Complete genome sequence of Desulfurispirillum indicum strain S5(T)

Desulfurispirillum indicum strain S5(T) is a strictly anaerobic bacterium isolated from river sediment in Chennai, India. D. indicum belongs to the deep branching phylum of Chrysiogenetes, which currently only includes three other cultured species. Strain S5(T) is the type strain of the species and it is capable of growth using selenate, selenite, arsenate, nitrate or nitrite as terminal electron acceptors. The 2,928,377 bp genome encodes 2,619 proteins and 49 RNA genes, and the information gained from its sequence will be relevant to the elucidation of microbially-mediated transformations of arsenic and selenium, in addition to deepening our knowledge of the underrepresented phylum of Chrysiogenetes.     

Viscosinamide-producing Pseudomonas fluorescens DR54 exerts a biocontrol effect on Pythium ultimum in sugar beet rhizosphere

Two repeated DNA sequences of European strains of the symbiotic fungus Tuber melanosporum were isolated and characterized. One of these, SS14, representing about 0.05% of the fungal genome, was shown to be a T. melanosporum-specific sequence by Southern and dot-blot hybridization. The second one, named SS15, is about 0.0025% of the entire genome, and it is specific not only to T. melanosporum but also to the Asian black truffle Tuber indicum. Neither of these two fragments hybridizes with any of the other European truffle species tested. By sequence analysis of these two fragments, PCR primers were designed and used to selectively amplify DNA from T. melanosporum ascocarps and ectomycorrhizae by simple and multiplex PCR. No amplification products were obtained with DNA from either mycorrhizal roots or fruit bodies of other ectosymbiotic fungi. The two identified genomic traits also provided useful information for a better understanding of the phylogenetic relationships among black truffle species and for testing T. melanosporum intraspecific variability.     

Genome sequencing of the important oilseed crop Sesamum indicum L

The Sesame Genome Working Group (SGWG) has been formed to sequence and assemble the sesame (Sesamum indicum L.) genome. The status of this project and our planned analyses are described.     

Genome Sequence of Sphingobium indicum B90A, a Hexachlorocyclohexane-Degrading Bacterium

Sphingobium indicum B90A, an efficient degrader of hexachlorocyclohexane (HCH) isomers, was isolated in 1990 from sugarcane rhizosphere soil in Cuttack, India. Here we report the draft genome sequence of this bacterium, which has now become a model system for understanding the genetics, biochemistry, and physiology of HCH degradation.     

Species recognition and cryptic species in the Tuber indicum complex

Morphological delimitation of Asian black truffles, including Tuber himalayense, T. indicum, T. sinense, T. pseudohimalayense, T. formosanum and T. pseudoexcavatum, has remained problematic and even phylogenetic analyses have been controversial. In this study, we combined five years of field investigation in China with morphological study and DNA sequences analyses (ITS, LSU and β-tubulin) of 131 Tuber specimens to show that T. pseudohimalayense and T. pseudoexcavatum are the same species. T. formosanum is a separate species based on its host plants and geographic distribution, combined with minor morphological difference from T. indicum. T. sinense should be treated as a synonym of T. indicum. Our results demonstrate that the present T. indicum, a single described morphological species, should include at least two separate phylogenetic species. These findings are of high importance for truffle taxonomy and reveal and preserve the richness of truffle diversity.     

印度块菌在未来气候变化情景下的空间分布模式——以云南省为例

以印度块菌（Tuber indicum）丰产区云南省为例,利用地理信息系统和物种分布模型,并通过影响印度块菌分布的主要环境因子和气候因子,共同模拟现在及未来生境分布模式。结果表明结合环境因子和气候因子,在建模过程中能提高模型预测准确度,在几类物种分布模型中,MAXENT模型具有最优的拟合效果。在大的空间尺度上,年降水,最湿季度降水,最冷月份最低温、地貌类型及土壤类型对印度块菌的生境分布影响最大。此外,在模型模拟的A2和B2未来气候变化情景下,印度块菌未来的新增生境均呈北上趋势,且B2情景下生境的适生程度低于A2情景。     

Molecular evidence for multiple polyploidization and lineage recombination in the Chrysanthemum indicum polyploid complex (Asteraceae)

The Chrysanthemum indicum polyploid complex comprises morphologically differentiated diploids, tetraploids and hybrids between C. indicum and C. lavandulifolium. The relationships between species and cytotypes within this complex remain poorly understood. Random amplified polymorphic DNAs (RAPDs), intersimple sequence repeats (ISSRs) and chloroplast SSR markers were used to elucidate the genetic diversity and relationships of the C. indicum polyploid complex. Molecular analysis of three diploid and nine tetraploid populations provided strong evidence for recurrent origins and lineage recombination in the C. indicum polyploid complex. The high similarity in molecular marker profiles and cpDNA haplotypes between the diploids and tetraploids distributed in the Shen-Nong-Jia Mountain area of China suggested an autopolyploid origin of the tetraploids, while the tetraploids from other populations may have originated via allopolyploidization. Lineage recombination was revealed by the extensive sharing of chloroplast haplotypes and genetic markers among the tetraploid populations with different origins. Multiple differentiation and hybridization/polyploidization cycles have led to an evolutionary reticulation in the C. indicum polyploid complex, and resulted in the difficulties in systematic classification.     

