Euglena gracilis Genome and Transcriptome: Organelles, Nuclear Genome Assembly Strategies and Initial Features

Abstract

Euglena gracilis is a major component of the aquatic ecosystem and together with closely related species, is ubiquitous worldwide. Euglenoids are an important group of protists, possessing a secondarily acquired plastid and are relatives to the Kinetoplastidae, which themselves have global impact as disease agents. To understand the biology of E. gracilis, as well as to provide further insight into the evolution and origins of the Kinetoplastidae, we embarked on sequencing the nuclear genome; the plastid and mitochondrial genomes are already in the public domain. Earlier studies suggested an extensive nuclear DNA content, with likely a high degree of repetitive sequence, together with significant extrachromosomal elements. To produce a list of coding sequences we have combined transcriptome data from both published and new sources, as well as embarked on de novo sequencing using a combination of 454, Illumina paired end libraries and long PacBio reads. Preliminary analysis suggests a surprisingly large genome approaching 2 Gbp, with a highly fragmented architecture and extensive repeat composition. Over 80% of the RNAseq reads from E. gracilis maps to the assembled genome sequence, which is comparable with the well assembled genomes of T. brucei and T. cruzi. In order to achieve this level of assembly we employed multiple informatics pipelines, which are discussed here. Finally, as a preliminary view of the genome architecture, we discuss the tubulin and calmodulin genes, which highlight potential novel splicing mechanisms.

Ferredoxin-dependent bilin reductases in eukaryotic algae: Ubiquity and diversity

“…Euglenids belong to the Excavata, an early-diverging eukaryotic supergroup (Burki et al, 2016). A prasinophyte plastid ancestor would be expected to contain PCYA, and we identified PCYA sequences in euglenid transcriptomes from Euglena gracilis and Eutreptiella isolates (Ebenezer et al, 2017; Keeling et al, 2014). …”

Comparative assessment of the Euglena gracilis var. saccharophila variant strain as a producer of the β‐1,3‐glucan paramylon under varying light conditions

“…There are also recent developments in the studies into the genome sequence and organization but no reports in high‐throughput proteomic studies with Euglena (Ebenezer et al. ).…”

Comparative molecular cell biology of phototrophic euglenids and parasitic trypanosomatids sheds light on the ancestor of Euglenozoa

“…While kinetoplastid nuclear genomes are relatively small (∼ 10 7 bp) (Gull, Alsford & Ersfeld, ; Berriman et al, ; Ivens et al, ; Jackson et al, ), euglenid nuclear genomes are much larger with estimated sizes in different species of approximately 3–24 Gb (reviewed in Ebenezer et al, ) which is equal to or greater than the size of the human genome (3 Gb). The size of the draft genome of the diplonemid D. papillatum has been estimated to be 176.5 Mb (Morales et al, ).…”

“…The size of the draft genome of the diplonemid D. papillatum has been estimated to be 176.5 Mb (Morales et al, ). The newest estimations of the E. gracilis nuclear genome size based on DNA sequencing (but not DNA content) range from less than 0.5 Gb to more than 2 Gb (Ebenezer et al, , ). One may conclude that the E. gracilis nuclear genome is approximately 10–100 times larger than kinetoplastid genomes ( B. saltans – 40 Mb, T. brucei – 26 Mb, L. major – 33 Mb, and T. cruzi – 28 Mb) (Jackson et al, ).…”

“…One may conclude that the E. gracilis nuclear genome is approximately 10–100 times larger than kinetoplastid genomes ( B. saltans – 40 Mb, T. brucei – 26 Mb, L. major – 33 Mb, and T. cruzi – 28 Mb) (Jackson et al, ). The analysis of the E. gracilis transcriptome found approximately 38 Mb of coding sequences (Ebenezer et al, , ) compared to kinetoplastid genomes with 31 Mb ( B. saltans ), 13 Mb ( T. brucei ), 16 Mb ( L. major ) or 17 Mb ( T. cruzi ) of coding sequences (Jackson et al, ). The size difference between the E. gracilis and kinetoplastid coding sequences is at most threefold, suggesting that the different sizes of the euglenid and kinetoplastid genomes are most likely due to the presence in the euglenid genome of much larger amounts of non‐coding DNA including introns, repetitive sequences and selfish mobile elements.…”