头花杜鹃、陇蜀杜鹃及杜鹃属植物叶绿体基因组比较分析

头花杜鹃(Rhododendron capitatum)和陇蜀杜鹃(R. przewalskii)是极具观赏价值的野生花卉和药用植物。为探讨头花杜鹃和陇蜀杜鹃叶绿体基因组的遗传结构及进化特征,该研究利用 Illumina HiSeq 4000 平台对头花杜鹃和陇蜀杜鹃的叶绿体全基因组进行测序,经组装和注释后,结合 7 个已发表的杜鹃属植物叶绿体全基因组进行比较基因组学分析和系统发育分析。结果表明:(1)头花杜鹃和陇蜀杜鹃叶绿体全基因组呈典型的环状四分体结构,均由一个大单拷贝区(105 990、109 191 bp)、一个小单拷贝区(2 617、2 606 bp)和一对反向重复区(45 825、47 516 bp)构成,全长分别为200 257、206 829 bp。(2)头花杜鹃和陇蜀杜鹃叶绿体基因组中共鉴定出 263 个SSR位点,大部分 SSR 偏好使用 A/T 碱基,密码子偏好使用 A/U 结尾。(3)杜鹃属植物叶绿体全基因组中普遍存在基因丢失以及基因组重排等结构变异现象。该研究丰富了杜鹃属植物的基因组资源,为头花杜鹃、陇蜀杜鹃的资源开发、遗传进化、育种及系统发育相关研究提供了理论参考。     

Sesqui-Ds , the chromosome-breaking insertion at bz-m1 , links double Ds to the original Ds element

The bz-m1 mutation in maize was one of the first to arise by direct transposition of the chromosome-breaking Ds element from its original or `standard' location in chromosome 9S to a known locus in the same chromosome arm. Thus, elucidation of its structure should shed light on the nature of the original Ds element described by McClintock in 1948. The Ds insertion in bz-m1 has been reported to be only 1.2 kb long – much shorter than other chromosome-breaking Ds elements that have been described. We have characterized here the Ds element in our bz-m1 stocks and have confirmed by genetic and molecular tests that, in the presence of Ac, it acts as a chromosome breaker. The Ds insertion at bz-m1 is 1260 bp long. Besides its normal 5′ and 3′ ends, it contains an internal 3′ end at the same junction as the chromosome-breaking double Ds element that has been found in several sh mutations. Thus, it appears to have arisen from the 4.1-kb double Ds by internal deletion of 2.9 kb. Because the element has lost one internal 5′ end, but retains the chromosome-breaking properties of double Ds, we have named it sesqui-Ds (sDs). The origin, structure and properties of sDs vis-à-vis double Ds support the hypothesis that double Ds corresponds to the chromosome-breaking Ds element at the `standard' location in 9S. Received: 10 March 1997 / Accepted: 2 May 1997     

Secondary metabolite profiling of Alternaria dauci, A. porri, A. solani, and A. tomatophila

Chemotaxonomy (secondary metabolite profiling) has been shown to be of great value in the classification and differentiation in Ascomycota. However, few studies have investigated the use of metabolite production for classification and identification purposes of plant pathogenic Alternaria species. The purpose of the present study was to describe the methodology behind metabolite profiling in chemotaxonomy using A. dauci, A. porri, A. solani, and A. tomatophila strains as examples of the group. The results confirmed that A. dauci, A. solani, and A. tomatophila are three distinct species each with their own specific metabolite profiles, and that A. solani and A. tomatophila both produce altersolanol A, altertoxin I, and macrosporin. By using automated chemical image analysis and other multivariate statistic analyses, three sets of species-specific metabolites could be selected, one each for A. dauci, A. solani, and A. tomatophila.     

Tokaramide A,a new cathepsin B inhibitor from the marine sponge Theonella aff. mirabilis

A new cathepsin B inhibitor, tokaramide A (1) has been isolated from the marine sponge Theonella aff. mirabilis. Its structure was determined by spectroscopic and chemical methods. Tokaramide A inhibits cathepsin B with an IC₅₀ value of 29.0 ng/mL.     

Cumanensic acid, a new chromene isolated from Piper cf. cumanense Kunth. (Piperaceae)

A new chromene, cumanensic acid (1), together with eight known compounds have been isolated from the aerial part of Piper cf. cumanense Kunth (Piperaceae). Chromene structure was identified on the basis of spectroscopic analysis and comparison with literature data. The compound showed antifungal activity against Fusarium oxysporum f. sp. dianthi and Botrytis cinerea.     

