Taxonomic scheme of the order Chaetophorales (Chlorophyceae, Chlorophyta) based on Chloroplast genomes

Abstract

Background: Order Chaetophorales currently includes six families, namely Schizomeridaceae, Aphanochaetaceae, Barrancaceae, Uronemataceae, Fritschiellaceae, and Chaetophoraceae. The phylogenetic relationships of Chaetophorales have been inferred primarily based on short and less informative rDNA sequences. This study aimed to phylogenetically reconstruct order Chaetophorales and determine the taxonomic scheme and to further the current understanding of the evolution of order Chaetophorales.Results: In the present study, seven complete and five fragmentary chloroplast genomes were harvested. Phylogenomic and comparative genomic analysis were performed to determine the taxonomic scheme within Chaetophorales. Consequently, Oedogoniales was found to be a sister to a clade linking Chaetophorales and Chaetopeltidales. Schizomeriaceae, and Aphanochaetaceae clustered into a well-resolved basal clade in Chaetophorales, inconsistent with the results of phylogenetic analysis based on rDNA sequences. Comparative genomic analyses revealed that the chloroplast genomes of Schizomeriaceae and Aphanochaetaceae were highly conserved and homologous, highlighting the closest relationship in this order. Germination types of zoospores precisely correlated with the phylogenetic relationships.Conclusions: chloroplast genome structure analyses, synteny analyses, and zoospore germination analyses were concurrent with phylogenetic analyses based on the chloroplast genome, and all of them robustly determined the unique taxonomic scheme of Chaetophorales and the relationships of Oedogoniales, Chaetophorales, and Chaetopeltidales.

Reassessment of suitable markers for taxonomy of Chaetophorales (Chlorophyceae, Chlorophyta) based on chloroplast genomes

“…Phylogenetic analyses based on concatenated seven genes presented limited ability to resolve the phylogenetic relationships within Chlorophyceae, especially those of the OCC clade. However, within the order Chaetophorales, the relationships were highly consistent with those based on the concatenated 58 protein-coding genes (Liu et al, 2020). The results obtained suggested that these concatenated seven genes are reliable and could replace phylogenetic analyses based on chloroplast genomes to some extent in determining the internal branching relationship of Chaetophorales.…”

“…Different genes support diverse topologies. Topology I is more reliable and has been verified using chloroplast genomes (Liu et al, 2020), whereas Topology II has been verified by nuclear genes (Caisová et al, 2011(Caisová et al, , 2013Liu et al, 2019Liu et al, , 2020. In the present study, 19 genes supported Topology I, and only 4 genes supported Topology II, which might explain why the phylogenetic trees constructed with concatenated 58 protein-coding genes supported Topology I for its absolute advantage in terms of the number of supported genes and variable information sites (Liu et al, 2020).…”

“…(1) at least one of the three treatments (phylogenetic analysis based on nucleotide sequence, amino acid sequence, or nucleotide without 3rd codon) for each gene, ML, and BI phylogenetic trees of the same processing method must be consistent and must satisfy the taxonomic scheme of the order Chaetophorales (Liu et al, 2020) (Figure 1; Topology I); and (2) there must be no introns in protein-coding genes so that the amplification primers can be designed to amplify the complete fragment to obtain more information sites.…”

“…Phylogenomics, with its unique advantages, has recently been considered as a useful approach to elucidate enigmatic evolutionary relationships among different plant taxa (Fučíková et al, 2016;Jansen et al, 2007;Moore et al, 2010;Sun et al, 2016;Wu et al, 2011;Zhong et al, 2011). To date, 15 chloroplast genomes, including all the main clades of Chaetophorales, have been sequenced (Bélanger et al, 2006;Brouard et al, 2011;Liu et al, 2020). Based on the data of chloroplast genomes, Liu et al (2020) determined the taxonomic scheme of the order Chaetophorales with robust evidence.…”

“…To date, 15 chloroplast genomes, including all the main clades of Chaetophorales, have been sequenced (Bélanger et al, 2006;Brouard et al, 2011;Liu et al, 2020). Based on the data of chloroplast genomes, Liu et al (2020) determined the taxonomic scheme of the order Chaetophorales with robust evidence. However, taxonomic problems below the family level are still not well resolved owing to the limited chloroplast genomes of Chaetophorales.…”