ABSTRACT

Chaetophora lobata is the type species of the polyphyletic genus Chaetophora. Clarification of its species identification, phylogenetic relationships, and plastome characteristics is helpful for taxonomic revisions and evolutionary studies of this genus. This study presents detailed information on morphology, culture, phylogenetic analysis, phylogenomics and comparative genomics of C. lobata. The complete morphological description and phylogenetic analyses based on nuclear rDNA and chloroplast protein-coding genes were robust for the identification of C. lobata. Moreover, de novo sequencing was used to determine the 222 213 bp chloroplast genome, which lacked inverted repeats as in all other members of the Chaetophorales. The chloroplast DNA (cpDNA) of C. lobata was found to be AT-rich (68.2%), consisting of 67 protein-coding genes, among which 62 genes were encoded on the plus strand and five genes were encoded on the minus strand with significant imbalance in distribution. Additionally, 28 tRNA genes, three rRNA genes, 16 introns and 18 putative open reading frames (ORFs) were annotated. Eight ORFs arranged in a row occupied about 18 kbp between psaA and atpI genes, and 16 introns (14 group I introns and 2 group II introns) were annotated in nine genes. Six genes contained nine intronic ORFs. Synteny and rearrangements analysis clearly showed the closest relationships between Chaetophora sp. and C. lobata. Substitution rate estimation indicated that the cpDNA of Chaetophorales was under purifying selection and most species were under similar evolutionary pressure. These findings can help advance research on the taxonomy and phylogeny of the order Chaetophorales.

摘要

Chaetophora lobata是Chaetophora多系属的模式种。阐明其物种鉴定、系统发育关系和质体特征有助于该属的分类学修订和进化研究。本研究提供了有关C. lobata的形态、培养、系统发育分析、系统基因组学和比较基因组学的详细信息。基于核 rDNA 和叶绿体蛋白编码基因的完整形态描述和系统发育分析对于鉴定C. lobata是稳健的. 此外，从头测序用于确定 222 213 bp 的叶绿体基因组，该基因组缺乏反向重复序列，与毛藻目的所有其他成员一样。C. lobata的叶绿体 DNA (cpDNA)富含 AT (68.2%)，由 67 个蛋白质编码基因组成，其中 62 个基因编码在正链上，5 个基因在负链上编码分布严重不平衡。此外，还注释了 28 个 tRNA 基因、3 个 rRNA 基因、16 个内含子和 18 个推定的开放阅读框 (ORF)。排成一排的八个 ORF 在psa A 和atp之间占据了大约 18 kbpI 基因和 16 个内含子（14 个 I 组内含子和 2 个 II 组内含子）被注释在 9 个基因中。六个基因包含九个内含子开放阅读框。Synteny 和重排分析清楚地显示了Chaetophora sp之间的最密切关系。和C. lobata。替代率估计表明，Chaetophorales的cpDNA处于纯化选择状态，大多数物种处于相似的进化压力下。这些发现有助于推进对角藻目分类学和系统发育的研究。