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Peer-reviewedCC BY 4.0Molecules

Whole-Genome Sequencing Identifies a New Aspergillus tubingensis Strain from Eremostachys isochila with Intraspecific Variation in Pharmaceutically Relevant Biosynthetic Gene Clusters

  • Farkhod Eshboev1
  • Mavjuda Kholikova2,3
  • Asifullah Khan1
  • Meixia Yang4
  • Alex X. Gao4
  • Kamila Mardieva5
  • Akhror Abdurashidov1,5
  • Saida Turaeva5
  • Vera Alferova6
  • Elvira Yusupova5
  • Zilola Kabirova2
  • Shokhista Tashmukhamedova2
4 more authors
  • Tina T. X. Dong5
  • Bakhodir Sagdullaev7
  • Shaknoz Azimova5
  • Karl W. K. Tsim4
7 affiliations
  1. 1Institute for Advanced Studies, New Uzbekistan University, Tashkent 100007, Uzbekistan
  2. 2Department of Biotechnology and Microbiology, National University of Uzbekistan, Tashkent 100174, Uzbekistan
  3. 3Institute of Fundamental and Applied Research, National Research University TIIAME, Tashkent 100000, Uzbekistan
  4. 4Division of Life Science and Center for Chinese Medicine R&D, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, China
  5. 5S.Yu. Yunusov Institute of the Chemistry of Plant Substances, Academy of Sciences of Uzbekistan, Tashkent 100170, Uzbekistan
  6. 6Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
  7. 7A.S. Sadykov Institute of Bioorganic Chemistry, Academy of Sciences of Uzbekistan, Tashkent 100143, Uzbekistan
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Abstract

Fungal endophytes are promising sources of pharmaceutically relevant secondary metabolites, yet the genomic basis of their biosynthetic potential remains poorly characterized. We sequenced the genome of endophyte S23, isolated from healthy Eremostachys isochila, and compared it with 13 reference genomes. ITS, multilocus, and genome-scale phylogenies identified S23 as Aspergillus tubingensis. CAZyme, secretome, effector, and virulence-factor analyses showed limited plant-pathogenic potential, with secreted LysM-domain proteins, chitinases, and β-1,3-glucanases as candidate determinants of endophytic adaptation. Biosynthetic gene cluster (BGC) mining identified 95 clusters, mostly conserved across A. tubingensis, including one S23-specific type I polyketide synthase cluster. S23 was identified as the only A. tubingensis genome carrying the complete ten-gene yanuthone D cluster, while the other five strains retained only three cluster genes and lacked the core polyketide synthase gene. This locus conflicts with the species phylogeny, arguing against simple vertical inheritance. The burnettiene A cluster showed a patchy intraspecific distribution, being complete in S23 but absent from three A. tubingensis strains. Nidulanin A and TAN-1612 BGCs were conserved, and the core kojic acid gene, kojA, was absent from all A. tubingensis genomes, including S23. These findings highlight distinctive biosynthetic features of S23 and provide targets for experimental validation of its metabolite production.

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Cite

BibTeXRIS
BibTeX
@article{eshboev2026wholegenome,
  title = {{Whole-Genome Sequencing Identifies a New Aspergillus tubingensis Strain from Eremostachys isochila with Intraspecific Variation in Pharmaceutically Relevant Biosynthetic Gene Clusters}},
  author = {Farkhod Eshboev and Mavjuda Kholikova and Asifullah Khan and Meixia Yang and Alex X. Gao and Kamila Mardieva and Akhror Abdurashidov and Saida Turaeva and Vera Alferova and Elvira Yusupova and Zilola Kabirova and Shokhista Tashmukhamedova and Tina T. X. Dong and Bakhodir Sagdullaev and Shaknoz Azimova and Karl W. K. Tsim},
  journal = {Molecules},
  year = {2026},
  month = nov,
  doi = {10.3390/molecules31213939},
  url = {https://www.mdpi.com/1420-3049/31/21/3939},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Whole-Genome Sequencing Identifies a New Aspergillus tubingensis Strain from Eremostachys isochila with Intraspecific Variation in Pharmaceutically Relevant Biosynthetic Gene Clusters
AU  - Farkhod Eshboev
AU  - Mavjuda Kholikova
AU  - Asifullah Khan
AU  - Meixia Yang
AU  - Alex X. Gao
AU  - Kamila Mardieva
AU  - Akhror Abdurashidov
AU  - Saida Turaeva
AU  - Vera Alferova
AU  - Elvira Yusupova
AU  - Zilola Kabirova
AU  - Shokhista Tashmukhamedova
AU  - Tina T. X. Dong
AU  - Bakhodir Sagdullaev
AU  - Shaknoz Azimova
AU  - Karl W. K. Tsim
PY  - 2026
DA  - 2026/11/01
JO  - Molecules
DO  - 10.3390/molecules31213939
UR  - https://www.mdpi.com/1420-3049/31/21/3939
AB  - Fungal endophytes are promising sources of pharmaceutically relevant secondary metabolites, yet the genomic basis of their biosynthetic potential remains poorly characterized. We sequenced the genome of endophyte S23, isolated from healthy Eremostachys isochila, and compared it with 13 reference genomes. ITS, multilocus, and genome-scale phylogenies identified S23 as Aspergillus tubingensis. CAZyme, secretome, effector, and virulence-factor analyses showed limited plant-pathogenic potential, with secreted LysM-domain proteins, chitinases, and β-1,3-glucanases as candidate determinants of endophytic adaptation. Biosynthetic gene cluster (BGC) mining identified 95 clusters, mostly conserved across A. tubingensis, including one S23-specific type I polyketide synthase cluster. S23 was identified as the only A. tubingensis genome carrying the complete ten-gene yanuthone D cluster, while the other five strains retained only three cluster genes and lacked the core polyketide synthase gene. This locus conflicts with the species phylogeny, arguing against simple vertical inheritance. The burnettiene A cluster showed a patchy intraspecific distribution, being complete in S23 but absent from three A. tubingensis strains. Nidulanin A and TAN-1612 BGCs were conserved, and the core kojic acid gene, kojA, was absent from all A. tubingensis genomes, including S23. These findings highlight distinctive biosynthetic features of S23 and provide targets for experimental validation of its metabolite production.
SN  - 1420-3049
ER  -