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Microbial Genomics logo Microbial Genomics

Volume 9, Issue 3

Highly contiguous genomes of human clinical isolates of reveal assemblage- and sub-assemblage-specific presence–absence variation in protein-coding genes Open Access

Abstract

(syn. ) is a widespread gastrointestinal protozoan parasite with debated taxonomic status. Currently, eight distinct genetic sub-groups, termed assemblages A–H, are defined based on a few genetic markers. Assemblages A and B may represent distinct species and are both of human public health relevance. Genomic studies are scarce and the few reference genomes available, in particular for assemblage B, are insufficient for adequate comparative genomics. Here, by combining long- and short-read sequences generated by PacBio and Illumina sequencing technologies, we provide nine annotated genome sequences for reference from new clinical isolates (four assemblage A and five assemblage B parasite isolates). Isolates chosen represent the currently accepted classification of sub-assemblages AI, AII, BIII and BIV. Synteny over the whole genome was generally high, but we report chromosome-level translocations as a feature that distinguishes assemblage A from B parasites. Orthologue gene group analysis was used to define gene content differences between assemblage A and B and to contribute a gene-set-based operational definition of respective taxonomic units. is tetraploid, and high allelic sequence heterogeneity (ASH) for assemblage B vs. assemblage A has been observed so far. Noteworthy, here we report an extremely low ASH (0.002%) for one of the assemblage B isolates (a value even lower than the reference assemblage A isolate WB-C6). This challenges the view of low ASH being a notable feature that distinguishes assemblage A from B parasites, and low ASH allowed assembly of the most contiguous assemblage B genome currently available for reference. In conclusion, the description of nine highly contiguous genome assemblies of new isolates of assemblage A and B adds to our understanding of the genomics and species population structure of this widespread zoonotic parasite.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): allelic sequence heterozygosity , comparative genomics , Giardia duodenalis and protozoa
Funding
This study was supported by the:
  • Horizon 2020 (Award 643476 (COMPARE project))
    • Principle Award Recipient: SimoneM. Cacciò
  • Western Norway Regional Health Authority (Award 911571 and 912245)
    • Principle Award Recipient: NinaLangeland
  • Western Norway Regional Health Authority (Award 911897)
    • Principle Award Recipient: KurtHanevik
  • Charles University, Prague, Czech Republic (Award PRIMUS/20/MED/008)
    • Principle Award Recipient: FilipWeisz
  • Horizon 2020 (Award 773830 (PARADISE project))
    • Principle Award Recipient: SimoneM. Cacciò
  • Horizon 2020 (Award 773830 (PARADISE project))
    • Principle Award Recipient: MarcoLalle
  • Horizon 2020 (Award 773830 (PARADISE project))
    • Principle Award Recipient: ChristianKlotz
  • Deutsche Forschungsgemeinschaft (Award Priority Program SPP 2332)
    • Principle Award Recipient: ToniAebischer
  • Deutsche Forschungsgemeinschaft (Award Priority Program SPP 2332)
    • Principle Award Recipient: ChristianKlotz
  • Deutsche Forschungsgemeinschaft (Award GRK2046 Research Training Program)
    • Principle Award Recipient: ToniAebischer
  • Deutsche Forschungsgemeinschaft (Award GRK2046 Research Training Program)
    • Principle Award Recipient: ChristianKlotz
© 2023 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2023-03-28
2025-01-17
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/content/journal/mgen/10.1099/mgen.0.000963
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Highly contiguous genomes of human clinical isolates of Giardia duodenalis reveal assemblage- and sub-assemblage-specific presence–absence variation in protein-coding genes
M Gen 9, 000963 (2023); https://doi.org/10.1099/mgen.0.000963
/content/journal/mgen/10.1099/mgen.0.000963
/content/journal/mgen/10.1099/mgen.0.000963
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