Complete chloroplast genome of the green alga Chaetophora lobata (Chlorophyceae, Chlorophyta): morphological features and phylogenetic and comparative analysis

Abstract

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.