球壳孢目真菌DNA GC含量及其分类学意义

利用热变性温度法测得球壳孢目5属14种19个菌株DNA G+C mol％的变化范围为48．08～53．7,平均值为51．12,与文献报道的丝孢茵类的平均值接近,也与子囊菌的平均值相差不大,提示该类群的种类及其与大多数丝孢菌间在系统演化上似具一定的同源性,与形态分类对半知菌的处理相吻合,也为其有性阶段大多属子囊菌这一事实提供了佐证;各属、种Gc值接近,且相互间有交叉,种内菌株间差异小于2％,方差分析显示属间差异不显著,故认为GC含量分析不宜用于球壳孢目属、种级分类单位的划分,但可作为排除性指标辅助某些种类的否定性判定。     

球壳孢目真菌DNA GC含量及其分类学意义

利用热变性温度法测得球壳孢目５属１４种１９个菌株ＤＮＡＧ＋Ｃｍｏｌ％的变化范围为４８．０８～５３．７平均值为５１．１２,与文献报道的丝孢菌类的平均值接近,也与子囊菌的平均值相差不大,提示该类群的种类及其与大多数丝孢菌间在系统演化上似具有一定的同源性,与形态分类对半知菌的处理相吻合,也为其有性阶段大多属子囊菌这一事实提供了佐证;各属,种ＧＣ值接近,且相互璋有交叉,种内菌株间差异小于２％,方差分析显示     

新疆的刺球座属、穴壳属及普氏腔孢属

本文报道了新疆腔菌纲座囊菌目刺球座属（Ｌａｓｉｏｂｏｔｒｙｓ）、穴壳属（Ｄｏｔｈｉｏｒａ）和普氏腔孢属（Ｐｌｏｗｒｉｇｈｔｉａ）的六种子囊菌,即：忍冬刺球座菌（Ｌ．ｌｏｎｉｃｅｒａｅ）、花揪穴壳菌（Ｄ．ｓｏｒｂｉ）及其无性阶段花揪疡壳孢（Ｄｏｔｈｉｃｈｉｚａ ｓｏｒｂｉ）、茶Ｂｉａｏ子普氏腔孢菌（Ｐ．ｒｉｂｅｓｉａ）、小檗普氏腔孢菌（Ｐ．ｂｅｒｂｅｒｉｄｉｓ）、沙棘普氏腔孢菌（Ｐ．ｈｉｐｐｏｐｈａ     

新疆的刺球座属、穴壳属及普氏腔孢属

本文报道了新疆腔菌纲座囊菌目刺球座属(Lasiobotrys)、穴壳属(Dothiora)和普氏腔孢属(Plowrightia)的六种子囊菌,即:忍冬刺球座菌(L.loniccrae)、花楸穴壳菌 (D.sorbi)及其无性阶段花楸疡壳孢(Dothichiza sorbi)、茶蔗子普氏腔孢菌(P.ribesia)、小檗普氏腔孢菌(P.berberidiJ)、沙棘普氏腔孢菌(P.hippophaeos)及雕刻普氏腔孢菌(P.insculpta)。这三个属的真菌在我国均未报道过,为我国新纪录属(种)。标本均采于新疆,保存于新疆八一农学院植保系真菌标本室(HMAAC)。     

西花蓟马高毒力虫生真菌筛选及其生防应用潜力的研究进展

西花蓟马是一种外来入侵的世界性害虫,对农林业危害巨大。查阅国内外相关文献,综述了当前防治西花蓟马的虫生真菌的种类、高毒力菌株的筛选及防治现状。现已知西花蓟马的寄生病原真菌有5种,包括蜡蚧轮枝菌(半知菌:丝孢目)、球孢白僵菌(半知菌:丝孢目)、金龟子绿僵菌(半知菌:丝孢目)、玫烟色棒束孢(半知菌:束梗孢目)和小孢新接霉。其中,球孢白僵菌、金龟子绿僵菌在西花蓟马的生物防治中应用最广,具有良好的开发应用潜力,部分防效好的虫生真菌已申请专利及实现工厂化生产。     

