。此外，鉴定出潜在的自絮凝蛋白编码基因将有助于研究该表型的分子机制，以便更好地控制和应用于生物技术。
