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The expanded genome of Hexamita inflata, a free-living diplomonad

Akdeniz, Zeynep ; Havelka, Michal ; Stoklasa, Michal ; Jiménez-González, Alejandro ; Žárský, Vojtěch ; Xu, Feifei ; Stairs, Courtney W. LU orcid ; Jerlström-Hultqvist, Jon ; Kolísko, Martin and Provazník, Jan , et al. (2025) In Scientific Data 12(1).
Abstract

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... (More)

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.

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publishing date
type
Contribution to journal
publication status
published
subject
in
Scientific Data
volume
12
issue
1
article number
192
publisher
Nature Publishing Group
external identifiers
  • scopus:85217731750
  • pmid:39893204
ISSN
2052-4463
DOI
10.1038/s41597-025-04514-x
language
English
LU publication?
yes
id
e5915ebc-35e2-4174-b65a-2cb1df5c3ab0
date added to LUP
2025-06-09 10:50:37
date last changed
2025-07-07 13:43:58
@article{e5915ebc-35e2-4174-b65a-2cb1df5c3ab0,
  abstract     = {{<p>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.</p>}},
  author       = {{Akdeniz, Zeynep and Havelka, Michal and Stoklasa, Michal and Jiménez-González, Alejandro and Žárský, Vojtěch and Xu, Feifei and Stairs, Courtney W. and Jerlström-Hultqvist, Jon and Kolísko, Martin and Provazník, Jan and Svärd, Staffan and Andersson, Jan O. and Tachezy, Jan}},
  issn         = {{2052-4463}},
  language     = {{eng}},
  number       = {{1}},
  publisher    = {{Nature Publishing Group}},
  series       = {{Scientific Data}},
  title        = {{The expanded genome of Hexamita inflata, a free-living diplomonad}},
  url          = {{http://dx.doi.org/10.1038/s41597-025-04514-x}},
  doi          = {{10.1038/s41597-025-04514-x}},
  volume       = {{12}},
  year         = {{2025}},
}