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Updated: May 9, 2025

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
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High-quality genome assembly and comparative analysis reveal extensive genomic variation in Talaromyces marneffei

Jinxia Luo1, Jingyuan Bian1, Michaela Murillo1

  • 1Department of Health Technology and Informatics, Faculty of Health and Social Science, The Hong Kong Polytechnic University, Hong Kong, PR China.

Microbial Genomics
|April 28, 2025
PubMed

Insights

This study presents a high-quality genome of Talaromyces marneffei, revealing significant genomic variations and duplications. These findings enhance understanding of fungal genetic diversity for improved diagnostics and surveillance.

Area of Science:

  • Mycology
  • Genomics
  • Infectious Diseases

Background:

  • Talaromyces marneffei is a dimorphic fungus causing severe infections, particularly in immunocompromised individuals in Southeast Asia.
  • Limited genomic data has hindered Talaromyces marneffei strain differentiation, diagnosis, and treatment strategies.
  • Genomic structural variations are crucial for understanding fungal pathogenicity and evolution.

Purpose of the Study:

  • To assemble a high-quality genome of Talaromyces marneffei ATCC 18224.
  • To identify and characterize genomic structural variations, including segmental duplications and retrotransposon activity.
  • To provide a foundation for improved Talaromyces marneffei genotyping, classification, and genomic surveillance.

Main Methods:

  • Third-generation Oxford Nanopore Technologies sequencing for genome assembly.
  • Identification of segmental duplications and long terminal repeat (LTR) retrotransposons.
  • Comparative genomic analysis across multiple Talaromyces marneffei strains.

Main Results:

  • A 28.9 Mb Talaromyces marneffei genome was assembled into 11 contigs.
  • A strain-specific 740-kb segmental duplication, potentially involving a Ty1/Copia LTR retrotransposon, was identified.
  • Significant genetic structural variations and recent Ty1/Copia retrotransposon expansions were observed in strain ATCC 18224.
  • Comparative analysis revealed large-scale rearrangements in other strains, prompting further investigation.

Conclusions:

  • The high-quality genome assembly and characterization of structural variations in Talaromyces marneffei advance our understanding of its genetic diversity.
  • Identified genomic features provide insights into the dimorphic transition and pathogenicity of Talaromyces marneffei.
  • This genomic resource will facilitate advancements in Talaromyces marneffei diagnostics, strain differentiation, and epidemiological surveillance.
Keywords:
Talaromyces marneffeicomparative genomicsgenomic structural variationlong terminal repeat (LTR) retrotransposons

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