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Fusarium oxysporum strain PkF01 is the causal agent of Polygonatum kingianum rhizome rot. Here, we report, for the first time, the genome assemblies of the F. oxysporum strain PkF01 using the PacBio Sequel system. We obtained a total base number of 51.27 Mb in 87 contigs. The number of scaffolds and scaffold N50 were 86 and 2.46 Mb, with a 47.55% GC content. The number of coding sequences was 17,265, with total length of 36.61 Mb, average length of 1.77 kb, and a gene density of 0.34 kb. A total of 11,447, 14,734, 10,759, and 4,434 genes were annotated using the Pfam, COG, GO, and KEGG databases, respectively. A total of 764, 335, 1,572, 216, 4,245, 1,591, 2,242, and 1,926 genes were annotated using the CAZy, CYP450, DFVF, CARD, PHI, SignalP, TCDB, and TMHMM databases, respectively. Collinearity analysis showed that the PkF01 genome shared more homologous genomic regions with F. oxysporum f. sp. lilii strain Fol39 than with F. oxysporum f. sp. lycopersici strain Fol4287, indicating that the PkF01 genome is more closely related to the Fol39 rather than the Fol4287 genome. The high-quality genome sequences of PkF01 will provide a valuable resource for not only investigating both the pathogenicity mechanism and host specificity in F. oxysporum but also exploring disease control measures. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Gastrodia elata BI. is an important cultivated medicinal plant in China. To analyze the genetic diversity and evolutionary relationship of the germplasm resources of G. elata, specific Single nucleotide polymorphism (SNP) markers were developed. SLAF analysis was used to compare 28 samples of the same G. elata cultivar. Plants from 4 different varieties or different habitats were collected to explore intraspecific variation and to lay a foundation for resource protection. This will facilitate improved variety breeding in future. In this study, Single nucleotide polymorphism (SNP) genetic variation and differentiation of G. elata f. glauca, G. elata f. viridis, and G. elata f. elata were analyzed using Specific-Locus Amplified Fragment Sequencing (SLAF-seq). A total of 75.95M reads with an average sequencing depth of 19.32 × and a mean Q30 of 91.71% were obtained. Based on the 19,675 polymorphic SLAF tags, 60,238 SNPs were identified and a subset of 22,737 SNPs with minor allele frequency > 0.05 and integrity > 0.5 were selected. A model-based analysis divided the accessions into two groups, wild type G. elata f. glauca and G. elata f. viridis groups. Phylogenetic analysis also clustered the samples into the two major groups. G. elata has high genetic diversity. Population diversity was highest in G. elata f. elata and lowest in G. elata f. viridis. Analysis of molecular variance (AMOVA) revealed significant variations within individuals (92.23%). This study provides new insights into the genetic variation and differentiation of G. elata, which can be exploited to improve existing commercial cultivars.

