Guozhong Tian

The genomic sequence of Wisteria vein mosaic virus and its similarities with other potyviruses

Summary.The complete nucleotide sequence of a Beijing isolate of Wisteria vein mosaic virus was determined to be 9695 nucleotides in length excluding the poly(A) tail. Sequence analysis predicted a single large open reading frame of 9279 nucleotides potentially encodes a polyprotein of 3092 amino acids. Phylogenetic analysis based on the genomic and deduced amino acid sequences support the current status of Wisteria vein mosaic virus (WVMV) as a distinct virus of the genus Potyvirus and a member of the Bean common mosaic virus (BCMV) subgroup. Sequence comparisons of WVMV and other members of the BCMV subgroup showed that WVMV is most closely related to both soybean mosaic virus and watermelon mosaic virus.

Molecular characterisation of two plasmids from paulownia witches’-broom phytoplasma and detection of a plasmid-encoded protein in infected plants

Two plasmids were cloned from paulownia witches’-broom phytoplasma-Nanyang strain (PaWBNy). Southern blotting using pPaWBNy-1ORF1 probe confirmed the existence of the two plasmids. The 4485xa0bp plasmid, designated pPaWBNy-1, had a nucleotide content of 24xa0mol% G+C and contained six putative open reading frames (ORFs). The 3837xa0bp plasmid, designated pPaWBNy-2, had a nucleotide content of 25.9xa0mol% G+C and contained five putative ORFs which showed similarity with ORFs in pPaWBNy-1. The two plasmids contained a series of tandem repeats and encoded a replication-associated protein (RepA) and a single-stranded DNA-binding protein (SSB), which were necessary for the replication of plasmids. Seven putative proteins encoded by two plasmids were predicted to contain one or more hydrophobic transmembrane domains, respectively, and presumably to be localised to the membrane. ORF4 from pPaWBNy-1 was partially cloned and the recombinant protein with His-tag expressed in Escherichia coli. The fusion protein was used for immunisation and the polyclonal antiserum to ORF4 protein detected the native expression of ORF4 protein in Western blot analysis from infected but not healthy plants.

Brenneria populi sp. nov., isolated from symptomatic bark of Populus×euramericana canker.

Five Gran-stain-negative, facultatively anaerobic, motile, bacterial strains were isolated from symptomatic bark tissue of Populus×euramericana canker. Strains grew at 4-41 °C, pH 4-10 and 0-6 % (w/v) salinity. They were positive with respect to catalase activity and negative for oxidase activity, nitrate reduction and the Voges-Proskauer reaction. Analysis of 16S rRNA gene sequences indicated that these five poplar isolates belong to the genus Brenneria, having highest sequence similarity of 95.98 % with Brenneria goodwinii LMG 26270(T). These five isolates formed a single cluster based on multilocus sequence analysis, indicating that they all belong to a single taxon within the genus Brenneria, which was confirmed by DNA-DNA hybridization. The DNA G+C content was 54.9-55.7 mol%, and the main fatty acids were C16 : 0, C18 : 1ω7c, C17 : 0 cyclo and C16 : 1ω7c/iso-C15 : 0 2-OH. Based on these results, we describe a novel species of the genus Brenneria with the proposed name Brenneria populi sp. nov. The type strain is D9-5(T) (u200a= CFCC 11963(T)u200a= KCTC 42088(T)).

Multilocus sequences confirm the close genetic relationship of four phytoplasmas of peanut witches'‐broom group 16SrII‐A

