Discussion

Euglena gracilis is a major component of the aquatic ecosystem and together with closely related species, is ubiquitous. Euglenoids are an important group of protists, possessing a secondarily acquired plastid and relatives to the Kinetoplastidae which themselves are global impacts as disease agents. To understand the biology of E. gracilis, and to provide further insight into the evolution and origins of Kinetoplastidae, we embarked on sequencing the nuclear genome. Earlier studies suggested an extensive nuclear DNA content, with likely a high degree of repetitive sequence, together with significance extrachromosomal elements. To produce a dataset of coding sequences we combined transcriptome data from both published and new data, as well as embarked on de novo genome sequencing using combination of 454, Illumina paired end libraries and PacBio platforms as well as transcriptomics and proteomics analysis under light and dark adaptations. Preliminary analysis suggests a surprising large genome approaching 2 Gbp, with highly fragmented architecture and extensive repeat composition. Over 80 % of the transcriptome maps to the genome, at par with T. brucei and T. cruzi. As a view of genome architecture, we have analyzed the tubulin and calmodulin genes together with several large genome contigs and which highlight potential novel splicing mechanisms. Analysis of the transcriptome and genome revealed a repertoire of E. gracilis genes conserved across all eukaryotes (~ 55 %) and others shared with specific eukaryotic lineages and evidence of LGT. Functional annotation via a web interface http://euglenadb.org suggests that of 36,526 predicted proteins, 23,833 (~ 46 %) have homology to NCBI-NR entries, while 23,866 (~ 65 %) have hits against the Interpro database. Overall, our data suggest that the Euglena genome is a chimera with highly significant proteome changes.