贵州赤水桫椤自然保护区桫椤内生真菌多样性研究

桫椤Alsophila spinulosa是白垩纪时期遗留的古老孑遗蕨类植物,具有较高的药用价值和观赏价值。本研究采用形态特征和ITS序列分析方法,从250个组织块中共分离获得84个菌株,隶属于2门3纲10目18科25属。子囊菌门Ascomycota为优势菌门,其相对丰度高达92.86%,而担子菌门Basidiomycota仅为2.38%;粪壳菌纲Sordariomycetes和座囊菌纲Dothideomycetes为优势纲,其相对丰度分别为78.57%和13.10%;小丛壳目Glomerellales和炭角菌目Xylariales为优势目,其相对丰度分别为33.33%和25.00%;小丛壳科Glomerellaceae和炭角菌科Xylariaceae为优势科,其相对丰度分别为32.14%和19.05%;刺盘孢属 Colletotrichum和炭角菌属Xylaria为优势属,其相对丰度分别为32.14%和14.29%。这些菌株存在一定的组织差异,属水平上,叶轴中共获得15属,特有属9属;羽状复叶中共获得16属,特有属10属,两组织间共有属为6属,其中刺盘孢属Colletotrichum和炭角菌属Xylaria均为两组织的优势属,但其相对丰度存在一定差异。从不同组织多样性来看,桫椤叶轴的Shannon、Simpson多样性指数和Pielou均匀度均高于桫椤叶。     

中国种子植物内生真菌资源及菌植协同进化

综述了中国种子植物内生真菌资源研究概况,比较了裸子植物和被子植物内生真菌种类,它们都具有肉座菌目(Hypocreales),粪壳菌目(Sordariales),散囊菌目(Eurotiales),毛霉目(Mucorales)及不产孢类(Myceliasterilia)内生真菌。裸子植物内生真菌涉及52个属,既包括高等的子囊菌和担子菌,也包括低等的卵菌(Oomycetes)和接合菌(Zygomycetes)类。被子植物涉及60个属,主要为高等的子囊菌(Ascomycetes)和担子菌(Basidiomycetes),低等的卵菌和接合菌报道很少。双子叶植物涉及40个属,单子叶植物内生真菌涉及30个属,两类被子植物所报道的内生真菌只有11个属相同。裸子植物与双子叶植物内生真菌相似程度较高,都具有炭角菌目(Xylariales)、格孢腔菌目(Pleosporales)、柔膜菌目(Helotiales)和白粉菌目(Erysiphales),刺盘孢菌属(Colletotrichum)、拟茎点霉属(Phomopsis)、枝孢霉属(Cladosporium)、地霉属(Geotrichum)等内真菌,共20个属相同。各类种子植物具有自己独特的一些内生真菌。还对植物与其内生真菌的协同进化关系进行了分析。     

球毛壳菌次级代谢产物及其生物活性研究进展

球毛壳菌(Chaetomium globosum)为属子囊菌纲、毛壳目、毛壳科丝状真菌,其在空气、土壤、植物和动物体中均有分布。已有研究表明,球毛壳菌的次生代谢产物种类多样、结构新颖,主要蕴含生物碱类、黄酮类、萜类、酯类等化合物,且多具抗肿瘤、抑菌、抗病毒等生物活性。本文综述了2015年以来所报道的球毛壳菌天然产物及其生物活性,为球毛壳菌真菌天然产物的研究奠定基础。     

山东省蔬菜保护地土壤真菌区系研究 Ⅰ.子囊菌

对我国重要保护地蔬菜生产基地的山东省 9个城市的 17个地区的蔬菜保护地进行了调查采样 ,采集土壤样品 87份。通过稀释平板法和采用孟加拉红培养基分离获得 5属 9种子囊菌 ,其中瓶束霉属 (Ascodes mis)为国内新记录属 ,球孢瓶束霉 (AscodesmissphaerosporaObrist.)为国内首次报道 ,瘤孢棒囊孢壳 [Corynascussepedonium (Emmons)V .Arx .]为国内已记录但未正式发表的种。本文对这两种子囊菌进行了描述 ,并附有照片和绘图 ,其余子囊菌以名录形式列出。     