Four witches‐broom diseases associated with Arachis hypogaea (peanut), Crotalaria pallida, Tephrosia purpurea, and Cleome viscosa were observed in Hainan Province, China during field surveys in 2004, 2005, and 2007. In previously reported studies, we identified these four phytoplasmas as members of subgroup 16SrII‐A, and discovered that their 16S rRNA gene sequences were 99.9–100% identical to one another. In this study, we performed extensive phylogenetic analyses to elucidate relationships among them. We analyzed sequences of the 16S rRNA gene and rplV–rpsC, rpoB, gyrB, dnaK, dnaJ, recA, and secY combined sequence data from two strains each of the four phytoplasmas from Hainan province, as well as strains of peanut witches‐broom from Taiwan (PnWB‐TW), “Candidatus Phytoplasma australiense”, “Ca. Phytoplasma mali AT”, aster yellows witches‐broom phytoplasma AYWB, and onion yellows phytoplasma OY‐M. In the 16S rRNA phylogenetic tree, the eight Hainan strains form a clade with PnWB‐TW. Analysis of the seven concatenated gene regions indicated that the four phytoplasmas collected from Hainan province cluster most closely with one another, but are closely related to PnWB‐TW. The results of field survey and phylogenetic analysis indicated that Cr. pallida, T. purpurea, and Cl. viscosa may be natural plant hosts of peanut witches‐broom phytoplasma.

Lampropedia puyangensis sp. nov., isolated from symptomatic bark of Populus × euramericana canker and emended description of Lampropedia hyalina (Ehrenberg 1832) Lee et al. 2004.

AbstractnA Gram-stain negative, Neisser-stain negative, aerobic, non-motile, non-spore-forming, slimy, glossy bacterial strain with single or clustered coccoid cells and white colony colour, designated as 2-binT, was isolated from cankered bark tissue of Populusxa0×xa0euramericana. The strain was found to grow at 15–40xa0°C and pH 5–10, with an optimum of 30xa0°C and pH 8.0. The strain was found to be negative with respect to catalase and positive for oxidase activity, nitrate reduction and Voges–Proskauer reaction. Analysis of 16S rRNA gene sequence data indicated that the isolate belongs to the genus Lampropedia, having sequence similarity of 96.24xa0% with Lampropedia hyalina ATCC11041T. DNA–DNA relatedness of strain 2-binT with L. hyalina JCM 21380T was 26.7xa0±xa04.6xa0%. The DNA G+C content of strain 2-binT was determined to be 57xa0% and the major cellular fatty acids were identified as C16:0, C16:1ω7c/C16:1ω6c and C18:1ω7c. The polar lipid profile of strain 2-binT was found to contain diphosphatidylglycerol, a glycolipid, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol, a phospholipid, phosphatidylmonomethylethanolamine and three unidentified lipids (L1, L2, L3). Based on molecular data and physiological and biochemical characteristics, strain 2-binT is considered to represent a novel species in the genus Lampropedia, for which the name Lampropedia puyangensis sp. nov. is proposed. The type strain is 2-binT (=xa0CFCC 10925Txa0=xa0KCTC 32235T).

Corticibacter populi gen. nov., sp. nov., a new member of the family Comamonadaceae, from the bark of Populus euramericana

Three novel endophytic strains, designated 17B10-2-12T, 26C10-4-4 and D13-10-4-9, were isolated from the bark of Populus euramericana in Heze, Shandong Province, China. They were Gram-reaction-negative, aerobic, non-motile, short-rod-shaped, oxidase-positive and catalase-negative. A phylogenetic analysis of the 16S rRNA gene showed that the three novel strains clustered with members of the family Comamonadaceae and formed a distinct branch. The isolates shared 100u2009% similarities among themselves and had the highest sequence similarity with Xenophilus azovorans DSM 13620T (95.2u2009%) and Xenophilus arseniciresistens YW8T (95.0u2009%), and less than 95.0u2009% sequence similarities with members of other species. Their major fatty acids were C16u2009:u20090, C17u2009:u20090 cyclo, C18u2009:u20091ω7c and C16u2009:u20091ω7c/C16u2009:u20091ω6c. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and three unknown aminophospholipids. The predominant quinone was ubiquinone-8 (Q-8). The DNA G+C content was 69.5–70.0u200amol%. Based on data from a polyphasic taxonomy study, the three strains represent a novel species of a novel genus of the family Comamonadaceae, for which the name Corticibacter populi gen. nov., sp. nov. is proposed. The type strain is 17B10-2-12T (u2009=u2009CFCC 12099Tu2009=u2009KCTC 42091T).

