Ng Poh-Kheng, Lin Showe-Mei, Lim Phaik-Eem, Liu Li-Chia, Chen Chien-Ming, Pai Tun-Wen
Institute of Marine Biology, National Taiwan Ocean University, Keelung, 20244, Taiwan.
Institute of Ocean and Earth Sciences, University of Malaya, Kuala Lumpur, 50603, Malaysia.
BMC Genomics. 2017 Jan 6;18(1):40. doi: 10.1186/s12864-016-3453-0.
The chloroplast genome of Gracilaria firma was sequenced in view of its role as an economically important marine crop with wide industrial applications. To date, there are only 15 chloroplast genomes published for the Florideophyceae. Apart from presenting the complete chloroplast genome of G. firma, this study also assessed the utility of genome-scale data to address the phylogenetic relationships within the subclass Rhodymeniophycidae. The synteny and genome structure of the chloroplast genomes across the taxa of Eurhodophytina was also examined.
The chloroplast genome of Gracilaria firma maps as a circular molecule of 187,001 bp and contains 252 genes, which are distributed on both strands and consist of 35 RNA genes (3 rRNAs, 30 tRNAs, tmRNA and a ribonuclease P RNA component) and 217 protein-coding genes, including the unidentified open reading frames. The chloroplast genome of G. firma is by far the largest reported for Gracilariaceae, featuring a unique intergenic region of about 7000 bp with discontinuous vestiges of red algal plasmid DNA sequences interspersed between the nblA and cpeB genes. This chloroplast genome shows similar gene content and order to other Florideophycean taxa. Phylogenomic analyses based on the concatenated amino acid sequences of 146 protein-coding genes confirmed the monophyly of the classes Bangiophyceae and Florideophyceae with full nodal support. Relationships within the subclass Rhodymeniophycidae in Florideophyceae received moderate to strong nodal support, and the monotypic family of Gracilariales were resolved with maximum support.
Chloroplast genomes hold substantial information that can be tapped for resolving the phylogenetic relationships of difficult regions in the Rhodymeniophycidae, which are perceived to have experienced rapid radiation and thus received low nodal support, as exemplified in this study. The present study shows that chloroplast genome of G. firma could serve as a key link to the full resolution of Gracilaria sensu lato complex and recognition of Hydropuntia as a genus distinct from Gracilaria sensu stricto.
鉴于真江蓠作为一种具有广泛工业应用的重要经济海洋作物，对其叶绿体基因组进行了测序。迄今为止，红藻纲仅公布了15个叶绿体基因组。除了呈现真江蓠完整的叶绿体基因组外，本研究还评估了基因组规模数据在解决红皮藻亚纲内系统发育关系方面的效用。还研究了真红藻纲各分类群叶绿体基因组的共线性和基因组结构。
真江蓠的叶绿体基因组图谱为一个187,001 bp的环状分子，包含252个基因，分布在两条链上，由35个RNA基因（3个rRNA、30个tRNA、tmRNA和一个核糖核酸酶P RNA成分）和217个蛋白质编码基因组成，包括未鉴定的开放阅读框。真江蓠的叶绿体基因组是迄今为止报道的江蓠科中最大的，其特征是有一个约7000 bp的独特基因间隔区，在nblA和cpeB基因之间散布着红藻质粒DNA序列的不连续遗迹。该叶绿体基因组与其他红藻纲分类群显示出相似的基因内容和顺序。基于146个蛋白质编码基因的串联氨基酸序列的系统基因组分析证实了紫菜纲和红藻纲的单系性，并得到了完全节点支持。红藻纲中红皮藻亚纲内的关系得到了中度到强的节点支持，江蓠目的单型科得到了最大支持。
叶绿体基因组包含大量信息，可用于解决红皮藻亚纲中难以确定的系统发育关系，该亚纲被认为经历了快速辐射，因此节点支持率较低，本研究就是例证。本研究表明，真江蓠的叶绿体基因组可以作为全面解析广义江蓠复合体以及将水云菜属识别为与狭义江蓠属不同的属的关键环节。