Characterization of CaGSP1, the Candida albicans RAN/GSP1 homologue

Gsp1p is a small nuclear-located GTP binding protein from the yeast Saccharomyces cerevisiae. It is highly conserved among eucaryotic cells and is involved in numerous cellular processes, including nucleocytoplasmic trafficking of macromolecules. To learn more about the GSP1 structure/function, we have characterized its Candida albicans homologue. CaGsp1p is 214 amino acids long and displays 91% identity to the ScGsp1p. There is functional complementation in S. cerevisiae, and its mRNA is constitutively expressed in the diploid C. albicans grown under various physiological conditions. Disruption of both alleles was not possible, suggesting that it could be an essential gene, but heterozygous mutants exhibited genomic instability.     

Microstructure and formation of the calcareous operculum in Pyrgopolonctenactis and Spirobranchusgiganteus (Annelida, Serpulidae)

The calcareous operculum of Pyrgopolon ctenactis is composed of spherulitic prismatic structures. The opercular cup consists of regular spherulitic prismatic crystals; the talon has two layers, an inner with an irregular spherulitic prismatic structure (150 μm thick) and an outer with a regular spherulitic prismatic structure (110 μm thick). The outer regular structure has thick (1 μm) organic interprismatic sheets unique in biomineralization of this group, but similar to that of Bivalvia. We infer that control over biomineralization is stronger during the formation of the outer regular layer, with its thick organic interprismatic sheets, than during the formation of the inner irregular spherulitic prismatic structure, without such sheets. In Spirobranchus giganteus, opercular formation differs from that of P. ctenactis. S. giganteus has numerous pores in its opercular plate, and calcification starts with the formation of an outer irregularly oriented prismatic structure followed by an oriented prismatic structure without interprismatic sheets.     

Taxonomy, molecular phylogeny, and ultrastructural morphology of Olpidiopsis porphyrae sp. nov. (Oomycetes, straminipiles), a unicellular obligate endoparasite of Bangia and Porphyra spp. (Bangiales, Rhodophyta)

Olpidiopsis porphyrae sp. nov., a marine oomycete endoparasite that infects the commercially cultivated red alga Porphyra yezoensis, is described and its phylogenetic position based on molecular data and ultrastructural morphology is discussed. O. porphyrae infects the host Porphyra by means of encysted zoospores. Spherical-shaped holocarpic thalli develop within the cytoplasm of its algal host, which produce monoplanetic, subapically biflagellate zoospores. The characteristic features of this isolate are the ellipsoidal, unicellular thallus and simple holocarpic zoosporangial development, which show morphological similarity with the genus Olpidiopsis. Laboratory infection experiments with a wide range of green, brown, and red algae revealed that O. porphyrae infects several stages of the bangialean red algae (the genera Bangia and Porphyra). Molecular phylogenetic analyses inferred from both SSU rRNA and cox2 genes showed O. porphyrae branched before the main saprolegnian and peronosporalean lineages within the monophyletic oomycete clade, indicating its phylogenetic separation from them. A single or double K-body-like organelle, which contains tubular inclusions, is found located to one side of the zoospore nucleus and shows similarities to homologous organelles previously described in O. saprolegniae. The ultrastructural morphology of O. porphyrae with zoospore initials containing K-bodies and tubular mitochondrial cristae is characteristic of oomycetes. Group I intron-like multiple insertions were found in the SSU rRNA gene of O. porphyrae. This is the first report of SSU group I introns in the class Oomycetes.     

红花檵木LcFLS1基因的克隆及其表达与转化研究

该研究以红花檵木(Loropetalum chinense var.rubrum)为材料,根据转录组测序结果和PCR方法克隆到1个黄酮醇合成酶(FLS)同源基因,命名为LcFLS1。生物信息学分析显示,LcFLS1的开放阅读框为996bp,编码331个氨基酸。氨基酸序列分析显示,LcFLS1具有典型的2-酮戊二酸和铁依赖性双加氧酶结构域;蛋白结构预测表明,球形蛋白结构的核心区域存在10个与2-酮戊二酸配体互作的位点。进化树分析结果表明,LcFLS1与茶树(Camellia sinensis)等木本植物的亲缘关系较近,而与拟南芥(Arabidopsis thaliana)等草本植物的亲缘关系较远。荧光定量PCR检测显示,LcFLS1在红花檵木的花中相对表达量最高,而在茎中最少。成功构建了LcFLS1基因的过表达载体pLcFLS1-SUPER1300,经农杆菌侵染花序法将pLcFLS1-SUPER1300质粒转入拟南芥中获得转基因植株,PCR鉴定表明获得了转LcFLS1基因拟南芥阳性植株。该研究结果为红花檵木黄酮醇的生物合成机制研究,以及药用价值的开发利用奠定了基础。     

