Diplomonads are anaerobic, flagellated protists, being part of the Metamonada group of Eukaryotes. Diplomonads either live as endobionts (parasites and commensals) of animals or free-living in low-oxygen environments. Genomic information is available for parasitic diplomonads like Giardia intestinalis and Spironucleus salmonicida, while little is known about the genomic arrangements of free-living diplomonads. We have generated the first reference genome of a free-living diplomonad, Hexamita inflata. The final version of the genome assembly is fragmented (1241 contigs) but substantially larger (142 Mbp) than the parasitic diplomonad genomes (9.8-14.7 Mbp). It encodes 79,341 proteins; 29,874 have functional annotations and 49,467 are hypothetical proteins. Interspersed repeats comprise 34% of the genome (9617 Retroelements, 2676 DNA transposons). The large expansion of protein-encoding capacity and the interspersed repeats are the major reasons for the large genome size. This genome from a free-living diplomonad will be the basis for further studies of the Diplomonadida lineage and the evolution of parasitism-free living style transitions.

Department of Biology Lund University Lund Sweden

Department of Cell and Molecular Biology Uppsala University Uppsala Sweden

Department of Parasitology Charles University Biotechnology and Biomedicine Centre in Vestec Staré Město Czech Republic

European Molecular Biology Laboratory Genomics Core Facility Heidelberg Germany

Institute of Parasitology Biology Centre Czech Academy of Sciences České Budějovice Czech Republic

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Burki, F., Sandin, M. M. & Jamy, M. Diversity and ecology of protists revealed by metabarcoding. PubMed DOI

Sibbald, S. J. & Archibald, J. M. More protist genomes needed. PubMed DOI

Kornalikova, M., Hampl, V. & Treitli, S. C. Investigation of the genome sizes and ploidy within the genus Monocercomonoides. PubMed DOI

Kolisko, M. PubMed DOI PMC

Keeling, P. J. & Doolittle, W. F. Widespread and ancient distribution of a noncanonical genetic code in diplomonads. PubMed DOI

Lloyd, D. & Williams, C. F. Comparative biochemistry of Giardia, Hexamita and Spironucleus: Enigmatic diplomonads. PubMed DOI

Sassera, D. PubMed DOI PMC

Rada, P., Kellerova, P., Verner, Z. & Tachezy, J. Investigation of the Secretory Pathway in Trichomonas vaginalis Argues against a Moonlighting Function of Hydrogenosomal Enzymes. PubMed DOI

None PubMed PMC

None

None

None

None

Chin, C. S. PubMed DOI

Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. PubMed DOI PMC

Walker, B. J. PubMed DOI PMC

Zimin, A. V. PubMed DOI PMC

De Maio, N. PubMed PMC

Xu, F. PubMed DOI PMC

None

Hudson, A. J. PubMed DOI PMC

Majoros, W. H., Pertea, M. & Salzberg, S. L. TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders. PubMed DOI

Hyatt, D. PubMed DOI PMC

Xu, F. PubMed DOI PMC

Xu, F. PubMed PMC

Xu, F., Jex, A. & Svard, S. G. A chromosome-scale reference genome for Giardia intestinalis WB. PubMed DOI PMC

Buchfink, B., Reuter, K. & Drost, H. G. Sensitive protein alignments at tree-of-life scale using DIAMOND. PubMed DOI PMC

Huerta-Cepas, J. PubMed DOI PMC

Jones, P. PubMed DOI PMC

Clark, C. G., Ali, I. K., Zaki, M., Loftus, B. J. & Hall, N. Unique organisation of tRNA genes in Entamoeba histolytica. PubMed DOI

Chan, P. P. & Lowe, T. M. tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences. PubMed DOI PMC

Deng, Z. L., Munch, P. C., Mreches, R. & McHardy, A. C. Rapid and accurate identification of ribosomal RNA sequences via deep learning. PubMed DOI PMC

Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. PubMed DOI

Manni, M., Berkeley, M. R., Seppey, M. & Zdobnov, E. M. BUSCO: Assessing Genomic Data Quality and Beyond. PubMed DOI

Salas-Leiva, D. E. PubMed DOI PMC

Tanifuji, G. PubMed DOI PMC

Emms, D. M. & Kelly, S. OrthoFinder: phylogenetic orthology inference for comparative genomics. PubMed DOI PMC

Xiong, J. PubMed DOI PMC