Ni Hong

• National University of Singapore

Viruses exploit autophagy to degrade host immune components for their successful infection. However, how viral factors sequester the autophagic substrates into autophagosomes remains largely unknown. In this study, we showed that p20 protein, a viral suppressor of RNA silencing (VSR) encoded by citrus tristeza virus (CTV), mediated autophagic degra...

Pear ring rot disease (Botryosphaeria dothidea) causes a significant threat to the healthy development of the pear industry. Recent research has identified the functional role of long noncoding RNAs (lncRNAs) in various biological processes of plants. The role of lncRNAs in pear defense response remains unknown. In this study, transcriptome sequenc...

Pear chlorotic leaf spot‐associated virus (PCLSaV) is a newly described emaravirus that infects pear trees. The virus genome consists of at least five single‐stranded, negative‐sense RNAs. The P5 encoded by RNA5 is unique to PCLSaV. In this study, the RNA silencing suppression (RSS) activity of P5 and its subcellular localization were determined in...

Apple stem pitting virus is a species in the genus Foveavirus in the family Betaflexiviridae . Apple stem pitting virus (ASPV) commonly infects apple and pear plants grown worldwide. In this study, by integrating bimolecular fluorescence complementation, split‐ubiquitin‐based membrane yeast two‐hybrid, and Agrobacterium ‐mediated expression assays,...

Pear ring rot disease is an important branch disease, caused by Botryosphaeria dothidea. With the discovery of fungal viruses, the use of their attenuated properties for biological control provides a new strategy for the biological control of fungal disease. RNA silencing is a major antiviral defense mechanism in plants, insects, and fungi. Viruses...

Diseases caused by Alternaria alternata and Botryosphaeria dothidea diminish pear yield and quality, and restrict the pear agricultural industry. Lignification is a conserved mechanism for plant resistance against pathogen invasion. The regulatory mechanisms underlying defence-induced lignification in pear in response to fungal pathogen infection r...

A novel plant virus with a double-stranded (ds) RNA genome was detected in Lilium spp. in China by high-throughput sequencing, tentatively named “Lily amalgavirus 2” (LAV2). The genomic RNA of LAV2 is 3432 nucleotides (nt) and encodes a large fusion protein with 1053 amino acids (aa). It encodes two open reading frames (ORFs). The two ORFs putative...

Viroid‐Like RNAs In article number 2204308, Wenxing Xu, Kaili Dong, and co‐workers characterize a novel class of viroid‐like RNAs naturally infecting a filamentous fungus Botryosphaeria dothidea isolated from apple and termed as mycoviroids. These mycoviroids replicate autonomously in the nucleus via a rolling‐circle mechanism following a symmetric...

Chinese jujube (Ziziphus jujuba Mill.) is a widely grown fruit crop at Aksu in Xinjiang Uygur Autonomous Region of China. Viral disease-like symptoms are common on jujube plants. Here, for the first time, we report a virus tentatively named persimmon ampelovirus jujube isolate (PAmpV-Ju) infecting jujube plants. The virus was identified using high-...

To date, viroids have been found to naturally infect only plants, resulting in substantial losses for some crops. Whether viroids or viroid‐like RNAs naturally infect non‐plant hosts remains unknown. Here the existence of a set of exogenous, single‐stranded circular RNAs, ranging in size from 157 to 450 nucleotides, isolated from the fungus Botryos...

Alternaria fungus can cause notable diseases in cereals, ornamental plants, vegetables, and fruits around the world. To date, an increasing number of mycoviruses have been accurately and successfully identified in this fungus. In this study, we discovered mycoviruses from 78 strains in 6 species of the genus Alternaria, which were collected from 10...

We report for the first time the complete genome sequence of a novel amalgavirus, tentatively designated as ‘lily amalgavirus 1’ (LAV-1), isolated from Lilium spp. in China. LAV-1 is a 3448-nt double-stranded RNA virus that encodes two putative proteins. Open reading frame 1 (ORF1) encodes a 394-aa protein with unknown function. ORF2 encodes a puta...

Here, a novel mycovirus, tentatively designated as “Botryosphaeria dothidea fusarivirus 2” (BdFV2), was discovered in Botryosphaeria dothidea strain JZ-3. The complete genome sequence is 6,271 nucleotides (nt) in length, excluding the poly(A) tail, and contains two putative open reading frames (ORFs). The larger ORF1 encodes a polypeptide of 1,552...

Viroids have been found to naturally infect only plants, resulting in big losses for some crops, but whether viroids or viroid-like RNAs naturally infect non-plant hosts remains unknown. Here we report the existence of a set of exogenous, single-stranded circular RNAs, ranging in size between 157-450 nucleotides (nt), isolated from the fungus Botry...