被子植物生散斑壳属若干种内和种间亲缘关系RAPD分析

采用9个重复性好的随机引物对被子植物上的28个散斑壳属(Lophoderm iumChevall.)菌株进行RAPD-PCR扩增,通过RAPD分析结果结合表型性状的比较和分析,确定了子囊果埋生位置,子座、子囊、子囊孢子、侧丝等形态学特征以及寄主种类差异在该类菌物种水平分类上的重要性,另外产地不同等对种内遗传多样性产生一定影响。进一步明确了被子植物生散斑壳属一些种内和种间的亲缘关系。     

核酸碱基组分与毛霉目的分类

本文对毛霉目中6科16属40个种共60株真菌DNA的G+C含量与分布作了系统的研究。在提取DNA时选用了Storck等人在Marmur提取细菌DNA方法基础上发展起来的真菌DNA提取法,经过一些修改后成功地提取了毛霉目真菌的DNA。经该法提取的DNA片段长、纯度高,在热变性时DNA的增色效应一般都大于35%。各个种的GC含量大致有一固定值。根据所测毛霉目16属各属真菌的平均GC含量,可将它们分为明显的三组:Gongronella, Haplosporangium, Mortierella及Syncephalastrum为一组,GC含量最高为46.0-49.8%; Cunninghamella单独成一组,GC含量最低只有28.8%;其他各属包括Absidia, Mucor, Rhizopus等GC含量介乎这两组之间,分布于34.9-41.9%。这一次序除Helicostylum与Circinella的数值低于他人的报道外,其余和文献报道值一致。一般属内GC含量变化小于10%,种内变化小于2%。所测得的G+C mol%对分Syncephalastrum monosporum Zheng et al.和Mortierella ramanniana (Moeller) Linneman的合理归属提供了佐证。对某些所测结果与文献报道值有出入的原因作了讨论和分析。对采用Mandel等1970年建议的公式GC=(Tm 0.1×SSC/50.2)-0.990来计算GC含量的依据也作了讨论。     

DNA barcoding Australia's fish species

Two hundred and seven species of fish, mostly Australian marine fish, were sequenced (barcoded) for a 655 bp region of the mitochondrial cytochrome oxidase subunit I gene (cox1). Most species were represented by multiple specimens, and 754 sequences were generated. The GC content of the 143 species of teleosts was higher than the 61 species of sharks and rays (47.1% versus 42.2%), largely due to a higher GC content of codon position 3 in the former (41.1% versus 29.9%). Rays had higher GC than sharks (44.7% versus 41.0%), again largely due to higher GC in the 3rd codon position in the former (36.3% versus 26.8%). Average within-species, genus, family, order and class Kimura two parameter (K2P) distances were 0.39%, 9.93%, 15.46%, 22.18% and 23.27%, respectively. All species could be differentiated by their cox1 sequence, although single individuals of each of two species had haplotypes characteristic of a congener. Although DNA barcoding aims to develop species identification systems, some phylogenetic signal was apparent in the data. In the neighbour-joining tree for all 754 sequences, four major clusters were apparent: chimaerids, rays, sharks and teleosts. Species within genera invariably clustered, and generally so did genera within families. Three taxonomic groups-dogfishes of the genus Squalus, flatheads of the family Platycephalidae, and tunas of the genus Thunnus-were examined more closely. The clades revealed after bootstrapping generally corresponded well with expectations. Individuals from operational taxonomic units designated as Squalus species B through F formed individual clades, supporting morphological evidence for each of these being separate species. We conclude that cox1 sequencing, or 'barcoding', can be used to identify fish species.     

