Intrageneric Variability Between the Chloroplast Genomes of Trachelomonas grandis and Trachelomonas volvocina and Phylogenomic Analysis of Phototrophic Euglenoids

Abstract

The latest studies of chloroplast genomes of phototrophic euglenoids yielded different results according to intrageneric variability such as cluster arrangement or diversity of introns. Although the genera Euglena and Monomorphina in those studies show high syntenic arrangements at the intrageneric level, the two investigated Eutreptiella species comprise low synteny. Furthermore Trachelomonas volvocina show low synteny to the chloroplast genomes of the sister genera Monomorphina aenigmatica, M. parapyrum, Cryptoglena skujae, Euglenaria anabaena, Strombomonas acuminata, all of which were highly syntenic. Consequently, this study aims at the analysis of the cpGenome of Trachelomonas grandis and a comparative examination of T. volvocina to investigate whether the cpGenomes are of such resemblance as could be expected for a genus within the Euglenaceae. Although these analyses resulted in almost identical gene content to other Euglenaceae, the chloroplast genome showed significant novelties: In the rRNA operon, we detected group II introns, not yet found in any other cpGenome of Euglenaceae and a substantially heterogeneous cluster arrangement in the genus Trachelomonas. The phylogenomic analysis with 84 genes of 19 phototrophic euglenoids and 18 cpGenome sequences from Chlorophyta and Streptophyta resulted in a well-supported cpGenome phylogeny, which is in accordance to former phylogenetic analyses.

Dynamic evolution of inverted repeats in Euglenophyta plastid genomes

“…The obtained phylogenetic tree (Fig. 2 ) confirmed sister relationship of Phacaceae and Euglenaceae 15 , 23 , 33 . The inferred relationships among genera of Euglenaceae are not well supported, and only those between closely related taxa are in accordance with multigene analyses on nuclear-encoded genes 14 , 15 .…”

“…We excluded also Colacium vesiculosum (JN674636), which has been previously shown to have the unstable position at phylogenomic trees, and its elimination doesn’t lead to different topology but could reinforce the support for the relationships within the tree 33 . As an outgroup, we used three species representing Chlorophyta, previously shown to be the close relatives of Euglenophyta 33 . For Maximum Likelihood (ML) analyses each protein-coding gene was divided into a separate partition, and one rRNA partition was applied, resulting in 58 partitions.…”

18S rDNA sequence–structure phylogeny of the Euglenophyceae (Euglenozoa, Euglenida)

“…Rapaza viridis was positioned at the base of Euglenophyceae , which is consistent with previous single‐gene studies using 18S rDNA (Cavalier‐Smith, 2016; Kolisko et al, 2020; Lukešová et al, 2020; Yamaguchi et al, 2012). In previous studies using 18S rDNA (Cavalier‐Smith, 2016; Kolisko et al, 2020; Lukešová et al, 2020; Marin et al, 2003; Yamaguchi et al, 2012) or multiple chloroplast genes (Dabbagh & Preisfeld, 2018), Eutreptiella branched off prior to Euglenales . This study supports this position.…”

“…E . archaeoplastidiata was not included in the main Euglena clade (Dabbagh & Preisfeld, 2018; Karnkowska et al, 2015; Kim et al, 2015; Kolisko et al, 2020) and several strains of E . velata were sister to Colacium (Kim et al, 2015).…”

“…Recent studies found that Euglena is not monophyletic. E. archaeoplastidiata was not included in the main Euglena clade (Dabbagh & Preisfeld, 2018;Karnkowska et al, 2015;Kim et al, 2015;Kolisko et al, 2020) and several strains of E. velata were sister to Colacium (Kim et al, 2015). Due to a lack of appropriate molecular data in NCBI, E.…”