Pear chlorotic leaf spot associated virus (PCLSaV) belongs to the genus Emaravirus and possesses a genome composed of five negative-sense single-stranded RNA (-ssRNA) segments. This study developed a SYBR green-based reverse transcription quantitative PCR (RT-qPCR) assay for the detection of PCLSaV infecting pear trees. A set of two primers q5-F2/q...

Botryosphaeria spp. are important phytopathogenic fungi that infect a wide range of woody plants, resulting in big losses worldwide each year. However, their pathogenetic mechanisms and the related virulence factors are rarely addressed. In this study, seven lignin peroxidase (LiP) paralogs were detected in Botryosphaeria kuwatsukai, named BkLiP1 t...

Citrus Huanglongbing (HLB) is one of the most devastating diseases causing unprecedented global economic losses and constituting a major hindrance to the development of the citrus industry. ‘Ca. Liberibacter asiaticus’ (CLas) is the most prevalent strain. Almost all commercial citrus cultivars are sensitive to it, and no curable method is available...

In this study, a novel positive-sense single-stranded RNA (+ssRNA) mycovirus, tentatively named Colletotrichum fructicola RNA virus 1 (CfRV1), was identified in the phytopathogenic fungus Colletotrichum fructicola. CfRV1 has seven genomic components, encoding seven proteins from open reading frames (ORFs) flanked by highly conserved untranslated re...

Viral seed transmission causes the spread of many plant viral diseases. Pyrusbetulifolia and P. calleryana are important rootstock germplasms for pear production in China. This study revealed the widespread infection of apple stem grooving virus (ASGV), apple chlorotic leaf spot virus (ACLSV), and apple stem pitting virus (ASPV) in maternal trees o...

Apple rubbery wood virus 2 (ARWV-2) and citrus virus A (CiVA) belong to a recently approved family Phenuiviridae in the order Bunyavirales and possess negative-sense single-stranded RNA genomes. In this study, the genome sequence of three ARWV-2 isolates (S17E2, LYC2, and LYXS) and a CiVA isolate (CiVA-P) infecting pear trees grown in China were ch...

We report firstly the complete genome sequence of a novel amalgavirus, tentatively designated as ‘Lily amalgavirus 1’(LAV-1), isolated from Lilium spp.in China. LAV-1 is a 3448-nt double-stranded RNA virus. It codes two putative proteins, open reading frame 1(ORF1) is 394 aa in length with unknown function. ORF2 encodes a putative RNA-dependent RNA...

Colletotrichum fructicola infects pear leaves, resulting in two major symptoms: tiny black spots (TS) followed by severe early defoliation and big necrotic lesions (BnL) without apparent damage depending on the pathotypes. How the same fungal species causes different symptoms remains unclear. To understand the molecular mechanism underlying the res...

A hypovirulent SZ-2-3y strain isolated from diseased Paris polyphylla was identified as Botrytis cinerea. Interestingly, SZ-2-3y was coinfected with a mitovirus, two botouliviruses, and a 3074 nt fusarivirus, designated Botrytis cinerea fusarivirus 8 (BcFV8); it shares an 87.2% sequence identity with the previously identified Botrytis cinerea fusar...

Here, we describe a novel mycovirus, tentatively designated as "Botryosphaeria dothidea mitovirus 3" (BdMV3), isolated from Botryosphaeria dothidea strain FJ, which causes pear ring rot disease in Fujian Province, China. The complete genome nucleotide sequence of BdMV3 is 2538 nt in length and contains a single 2070-nt open reading frame (ORF) enco...

Diaporthe species are significant pathogens, saprobes, and endophytes, with comprehensive host association and geographic distribution. These fungi cause severe dieback, cankers, leaf spots, blights, and stem-end rot of fruits on different plant hosts. This study, explored the occurrence, diversity and pathogenicity of Diaporthe spp. associated wit...

In March 2021, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. The phylum was expanded by four families (Aliusviridae, Crepuscuviridae, Myriaviridae, and Natareviridae), three subfamilies (Alpharhabdovirinae, Betarhabdovirinae, a...

A novel cytorhabdovirus, tentatively named Actinidia virus D (AcVD), was identified from kiwifruit (Actinidia chinensis) in China using high‐throughput sequencing technology. The genome of AcVD consists of 13,589 nucleotides and is organized into seven open reading frames (ORFs) in its antisense strand, coding for proteins in the order N‐P‐P3‐M‐G‐P...

Species of Diaporthe infect a wide range of plants and live in vivo as endophytes, saprobes or pathogens. However, those in peach plants are poorly characterized. In this study, 52 Diaporthe strains were isolated from peach branches with buds, showing constriction canker symptoms. Phylogenetic analyses were conducted using five gene regions: intern...

Citrus tristeza virus is a member of the genus Closterovirus in the family Closteroviridae. The p23 of citrus tristeza virus (CTV) is a multifunctional protein and RNA silencing suppressor. In this study, we identified a p23 interacting partner, FK506-binding protein (FKBP) 17-2, from Citrus aurantifolia (CaFKBP17-2), a susceptible host, and Nicoti...

