Complete genome sequence of a novel totivirus isolated from the leaves of Myrica rubra.

Chinese bayberry is a fruit that is appreciated for its taste. A novel totivirus associated with rolling, disfiguring, chlorotic and vein-clearing symptoms on the leaf apices of Chinese bayberry was identified by transcriptome sequencing and reverse transcription PCR (RT-PCR). The complete genome of the virus was determined to be 4959 nucleotides long, and it contains two open reading frames (ORFs). Its genomic organization is similar to that of previously reported totiviruses. ORF1 encodes a putative coat protein (CP) of 765 aa, and ORF2 encodes an RNA-dependent RNA polymerase (RdRp) of 815 aa. These two putative proteins share 55.1% and 62.6%, amino acid sequence identity, respectively, with the corresponding proteins of Panax notoginseng virus A, respectively. According to the demarcation criteria for totivirus species established by the International Committee on Taxonomy of Viruses (ICTV), the new virus should be considered a member of a new species in the genus totivirus, family Orthototiviridae, which we have tentatively named ''Myrica rubra-associated totivirus'' (MRaTV).

Complete genome sequence of polygonatum mosaic-associated virus 1, a novel member of the genus Potyvirus in China.

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).

Complete genome sequence analysis of a new potyvirus isolated from Paris polyphylla var. yunnanensis.

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).

First report of Didymella curtisii causing leaf scorch on spider lily (Hymenocallis littoralis) in China.

Hymenocallis littoralis (Jacq.) Salisb, commonly known as spider lily, is a Amaryllidaceae species widely cultivated in southern China for ornamental and medicinal purposes (Anusha et al., 2016). In 2020, there was a devastating outbreak of leaf scorch of H. littoralis from July to September in Kunming city, Yunnan province of China (E102.8268°, N24.8371°), with 97% disease incidence. The initial spots were small and reddish-brown but gradually expanded to large irregular lesions with yellow centers. The leaves then turned yellow and withered from tip towards the petiole in the severely infected plants. For identification, leaf sections (5 × 5 mm2) cut from the margins of the lesions were surface-sterilized for 3 min with 1% sodium hypochlorite, rinsed three times with sterile distilled water, placed on potato dextrose agar (PDA), and incubated at 28°C at a 12-h photoperiod for three days. One fungus was isolated from 90% of the samples, of which three monosporic isolates were selected using a method of agar dilution lineation separation. After 4 days of incubation, colonies were white-yellowish, and changed to beige-mustard after 7 days. The pycnidia were produced after 10 days incubation on oatmeal agar (OA), and they were black-brown, subglobose, and ostiolate. Chlamydospores mainly formed in the aerial mycelia, globose, often in chains, brown or pale. The conidia were ellipsoidal or clavate, (0-)1-3-septate, 2.1 to 10.8 × 1.0 to 3.2 µm (n=60). The total genomic DNA of three isolates was extracted from mycelia. The nuclear ribosomal internal transcribed spacer region (ITS), the second largest subunit of nuclear DNA-dependent RNA polymerase II (rpb2), the 28S nuclear ribosomal large subunit rRNA gene (LSU), and beta-tubulin gene (tub2) were amplified using the ITS1/ITS4 (White et al., 1990), fRPB2-5F/fRPB2-7cR (Liu et al., 1999), LR0R/LR5 (Schoch et al., 2012), and Btub2Fd/Btub4Rd (Woudenberg et al., 2009) primer pairs, respectively. The amplicons were cloned in the pMD19-T vector (Code No. 6013, Takara, Kusatsu, Japan) and sequenced bi-directionally. These three isolates had the same nucleotide sequences, one of which was submitted to NCBI (ITS, OM279485; rpb2, OM304305; LSU, OP800249; tub2, OQ108870). BLASTn analyses showed that ITS, rpb2, LSU, and tub2 were genetically 100%, 98.49%, 99.89%, and 97.89%, respectively, identical with MN973518, MT018130, MN943724, and MT005618 genes of Didymella curtisii strain CBS 288.29. Phylogenetic tree was constructed with MEGAX based on the nucleotide sequences of ITS, rpb2, LSU, and tub2 using the maximum likelihood method. The fungus isolated from diseased leaves of H. littoralis was grouped into the same clade with D. curtisii. According to the morphology and sequence analyses, the isolate was D. curtisii (Chen et al., 2015) and was named isolate HlDc1. To confirm the causal agent of the disease, a spore suspension with 106 spores of HlDc1/mL was smeared on healthy leaves of six months old with brushes. Leaves in the control group were smeared with sterile water. All inoculated plants were incubated at 28°C under a 12-h photoperiod in a moisture chamber. The pathogenicity tests were conducted three times with six plants each time. Fifteen days post-inoculation, the leaves inoculated with HlDc1 developed red-brown lesions, whereas the control leaves remained asymptomatic. Isolate HlDc1 was re-isolated from infected leaves. To our knowledge, this is the first report of leaf scorch on H. littoralis in Yunnan province, China, caused by D. curtisii. The results laid the foundation for epidemiological forecasting and scientific control of this disease.

