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Abstract Objectives Knoxia roxburghii is a member of the madder (Rubiaceae) family. This plant is cultivated in different areas of China and recognized for its medicinal properties, which leads to its use in traditional Chinese medicine. The incidence of root rot was 10–15%. In June 2023, the causal agent of root rot on K. roxburghii was identified as Fusarium oxysporum. To the best of our knowledge, this is the first report of the complete genome of F. oxysporum strain ByF01 that is the causal agent of root rot of K. roxburghii in China. The results will provide effective resources for pathogenesis on K. roxburghii and the prevention and control of root rot on this host in the future. Data description To understand the molecular mechanisms used by F. oxysporum to cause root rot on K. roxburghii, strain ByF01 was isolated from diseased roots and identified by morphological and molecular methods. The complete genome of strain ByF01 was then sequenced using a combination of the PacBio Sequel IIe and Illumina sequencing platforms. We obtained 54,431,725 bp of nucleotides, 47.46% GC content, and 16,705 coding sequences.

The microbial communities in rhizosphere soil play important roles in plant health and crop productivity. However, the microbial community structure of rhizosphere soil still remains unclear. In this study, the composition, diversity and function of the microbial communities in the rhizosphere soil of healthy and diseased plants were compared using Illumina MiSeq high-throughput sequencing. The Sobs (richness) and Shannon (diversity) indices of the soil microbial communities were higher in the rhizospheres of 2- and 3-year-old susceptible plants than in those of the healthy plants. With the increase in planting time, the numbers of fungi tended to decrease, while those of the bacteria tended to increase. Fungal diversity could be used as a biological indicator to measure the health of Knoxia roxburghii. The microbial composition and differential analyses revealed that the rhizosphere soil infested with fungi had a higher relative abundance at the phylum level in Ascomycota and Basidiomycota, while the bacteria had a higher relative abundance of Chloroflexi and a lower relative abundance of Actinobacteriota. At the genus level, the rhizosphere soil infested with fungi had relatively more abundant unclassified_f__Didymellaceae and Solicoccozyma and relatively less abundant Saitozyma and Penicillium. The bacterial genus norank_f__Gemmatimonadaceae was the most abundant, while Arthrobacter was less abundant. In addition, the abundance of Fusarium in the fungal community varied (p = 0.001). It tended to increase in parallel with the planting years. Therefore, it was hypothesized that the change in the community composition of Fusarium may be the primary reason for the occurrence of root rot in K. roxburghii, and the change in the abundance of Fusarium OTU1450 may be an indication of the occurrence of root rot in this species. The community function and prediction analyses showed that the pathogenic fungi increased with the increase in planting years. In general, soil fungi can be roughly divided into three types, including pathotrophs, symbiotrophs, and saprotrophs. An analysis of the differences in the prediction of different rhizosphere functions showed that D and L were significantly different in the COG enrichment pathway of the K. roxburghii rhizosphere bacteria (p < 0.05). The soil physical and chemical properties, including the pH, AK, total potassium (TK), and catalase (S_CAT), had the most significant effect on the soil fungal community, and most of the soil physical and chemical properties significantly correlated with the bacterial community. This study demonstrated that the occurrence of root rot had an important effect on the diversity, structure and composition of microbial communities. In addition, the results will provide a theoretical basis to prevent and control root rot in K. roxburghii. [ABSTRACT FROM AUTHOR]

