Zhang Lei, Wang Xumin, Liu Tao, Wang Haiyang, Wang Guoliang, Chi Shan, Liu Cui
Laboratory of Genetics and Breeding of Marine Organism, College of Marine Life Sciences, Ocean University of China, Qingdao, People's Republic of China.
CAS Key Laboratory of Genome Sciences and Information, Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, People's Republic of China.
PLoS One. 2015 Oct 7;10(10):e0140144. doi: 10.1371/journal.pone.0140144. eCollection 2015.
Costaria costata is a commercially and industrially important brown alga. In this study, we used next-generation sequencing to determine the complete plastid genome of C. costata. The genome consists of a 129,947 bp circular DNA molecule with an A+T content of 69.13% encoding a standard set of six ribosomal RNA genes, 27 transfer RNA genes, and 137 protein-coding genes with two conserved open reading frames (ORFs). The overall genome structure of C. costata is nearly the same as those of Saccharina japonica and Undaria pinnatifida. The plastid genomes of these three algal species retain a strong conservation of the GTG start codon while infrequently using TGA as a stop codon. In this regard, they differ substantially from the plastid genomes of Ectocarpus siliculosus and Fucus vesiculosus. Analysis of the nucleic acid substitution rates of the Laminariales plastid genes revealed that the petF gene has the highest substitution rate and the petN gene contains no substitution over its complete length. The variation in plastid genes between C. costata and S. japonica is lower than that between C. costata and U. pinnatifida as well as that between U. pinnatifida and S. japonica. Phylogenetic analyses demonstrated that C. costata and U. pinnatifida have a closer genetic relationship. We also identified two gene length mutations caused by the insertion or deletion of repeated sequences, which suggest a mechanism of gene length mutation that may be one of the key explanations for the genetic variation in plastid genomes.
鹿角菜是一种具有商业和工业重要性的褐藻。在本研究中，我们使用下一代测序技术来确定鹿角菜的完整质体基因组。该基因组由一个129,947 bp的环状DNA分子组成，A+T含量为69.13%，编码一套标准的六个核糖体RNA基因、27个转移RNA基因和137个蛋白质编码基因，还有两个保守的开放阅读框（ORF）。鹿角菜的整体基因组结构与海带和裙带菜的几乎相同。这三种藻类的质体基因组在起始密码子使用GTG方面保持高度保守，而很少使用TGA作为终止密码子。在这方面，它们与硅藻和墨角藻的质体基因组有很大不同。对海带目质体基因的核酸替换率分析表明，petF基因的替换率最高，而petN基因在其全长范围内没有替换。鹿角菜和海带之间质体基因的变异低于鹿角菜和裙带菜之间以及裙带菜和海带之间的变异。系统发育分析表明，鹿角菜和裙带菜有更密切的遗传关系。我们还鉴定出由重复序列的插入或缺失引起的两个基因长度突变，这表明基因长度突变机制可能是质体基因组遗传变异的关键解释之一。
