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

Abstract

A comparative analysis of the chloroplast genome of Euglena mutabilis underlined a high diversity in the evolution of plastids in euglenids. Gene clusters in more derived Euglenales increased in complexity with only a few, but remarkable changes in the genus Euglena. Euglena mutabilis differed from other Euglena species in a mirror-inverted arrangement of 12 from 15 identified clusters, making it very likely that the emergence at the base of the genus Euglena, which has been considered a long branch artifact, is truly a probable position. This was corroborated by many similarities in gene arrangement and orientation with Strombomonas and Monomorphina, rendering the genome organization of E. mutabilis in certain clusters as plesiomorphic feature. By RNA analysis exact exon-intron boundaries and the type of the 77 introns identified were mostly determined unambiguously. A detailed intron study of psbC pointed at two important issues: First, the number of introns varied even between species, and no trend from few to many introns could be observed. Second, mat1 was localized in Eutreptiales exclusively in intron 1, and mat2 was not identified. With the emergence of Euglenaceae in most species, a new intron containing mat2 inserted in front of the previous intron 1 and thereby became intron 2 with mat1.

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

“…As it is known that intrageneric comparisons of Euglena species (with the exception of E. archaeoplastidiata ) and Monomorphina species have shown high synteny and that the Eutreptiella species comprise low synteny (Bennett and Triemer ; Bennett et al. , ; Dabbagh and Preisfeld ; Dabbagh et al. ; Hrdá et al.…”

“…Trachelomonas grandis strain SAG 204.80 (EPSAG, Germany) was grown in WEES medium (Kies ) at 20–23 °C under 12 h light–dark cycle using fluorescent tubes, which supplied approximately 30 μmol photons/m 2 /s 2 of light. Cells were concentrated and washed, chloroplasts isolated, and DNA extracted as described previously (Dabbagh and Preisfeld ), with the following modification: To isolate the chloroplast, cells were disrupted by ultrasonic probe six times for three seconds with the amplitude set at 80% and a 0.1 s puls rate (Bandelin Sonoplus HD 60, Berlin, Germany) with intermediate washing steps on ice. After the Percoll gradient was centrifuged, the chloroplast fraction was recovered from the 30% layer.…”

“…The phylogenomic analysis of all sequenced euglenoid cpGenomes up to date expands the taxon sampling of further studies (Bennett and Triemer ; Bennett et al. ; Dabbagh and Preisfeld ; Dabbagh et al. ; Kasiborski et al.…”

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).…”

Euglena Transcript Processing

“…Most recently, much of what has been deduced about Euglena choloroplast genome RNA-coding capacity has been through the determination of complete chloroplast genome structures from a collection of representative species from the Euglenaceae (Hrdá et al 2012;Wiegert et al 2012;Dabbagh and Preisfeld 2017;Bennett and Triemer 2015) and comparison to the much earlier determined choloroplast genome structure of Euglena gracilis Strain Z ). An examination of transcription patterns of the 96 genes contained on the E. gracilis plastid genome under different physiological states and stress conditions has also been performed (Geimer et al 2009).…”