Yang Qihong, Mao Zhenchuan, Hao Yali, Zheng Shijie, Zhao Jianlong, Li Yan, Yang Yuhong, Xie Bingyan, Ling Jian, Li Yanlin
College of Horticulture, Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding (Ministry of Education), Hunan Mid-Subtropical Quality Plant Breeding and Utilization Engineering Technology Research Center, Hunan Agricultural University, Changsha, China.
State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
Front Microbiol. 2024 Feb 1;15:1342584. doi: 10.3389/fmicb.2024.1342584. eCollection 2024.
exhibits a strong biological control effect on many important plant pathogens, such as , , and . However, its biocontrol effectiveness is weakened or reduced under salt stress. The aim of this study was to investigate the molecular response of to salt stress at the whole-genome level. Here, we present a 44.47 Mb near-complete genome assembly of the qt40003 strain for the first time, which was assembled with 7.59 Gb Nanopore sequencing long reads (170-fold) and 5.2 Gb Illumina short reads (116-fold). The assembled qt40003 genome contains 12 contigs, with a contig N50 of 4.81 Mb, in which four of the 12 contigs were entirely reconstructed in a single chromosome from telomere to telomere. The qt40003 genome contains 4.27 Mb of repeat sequences and 12,238 protein-coding genes with a BUSCO completeness of 97.5%, indicating the high accuracy and completeness of our gene annotations. Genome-wide transcriptomic analysis was used to investigate gene expression changes related to salt stress in qt40003 at 0, 2% (T2), and 4% (T4) sodium chloride concentrations. A total of 2,937 and 3,527 differentially expressed genes (DEGs) were obtained under T2 and T4 conditions, respectively. GO enrichment analysis showed that the T2-treatment DEGs were highly enriched in detoxification ( < 0.001), while the T4 DEGs were mainly enriched in cell components, mostly in cellular detoxification, cell surface, and cell wall. KEGG metabolic pathway analysis showed that 91 and 173 DEGs were significantly enriched in the T2 and T4 treatments, respectively ( < 0.01), mainly in the glutathione metabolism pathway. We further experimentally analyzed the differentially expressed glutathione transferase genes in the glutathione metabolic pathway, most of which were downregulated (13/15). In addition, we screened 13 genes related to active oxygen clearance, including six upregulated and seven downregulated genes, alongside five fungal hydrophobic proteins, of which two genes were highly expressed. Our study provides high-quality genome information for the use of for biological control and offers significant insights into the molecular responses of under salt-stress conditions.
对许多重要的植物病原体具有很强的生物防治效果，如 、 和 。然而，在盐胁迫下其生物防治效果会减弱或降低。本研究的目的是在全基因组水平上研究 对盐胁迫的分子反应。在此，我们首次展示了qt40003菌株44.47 Mb的近乎完整的基因组组装，该组装使用了7.59 Gb纳米孔测序长读段（约170倍）和5.2 Gb Illumina短读段（约116倍）。组装的qt40003基因组包含12个重叠群，重叠群N50为4.81 Mb，其中12个重叠群中的4个从端粒到端粒在一条单染色体上完全重建。qt40003基因组包含4.27 Mb的重复序列和12238个蛋白质编码基因，BUSCO完整性为97.5%，表明我们基因注释的高精度和完整性。全基因组转录组分析用于研究qt40003在0、2%（T2）和4%（T4）氯化钠浓度下与盐胁迫相关的基因表达变化。在T2和T4条件下分别获得了2937个和3527个差异表达基因（DEG）。GO富集分析表明，T2处理的DEG在解毒方面高度富集（ ＜0.001），而T4的DEG主要富集在细胞成分中，大多在细胞解毒、细胞表面和细胞壁。KEGG代谢途径分析表明，T2和T4处理分别有91个和173个DEG显著富集（ ＜0.01），主要在谷胱甘肽代谢途径。我们进一步通过实验分析了谷胱甘肽代谢途径中差异表达的谷胱甘肽转移酶基因，其中大部分被下调（13/15）。此外，我们筛选了13个与活性氧清除相关的基因，包括6个上调基因和7个下调基因，以及5个真菌疏水蛋白，其中2个基因高表达。我们的研究为利用 进行生物防治提供了高质量的基因组信息，并为盐胁迫条件下 的分子反应提供了重要见解。
