Deciphering the Genome Evolution and Cryptic Biosynthetic Potential in Rare Lentzea spp.
- 1College of Life Science and Technology & Xinjiang Production & Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar 843300, China.
- 2State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
Abstract
Background/Objectives: Rare actinomycetes are considered underexplored reservoirs of bioactive natural products, yet genus-level evolutionary processes underlying diversity and novelty in specialized metabolite biosynthetic potential remain poorly understood. Methods: We analyzed 652 high-quality, non-redundant Pseudonocardiaceae genomes, including 59 Lentzea genomes, using phylogenomics, pangenome analysis, antiSMASH, BiG-SCAPE/MIBiG comparisons, orthogroup-informed BGC conservation analysis, and five genomic context criteria for MGE association. Results: Phylogenomics confirmed the monophyly of Lentzea spp. and resolved six intrageneric clades. Pangenome analysis revealed an open architecture with core-accessory functional differentiation. Comparative genome mining revealed a rich BGC repertoire in Lentzea spp., with no significant correlation between BGC abundance and genome size. Family-scale BiG-SCAPE clustering identified numerous Lentzea-specific, putatively novel GCFs in RiPP, terpene, and NRPS classes. Six lineage-associated BGC groups retained conserved biosynthetic backbones alongside local gene content and domain architecture variation, whereas MGE-associated BGCs were enriched among lower-prevalence GCFs. Sensitivity analyses supported conservation and mobility association patterns. Conclusions: Findings support a dual-pattern model of BGC conservation and mobility-associated diversification in Lentzea, providing complementary criteria for prioritizing biosynthetic candidates and a practical framework for genome-guided natural product discovery in rare actinomycetes.
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BibTeX
@article{hua2026deciphering,
title = {{Deciphering the Genome Evolution and Cryptic Biosynthetic Potential in Rare Lentzea spp.}},
author = {Linqi Hua and Xingzhi Jiao and Wei Huang and Xing Fan and Wei Sun and Jie Xu and Lin Zhou and Wenjing Niu and Xiaoxia Luo and Chuanxing Wan and Linquan Bai and Qianjin Kang},
journal = {Antibiotics (Basel, Switzerland)},
year = {2026},
month = sep,
doi = {10.3390/antibiotics15100967},
url = {https://europepmc.org/article/MED/42938708},
note = {CC BY},
}
RIS
TY - JOUR
TI - Deciphering the Genome Evolution and Cryptic Biosynthetic Potential in Rare Lentzea spp.
AU - Linqi Hua
AU - Xingzhi Jiao
AU - Wei Huang
AU - Xing Fan
AU - Wei Sun
AU - Jie Xu
AU - Lin Zhou
AU - Wenjing Niu
AU - Xiaoxia Luo
AU - Chuanxing Wan
AU - Linquan Bai
AU - Qianjin Kang
PY - 2026
DA - 2026/09/30
JO - Antibiotics (Basel, Switzerland)
DO - 10.3390/antibiotics15100967
UR - https://europepmc.org/article/MED/42938708
AB - Background/Objectives: Rare actinomycetes are considered underexplored reservoirs of bioactive natural products, yet genus-level evolutionary processes underlying diversity and novelty in specialized metabolite biosynthetic potential remain poorly understood. Methods: We analyzed 652 high-quality, non-redundant Pseudonocardiaceae genomes, including 59 Lentzea genomes, using phylogenomics, pangenome analysis, antiSMASH, BiG-SCAPE/MIBiG comparisons, orthogroup-informed BGC conservation analysis, and five genomic context criteria for MGE association. Results: Phylogenomics confirmed the monophyly of Lentzea spp. and resolved six intrageneric clades. Pangenome analysis revealed an open architecture with core-accessory functional differentiation. Comparative genome mining revealed a rich BGC repertoire in Lentzea spp., with no significant correlation between BGC abundance and genome size. Family-scale BiG-SCAPE clustering identified numerous Lentzea-specific, putatively novel GCFs in RiPP, terpene, and NRPS classes. Six lineage-associated BGC groups retained conserved biosynthetic backbones alongside local gene content and domain architecture variation, whereas MGE-associated BGCs were enriched among lower-prevalence GCFs. Sensitivity analyses supported conservation and mobility association patterns. Conclusions: Findings support a dual-pattern model of BGC conservation and mobility-associated diversification in Lentzea, providing complementary criteria for prioritizing biosynthetic candidates and a practical framework for genome-guided natural product discovery in rare actinomycetes.
SN - 2079-6382
ER -