Table_5_Six Newly Sequenced Chloroplast Genomes From Trentepohliales: The Inflated Genomes, Alternative Genetic Code and Dynamic Evolution.XLSX

Cephaleuros is often known as an algal pathogen with 19 taxonomically valid species, some of which are responsible for red rust and algal spot diseases in vascular plants. No chloroplast genomes have yet been reported in this genus, and the limited genetic information is an obstacle to understanding the evolution of this genus. In this study, we sequenced six new Trentepohliales chloroplast genomes, including four Cephaleuros and two Trentepohlia. The chloroplast genomes of Trentepohliales are large compared to most green algae, ranging from 216 to 408 kbp. They encode between 93 and 98 genes and have a GC content of 26–36%. All new chloroplast genomes were circular-mapping and lacked a quadripartite structure, in contrast to the previously sequenced Trentepohlia odorata, which does have an inverted repeat. The duplicated trnD-GTC, petD, and atpA genes in C. karstenii may be remnants of the IR region and shed light on its reduction. Chloroplast genes of Trentepohliales show elevated rates of evolution, strong rearrangement dynamics and several genes display an alternative genetic code with reassignment of the UGA/UAG codon presumably coding for arginine. Our results present the first whole chloroplast genome of the genus Cephaleuros and enrich the chloroplast genome resources of Trentepohliales.

Cephaleuros（头孢藻属）常被视为藻类病原菌，该属共计19个分类学上有效的物种，其中部分物种可引发维管植物的红锈病与藻斑病。目前该属尚未见叶绿体基因组的相关报道，有限的遗传信息阻碍了对该属演化历程的解析。本研究测序获得6个全新的Trentepohliales（橘色藻目）叶绿体基因组，其中包含4个头孢藻属物种与2个Trentepohlia（橘藻属）物种。橘色藻目叶绿体基因组的规模相较于多数绿藻更大，长度介于216至408千碱基对（kbp）之间；其编码基因数量为93至98个，GC含量为26%~36%。所有新测序的叶绿体基因组均呈环状图谱结构，且不具备四分体结构，这与此前已测序的Trentepohlia odorata（香橘藻）存在显著差异——后者含有反向重复（IR）区域。C. karstenii（卡氏头孢藻）中重复的trnD-GTC、petD与atpA基因可能是反向重复区域的残留序列，可为该区域的退化过程提供研究线索。橘色藻目的叶绿体基因展现出较高的演化速率与强烈的基因组重排动态特征，部分基因采用替代性遗传密码，其UGA/UAG密码子被重新分配为编码精氨酸。本研究首次报道了头孢藻属的完整叶绿体基因组，丰富了橘色藻目的叶绿体基因组资源。