Yan Liu

Wheat dwarf virus (WDV, genus Mastrevirus, family Geminiviridae) is one of the causal agents of wheat viral disease, which severely impacts wheat production in most wheat-growing regions in the world. Currently, there is little information about natural resistance against WDV in common wheat germplasms. CRISPR/Cas9 technology is being utilized to manufacture transgenic plants resistant to different diseases. In the present study, we used the CRISPR/Cas9 system targeting overlapping regions of coat protein (CP) and movement protein (MP) (referred to as CP/MP) or large intergenic region (LIR) in the wheat variety ‘Fielder’ to develop resistance against WDV. WDV-inoculated T₁ progenies expressing Cas9 and sgRNA for CP/MP and LIR showed complete resistance against WDV and no accumulation of viral DNA compared with control plants. Mutation analysis revealed that the CP/MP and LIR targeting sites have small indels in the corresponding Cas9-positive plants. Additionally, virus inhibition and indel mutations occurred in T₂ homozygous lines. Together, our work gives efficient results of the engineering of CRISPR/Cas9-mediated WDV resistance in common wheat plants, and the specific sgRNAs identified in this study can be extended to utilize the CRISPR/Cas9 system to confer resistance to WDV in other cereal crops such as barley, oats, and rye.

Although most known viruses infecting fungi pathogenic to higher eukaryotes are asymptomatic or reduce the virulence of their host fungi, those that confer hypervirulence to entomopathogenic fungus still need to be explored. Here, we identified and studied a novel mycovirus inMetarhizium flavoviride, isolated from small brown planthopper (Laodelphax striatellus). Based on molecular analysis, we tentatively designated the mycovirus as Metarhizium flavoviride partitivirus 1 (MfPV1), a species in genusGammapartitivirus, familyPartitiviridae. MfPV1 has two double-stranded RNAs as its genome, 1,775 and 1,575 bp in size respectively, encapsidated in isometric particles. When we transfected commercial strains ofMetarhizium anisopliaeandMetarhizium pingshaensewith MfPV1, conidiation was significantly enhanced (ttest;P-value < 0. 01), and the significantly higher mortality rates of the larvae of diamondback moth (Plutella xylostella) and fall armyworm (Spodoptera frugiperda), two important lepidopteran pests were found in virus-transfected strains (ANOVA;P-value < 0.05). Transcriptomic analysis showed that transcript levels of pathogenesis-related genes in MfPV1-infectedM. anisopliaewere obviously altered, suggesting increased production of metarhizium adhesin-like protein, hydrolyzed protein, and destruxin synthetase. Further studies are required to elucidate the mechanism whereby MfPV1 enhances the expression of pathogenesis-related genes and virulence ofMetarhiziumto lepidopteran pests. This study presents experimental evidence that the transfection of other entomopathogenic fungal species with a mycovirus can confer significant hypervirulence and provides a good example that mycoviruses could be used as a synergistic agent to enhance the biocontrol activity of entomopathogenic fungi.

Here, we report a novel wheat-infecting marafivirus, tentatively named "Triticum aestivum marafivirus" (TaMRV). The full-length genome sequence of TaMRV comprises 6,437 nucleotides, excluding the poly(A) tail. Pairwise sequence comparisons and phylogenetic analysis revealed that TaMRV may represent a novel species within the genus Marafivirus in the family Tymoviridae. We also observed a mass of isometric particles with a diameter of about 30 nm in ultrathin sections of infected wheat leaf tissue. In addition, the leafhopper Psammotettix alienus was identified as a vector for this virus. This is the first report of the occurrence of a wheat-infecting marafivirus.

