Complete genome sequence of a new virus, a tentative member of the family Geminiviridae, infecting hedge bindweed (Calystegia sepium) in South Korea.

The family Convolvulaceae comprises approximately 50-60 genera with approximately 1600-1700 species, exhibiting a rich diversity of morphological characteristics and occupying a broad range of ecological habitats. High-throughput sequencing identified a tentative new virus in the family Geminiviridae infecting Calystegia sepium var. japonica in South Korea. The 2,706 nt long genome comprises six open reading frames (ORFs). The analysis of the nucleotide sequence of the genome and the putative amino acid sequences of ORFs indicated that the virus was closely related to the members of the family Geminiviridae. The genome organization of the virus was similar to that of members of the genus Topilevirus in terms of the number of ORFs and splicing signal. However, the virus, tentatively named bindweed mottle virus (BWMV), may not be assigned to current genera into the family Geminiviridae.

Genetic diversity assessment and genome-wide association study reveal candidate genes associated with component traits in sweet potato (Ipomoea batatas (L.) Lam).

The Korean sweet potatoes were bred by various cultivars introduced from Japanese, American, Porto Rico, China, and Burundi. This issue enriched their genetic diversity but also resulted in a mixture of cultivars. For genotyping, we collected and sequenced 66 sweet potato germplasms from different localities around Korea, including 36 modern cultivars, 5 local cultivars, and 25 foreign cultivars. This identified 447.6 million trimmed reads and 324.8 million mapping reads and provided 39,424 single nucleotide polymorphisms (SNPs) markers. Phylogenetic clustering and population structure analysis distinctly classified these germplasms into 5 genetic groups, group 1, group 2, group 3, group 4, and group 5, containing 20, 15, 10, 7, and 14 accessions, respectively. Sixty-three significant SNPs were selected by genome-wide association for sugar composition-related traits (fructose, glucose, and total sugars), total starch, amylose content, and total carotenoid of the storage root. A total of 37 candidate genes encompassing these significant SNPs were identified, among which, 7 genes were annotated to involve in sugar and starch metabolism, including galactose metabolism (itf04g30630), starch and sucrose metabolism (itf03g13270, itf15g09320), carbohydrate metabolism (itf14g10250), carbohydrate and amino acid metabolism (itf12g19270), and amino sugar and nucleotide sugar metabolism (itf03g21950, itf15g04880). This results indicated that sugar and starch are important characteristics to determine the genetic diversity of sweet potatoes. These findings not only illustrate the importance of component traits to genotyping sweet potatoes but also explain an important reason resulting in genetic diversity of sweet potato.

Comprehensive transcriptome profiling of Caragana microphylla in response to salt condition using de novo assembly.

OBJECTIVE: To investigate the response of Caragana microphylla in salt condition, transcriptome analysis, differentially expressed genes (DEGs) comparison with Arabidopsis thaliana, and the chlorophyll content analysis were performed. RESULTS: Gene Ontology (GO) term, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of DEGs indicated that salt condition affected photosynthesis and chlorophyll in C. microphylla. The DEGs compared with salt responsive genes of A. thaliana indicated that C. microphylla's responses to salt differed greatly from those of the model plant and that the results also indicated up-regulated genes related to photosynthesis and chlorophyll in C. microphylla. Moreover, we confirmed that salt-treated C. microphylla increased chlorophyll content, and the genes of protoporphyrin IX downstream in chlorophyll biosynthesis were induced in the heatmap analysis. CONCLUSIONS: These results showed a similar pattern to some halophytes plants with increased chlorophyll at a certain salt concentration, and we assumed that C. microphylla also has a mechanism to adapt or tolerate moderate salt conditions.

Enhanced binding and inhibition of SARS-CoV-2 by a plant-derived ACE2 protein containing a fused mu tailpiece.

Infectious diseases such as Coronavirus disease 2019 (COVID-19) and Middle East respiratory syndrome (MERS) present an increasingly persistent crisis in many parts of the world. COVID-19 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The angiotensin-converting enzyme 2 (ACE2) is a crucial cellular receptor for SARS-CoV-2 infection. Inhibition of the interaction between SARS-CoV-2 and ACE2 has been proposed as a target for the prevention and treatment of COVID-19. We produced four recombinant plant-derived ACE2 isoforms with or without the mu tailpiece (µ-tp) of immunoglobulin M (IgM) and the KDEL endoplasmic reticulum retention motif in a plant expression system. The plant-derived ACE2 isoforms bound whole SARS-CoV-2 virus and the isolated receptor binding domains of SARS-CoV-2 Alpha, Beta, Gamma, Delta, and Omicron variants. Fusion of µ-tp and KDEL to the ACE2 protein (ACE2 µK) had enhanced binding activity with SARS-CoV-2 in comparison with unmodified ACE2 protein derived from CHO cells. Furthermore, the plant-derived ACE2 µK protein exhibited no cytotoxic effects on Vero E6 cells and effectively inhibited SARS-CoV-2 infection. The efficient and rapid scalability of plant-derived ACE2 µK protein offers potential for the development of preventive and therapeutic agents in the early response to future viral outbreaks.

High-quality genome assembly and genetic mapping reveal a gene regulating flesh color in watermelon (Citrullus lanatus).

