Global genetic diversity and evolutionary patterns among Potato leafroll virus populations

Potato leafroll virus (PLRV) is a widespread and one of the most damaging viral pathogens causing significant quantitative and qualitative losses in potato worldwide. The current knowledge of the geographical distribution, standing genetic diversity and the evolutionary patterns existing among global PLRV populations is limited. Here, we employed several bioinformatics tools and comprehensively analyzed the diversity, genomic variability, and the dynamics of key evolutionary factors governing the global spread of this viral pathogen. To date, a total of 84 full-genomic sequences of PLRV isolates have been reported from 22 countries with most genomes documented from Kenya. Among all PLRV-encoded major proteins, RTD and P0 displayed the highest level of nucleotide variability. The highest percentage of mutations were associated with RTD (38.81%) and P1 (31.66%) in the coding sequences. We detected a total of 10 significantly supported recombination events while the most frequently detected ones were associated with PLRV genome sequences reported from Kenya. Notably, the distribution patterns of recombination breakpoints across different genomic regions of PLRV isolates remained variable. Further analysis revealed that with exception of a few positively selected codons, a major part of the PLRV genome is evolving under strong purifying selection. Protein disorder prediction analysis revealed that CP-RTD had the highest percentage (48%) of disordered amino acids and the majority (27%) of disordered residues were positioned at the C-terminus. These findings will extend our current knowledge of the PLRV geographical prevalence, genetic diversity, and evolutionary factors that are presumably shaping the global spread and successful adaptation of PLRV as a destructive potato pathogen to geographically isolated regions of the world

Identification and Genetic Characterization of Ralstonia solanacearum Species Complex Isolates from Cucurbita maxima in China

Ralstonia solanacearum species complex is a devastating phytopathogen with an unusually wide host range, and new host plants are continuously being discovered. In June 2016, a new bacterial wilt on Cucurbita maxima was observed in Guangdong province, China. Initially, in the adult plant stage, several leaves of each plant withered suddenly and drooped; the plant then wilted completely, and the color of their vasculature changed to dark brown, ultimately causing the entire plant to die. Creamy-whitish bacterial masses were observed to ooze from crosscut stems of these diseased plants. To develop control strategies for C. maxima bacterial wilt, the causative pathogenic isolates were identified and characterized. Twenty-four bacterial isolates were obtained from diseased C. maxima plants, and 16S rRNA gene sequencing and pathogenicity analysis results indicated that the pathogen of C. maxima bacterial wilt was Ralstonia solanacearum. The results from DNA-based analysis, host range determination and bacteriological identification confirmed that the 24 isolates belonged to R. solanacearum phylotype I, race 1, and eight of these isolates belonged to biovar 3, while 16 belonged to biovar 4. Based on the results of partial egl gene sequence analysis, the 24 isolates clustered into three egl- sequence type groups, sequevars 17, 45, and 56. Sequevar 56 is a new sequevar which is described for the first time in this paper. An assessment of the resistance of 21 pumpkin cultivars revealed that C. moschata cv. Xiangyu1 is resistant to strain RS378, C. moschata cv. Xiangmi is moderately resistant to strain RS378, and 19 other pumpkin cultivars, including four C. maxima cultivars and 15 C. moschata cultivars, are susceptible to strain RS378. To the best of our knowledge, this is the first report of C. maxima bacterial wilt caused by R. solanacearum race 1 in the world. Our results provide valuable information for the further development of control strategies for C. maxima wilt disease

Effects of Companion Chives on Bacterial Wilt and the Micro-ecological Characteristics of Tomato Rhizosphere

【Objective】The aim of this study was to elucidate the effect of associated chives on bacterial wilt and microecological characteristics of tomato rhizosphere, and to reveal the mechanism of reducing incidence of tomato bacterial wilt.【Method】Two treatments of tomato monoculture and tomatoes with chives were set for field experiments, and rhizosphere soils of diseased tomatoes in tomato monoculture treatment (QK), healthy tomatoes in tomato monoculture treatment (NBS) and tomatoes with chives treatment (BS) were collected. And the effects of companion chives on the micro-ecological characteristics of tomato rhizosphere were investigated by using 16S rDNA high-throughput sequencing and liquid chromatography-mass spectrometry.【Result】The results of field experiments showed that the average disease incidence of tomato bacterial wilt were 50.48% in tomato monoculture treatment and 31.43% in companion chives treatment. The control effect of companion chives on tomato bacterial wilt was 37.74%. According to the resulyts of 16S rDNA high-throughput sequencing, the relative abundance and diversity of bacterial communities in the rhizosphere soils of BS and NBS were significantly higher than those of QK. Compared with QK, the relative abundance of Ralstonia in the rhizosphere soils of BS and NBS was significantly lower than that of QK, and the relative abundance of Bacillus was higher than that of QK. Moreover, compared with NBS, the relative abundance of Ralstonia in the rhizosphere soil of BS was reduced, and the relative abundance of Bacillus was significantly enhanced. A total of 586 metabolites in tomato rhizosphere soil were identified by using LC-MS, including 320 positive ion mode metabolites and 266 negative ion mode metabolites. The functions of metabolites were annotated to metabolic pathways such as metabolism, genetic information processing and environmental information processing. Compared with NBS, the contents of valine, L-asparagine and citric acid in BS rhizosphere soil were significantly lower than those in NBS, and the contents of L-lysine, glutamic acid, D-glutamine and isoleucine in rhizosphere soil of BS were also lower than those of NBS, though, the difference was not significant.【Conclusion】The companion chives significantly reduced the disease incidence of tomato bacterial wilt in the field, and changed the bacterial community structure and metabolite contents in tomato rhizosphere soil