杜鹃属植物与杜鹃灌丛群落的研究进展

对杜鹃属(Rhododendron L.)植物起源、中国分布、适应性、灌丛群落结构特征和演替特征等问题进行了综述,并对杜鹃属植物的深入研究和合理利用进行展望。中国西南地区以及喜马拉雅至缅甸北部地区为杜鹃属植物的起源中心,贵州百里杜鹃林是全球最大野生杜鹃资源库。杜鹃属植物的适应性与所在区系的同质性、海拔相似度、进化程度、关键功能性状等密切相关,基于进化-形态功能特征的比较为选育适应性优良的杜鹃品种提供了参考。杜鹃灌丛群落具有特殊性,表现出复杂的多层次垂直结构、镶嵌式水平结构和明显的年龄结构特征。依据群落具备优势种生态位宽度大且种群间的生态位相似性比例较小来判定杜鹃灌丛群落已演替至顶级的观点仍有待考证。     

Revision of the genus Absidia (Mucorales, Zygomycetes) based on physiological, phylogenetic, and morphological characters; thermotolerant Absidia spp. form a coherent group, Mycocladiaceae fam. nov.

The genus Absidia comprises ubiquitously distributed soil fungi inhabiting different growth temperature optima ranging from 20–42 °C. Some of the mesophilic species are important biotechnologically in the biotransformation of steroids or as producers of rennin-like components, whereas species with higher growth temperature optima are of clinical relevance as opportunistic human pathogens. The aim of this study was to investigate the phylogenetic relationships between these species and to establish a revision of their systematics. For this purpose single and combined genealogies based on distance, MP, ML, and Bayesian analyses of aligned nucleotide sequences of the nuclear-encoded genes for actin (act) and for the 5.8S ribosomal RNA flanked by the ITS regions 1 and 2 (comprising 807 and 828 characters, respectively) of 16 Absidia species were reconstructed. The phylogenetic reconstructions suggest a trichotomy of the Absidia genus consisting of a mesophilic, a fast-growing thermotolerant, and a slowly-growing mycoparasitic Absidia group. The trichotomous phylogenetic grouping is concordant with the morphology of the zygospores, which are zygotes resulting from sexual conjugation between two compatible mating partners. Whereas the mesophilic group comprises the majority of absidiaceaeous species forming sterile hair-like, mycelial appendages on the suspensors of their zygospores, the thermotolerant group is characterised by the formation of smooth-walled zygospores, and the mycoparasitic group, namely Absidia parricida and A. zychae, by Mucor-like rough-walled zygospores. Based on the phylogenetic coherence of mesophilic and thermotolerant Absidia species, we propose that the two groups are separated into two distinct genera, Absidia for the mesophilic Absidia species resembling the Absidiaceae and Mycocladus for the thermotolerant species A. corymbifera, A. blakesleeana and A. hyalospora. Because Mycocladus is physiologically, phylogenetically, and morphologically distinct from the Absidiaceae s. str. we suggest that they are classified as a separate family, Mycocladiaceae fam. nov., which comprises the three species M. corymbifer, M. blakesleeanus and M. hyalospora.     

Genome constitutions of Pseudoroegneriageniculata, P. geniculata ssp. scythica and P. geniculata ssp. pruinifera (Poaceae: Triticeae) revealed by genomic in situ hybridization

Genomic constitutions of three taxa of Pseudoroegneria á. L?ve, P. geniculata, P. geniculata ssp. scythica, and P. geniculata ssp. pruinifera, were characterized using genomic in situ hybridization (GISH). The results indicated that ploidy level and genomic constitution in the three Pseudoroegneria taxa studied were as follows: P. geniculata (2n = 4x = 28; genomic formula StSt ^g ), P. geniculata ssp. scythica (2n = 4x = 28; genomic formula ESt), and P. geniculata ssp. pruinifera (2n = 6x = 42; genomic formula EESt). P. geniculata ssp. scythica and P. geniculata ssp. pruinifera should be transferred to Trichopyrum á. L?ve following L?ve’s principles and treated as T. scythicum and T. pruiniferum, respectively.     

