The chloroplast genome of Phacus orbicularis (Euglenophyceae): an initial datum point for the phacaceae

Abstract

The Euglenophyceae chloroplast was acquired when a heterotrophic euglenoid engulfed a green alga and subsequently retained the algal chloroplast, in a process known as secondary endosymbiosis. Since this event, Euglenophyceae have diverged widely and their chloroplast genomes (cpGenomes) have as well. Changes to the cpGenome include extensive gene rearrangement and the proliferation of introns, the analyses of which have proven to be useful in examining cpGenome changes throughout the Euglenophyceae. The Euglenales fall into two families, Euglenaceae and Phacaceae. Euglenaceae contains eight genera and at least one cpGenome has been published for each genus. Phacaceae, on the other hand, contains three genera, none of which have had a representative chloroplast genome sequenced. Members of this family have many small disk-shaped chloroplasts that lack pyrenoids. We sequenced and annotated the cpGenome of Phacus orbicularis in order to fill in the large gap in our understanding of Euglenophyceae cpGenome evolution, especially in regard to intron number and gene order. We compared this cpGenome to those of species from both the Euglenaceae and Eutreptiales of the Euglenophyceae phylogenetic tree. The cpGenome showed characteristics that were more derived than that of the basal species Eutreptia viridis, with extensive gene rearrangements and nearly three times as many introns. In contrast, it contained fewer introns than all but one of the previously reported Euglenaceae cpGenomes, had a smaller estimated genome size, and shared greater synteny with two main branches of that family.

Proliferation of group II introns in the chloroplast genome of the green algaOedocladium carolinianum(Chlorophyceae)

“…In euglenids, multiple waves of group II intron acquisition undoubtedly took place, because there are remarkable differences in intron content among the chloroplast genomes of the numerous taxa that have been investigated (Hallick et al, 1993; Hrda et al, 2012; Pombert et al, 2012; Bennett & Triemer, 2015; Dabbagh & Preisfeld, 2016; Kasiborski, Bennett & Linton, 2016). The number of introns ranges from a single group II intron in the closest relative of euglenid chloroplasts, the prasinopyte Pyramimonas parkeae (Turmel et al, 2009), to over 150 introns in the Euglena gracilis chloroplast genome (Hallick et al, 1993).…”

“…The number of introns ranges from a single group II intron in the closest relative of euglenid chloroplasts, the prasinopyte Pyramimonas parkeae (Turmel et al, 2009), to over 150 introns in the Euglena gracilis chloroplast genome (Hallick et al, 1993). Although the evolutionary patterns of euglenid introns remain poorly understood, the currently available data suggest that an intron in the psbC gene, which encodes the reverse transcriptase/maturase ycf13 , is the ancestral intron from which all other euglenid introns were derived and that independent waves of proliferation were associated with the acquisition of additional maturase genes (Pombert et al, 2012; Bennett & Triemer, 2015; Kasiborski, Bennett & Linton, 2016). Among the four classes that were sampled within the red algae, only the Porphyrididiophyceae was found to exhibit a high diversity of group II introns, with 41 intron insertion sites conserved in all five investigated strains of the unicellular Porphyridium purpurea in addition to the six sites displaying lineage-specific patterns of recent intron gains/losses (Tajima et al, 2014; Perrineau et al, 2015).…”

The Chloroplast Genome of Euglena mutabilis—Cluster Arrangement, Intron Analysis, and Intrageneric Trends

“…The cpGenome of Phacus orbicularis Hübner 1886 was sequenced very recently (Kasiborski et al. ), but is not included in this analysis. All cpGenomes present a large amount of cluster similarity and many highly conserved genes.…”

“…The other two (Bennett and Triemer 2015) and Euglenaformis proxima (Dangeard) Triemer 2014 (Bennett et al 2014) added to previously analyzed cpGenomes (Table 1), all lineages in the Euglenaceae have been covered and allowed for a diagrammatic phylogeny revealing first evolutionary trends (Bennett and Triemer 2015). The cpGenome of Phacus orbicularis H€ ubner 1886 was sequenced very recently (Kasiborski et al 2016), but is not included in this analysis. All cpGenomes present a large amount of cluster similarity and many highly conserved genes.…”

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

“…; Kasiborski et al. ). It was further carried out to examine the available phylogenetic information and to determine the positions of Euglena archaeoplastidiata , a species in need of revision and Colacium vesiculosum , since molecular data at the moment are quite contradictory (Karnkowska et al.…”