First Report of Root Rot on Paris polyphylla var. yunnanensis caused by Fusarium solani in Yunnan, China.

Paris polyphylla var. yunnanensis is a perennial herb with diverse chemical components having wide-ranging pharmacological effects. The demand for P. polyphylla var. yunnanensis as a raw material increases greatly and currently exceeds 1,000 tons per year (Zhou et al. 2021). In September 2021, root rot was observed on P. polyphylla var. yunnanensis in Mangshi, Yunnan province, China. Average disease incidences in the fields reached 15%, with diseased plants exhibiting yellowing and wilting leaves, as well as browning and rotting roots. Cross sections (5 × 5 mm2) cut from the margin of symptomatic and asymptomatic root tissues were surface-sterilized for 30 s with 75% ethanol, followed by 180 s with 1% sodium hypochlorite. After rinsing thrice with sterile distilled water, the fragments were transferred to potato dextrose agar (PDA) plates and incubated at 28°C in the dark. Ten isolates were obtained, and single spore isolation was performed. These isolates showed similar morphological characters, with colonies ranging in color from white to pale cream and sparse mycelia. Conidia were produced on the top or side of phialides. Microconidia were oval or reniform, 0- or 1-septate, with a diameter of 5.1-10.7 µm × 1.6-3.9 µm (average 7.6 µm × 2.8 µm) (n=30). The macroconidia were straight to slightly curved or sickle-shaped, 3- to 5-septate, with a diameter of 15.1-27.9 µm × 2.8-4.0 µm (average 21.0 µm × 3.6 µm). Chlamydospores were smooth, nearly round, and 3.3-6.6 (average 4.9) µm in diameter. Genomic DNA were extracted from mycelia of the two isolates. The nuclear ribosomal internal transcribed spacer (ITS), translation elongation factor 1 alpha (EF1α), and the second largest subunit of nuclear DNA-directed RNA polymerase II (RPB2) were amplified with the primer pairs of ITS1/ITS4 (White et al. 1990), EF1-728F/EF1-986R (Carbone and Kohn 1999), and fRPB2-5F/fRPB2-7cR (Liu et al. 1999), respectively. These two isolates exhibited the same nucleotide sequences (ITS, OP646781; EF1α, OP661172; RPB2, OP661173), with BLASTn analyses showing 100%, 99.66%, and 99.65% identity, respectively, with Fusarium solani (syn. Neocosmospora solani) (Crespo et al. 2019) strain NRRL 43474 (ITS, EF453097; EF1α, EF452945; RPB2, EF469984). A phylogenetic tree was constructed using MEGAX based on the nucleotide sequences of ITS, EF1α, and RPB2, using the maximum likelihood method. The isolate was classified into the F. solani clade. According to the morphology and sequence analyses, the isolate was identified as F. solani (Chehri et al. 2015), and named PpFs1. To test the pathogenicity of the isolate PpFs1, the roots of four years old P. polyphylla var. yunnanensis plants were dipped in 107 spore/mL suspension filtered from potato dextrose broth (PDB) for 30 min, while control roots were dipped in sterile water. After inoculation, all plants were transplanted in pots filled with sterile soil and kept at 25°C with a 12/12-h light/darkness photoperiod. Six plants were used for each treatment, and repeated thrice. Two months after inoculation, the infected plants showed wilted leaves and rotted roots, while controls remained asymptomatic. PpFs1, identified by morphology and ITS, was re-isolated from infected plants, and was found to comply with Koch's postulates. To the best of our knowledge, F. oxysporum and F. concentricum causes Paris polyphylla var. Chinensis stem rot in China. But this is the first report of root rot on P. polyphylla var. yunnanensis being caused by F. solani in Yunnan, China.

First report of Impatiens necrotic spot orthotospovirus infecting Tulbaghia violacia Harv. in China.

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.

Transcriptomic responses to drought stress in Polygonatum kingianum tuber.