The microbial communities in rhizosphere soil play important roles in plant health and crop productivity. However, the microbial community structure of rhizosphere soil still remains unclear. In this study, the composition, diversity and function of the microbial communities in the rhizosphere soil of healthy and diseased plants were compared using Illumina MiSeq high-throughput sequencing. The Sobs (richness) and Shannon (diversity) indices of the soil microbial communities were higher in the rhizospheres of 2- and 3-year-old susceptible plants than in those of the healthy plants. With the increase in planting time, the numbers of fungi tended to decrease, while those of the bacteria tended to increase. Fungal diversity could be used as a biological indicator to measure the health of Knoxia roxburghii . The microbial composition and differential analyses revealed that the rhizosphere soil infested with fungi had a higher relative abundance at the phylum level in Ascomycota and Basidiomycota, while the bacteria had a higher relative abundance of Chloroflexi and a lower relative abundance of Actinobacteriota. At the genus level, the rhizosphere soil infested with fungi had relatively more abundant unclassified&#95;f&#95;&#95;Didymellaceae and Solicoccozyma and relatively less abundant Saitozyma and Penicillium . The bacterial genus norank&#95;f&#95;&#95;Gemmatimonadaceae was the most abundant, while Arthrobacter was less abundant. In addition, the abundance of Fusarium in the fungal community varied ( p = 0.001). It tended to increase in parallel with the planting years. Therefore, it was hypothesized that the change in the community composition of Fusarium may be the primary reason for the occurrence of root rot in K. roxburghii , and the change in the abundance of Fusarium OTU1450 may be an indication of the occurrence of root rot in this species. The community function and prediction analyses showed that the pathogenic fungi increased with the increase in planting years. In general, soil fungi can be roughly divided into three types, including pathotrophs, symbiotrophs, and saprotrophs. An analysis of the differences in the prediction of different rhizosphere functions showed that D and L were significantly different in the COG enrichment pathway of the K. roxburghii rhizosphere bacteria ( p < 0.05). The soil physical and chemical properties, including the pH, AK, total potassium (TK), and catalase (S&#95;CAT), had the most significant effect on the soil fungal community, and most of the soil physical and chemical properties significantly correlated with the bacterial community. This study demonstrated that the occurrence of root rot had an important effect on the diversity, structure and composition of microbial communities. In addition, the results will provide a theoretical basis to prevent and control root rot in K. roxburghii ., Competing Interests: HL was employed by R&D Center of Yunnan Yuntianhua Co., Ltd. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Liu, Li, Dong, He, Zhang and Qiu.)

Knoxia roxburghii (syn. Knoxia valerianoides), locally known as 'Zi Daji', is a perennial herb that belongs to the Rubiaceae family, cultivated in different areas of China and recognized for its medicinal properties in traditional Chinese medicine (Chen et al. 2022). In 2021, root rot was observed during summer on K. roxburghii in Xiangyun and Dali, Yunnan Province (25°25'N, 100°40'E), China. Root rots were characterized by dark brown tissue from stem base to root, loss of vitality in tender leaves and wither. Three symptomatic root samples of K. roxburghii collected from different fields were rinsed with running water, and 0.5-1 cm2 fragments of diseased tissues were cut and surface-disinfested with 75% ethanol for 30 s, and 1% NaClO for 180 s. The fragments were then washed with sterile water, transferred to potato dextrose agar (PDA, 4.6%) and incubated at 28℃ in the dark for 3 days. A total of 13 isolates with consistent appearances were obtained by single spore isolation. These colonies on PDA showed gray and light brown obverse, and light green reverse after 10 days. The average growth rate was 3 mm per day. Conidia were nearly spherical or broadly elliptic, greyish-green, and 1.4-2.4×1.3-2.2 μm in size (n=50). The conidiophore has symmetrical or asymmetrical broom branches from the tip, with 2-4 small stems. The conidiophore branching patterns were predominantly biverticillate; stipes coarsely roughened, 80-210×2.6-3.0 μm; metulae were usually appressed verticils of 3-6, 6.4-12.5×1.6-3.0 μm; phialides were short and wide neck, 3.8-4.8×1.1-1.8 μm (n=30). The morphological characteristics of the fungus were identical to Penicillium (Mansouri et al. 2013). To further identify the isolate, one isolate (ByF10) was randomly selected for identification. DNA was extracted from mycelia using a simplified CTAB method. Primer pairs, ITS1/ITS4 and Bt2a/Bt2b were used to amplify the partial regions of rDNA internal transcribed spacer (ITS) and β-tubulin (TUB), respectively (White et al. 1990; Glass and Donaldson 1999). Blast searches showed that the sequences of ITS (OQ954757) and TUB (OQ970059) of isolate ByF10 were 99% (MH865456) and 100% (KC797611) identical with P. subrubescens CBS 130205 and CBS 129617, respectively. A concatenated phylogenetic tree (ITS+TUB) constructed using the maximum likelihood method showed that ByF10 was closely grouped next to isolates of P. subrubescens. Pathogenicity test was carried out using 1-year-old healthy seedlings of K. roxburghii cv. Yunji-1 growing on autoclaved soil (n=10). Ten plants were inoculated with mycelial blocks (5 mm2), which were taken from the colony margins of a 10-day-old culture (PDA) colony, and placed on the roots near the soil. Five control plants were inoculated with non-colonized PDA plugs. The pathogenicity test was repeated three times. All plants were kept at 25℃, 70% relative air humidity, and 12 h light/12 h regime dark for 35 days. After that period 95% of inoculated plants showed typical symptoms of root browning. P. subrubescens was only re-isolated from the inoculated plants, and identified based on morphological and molecular characteristics. No symptoms were observed in the controls. To the best of our knowledge, this is the first report of P. subrubescens causing root rot on K. roxburghii in China and the world.