Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea.
Aquatic Plant Variety Center, National Institute of Fisheries Science, Mokpo, 58746, Korea.
J Phycol. 2019 Feb;55(1):214-223. doi: 10.1111/jpy.12811. Epub 2018 Dec 18.
To better understand organelle genome evolution of the ulvophycean green alga Capsosiphon fulvescens, we sequenced and characterized its complete chloroplast genome. The circular chloroplast genome was 111,561 bp in length with 31.3% GC content that contained 108 genes including 77 protein-coding genes, two copies of rRNA operons, and 27 tRNAs. In this analysis, we found the two types of isoform, called heteroplasmy, were likely caused by a flip-flop organization. The flip-flop mechanism may have caused structural variation and gene conversion in the chloroplast genome of C. fulvescens. In a phylogenetic analysis based on all available ulvophycean chloroplast genome data, including a new C. fulvescens genome, we found three major conflicting signals for C. fulvescens and its sister taxon Pseudoneochloris marina within 70 individual genes: (i) monophyly with Ulotrichales, (ii) monophyly with Ulvales, and (iii) monophyly with the clade of Ulotrichales and Ulvales. Although the 70-gene concatenated phylogeny supported monophyly with Ulvales for both species, these complex phylogenetic signals of individual genes need further investigations using a data-rich approach (i.e., organelle genome data) from broader taxon sampling.
为了更好地理解 Ulvophycean 绿藻 Capsosiphon fulvescens 的细胞器基因组进化，我们对其完整的叶绿体基因组进行了测序和特征描述。这个圆形的叶绿体基因组长 111561bp，GC 含量为 31.3%，包含 108 个基因，包括 77 个蛋白编码基因、两个 rRNA 操纵子和 27 个 tRNA。在这个分析中，我们发现了两种类型的同工型，称为异质体，可能是由翻转组织引起的。翻转机制可能导致了 C. fulvescens 叶绿体基因组的结构变异和基因转换。在基于所有可用的 Ulvophycean 叶绿体基因组数据的系统发育分析中，包括一个新的 C. fulvescens 基因组，我们在 70 个单独的基因中发现了三个与 C. fulvescens 和其姐妹分类群 Pseudoneochloris marina 相关的主要冲突信号：（i）与 Ulotrichales 的单系性，（ii）与 Ulvales 的单系性，以及（iii）与 Ulotrichales 和 Ulvales 的分支的单系性。尽管 70 个基因串联的系统发育树支持这两个物种与 Ulvales 的单系性，但这些单个基因的复杂系统发育信号需要进一步使用来自更广泛分类群采样的富含数据的方法（即细胞器基因组数据）进行调查。