Here, we describe a novel mycovirus, Botryosphaeria dothidea mitovirus 2 (tentatively designated as BdMV2), isolated from Botryosphaeria dothidea FJ strain causing pear ring rot disease in Fujian Province, China. The complete genome nucleotide sequence of BdMV2 is 2538 nt in length and contains a single 2070 nt open reading frame (ORF) encoding a p...

Fungi are generally thought to live in host plants with a single lifestyle, being parasitism, commensalism, or mutualism. The former, known as phytopathogenic fungi, cause various plant diseases that result in significant losses every year; while the latter, such as endophytic fungi, can confer fitness to the host plants. It is unclear whether biol...

Chinese jujube (Ziziphus jujuba Mill.) is a native fruit crop in China. Leaf mottle and dapple fruit disease is prevalent in cultivated jujube plants grown at Aksu in Xinjiang Uygur Autonomous Region of China. Jujube yellow mottle-associated virus (JYMaV), a tentative member in the genus Emaravirus, was recently identified from mottle-diseased juju...

Kiwifruit (Actinidia spp.) is native to China. Viral disease–like symptoms are common on kiwifruit plants. In this study, six libraries prepared from total RNA of leaf samples from 69 kiwifruit plants were subjected to next-generation sequencing (NGS). Actinidia virus 1 (AcV-1), a tentative species in the family Closteroviridae, was discovered in t...

In this study, we report the molecular characterization of a novel positive-sense single-stranded RNA (+ssRNA) mycovirus from Botryosphaeria dothidea strain G91, which we name “Botryosphaeria dothidea botourmiavirus 1” (BdBOV-1). The complete genome of BdBOV-1 is 2547 nucleotides (nt) long, contains one open reading frame (ORF) potentially encoding...

Pear chlorotic leaf spot (PCLS) is a recently emerged disease of commercially cultivated sandy pear (Pyrus pyrifolia) trees in central and southern China. By integrating high-throughput sequencing and conventional Sanger sequencing of reverse-transcription (RT)-PCR products, a novel emaravirus infecting pear trees was identified and molecularly cha...

Viruses in the genus Emaravirus contain 5-8 negative genomic RNAs and cause severe diseases of plants. In this study, a novel emaravirus, provisionally named Actinidia emaravirus 2 (AcEV-2), was identified from a kiwifruit tree showing leaf mottle and chlorosis symptoms. The genome of AcEV-2 consisted of at least six RNAs (RNAs 1-6) with sizes of 7...

The severe strain of citrus tristeza virus (CTV) causes quick decline of citrus trees. However, the CTV mild strain causes no symptoms and commonly presents in citrus trees. Viral suppressor of RNA silencing (VSR) plays an important role in the successful invasion of viruses into plants. For CTV, VSR has mostly been studied in severe strains. In th...

Colletotrichum species are plant pathogens, saprobes, and endophytes on a range of economically important hosts. However, the species occurring on pear remain largely unresolved. To determine the morphology, phylogeny and biology of Colletotrichum species associated with Pyrus plants, a total of 295 samples were collected from cultivated pear speci...

Banana trees, citrus fruit trees, pome fruit trees, grapevines, mango trees, and stone fruit trees are major fruit trees cultured worldwide and correspond to nearly 90% of the global production of woody fruit trees. In light of the above, the present manuscript summarizes the viruses that infect the major fruit trees, including their taxonomy and m...

Pear ring rot disease, mainly caused by Botryosphaeria dothidea, is widespread in most pear and apple-growing regions. Mycoviruses are used for biocontrol, especially in fruit tree disease. BdCV1 (Botryosphaeria dothidea chrysovirus 1) and BdPV1 (Botryosphaeria dothidea partitivirus 1) influence the biological characteristics of B. dothidea strains...

Background A disease of unknown etiology in water chestnut plants (Eleocharis dulcis) was reported in China between 2012 and 2014. High throughput sequencing of small RNA (sRNA) combined with bioinformatics, and molecular identification based on PCR detection with virus-specific primers and DNA sequencing is a desirable approach to identify an unkn...

Citrus yellow vein clearing virus is a newly accepted member of the genus Mandarivirus in the family Alphaflexiviridae. The triple gene block proteins (TGBp1, TGBp2 and TGBp3) encoded by plant viruses in this family function on facilitating virus movement. However, the protein function of citrus yellow vein clearing virus (CYVCV) have never been ex...

A double-stranded RNA (dsRNA) virus was isolated and characterized from strain EW220 of the phytopathogenic fungus Botryosphaeria dothidea. The full-length cDNAs of the dsRNAs were 6434 bp and 5986 bp in size, respectively. The largest dsRNA encodes a cap-pol fusion protein that contains a coat protein gene and an RNA-dependent RNA polymerase (RdRp...