Maize yellow mosaic virus (MaYMV), a new species in the genus Polerovirus (family Solemoviridae), was reported in maize for the first time in China in 2016 (Chen et al., 2016). Later, MaYMV was found in other gramineous species including sugarcane (Saccharum spp.), itch grass (Rottboellia cochinchinensis), millet (Panicum miliaceum) and sorghum (Sorghum bicolor) in several countries in Asia, Africa, and South America (Yahaya et al. 2017; Lim et al. 2018; Sun et al. 2019; Nithya et al. 2021). Here, we report its presence in cultivated wheat (Triticum aestivum), detected using high-throughput sequencing (HTS). In 2021 in Henan Province, China, wheat plants with virus-like symptoms such as yellowing, stunting, and vein clearing were collected from fields in Luoyang (three plants, cv. Luohan 6), Nanyang (two plants, cv. Xinong 979), and Anyang (one plant, cv. Bainong 207). RNA was extracted from symptomatic leaves of each plant sample using TRIzol reagent (Invitrogen, Carlsbad, CA, USA). From each sample, 1 μg of RNA was mixed into a single pool to construct an rRNA-depleted RNA-seq library using a TruSeq RNA Sample Prep Kit for sequencing on the HiSeq X-Ten platform as 150-bp paired-end reads. A total of 88,892,804 clean reads were obtained after removing adaptor sequences and low-quality reads. Reads were mapped against the wheat genome database (IWGSC RefSeq v2.1) using the hisat2 v2.0.5 program. Remaining sequences were de novo assembled into contigs with Trinity program. Contigs from barley yellow dwarf virus PAV (BYDV-PAV), and BYDV-GAV were identified using a Blast search of the NCBI nr/nt database, all previously reported in wheat in China. Interestingly, four contigs with high similarity (>95%, at the nucleotide level) to MaYMV were also identified. Using the sequence of MaYMV isolate Yunnan 9 (KU291105) as reference, a total of 1,260 reads from HTS mapped to the virus genome with a coverage of 75.5% (average coverage: 33.5×). For verifying the presence of MaYMV in the source samples, MaYMV-specific primers MV-fw/MV-rev were designed to amplify the 513-bp fragment of the RdRp gene by a reverse transcription-polymerase chain reaction (RT-PCR) using the original total RNA. RT-PCR assay revealed that only 1 of the 6 samples tested positive for MaYMV, while the remaining plants were positive for other viruses (BYDV-PAV and BYDV-GAV that produce similar symptoms; viral-specific primers as previously described [Liu et al., 2020]). A subsequent survey of 17 winter wheat fields in 2021 confirmed that 6 of 286 wheat samples with virus symptoms were infected with MaYMV; 4 positives were from Linfen, Shanxi Province and 1 each from Yuanyang and Anyang, Henan Province. The full genome of wheat-infecting MaYMV isolate Anyang1 was then sequenced using RT-PCR with Sanger sequencing technology; the genomic sequence (5,642 nt) was deposited in GenBank as accession OK331995. BLASTn search showed that the complete genome sequence of this virus is 99.0%, 98.9% and 98.7% identical to isolate SC1 (MK652148), Guizhou1 (KU291107) and Yunnan 11 (KU248489), respectively. Also, the MaYMV isolate Anyang1 obtained in this study clustered with other MaYMV isolates in a phylogenetic analysis based on MaYMV full genomes. To the best of our knowledge, this is the first report of MaYMV in wheat worldwide. The presence of MaYMV in wheat is important because winter wheat could serve as an overwintering reservoir of MaYMV and perpetuate the virus in wheat-maize rotation systems in northern China.

A novel wheat-infecting polerovirus, tentatively named “wheat yellow dwarf virus” (WYDV), was identified from winter wheat in China using transcriptome sequencing (RNA-seq) combined with RT-PCR and RACE amplification. WYDV has a single-stranded RNA genome of 5,650 nucleotides (nt) and contains seven putative open reading frames (ORFs). WYDV was found to share the highest sequence identity with cereal yellow dwarf virus RPV (CYDV-RPV, genus Polerovirus), 71.1% for the nucleotide sequence of the whole genome, and 77.3% and 70.0% for the amino acid sequences of the coat protein (CP) and RNA-dependent RNA polymerase protein (RdRp), respectively. Phylogenetic analysis based on the complete genome and CP and RdRp amino acid sequences showed that WYDV is most closely related to the cereal-infecting poleroviruses CYDV-RPV, CYDV-RPS, and barley yellow dwarf virus-GPV. These data suggest that WYDV, which is associated with a newly emerging yellow dwarf disease in wheat fields in central China, should be classified as a new member of the genus Polerovirus.

