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对[具体真菌名称] f. sp. 进行全基因组测序和功能注释，以揭示毒力和次生代谢物生物合成基因簇。

Whole genome sequencing and functional annotation of f. sp. to unravel virulence and secondary metabolite biosynthesis gene clusters.

作者信息

Kharte Sanjay, Kumar Ashish, Mishra Priyamvada, Ramakrishnan R S, Sharma Stuti, Mishra Nishi, Chauhan Puneet Singh, Sharma Radheshyam, Gautam Vedant, Tiwari Shweta, Goyal Vinod, Sharma Sonu, Koutu G K, Joshi N K

机构信息

Department of Plant Pathology, Jawaharlal Nehru Agricultural University, Jabalpur, Madhya Pradesh, India.

CSIR-National Botanical Research Institute, Lucknow, Uttar Pradesh, India.

出版信息

Front Genet. 2025 Jun 18;16:1585510. doi: 10.3389/fgene.2025.1585510. eCollection 2025.

DOI:10.3389/fgene.2025.1585510
PMID:40606672
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12213878/
Abstract

BACKGROUND

f. sp. is a major fungal pathogen that causes vascular wilt in lentil crops, leading to significant reductions in yield. Despite its importance, the genetic underpinnings of this pathogen remain poorly understood.

METHODS

We performed whole-genome sequencing of f. sp. using the Illumina Shotgun Sequencing platform. The resulting high-quality genome assembly consisted of 12,366 contigs with a total length of 124.48 Mb. Genome completeness was evaluated using Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis, and functional annotation was performed through comparisons with several public databases, including Uniprot, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Pfam, and Clusters of Orthologous Groups (COG). Pathogenicity-related genes were identified using the PHI-base database, and secondary metabolite biosynthesis was analyzed with AntiSMASH.

RESULTS

The genome assembly achieved 99% completeness, identifying 116,998 protein-coding genes. A total of 16,779 carbohydrate-active enzymes (CAZymes) could be detected, highlighting the pathogen's potential for plant cell wall degradation. Pathogenicity analysis revealed genes linked with moderate virulence. AntiSMASH detected 77 biosynthetic gene clusters (BGCs), including those encoding Type I polyketide synthases (T1PKS) and non-ribosomal peptide synthetases (NRPS), which may contribute to pathogenicity.

DISCUSSION

The comprehensive genomic analysis of f. sp. offers valuable insights into its pathogenic mechanisms, including plant cell wall degradation and secondary metabolite production. These findings pave the way for future research on host-pathogen interactions and the development of targeted disease management strategies.

摘要

背景

[病原菌名称]是一种主要的真菌病原体，可导致小扁豆作物发生维管束萎蔫病，从而使产量大幅降低。尽管其具有重要性，但对该病原体的遗传基础仍知之甚少。

方法

我们使用Illumina鸟枪法测序平台对[病原菌名称]进行了全基因组测序。所得的高质量基因组组装由12366个重叠群组成，总长度为124.48 Mb。使用基准通用单拷贝直系同源基因（BUSCO）分析评估基因组完整性，并通过与多个公共数据库进行比较进行功能注释，这些数据库包括Uniprot、基因本体（GO）、京都基因与基因组百科全书（KEGG）、Pfam和直系同源基因簇（COG）。使用PHI-base数据库鉴定与致病性相关的基因，并使用AntiSMASH分析次生代谢物生物合成。

结果

基因组组装的完整性达到99%，鉴定出116998个蛋白质编码基因。总共可检测到16779种碳水化合物活性酶（CAZyme），突出了该病原体降解植物细胞壁的潜力。致病性分析揭示了与中等毒力相关的基因。AntiSMASH检测到77个生物合成基因簇（BGC），包括那些编码I型聚酮合酶（T1PKS）和非核糖体肽合成酶（NRPS）的基因簇，这些基因簇可能与致病性有关。

讨论

对[病原菌名称]的全面基因组分析为其致病机制提供了有价值的见解，包括植物细胞壁降解和次生代谢物产生。这些发现为未来关于宿主-病原体相互作用的研究以及针对性病害管理策略的开发铺平了道路。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fe6d/12213878/f6305b9757bd/fgene-16-1585510-g014.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fe6d/12213878/1f6c6f08f03a/fgene-16-1585510-g010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fe6d/12213878/3c44027c5285/fgene-16-1585510-g011.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fe6d/12213878/4f4ee6d27798/fgene-16-1585510-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fe6d/12213878/161d4d7a0911/fgene-16-1585510-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fe6d/12213878/2a6f5ca27979/fgene-16-1585510-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fe6d/12213878/095d5cdf8576/fgene-16-1585510-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fe6d/12213878/8676d8eed2b8/fgene-16-1585510-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fe6d/12213878/0681820097c4/fgene-16-1585510-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fe6d/12213878/c6a2a59d65e1/fgene-16-1585510-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fe6d/12213878/1f6c6f08f03a/fgene-16-1585510-g010.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fe6d/12213878/3c44027c5285/fgene-16-1585510-g011.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fe6d/12213878/4a22ee519d08/fgene-16-1585510-g012.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fe6d/12213878/3f91c23c8022/fgene-16-1585510-g013.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/fe6d/12213878/f6305b9757bd/fgene-16-1585510-g014.jpg

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