茎瘤芥根际一株产紫色杆菌素杜擀氏菌的分离鉴定及其基因组分析

【目的】对茎瘤芥根际微生物进行分离鉴定,分析微生物菌群构成,选择具有优良特性的菌株,评估其次级代谢产物合成能力,为茎瘤芥根际微生物多样性和菌种资源的挖掘利用奠定基础。【方法】采集重庆市涪陵区二渡村和邓家村的茎瘤芥根,分离培养根际微生物菌株,通过菌株形态观察和看家基因的序列分析,对菌株进行初步鉴定、归类和保存。选择具有优良性状的菌株,利用Pacbio RS II和Illumina HiSeq平台完成全基因组测序,通过antiSMASH分析评估其次级代谢产物合成潜力,克隆目的基因簇并进行异源表达和产物鉴定。【结果】分离得到256株微生物,初步鉴定120株;从中鉴定了一株产紫色杆菌素的杜擀氏菌BjR8,完成了基因组测序及分析,发现该菌基因组为一条环状染色体,全长7 205 593 bp,GC含量为64.67%,含有6 241个编码基因。生物信息学分析发现基因组含有9个次级代谢产物生物合成基因簇,其中7个基因簇与已知化合物编码基因簇同源性较低,说明该菌具有产生多种新型次级代谢产物的潜力;克隆得到紫色杆菌素生物合成基因簇,并在变铅青链霉菌TK23中完成了异源表达。【结论】从茎瘤芥根际分离得到25...     

The phylogenetic placement of the Leucogastrales, including Mycolevis siccigleba (Cribbeaceae), in the Albatrellaceae using morphological and molecular data

The morphology of many hypogeous fungi converges on a homogeneous reduced form, suggesting that disparate lineages are subject to a uniform selection pressure. The primary goal of this study was to evaluate the morphology and infer the phylogeny of the Leucogastrales with Mycolevis siccigleba using a Bayesian methodology. A comprehensive morphological assessment was used for an a priori phylogenetic inference to guide the sequencing effort. All structures except spore ornamentation pointed to the Albatrellaceae as the most likely sister taxon. Polyporoletus sublividus, a close relative of Albatrellus, produces ornamented basidiospores with a similar structure to M. siccigleba basidiospores. The ITS from 30 taxa was used for the molecular phylogenetic analysis. P. sublividus was found sister to Mycolevis. Leucophleps spinispora and L. magnata formed a group sister to the Polyporoletus/Mycolevis group, whereas Leucogaster was polyphyletic with respect to the core of the Leucogastrales and sister to A. caeruleoporus. This relationship was expected as previously undescribed chlamydospores produced by members of Albatrellus had a similar morphology to the basidiospores of L. rubescens.     

药用植物华重楼(黑药花科)叶绿体全基因组研究

为探究华重楼(Paris polyphylla var. chinensis)的叶绿体基因组特征,利用叶绿体系统发育基因组学方法,对华重楼与其它百合目植物的叶绿体全基因组进行了比较。结果表明,华重楼的叶绿体全基因组长158307 bp,由4个区组成,包括2个反向重复区(IRA和IRB,27473 bp)、1个小单拷贝区(SSC,18175 bp)和1个大单拷贝区(LSC,85187 bp)。其叶绿体基因组有115个基因,包括81个编码蛋白质基因、30个转运RNA基因和4 个核糖体RNA基因。11种百合目植物的叶绿体全基因组的基因组成和基因顺序相似。华重楼的cemA基因是假基因,其起始密码子后有多聚核苷酸poly(A)及CA双核苷酸重复序列,编码序列中出现多个终止密码子, 且与北重楼(Paris verticillata)的cemA编码序列中的终止密码子位置不同。因此,华重楼叶绿体基因组比较保守;cemA结构及假基因化现象可能具有重要的进化与系统发育信息,其编码序列中的终止密码子可以区分华重楼和北重楼。     

马尾松R2R3-MYB基因特征及进化和表达分析

MYB类转录因子在植物生长发育、代谢、应答生物胁迫和非生物胁迫的响应等生物过程发挥重要作用。为探究马尾松R2R3-MYB基因结构及功能,该研究以转录组数据为研究区域,从中筛选获得了17个马尾松R2R3-MYB基因,利用生物信息学对基因进行理化性质、系统进化树等分析,同时利用荧光定量PCR技术分析基因的组织特异性以及在花发育时期和非生物胁迫下的表达模式。结果表明：(1)17个PmMYBs亚细胞定位于细胞核,均无跨膜结构,且均含有Motif1、Motif2保守基序。系统发育进化树将马尾松PmMYBs划分为9个亚家族,且与火炬松、白云杉等裸子针叶植物关系较近。(2)17个基因均属于组成型表达,但在不同组织的表达量不同;所有基因均参与了花发育和非生物胁迫,不同基因在花发育不同时期的表达存在差异,有7个基因可能参与了雌雄性状转变;大部分基因响应非生物胁迫上调表达,但响应胁迫的时间存在差异;少数基因在胁迫中下调表达,尤其是PmMYB11基因在所有胁迫中均明显下调表达。该研究较系统地分析了马尾松R2R3-MYB基因的结构特征、系统进化及其在花发育时期和非生物胁迫下的表达模式,为深入探究马尾松R2R3...     