BACKGROUND: Polygonatum kingianum Coll. et Hemsl. is an important plant in Traditional Chinese Medicine. The extracts from its tubers are rich in polysaccharides and other metabolites such as saponins. It is a well-known concept that growing medicinal plants in semi-arid (or drought stress) increases their natural compounds concentrations. This study was conducted to explore the morpho-physiological responses of P. kingianum plants and transcriptomic signatures of P. kingianum tubers exposed to mild, moderate, and severe drought and rewatering. RESULTS: The stress effects on the morpho-physiological parameters were dependent on the intensity of the drought stress. The leaf area, relative water content, chlorophyll content, and shoot fresh weight decreased whereas electrolyte leakage increased with increase in drought stress intensity. A total of 53,081 unigenes were obtained; 59% of which were annotated. We observed that 1352 and 350 core genes were differentially expressed in drought and rewatering, respectively. Drought stress driven differentially expressed genes (DEGs) were enriched in phenylpropanoid biosynthesis, flavonoid biosynthesis, starch and sucrose metabolism, and stilbenoid diarylheptanoid and gingerol biosynthesis, and carotenoid biosynthesis pathways. Pathways such as plant-pathogen interaction and galactose metabolism were differentially regulated between severe drought and rewatering. Drought reduced the expression of lignin, gingerol, and flavonoid biosynthesis related genes and rewatering recovered the tubers from stress by increasing the expression of the genes. Increased expression of carotenoid biosynthesis pathway related genes under drought suggested their important role in stress endurance. An increase in starch and sucrose biosynthesis was evident from transcriptomic changes under drought stress. Rewatering recovered the drought affected tubers as evident from the contrasting expression profiles of genes related to these pathways. P. kingianum tuber experiences an increased biosynthesis of sucrose, starch, and carotenoid under drought stress. Drought decreases the flavonoids, phenylpropanoids, gingerol, and lignin biosynthesis. These changes can be reversed by rewatering the P. kingianum plants. CONCLUSIONS: These results provide a transcriptome resource for P. kingianum and expands the knowledge on the effect of drought and rewatering on important pathways. This study also provides a large number of candidate genes that could be manipulated for drought stress tolerance and managing the polysaccharide and secondary metabolites' contents in P. kingianum.

Identification of Potential Biomarkers from Aconitum carmichaelii, a Traditional Chinese Medicine, Using a Metabolomic Approach.

Despite their well-known toxicity, Aconitum species are important traditional medicines worldwide. Aconitum carmichaelii, known in Chinese as (fuzi), is an officially recognized traditional Chinese medicine with characteristic analgesic and anti-inflammatory activities, whose principal pharmacological ingredients are considered as aconitine-type diterpene alkaloids. Notwithstanding the long-recorded use of A. carmichaelii in traditional Chinese medicine, no single-entity aconitum alkaloid drug has been developed for clinical use. UPLC-Q-TOF-MS was used to investigate the marker compounds that can be used to differentiate A. carmichaelii from seven other Aconitum species collected in Yunnan Province. Nontargeted principle component analysis scores plots found that all the tested Aconitum species clustered into three distinct groups, and A. carmichaelii was significantly different chemically than the other seven species. Furthermore, the primary and lateral roots of A. carmichaelii also showed significant differences. Using orthogonal partial least squares discriminate analysis analysis, eight marker compounds were identified, including 14-acetylkarakoline, aconitine, carmichaeline, fuziline, hypaconitine, mesaconitine, neoline, and talatisamine. Four of these aconitum alkaloids, fuziline, hypaconitine, mesaconitine, and neoline, showed significant analgesic activity in a dose-dependent manner compared to the negative and positive controls. However, hypaconitine, mesaconitine, and neoline exhibited significant acute toxicity activity, while fuziline showed no acute toxicity in mice, suggesting the relative safety of this alkaloid. This study provides a good example of how to differentiate an authentic medicinal plant from common adulterants using a metabolomics approach, and to identify compounds that may be developed into new drugs.

[Testing methods for seed quality of Bletilla striata].

In order to provide a basis for establishing seed testing rules and seed quality standard of Bletilla striata, the seed quality of B.striata from different producing area was measured referring to the Rules for Agricultural Seed Testing(GB/T 3543-1995).The results showed that the seeds of B.striata passed through 20-mesh sieve for purity analysis.The weight of seeds was measured by 1000-seed method and the water content was measured at the higher temperature (133±2) ℃ for 3 hours.The seeds were cultured on the wet filter paper at 30 ℃ for 4-20 days in light for germination testing.The method of testing seed viability was that seeds were dipped into 1% TTC solution for 7 hours at temperature of 40 ℃.