The unique color and type characteristics of watermelon fruits are regulated by many molecular mechanisms. However, it still needs to be combined with more abundant genetic data to fine-tune the positioning. We assembled genomes of two Korean inbred watermelon lines (cv. 242-1 and 159-1) with unique color and fruit-type characteristics and identified 23,921 and 24,451 protein-coding genes in the two genomes, respectively. To obtain more precise results for further study, we resequenced one individual of each parental line and an F2 population composed of 87 individuals. This identified 1,539 single-nucleotide polymorphisms (SNPs) and 80 InDel markers that provided a high-density genetic linkage map with a total length of 3,036.9 cM. Quantitative trait locus mapping identified 15 QTLs for watermelon fruit quality-related traits, including ß-carotene and lycopene content in fruit flesh, fruit shape index, skin thickness, flesh color, and rind color. By investigating the mapping intervals, we identified 33 candidate genes containing variants in the coding sequence. Among them, Cla97C01G008760 was annotated as a phytoene synthase with a single-nucleotide variant (A → G) in the first exon at 9,539,129 bp of chromosome 1 that resulted in the conversion of a lysine to glutamic acid, indicating that this gene might regulate flesh color changes at the protein level. These findings not only prove the importance of a phytoene synthase gene in pigmentation but also explain an important reason for the color change of watermelon flesh.

Differential expression pattern of novel MADS-box genes in early root formation and differentiation of sweet potato.

MADS-box genes are important transcription factors affecting overall development, but their role in sweet potato [Ipomoea batatas (L.) Lam.] has not been fully studied. This study isolated six novel MADS-box genes (IbSOC1, IbFUL1, IbAGL6, IbSVP1, IbSVP2, and IbSVP3) from sweet potato [Ipomoea batatas (L.) Lam. cv. Annouimo] during the early root differentiation stage using the de novo transcriptome assembly sequencing method. At the early root differentiation (between 0 and 3 days after transplanting), the IbSOC1, IbFUL1, and IbSVP2 genes decreased rapidly, whereas the IbSVP3 gene decreased gradually. In the early stages of root formation (0-30 days), the levels of IbSVP1 and IbSVP3 expression were steady, but the levels of IbSOC1 expression decreased gradually. The expression of six novel genes was also conducted in the tuberous root formation stage (30-90 days), and the IbSVP3 gene increased significantly according to the formation of the tuberous root. Six novel MADS-box genes that were believed to influence the entire root formation of sweet potato were isolated from the sweet potato. This study provides a genetic basis for further research on sweet potato root formation and development.

Functional genomics by integrated analysis of transcriptome of sweet potato (Ipomoea batatas (L.) Lam.) during root formation.

BACKGROUND: Sweet potato is easily propagated by cuttings. But the molecular biological mechanism of adventitious root formation are not yet clear. OBJECTIVE: To understand the molecular mechanisms of adventitious root formation from stem cuttings in sweet potato. METHODS: RNA-seq analysis was performed using un-rooted stem (0 day) and rooted stem (3 days). Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, comparison with Arabidopsis transcription factors (TFs) of DEGs were conducted to investigate the characteristics of genes and TFs involved in root formation. In addition, qRT-PCR analysis using roots at 0, 3, 6, 9, and 12 days after planting was performed to confirm RNA-seq reliability and related genes expression. RESULTS: 42,459 representative transcripts and 2092 DEGs were obtained through the RNA-seq analysis. The DEGs indicated the GO terms related to the single-organism metabolic process and cell periphery, and involved in the biosynthesis of secondary metabolites, and phenylpropanoid biosynthesis in KEGG pathways. The comparison with Arabidopsis thaliana TF database showed that 3 TFs (WRKY, NAC, bHLH) involved in root formation of sweet potato. qRT-PCR analysis, which was conducted to confirm the reliability of RNA-seq analysis, indicated that some metabolisms including oxidative stress and wounding, transport, hormone may be involved in adventitious root formation. CONCLUSIONS: The detected genes related to secondary metabolism, some hormone (auxin, gibberellin), transports, etc. and 3 TFs (WRKY, NAC, bHLH) may have functions in adventitious roots formation. This results provide valuable resources for future research on the adventitious root formation of sweet potato.

Physiological and proteomic analysis of plant growth enhancement by the rhizobacteria Bacillus sp. JS.

In this study, the effects of the plant growth-promoting rhizobacterium (PGPR), Bacillus sp. JS on the growth of tobacco (Nicotiana tabacum 'Xanthi') and lettuce (Lactuca sativa 'Crispa'), were evaluated by comparing various growth parameters between plants treated with the bacterium and those exposed to water or nutrient broth as control. In both tobacco and lettuce, fresh weight and length of shoots were increased upon exposure to Bacillus sp. JS. To explain the overall de novo expression of plant proteins by bacterial volatiles, two-dimensional gel electrophoresis was performed on samples from PGPR-treated tobacco plants. Our results showed that chlorophyll a/b binding proteins were significantly up-regulated, and total chlorophyll content was also increased. Our findings indicate the potential benefits of using Bacillus sp. JS as a growth-promoting factor in agricultural practice, and highlight the need for further research to explore these benefits.