Zhang Lei, Wang Xumin, Liu Tao, Wang Guoliang, Chi Shan, Liu Cui, Wang Haiyang
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 1;10(10):e0139366. doi: 10.1371/journal.pone.0139366. eCollection 2015.
In this study, we fully sequenced the circular plastid genome of a brown alga, Undaria pinnatifida. The genome is 130,383 base pairs (bp) in size; it contains a large single-copy (LSC, 76,598 bp) and a small single-copy region (SSC, 42,977 bp), separated by two inverted repeats (IRa and IRb: 5,404 bp). The genome contains 139 protein-coding, 28 tRNA, and 6 rRNA genes; none of these genes contains introns. Organization and gene contents of the U. pinnatifida plastid genome were similar to those of Saccharina japonica. There is a co-linear relationship between the plastid genome of U. pinnatifida and that of three previously sequenced large brown algal species. Phylogenetic analyses of 43 taxa based on 23 plastid protein-coding genes grouped all plastids into a red or green lineage. In the large brown algae branch, U. pinnatifida and S. japonica formed a sister clade with much closer relationship to Ectocarpus siliculosus than to Fucus vesiculosus. For the first time, the start codon ATT was identified in the plastid genome of large brown algae, in the atpA gene of U. pinnatifida. In addition, we found a gene-length change induced by a 3-bp repetitive DNA in ycf35 and ilvB genes of the U. pinnatifida plastid genome.
在本研究中，我们对一种褐藻——裙带菜的环状质体基因组进行了全测序。该基因组大小为130,383碱基对（bp）；它包含一个大单拷贝区（LSC，76,598 bp）和一个小单拷贝区（SSC，42,977 bp），这两个区域被两个反向重复序列（IRa和IRb：5,404 bp）隔开。该基因组包含139个蛋白质编码基因、28个tRNA基因和6个rRNA基因；这些基因均不包含内含子。裙带菜质体基因组的组织和基因内容与海带的相似。裙带菜的质体基因组与之前测序的三种大型褐藻物种的质体基因组之间存在共线性关系。基于23个质体蛋白质编码基因对43个分类单元进行的系统发育分析将所有质体分为红系或绿系。在大型褐藻分支中，裙带菜和海带形成了一个姐妹进化枝，与硅藻的关系比与墨角藻的关系更为密切。首次在大型褐藻的质体基因组中，即在裙带菜的atpA基因中鉴定出起始密码子ATT。此外，我们在裙带菜质体基因组的ycf35和ilvB基因中发现了由一个3 bp重复DNA引起的基因长度变化。