Identification, molecular characterization and phylogenetic analysis of a novel nucleorhabdovirus infecting Paris polyphylla var. yunnanensis.

A novel betanucleorhabdovirus infecting Paris polyphylla var. yunnanensis, tentatively named Paris yunnanensis rhabdovirus 1 (PyRV1), was recently identified in Yunnan Province, China. The infected plants showed vein clearing and leaf crinkle at early stage of infection, followed by leaf yellowing and necrosis. Enveloped bacilliform particles were observed using electron microscopy. The virus was mechanically transmissible to Nicotiana bethamiana and N. glutinosa. The complete genome of PyRV1 consists of 13,509 nucleotides, the organization of which was typical of rhabdoviruses, containing six open reading frames encoding proteins N-P-P3-M-G-L on the anti-sense strand, separated by conserved intergenic regions and flanked by complementary 3'-leader and 5'-trailer sequences. The genome of PyRV1 shared highest nucleotide sequence identity (55.1%) with Sonchus yellow net virus (SYNV), and the N, P, P3, M, G, and L proteins showed 56.9%, 37.2%, 38.4%, 41.8%, 56.7%, and 49.4% amino acid sequence identities with respective proteins of SYNV, suggesting RyRV1 belongs to a new species of the genus Betanucleorhabdovirus.

Phylogeography of Camellia taliensis (Theaceae) inferred from chloroplast and nuclear DNA: insights into evolutionary history and conservation.

BACKGROUND: As one of the most important but seriously endangered wild relatives of the cultivated tea, Camellia taliensis harbors valuable gene resources for tea tree improvement in the future. The knowledge of genetic variation and population structure may provide insights into evolutionary history and germplasm conservation of the species. RESULTS: Here, we sampled 21 natural populations from the species' range in China and performed the phylogeography of C. taliensis by using the nuclear PAL gene fragment and chloroplast rpl32-trnL intergenic spacer. Levels of haplotype diversity and nucleotide diversity detected at rpl32-trnL (h = 0.841; π = 0.00314) were almost as high as at PAL (h = 0.836; π = 0.00417). Significant chloroplast DNA population subdivision was detected (GST = 0.988; NST = 0.989), suggesting fairly high genetic differentiation and low levels of recurrent gene flow through seeds among populations. Nested clade phylogeographic analysis of chlorotypes suggests that population genetic structure in C. taliensis has been affected by habitat fragmentation in the past. However, the detection of a moderate nrDNA population subdivision (GST = 0.222; NST = 0.301) provided the evidence of efficient pollen-mediated gene flow among populations and significant phylogeographical structure (NST > GST; P < 0.01). The analysis of PAL haplotypes indicates that phylogeographical pattern of nrDNA haplotypes might be caused by restricted gene flow with isolation by distance, which was also supported by Mantel's test of nrDNA haplotypes (r = 0.234, P < 0.001). We found that chlorotype C1 was fixed in seven populations of Lancang River Region, implying that the Lancang River might have provided a corridor for the long-distance dispersal of the species. CONCLUSIONS: We found that C. taliensis showed fairly high genetic differentiation resulting from restricted gene flow and habitat fragmentation. This phylogeographical study gives us deep insights into population structure of the species and conservation strategies for germplasm sampling and developing in situ conservation of natural populations.

[Genetic diversity of ancient tea gardens and tableland tea gardens from Yunnan Province as revealed by AFLP marker].

This study was conducted to evaluate the genetic diversity within and among the plants of four ancient tea gardens and two tableland tea gardens form Yunnan Province, China by AFLP technique. The percentage of polymorphic loci (P) of the plants from six tea gardens was 92.31%. The genetic diversity within the six gardens demonstrated by Nei cents genetic diversity (He) was estimated to be 0.1366, while Shannon indices (Ho) were 0.2323. The percentage of polymorphic loci of the four ancient tea populations was 45.55% on average, with a range of 36.44% (Mengsong) to 59.11% (Mengla). But the percentages of polymorphic loci of the plants from two tableland gardens were 13.77% (Yunkang 10) and 24.2% (Menghai Daye), respectively. There was a great genetic difference between ancient tea gardens and tableland tea gardens. The genetic diversity among the plants of the ancient tea garden was higher than those of the sexual tableland tea garden and the clone tableland tea garden based on P valve. The four ancient tea gardens and two tableland gardens could be differentiated with AFLP markers. The results show that AFLP marker is an effective tool in the discrimination of tea germplasm, as well as sundried green tea.