Tulbaghia violacea Harv. indigenous to southern African countries, is an herbaceous perennial bulbous plant belonging to the family Amaryllidaceae. It is a popular garden plant in China. This attractive plant is traditionally used as medicine and repellent (Kubec et al. 2002; Moodley et al. 2015). In June 2021, T. violacea plants showing typical tospovirus-like symptoms of chlorotic rings patterns, were found at the campus of Yunnan University of Chinese Medicine (Fig.S1). Disease incidence was about 11.0% during the field survey. Total RNA was extracted from symptomatic leaves of T. violacea plants using the TRIzol reagent (ambio, Carlsbad, CA). Reverse transcription (RT)-PCR was conducted to identify the virus using RNA extract as the template. The degenerate primers (dTospo-F2 and dTospo-R2) (Huang et al. 2018) were used to amplify the conserved regions of the orthotospoviral L RNA sequences. No amplification was obtained from extracts of two asymptomatic plants. The amplicons from four symptomatic samples were cloned into the pMD19-T vector (TaKaRa) and sequenced (three clones for each amplicon) by Tsingke (Shanghai, China). The obtained DNA fragments were determined to be 312 bp. The sequences from four symptomatic samples were identical (GenBank acc.no. OK258285) and shared the highest nucleotide identities (98.0%) with a corresponding sequence of segment L of impatiens necrotic spot virus (INSV) isolated (GQ336991) from Phalaenopsis amabilis in Yunnan province, China. To further confirm the INSV infection to T. violacea, the samples were analyzed with the specific primers for the N, NSs and NSm genes of INSV (Table S1), respectively. Amplicons of the expected size, 789 bp, 1344 bp and 912 bp, were produced, respectively. Amplicons were cloned and sequenced. The 789-bp N (ON529554) and 1344-bp NSs (ON529554) gene sequences had 99.1% and 99.3% nucleotide identities with the corresponding region of previously described INSV Phalenopsis isolate (GQ336989), respectively. The 912-bp NSm (ON529553) gene sequence shared 99.5% nucleotide identity with the corresponding region of INSV Phalenopsis isolate (GQ336990). Metavirome and Sanger sequencing were used to complete the genome of INSV from T. violacea. The leaves of the symptomatic sample were used to construct an rRNA-depleted library using Nextera XT reagents (Illumina, San Diego, CA). The library was subjected to RNA-Seq a NovaSeq 6000 platform (Illumina, San Diego, CA). A total of 33,193,233 quality-filtered reads were obtained using BBMAP (https://github.com/BioInfoTools/BBMapBBMap - Bushnell B. - sourceforge.net/projects/bbmap/). Among 161052 reads mapped to virus sequences, 151407 reads (read ratios 94.0%) were mapped to INSV. Three complete segments of INSV genome were determined to 8,778 nt (L segment, Acc. No. ON529552), 4,958 nt (M segment, Acc. No. ON529553), and 2,983 nt (S segment, Acc. No. ON529554) in length. These segments were validated by RT-PCR and Sanger sequencing. Three segments share nucleotide sequence identities of 99.6%, 99.3% and 98.9% with the L (GQ336991), M (GQ336990) and S segments (GQ336989) of INSV Phalenopsis isolate, respectively. The results of sequence comparisons showed no evidence of reassortment between INSV and another orthotospovirus. There was a report of tomato spotted wilt virus infecting T. violacea in Florida, USA (Dey et al. 2019). No other virus infecting T. violacea was reported. INSV has been reported to infect several economically important crops including Phalenopsis, pepper etc. in China (Chen et al. 2016). INSV-infected T. violacea not only losses landscaping value but also plays an important intermedia host role in the spread of INSV. Additional surveys and evaluation will be needed to understand the potential medicinal effect of this virus on this plant. To our knowledge, this is first report of INSV in T. violacea.

The complete genome sequence of a putative novel potyvirus, tentatively named "polygonatum mosaic-associated virus 1" (PMaV1), was sequenced from naturally infected Polygonatum cyrtonema Hua in China. PMaV1 has a typical genome organization of potyviruses with a single large open reading frame (nt 119-9448) that encodes a 3109-aa polyprotein that is predicted to be cleaved into 10 mature proteins by virus-encoded proteases. Pairwise comparisons revealed that PMaV1 shares 71.50% complete genome sequence identity with Polygonatum kingianum virus 4 and 80.00% amino acid sequence identity with Polygonatum kingianum virus 3 of the genus Potyvirus. Phylogenetic analysis indicated that PMaV1 clustered with other potyviruses and that it was most closely related to Polygonatum kingianum virus 3 and Polygonatum kingianum virus 4. These results suggest that PMaV1 is a new member of the genus Potyvirus of the family Potyviridae (Nucleotide sequence data reported are available in the GenBank databases under the accession number OP380926).

The complete genomic sequence of a new potyvirus was determined from Paris polyphylla var. yunnanensis. Its genomic RNA consists of 9571 nucleotides (nt) excluding the 3’ -terminal poly (A) tail, containing the typical open reading frame (ORF) of potyviruses and encoding a putative large polyprotein of 3061 amino acids. The virus shares 54.20-59.60% nt sequence identities and 51.80-57.90% amino acid sequence identities with other potyviruses. Proteolytic cleavage sites and conserved motifs of the potyviruses were identified in the polyprotein and within individual proteins. Phylogenetic analysis indicated that the virus was most closely related to lily yellow mosaic virus. The results suggest that the virus should be classified as a novel species within the genus Potyvirus, which we tentatively name “Paris yunnanensis mosaic chlorotic virus” (PyMNV).11Note: Nucleotide sequence data reported are available in the GenBank databases under the accession number no.ON871824.

The complete genome sequence of a new potyvirus from Paris polyphylla var. yunnanensis was determined. Its genomic RNA consists of 9571 nucleotides (nt), excluding the 3'-terminal poly(A) tail, containing the typical open reading frame (ORF) of potyviruses and encoding a putative large polyprotein of 3061 amino acids. The virus shares 54.20%-59.60% nt sequence identity and 51.80%-57.90% amino acid sequence identity with other potyviruses. Proteolytic cleavage sites and conserved motifs of potyviruses were identified in the polyprotein and within individual proteins. Phylogenetic analysis indicated that the virus was most closely related to lily yellow mosaic virus. The results suggest that the virus should be classified as a member of a novel species within the genus Potyvirus, and we have tentatively named this virus "Paris yunnanensis mosaic chlorotic virus" (PyMCV).