Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China.
School of Biomedical Engineering, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
BMC Plant Biol. 2018 May 25;18(1):94. doi: 10.1186/s12870-018-1309-2.
Red algae are economically valuable for food and in industry. However, their genomic information is limited, and the genomic data of only a few species of red algae have been sequenced and deposited recently. In this study, we annotated a draft genome of the macroalga Gracilariopsis lemaneiformis (Gracilariales, Rhodophyta).
The entire 88.98 Mb genome of Gp. lemaneiformis 981 was generated from 13,825 scaffolds (≥500 bp) with an N50 length of 30,590 bp, accounting for approximately 91% of this algal genome. A total of 38.73 Mb of scaffold sequences were repetitive, and 9281 protein-coding genes were predicted. A phylogenomic analysis of 20 genomes revealed the relationship among the Chromalveolata, Rhodophyta, Chlorophyta and higher plants. Homology analysis indicated phylogenetic proximity between Gp. lemaneiformis and Chondrus crispus. The number of enzymes related to the metabolism of carbohydrates, including agar, glycoside hydrolases, glycosyltransferases, was abundant. In addition, signaling pathways associated with phytohormones such as auxin, salicylic acid and jasmonates are reported for the first time for this alga.
We sequenced and analyzed a draft genome of the red alga Gp. lemaneiformis, and revealed its carbohydrate metabolism and phytohormone signaling characteristics. This work will be helpful in research on the functional and comparative genomics of the order Gracilariales and will enrich the genomic information on marine algae.
红藻在食品和工业方面具有经济价值。然而，它们的基因组信息有限，最近只有少数几种红藻的基因组数据被测序和提交。在本研究中，我们对大型红藻条斑紫菜（Gracilariales，红藻门）的基因组草案进行了注释。
Gp. lemaneiformis 981 的整个 88.98 Mb 基因组由 13825 个大于等于 500bp 的支架（scaffold）组成，N50 长度为 30590bp，约占该藻类基因组的 91%。总共 38.73 Mb 的支架序列是重复的，预测到 9281 个蛋白质编码基因。对 20 个基因组的系统发育基因组学分析揭示了 Chromalveolata、红藻、绿藻和高等植物之间的关系。同源分析表明 Gp. lemaneiformis 与角叉菜（Chondrus crispus）亲缘关系较近。与碳水化合物代谢相关的酶（包括琼脂、糖苷水解酶、糖基转移酶）数量丰富。此外，还首次报道了与植物激素（如生长素、水杨酸和茉莉酸）相关的信号通路。
我们对红藻 Gp. lemaneiformis 的基因组草案进行了测序和分析，揭示了其碳水化合物代谢和植物激素信号特征。这项工作将有助于 Gracilariales 目的功能和比较基因组学的研究，并丰富海洋藻类的基因组信息。