A double-stranded RNA (dsRNA) virus was isolated and characterized from a strain EW220 of the phytopathogenic fungus Botryosphaeria dothidea. The full-length cDNAs of dsRNAs were 6,434 bp and 5,986 bp in size, respectively. The largest dsRNA of BdBRV1 encodes a cap-pol fusion protein that contains part coat protein gene and a RNA-dependent RNA poly...

A highly sensitive nested multiplex reverse transcription-polymerase chain reaction (nmRT-PCR) assay was developed for the simultaneous detection of Apple chlorotic leaf spot virus (ACLSV), Apple stem grooving virus (ASGV) and Apple stem pitting virus (ASPV) infecting pear trees. In the assay, a set of three forward primers specific to each of the...

Background: Pear ring rot, caused by Botryosphaeria species, is responsible for substantial economic losses by causing severe recession of pear tree growth in China. Mycovirus-mediated hypovirulence in plant pathogenic fungi is a crucial biological method to control fungal diseases. Methods: We conducted a large-scale and comprehensive transcrip...

In 2018, the family Arenaviridae was expanded by inclusion of 1 new genus and 5 novel species. At the same time, the recently established order Bunyavirales was expanded by 3 species. This article presents the updated taxonomy of the family Arenaviridae and the order Bunyavirales as now accepted by the International Committee on Taxonomy of Viruses...

A novel hepta-segmented double-stranded RNA (dsRNA) virus was isolated and characterized from the strain FJ-4 of the phytopathogenic fungus Colletotrichum fructicola, and was named Colletotrichum fructicola chrysovirus 1 (CfCV1). The full-length cDNAs of dsRNA1–7 were 3620, 2801, 2687, 2437, 1750, 1536, and 1211 bp, respectively. The 5′- and 3′-unt...

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Viruses with double-stranded RNA genomes form isometric particles or are capsidless. Here we report a double-stranded RNA virus, Colletotrichum camelliae filamentous virus 1 (CcFV-1) isolated from a fungal pathogen, that forms filamentous particles. CcFV-1 has eight genomic double-stranded RNAs, ranging from 990 to 2444 bp, encoding 10 putative ope...

Alternaria fungi are important pathogens infecting a wide variety of organisms. Here, we report a novel double-stranded RNA (dsRNA) mycovirus named Alternaria botybirnavirus 1 (ABRV1) isolated from a phytopathogenic Alternaria sp. strain (SCFS-3) infecting a pear tree in China. ABRV1 has two dsRNA components (dsRNAs 1 and 2) with the sizes of 6,188...

A disease causing smaller and cracked fruit affects peach [Prunus persica (L.) Batsch], resulting in significant decreases in yield and quality. In this study, peach tree leaves showing typical symptoms were subjected to deep sequencing of small RNAs for a complete survey of presumed causal viral pathogens. The results revealed two known viroids (H...

Virus infection is common in pear (Pyrus spp.) trees commercially cultivated in China. In this study, the growth speed, root development and phytohormone levels of virus-free and virus-infected pear cultures were comparatively investigated. Results showed that the co-infection of Apple stem grooving virus (ASGV) and Apple stem pitting virus (ASPV)...

A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for the detection of Apple chlorotic leaf spot virus (ACLSV) and Apple stem pitting virus (ASPV), two important viruses frequently occurring in pear trees. A set of four RT-LAMP primers designed based on the highly conserved region of each CP gene of the tw...

A novel disease characterized by small brown-black spots (1 to 2 mm in diameter) on tender tea leaves (Camellia sinensis) has been observed in many regions of Hubei Province, China, which severely affects the yield and quality of tea. Tea leaf samples with typical symptoms were collected from three major tea-cultivation regions of Hubei, and were s...

Purple Cai-tai (Brassica campestris L. var. purpuraria L. H. Bailey) is one of the most popular vegetable crops in the south of China, and has been cultivated over thousands of years. From March 2010 to December 2016, the incidence of Cucumber mosaic virus (CMV, genus Cucumovirus, family Bromoviridae) in purple Cai-tai was investigated in Wuhan, Hu...

Efficient recovery of high quality RNA is very important for successful RT-PCR detection of plant RNA viruses. High levels of polyphenols and polysaccharides in plant tissues can irreversibly bind to and/or co-precipitate with RNA, which influences RNA isolation. In this study, a silica spin column-based RNA isolation method was developed by using...

Non-heading Chinese cabbage [Brassica rapa L. var. chinensis (Linnaeus) Kitamura] is a variant of Chinese Cabbage. It is characterized by well-developed edible flower stalks. This vegetable has been cultivated over one thousand years in China, mostly in the Yangtze River region. Nowadays, it has become globalized with cultivation in Southeast Asia,...