Additional file 1: of High genetic homogeneity points to a single introduction event responsible for invasion of Cotton leaf curl Multan virus and its associated betasatellite into China

GenBank accessions and sequences of Chinese isolates of CLCuMuVs in this study. (FAS 111 kb

Comparative genomics and host range analysis of four Ralstonia pseudosolanacearum strains isolated from sunflower reveals genomic and phenotypic differences

Abstract Background Bacterial wilt caused by Ralstonia solanacearum species complex (RSSC) is one of the devastating diseases in crop production, seriously reducing the yield of crops. R. pseudosolanacearum, is known for its broad infrasubspecific diversity and comprises 36 sequevars that are currently known. Previous studies found that R. pseudosolanacearum contained four sequevars (13, 14, 17 and 54) isolated from sunflowers sown in the same field. Results Here, we provided the complete genomes and the results of genome comparison of the four sequevars strains (RS639, RS642, RS647, and RS650). Four strains showed different pathogenicities to the same cultivars and different host ranges. Their genome sizes were about 5.84 ~ 5.94 Mb, encoding 5002 ~ 5079 genes and the average G + C content of 66.85% ~ 67%. Among the coding genes, 146 ~ 159 specific gene families (contained 150 ~ 160 genes) were found in the chromosomes and 34 ~ 77 specific gene families (contained 34 ~ 78 genes) in the megaplasmids from four strains. The average nucleotide identify (ANI) values between any two strains ranged from 99.05% ~ 99.71%, and the proportion of the total base length of collinear blocks accounts for the total gene length of corresponding genome was all more than 93.82%. Then, we performed a search for genomic islands, prophage sequences, the gene clusters macromolecular secretion systems, type III secreted effectors and other virulence factors in these strains, which provided detailed comparison results of their presence and distinctive features compared to the reference strain GMI1000. Among them, the number and types of T2SS gene clusters were different in the four strains, among which RS650 included all five types. T4SS gene cluster of RS639 and RS647 were missed. In the T6SS gene cluster, several genes were inserted in the RS639, RS647, and RS650, and gene deletion was also detected in the RS642. A total of 78 kinds of type III secreted effectors were found, which included 52 core and 9 specific effectors in four strains. Conclusion This study not only provided the complete genomes of multiple R. pseudosolanacearum strains isolated from a new host, but also revealed the differences in their genomic levels through comparative genomics. Furthermore, these findings expand human knowledge about the range of hosts that Ralstonia can infect, and potentially contribute to exploring rules and factors of the genetic evolution and analyzing its pathogenic mechanism

The complete chloroplast genome of Gentiana apiata (Gentianaceae), an endemic species to Qinba Mountain in China

Gentiana apiata N. E. Br., is a perennial medicinal plant in the family Gentianaceae, which is recorded as near-threatened (NT) species in the Red List and endemic species only distributed in Qinba Mountain, China. The complete chloroplast genome sequence of G. apiata was sequenced using the Illumina Hiseq 4000 platform. The size of the G. apiata chloroplast genome is 151,069 bp, with an average GC content of 37.6%. This circular molecule has a typical quadripartite structure containing a large single-copy (LSC) region of 83,023 bp, a small single-copy (SSC) region of 17,256 bp, and two inverted (IRs) repeat regions of 25,395 bp. A total of 134 genes were successfully annotated containing 86 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 3 pseudogenes (rps19, ycf1, infA). A maximum likelihood (ML) phylogenetic tree supported the fact that the chloroplast genome of G. apiata is closely related to that of Gentiana hexaphylla

Bacterial Wilt in China: History, Current Status, and Future Perspectives

Bacterial wilt caused by plant pathogenic Ralstonia spp. is one of the most important diseases affecting the production of many important crops worldwide. In China, a large scientific community has been dedicated to studying bacterial wilt and its causative agent, Ralstonia pseudosolanacearum and R. solanacearum. Most of their work was published in Chinese, which has hindered international communication and collaboration in this field. In this review, we summarize the status of knowledge on geographical distribution, diversity, and host range of Ralstonia spp., as well as, the impact of bacterial wilt on important crops and disease control approaches, in China. We present areas of research and publications by Chinese scientists and propose the promotion of collaborative research within China and with the international community

Additional file 1 of Comparative genomics and host range analysis of four Ralstonia pseudosolanacearum strains isolated from sunflower reveals genomic and phenotypic differences

Supplementary file 1