Full genome sequence of jujube mosaic-associated virus, a new member of the family Caulimoviridae

We report a new circular DNA virus identified from a Chinese jujube tree showing mosaic-like symptoms. The genome of this virus is 7194 bp in length and contains five putative open reading frames (ORFs), all on the plus-strand of the genome. The genomic organization, primer binding sites and the sizes of the ORFs were similar to those reported for other badnaviruses (family Caulimoviridae), except for ORF3, which was split into ORF3a and ORF3b with a 70-nt intergenic region. Furthermore, this new virus shares low nucleotide sequence identity (<50%) with other members of the family Caulimoviridae. Consequently, we propose this virus as a new member of the family Caulimoviridae and refer to it as jujube mosaic-associated virus (JuMaV).

Multilocus sequence analysis of the genus Kurthia, and a description of Kurthia populi sp. nov.

Four novel bacteria strains, belonging to the genus Kurthia, were isolated from the surface of Curculionidae (Kurthia strain 10y-14T), and from hybrid poplar, Populus × euramericana (Kurthia strains 6-3, 2-5, and 06C10-3-14), different bark samples in Puyang, Henan Province, China. Phylogenetic analyses of the 16S rRNA gene and MLSA data showed that the four strains form a distinct cluster in the genus Kurthia, indicating that they all belong to a single taxon within the genus. DNA-DNA hybridization levels between the 10y-4T and Kurthia huakuii LAM0618T and Kurthia massiliensis DSM 24639T were 58.31% and 53.92%, respectively. This indicates that the four novel strains represent a species distinct from these closely two species. DNA G+C content of the type strain is 42.1-42.6%. The major fatty acids are iso-C15:0 and anteiso-C15:0. The major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, and an unknown phospholipid and unidentified aminophospholipids. The predominant menaquinones were MK-7 (90%) and MK-6 (10%). The major cell wall amino acids were lysine, alanine, glutamic acid, glycine. On the basis of the MLSA and 16S rRNA gene phylogenetic analyses, percentage of DNA-DNA reassociation, DNA base composition, and biochemical and phenotypic characteristics, the four strains represent a new species within the genus Kurthia, for which the name Kurthia populi sp. nov. is proposed. The type strain is 10y-14T (=CFCC 11600T=KCTC 33522T).Four novel bacterial strains belonging to the genus Kurthia were isolated from the surface of a weevil of the family Curculionidae (strain 10y-14T), and from bark samples of hybrid poplar, Populusu2009×u2009euramericana (strains 6-3, 2-5 and 06C10-3-14), in Puyang, Henan Province, China. Phylogenetic analyses of the 16S rRNA gene and multilocus sequence analysis (MLSA) data showed that the four strains form a distinct cluster in the genus Kurthia, indicating that they all belong to a single taxon within the genus. DNA-DNA hybridization levels between strain 10y-4T and Kurthia huakuii LAM0618T and Kurthia massiliensis DSM 24639T were 58.31 and 53.92u2009%, respectively. This indicates that the four novel strains represent a species distinct from these two closely related species. The DNA G+C content of the novel strains was 42.1-42.6u2009%. The major fatty acids were iso-C15u2009:u20090 and anteiso-C15u2009:u20090.The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, an unknown phospholipid and unidentified aminophospholipids. The predominant menaquinones were MK-7 (90u2009%) and MK-6 (10u2009%). The major cell-wall amino acids were lysine, alanine, glutamic acid and glycine. On the basis of the MLSA and 16S rRNA gene sequence phylogenetic analyses, DNA-DNA reassociation values, DNA base composition, and biochemical and phenotypic characteristics, the four strains are considered to represent a novel species within the genus Kurthia, for which the name Kurthia populi sp. nov. is proposed. The type strain is 10y-14T (u2009=u2009CFCC 11600Tu2009=u2009KCTC 33522T).