While altered transcription is a cardinal feature of acute myeloid leukemia (AML), how mutations synergize to remodel the epigenetic landscape and rewire three-dimensional DNA topology is unknown. In this study, the authors utilized RNA-seq, ATAC-seq, ChIP-seq, and HiC to determine the impacts of FLT3-ITD and NPM mutation on gene transcription, chromatin accessibility, and 3D chromatin structure in murine hematopoietic stem and progenitor cells. They discovered that Flt3-ITD signals to chromatin to alter the epigenetic environment and synergizes with mutations in Npm1c to alter gene expression and drive leukemia induction. They also identified long-range cis-regulatory circuits, including a previously unknown superenhancer of Hoxa locus, as well as larger and more detailed gene-regulatory networks, driven by transcription factors including PU.1 and IRF8, whose importance were demonstrated through perturbation of network members. Overall, this study is very exciting and innovative, underscoring the importance of oncogenic driver mutations in remodeling the epigenetic landscape and rewiring the 3D DNA topology to dysregulate transcription, thereby promoting leukemia development.

In March 2020, following the annual International Committee on Taxonomy of Viruses (ICTV) ratification vote on newly proposed taxa, the phylum Negarnaviricota was amended and emended. At the genus rank, 20 new genera were added, two were deleted, one was moved, and three were renamed. At the species rank, 160 species were added, four were deleted, ten were moved and renamed, and 30 species were renamed. This article presents the updated taxonomy of Negarnaviricota as now accepted by the ICTV.

A novel double-stranded RNA (dsRNA) virus designated Psammotettix alienus reovirus (PARV) was found in the leafhopper Psammotettix alienus in China. Spherical particles approximately 70 nm in diameter arranged in a crystalline array were observed in the salivary gland tissues of infected leafhoppers by transmission electron microscopy. Some viral particles were also encased in tubules, similar to those of previously described reoviruses. Whole-genome sequencing revealed that the dsRNA genome of PARV consists of 29 569 nucleotides (nt) divided into 10 segments ranging from 4403 to 1476 nt, with low G+C content (29.5–36.5 %). All segments contained conserved terminal sequences (5′AAC…GUCA3′) and specific panhandle structures formed by inverted terminal repeats in the noncoding regions. Phylogenetic analysis based on the deduced RNA-dependent RNA polymerase (RdRp) revealed that PARV was in the fijivirus clade, but in a monophyletic lineage with an unassigned insect reovirus (Hubei insect virus 2, HBIV-2), although PARV and HBIV-2 are distinct enough to represent a new group within the genus Fijivirus. Biological assays showed that PARV infects P. alienus but not wheat plants, implying that it is a new insect-specific reovirus in the leafhopper. Given these features, PARV should be considered as a new species in the genus Fijivirus, family Reoviridae.

A novel iflavirus, tentatively named “Langfang leafhopper iflavirus” (LfLHV) was detected in leafhopper (Psammotettix alienus) by total RNA sequencing, and its genome sequence was confirmed by Sanger sequencing. The complete genome consisted of 10,700 nucleotides (nt) excluding the poly A tail and included one open reading frame (9,453 nt in length), encoding a polyprotein of 3,150 amino acids (aa). The nucleotide sequence of the complete genome was shared 44.1–53.3% identical, and the deduced amino acid sequence RNA-dependent RNA polymerase (RdRp) 22–74% identical to those of other iflaviruses. These values were all below the species demarcation threshold of 90%. Conserved motifs for structural proteins, helicase, protease, and RdRp were also similar to those in other iflaviruses. These results, as well as those of phylogenetic analysis based on the deduced amino acid sequences of the polyprotein and RdRp of LfLHV and other iflaviruses, indicate that the sequence represents a novel virus of the family Iflaviridae.