中国块菌要览及其保护策略

截至目前报道的中国块菌有28种,其中黑块菌4种,白块菌24种.具有重要经济价值和生态价值的黑块菌类有印度块菌复合种和中国夏块菌,其中印度块菌复合种与欧洲法国黑孢块菌属于姊妹类群,中国夏块菌与欧洲夏块菌也是姊妹类群.虽然欧洲意大利白块菌在中国尚未找到、波氏块菌在中国的存在尚待最终确认,但是,最近的更多白块菌新种的发现,说...     

Trichodesma mudgalii (Boraginaceae)—a new species from Madhya Pradesh, India

Trichodesma mudgalii (Boraginaceae) is described and illustrated as a new species from Madhya Pradesh (Betul district), India. The species is closely allied to T. indicum var. indicum and T. stocksii but differs from the former in having epidermis (on stem) peeling off in flakes with age, leaves crowded, 2–6 mm broad, strongly revolute and covered on abaxial surface with simple, short, thin hairs intermixed with long, bulbous-based hairs and from the latter in having apices of connectives strongly spirally twisted, ovoid nutlets and emarginate.     

Phylogenetic relationships between European and Chinese truffles based on parsimony and distance analysis of ITS sequences

Phylogenetic relationships among truffle species from Europe and China were investigated through parsimony analysis of the ITS sequences. Three major clades were obtained among the species analysed. The so-called white truffles appeared polyphyletic since Tuber magnatum was grouped with brown truffles and not with the other white species (T. maculatum, T. borchii, T. dryophilum, T. puberulum). The black truffles investigated in this study, T. brumale, T. melanosporum, T. indicum and T. himalayense, were grouped in an independent clade. The Périgord black truffle T. melanosporum and the Chinese black truffles T. indicum and T. himalayense, were very closely related. The delimitation of these species was estimated by a distance analysis on several isolates collected from different geographic areas. In spite of intraspecific variations of the internal transcribed spacers (ITS) sequences, T. melanosporum and the Chinese black truffles can be unambiguously attributed to distinct taxa.     

Phylogenetic relationships between Tuber pseudoexcavatum, a Chinese truffle, and other Tuber species based on parsimony and distance analysis of four different gene sequences

Phylogenetic relationships between Tuber pseudoexcavatum and other Tuber species were investigated by studying the sequences of four genes: 5.8S-ITS2, beta-tubulin, protein kinase C and elongation factor 1alpha. The four phylogenetic trees allowed to differentiate the black truffle clade, composed of two subclades, one comprising the Asian black truffles (T. indicum, T. sinense, T. himalayense) and the Perigord black truffle (T. melanosporum), the second comprising T. pseudoexcavatum and T. brumale. These two subclades diverged relatively early. We propose a common ancestor, located between Europe and China, to all the black truffles. The T. brumale/pseudoexcavatum subclade would have started to diverge and migrate first, T. brumale towards Europe through a northern route and T. pseudoexcavatum towards China. Later the T. melanosporum subclade would have started to migrate through the same route, T. melanosporum towards Europe and T. indicum towards China, leading to vicariant species.     

Genome analysis of phage JS98 defines a fourth major subgroup of T4-like phages in Escherichia coli

Numerous T4-like Escherichia coli phages were isolated from human stool and environmental wastewater samples in Bangladesh and Switzerland. The sequences of the major head gene (g23) revealed that these coliphages could be placed into four subgroups, represented by the phages T4, RB69, RB49, and JS98. Thus, JS98 defines a new major subgroup of E. coli T4-like phages. We conducted an analysis of the 169-kb JS98 genome sequence. Overall, 198 of the 266 JS98 open reading frames (ORFs) shared amino acid sequence identity with the reference T4 phage, 41 shared identity with other T4-like phages, and 27 ORFs lacked any database matches. Genes on the plus strand encoded virion proteins, which showed moderate to high sequence identity with T4 proteins. The right genome half of JS98 showed a higher degree of sequence conservation with T4 and RB69, even for the nonstructural genes, than did the left genome half, containing exclusively nonstructural genes. Most of the JS98-specific genes were found in the left genome half. Two came as a hypervariability cluster, but most represented isolated genes, suggesting that they were acquired separately in multiple acquisition events. No evidence for DNA exchange between JS98 phage and the E. coli host genome or coliphages other than T4 was observed. No undesired genes which could compromise its medical use were detected in the JS98 genome sequence.     