Reducing the allelopathic effect of Partheniumhysterophorus L. on wheat (Triticumaestivum L.) by Pseudomonasputida

The present study evaluates the role of Pseudomonas putida NBRIC19 in alleviating biotic stress of Parthenium hysterophorus (Parthenium) in Triticum aestivum. Due to presence of Parthenium there was 43.76, 53.08 and 78.65% inhibition in root length, shoot length and dry weight of wheat respectively. This inhibition was recovered when P. putida NBRIC19 treatment resulted in 52.29, 28.73 and 76.31% increase in root length, shoot length and dry weight respectively as compared to control. P. putida NBRIC19 was able to form more biofilm under toxic environment of allelochemicals and enhanced expression of stress responsive genes in wheat. Inoculated wheat plants showed lower activity of catalase and ascorbate peroxidase under biotic stress of Parthenium indicating that inoculated plants felt less stress as compared to uninoculated plants. Microbial community structure in bacterized and nonbacterized wheat rhizosphere in presence and absence of Parthenium, was investigated using Biolog. There was significant increase in microbial diversity in P. putida NBRIC19 bacterized wheat rhizosphere. Functional microbial diversity revealed that P. putida NBRIC19 had shifted the microflora in such a manner that utilization of phytotoxic allelochemicals increased to lessen its toxic effect and finally it resulted in better growth of wheat in presence of Parthenium. Principal component analysis showed that microbial community function in nonbacterized wheat rhizosphere in presence (WPC) and absence (WC) of Parthenium is totally different from each other but due to P. putida NBRIC19 treatment there was close clustering of WPT and WT indicating a total shift in microbial community structure.     

Taxonomic differences among closely related pines Pinus sylvestris, P. mugo, P. uncinata, P. rotundata and P. uliginosa as revealed in needle sclerenchyma cells

The purpose of the present study was to test the taxonomic value of sclerenchyma in distinguishing Pinus sylvestris and P. mugo, P. uncinata, P. rotundata and P. uliginosa, all representing the subsection Sylvestres within the genus Pinus. Thirty-six samples were gathered in natural populations. Every sample was represented with 30 individuals, every individual with 10 brachyblasts. Three types of sclerenchymatic cells surrounding the resin canals and four between vascular bundles were distinguished. Relations among samples and taxa were verified using discriminant analysis and clustering based on Euclidean distances. The types of sclerenchymatic cells surrounding the resin canals and located between the vascular bundles differentiate the compared taxa when used as average frequencies but are extremely variable and do not allow the classification of every individual. The study demonstrated that the type of sclerenchymatic cells surrounding the resin canals and between the vascular bundles in needles could have an important taxonomic value in distinguishing the taxa of two-needle pines of the subsection Sylvestres in Europe at the population level. The distinguishing of individuals was difficult because of very high variation of sclerenchyma characters.     

Molecular cytogenetic study of three common Mediterranean limpets, Patella caerulea, P. rustica and P. ulyssiponensis (Archaeogastropoda, Mollusca)

The present paper shows the results of chromosome banding and rDNA-FISH study performed on several specimens of different populations of Patella caerulea, Patella rustica and Patella ulyssiponensis. The taxonomic attribution of specimens was ascertained by the molecular phylogenetic analysis of the mitochondrial 16S rRNA gene. P. caerulea and P. rustica had 2n = 18 chromosomes with first seven of biarmed pairs and the remaining two uniarmed pairs. P. ulyssiponensis had 2n = 16 with all biarmed chromosomes. Ag-NOR loci were on the short arms of the first metacentric pair in the three studied limpets, whereas they showed a different pattern of heterochromatin distribution and composition. A chromosome mosaicism was observed in several P. caerulea specimens, which exhibited an unpaired metacentric element and loss of a telocentric pair. The obtained results suggest that in the genus Patella specific diversification was accompanied by variations in heterochromatin distribution and composition and reduction of chromosome number by Robertsonian centric fusion.