印度块菌子囊果内部解剖结构的扫描电镜观察

利用扫描电镜对成熟印度块菌子囊果的内部结构进行了观察,以系统揭示其子囊果内部组织特征,为块菌属的分类以及块菌属真菌子囊果的生理研究奠定基础。观察结果进一步证明,成熟印度块菌子囊果横切面上的白色迷宫状脉络是由不育的侧丝构成,而暗脉则是被侧丝缠绕并包裹着的可育的菌丝组织,即产孢组织,这些白色脉络和暗脉就构成了印度块菌子囊果横切面上迷宫状的纹脉;产孢组织中,可观察到正在发育的大大小小的子囊被缠绕在一起的大量产囊丝与侧丝包裹着,形成密密麻麻微小的类似蜂巢状结构;子囊孢子游离于子囊中,成熟子囊孢子表面有刺状纹饰,刺的顶端有小弯钩。单个子囊内含的子囊孢子大小与其内含的子囊孢子数目有关,子囊内所含的子囊孢子越多,子囊孢子就越小。     

Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1(T))

Parvibaculum lavamentivorans DS-1(T) is the type species of the novel genus Parvibaculum in the novel family Rhodobiaceae (formerly Phyllobacteriaceae) of the order Rhizobiales of Alphaproteobacteria. Strain DS-1(T) is a non-pigmented, aerobic, heterotrophic bacterium and represents the first tier member of environmentally important bacterial communities that catalyze the complete degradation of synthetic laundry surfactants. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,914,745 bp long genome with its predicted 3,654 protein coding genes is the first completed genome sequence of the genus Parvibaculum, and the first genome sequence of a representative of the family Rhodobiaceae.     

昆明地区印度块菌子囊果的解剖结构研究

通过印度块菌子囊果石蜡切片的显微观察,对印度块菌子囊果包被及子实层的显微结构、子囊及子囊孢子的发育过程进行研究.结果表明:(1)印度块菌子囊果是由包被和子实层构成,子囊果的表面密被大量大小不一的疣状突起,包被由外皮层和内皮层构成;子实层由封闭的、大小不一的产孢组织构成,在产孢组织中包含有侧丝、产囊丝、子囊和子囊内的子囊孢子;(2)成熟印度块菌子囊果横切面上有明暗相间的迷宫状纹脉;(3)子囊卵形,由产囊丝顶端的细胞发育而来;(4)成熟子囊孢子红褐色,椭圆形至近球形不等,子囊孢子双层壁,外壁密布有刺状纹饰.子囊孢子在子囊内的发育过程中常出现败育现象,每个成熟子囊中含有1～5个子囊孢子(常见4个).     

Genome sequence of the phototrophic betaproteobacterium Rubrivivax benzoatilyticus strain JA2T

Herein we report the draft genome sequence of a phototrophic bacterium, Rubrivivax benzoatilyticus strain JA2(T), which apparently is the first genome sequence report of a phototrophic member belonging to the class Betaproteobacteria. The unique feature of this strain is its capability to synthesize carotenoids through both spirilloxanthin and spheroidenone pathways. Strain JA2(T) produces several novel secondary metabolites, and the genome insights help in understanding the unique machinery that the strain adapted.     

Cytotaxonomic studies in the Adiantum caudatum complex of Africa and Asia

Study of meiosis in synthesized hybrids has permitted a genome analysis to be carried out with respect to the holotype of A. indicum Ghatak, 4x, originally found wild near Calcutta. The two differentiated diploids from which A. indicum , 4x, seems to have arisen are represented in the analysis by A. zollingeri from Ceylon and by two strains of an Indian diploid provisionally designated A. incisum sens. lat. 2x. Supplementary information excluding an autopolyploid origin for A. indicum is provided by hybrids between A. indicum 4x and an unrelated tetraploid, A. malesianum Ghatak. Ecological information is supplied for the material of A. zollingeri , indicating that it occupies a specialized habitat which might be found in India if search is made in the right kind of territory. A. incisum 2x is shown to be much more widespread and to be present in hill country, or occasionally in lowlands, from the Himalayas to South India inclusive. It contains a number of genetically determined biotypes differing slightly in morphology but behaving as members of one species when combined into hybrids. Further morphological information and a revised key for separating the specimens used in the investigation is provided in an Appendix.     

Draft Genome Sequence of the Hydrocarbon-Degrading and Emulsan-Producing Strain Acinetobacter venetianus RAG-1T

We report the draft genome sequence of Acinetobacter venetianus strain RAG-1(T), which is able to degrade hydrocarbons and to synthesize a powerful biosurfactant (emulsan) that can be employed for oil removal and as an adjuvant for vaccine delivery. The genome sequence of A. venetianus RAG-1(T) might be useful for bioremediation and/or clinical purposes.