Nucleotide Composition of Deoxyribonucleic Acid of Some Species of Cryptococcus, Rhodotorula, and Sporobolomyces

The buoyant density of deoxyribonucleic acid (DNA) from nine species and two varieties of Cryptococcus, three species and two varieties of Rhodotorula, and six species of Sporobolomyces was determined by CsCl density gradient equilibrium centrifugation. Several species were represented by two to four different strains. Expressed in moles per cent of guanine plus cytosine (GC content) the ranges were 49 to 65%, 52 to 70%, and 51 to 65% for Cryptococcus, Rhodotorula, and Sporobolomyces, respectively. For each genus, the GC content was distributed into two discrete groups with averages ranging from 52 to 54 and 60 to 66, respectively. An analysis of these results suggested that the determination of GC content of DNA had a taxonomic value for these yeast genera.     

球壳孢目真菌个体发育研究Ⅰ:壳二胞等四属

人工培养条件下,用光学显微镜和透射电子显微镜对球壳孢目（Sphaerosidales）的Ascochyta,Phyllosticta,Phomopsis,Septoria四属进行个体发育研究,明确了其产孢方式：Ascochyta和Phyllosticta为内壁芽生瓶梗式;Phomopsis为全壁芽生瓶梗式;Septoria为全壁芽生合轴式,这一结果为属级分类提供了可靠的依据。产孢方式是属内共同具有的稳定特征,分生孢子的形成方式类型、产孢细胞及分生孢子的形态是划分属的首要标准。以寄主植物属为基础确定的同属大多数种在个体发育上无明显差别,分生孢子的形态及大小是分种的一个重要依据。     

ITS1: a DNA barcode better than ITS2 in eukaryotes?

A DNA barcode is a short piece of DNA sequence used for species determination and discovery. The internal transcribed spacer (ITS/ITS2) region has been proposed as the standard DNA barcode for fungi and seed plants and has been widely used in DNA barcoding analyses for other biological groups, for example algae, protists and animals. The ITS region consists of both ITS1 and ITS2 regions. Here, a large‐scale meta‐analysis was carried out to compare ITS1 and ITS2 from three aspects: PCR amplification, DNA sequencing and species discrimination, in terms of the presence of DNA barcoding gaps, species discrimination efficiency, sequence length distribution, GC content distribution and primer universality. In total, 85 345 sequence pairs in 10 major groups of eukaryotes, including ascomycetes, basidiomycetes, liverworts, mosses, ferns, gymnosperms, monocotyledons, eudicotyledons, insects and fishes, covering 611 families, 3694 genera, and 19 060 species, were analysed. Using similarity‐based methods, we calculated species discrimination efficiencies for ITS1 and ITS2 in all major groups, families and genera. Using Fisher's exact test, we found that ITS1 has significantly higher efficiencies than ITS2 in 17 of the 47 families and 20 of the 49 genera, which are sample‐rich. By in silico PCR amplification evaluation, primer universality of the extensively applied ITS1 primers was found superior to that of ITS2 primers. Additionally, shorter length of amplification product and lower GC content was discovered to be two other advantages of ITS1 for sequencing. In summary, ITS1 represents a better DNA barcode than ITS2 for eukaryotic species.     

Effect of the GC content of DNA on the distribution of UVB-induced bipyrimidine photoproducts.

Solar UV radiation is a major mutagen that damages DNA through the formation of dimeric photoproducts between adjacent thymine and cytosine bases. A major effect of the GC content of the genome is thus anticipated, in particular in prokaryotes where this parameter significantly varies among species. We quantified the formation of UV-induced photolesions within both isolated and cellular DNA of bacteria of different GC content. First, we could unambiguously show the favored formation of cytosine-containing photoproducts with increasing GC content (from 28 to 72%) in isolated DNA. Thymine-thymine cyclobutane dimer was a minor lesion at high GC content. This trend was confirmed by an accurate and quantitative analysis of the photochemical data based on the exact dinucleotide frequencies of the studied genomes. The observation of the effect of the genome composition on the distribution of photoproducts was then confirmed in living cells, using two marine bacteria exhibiting different GC content. Because cytosine-containing photoproducts are highly mutagenic, it may be predicted that species with genomes exhibiting a high GC content are more susceptible to UV-induced mutagenesis.     

Deoxyribonucleic Acid Base Composition in Yeasts

The deoxyribonucleic acid base composition of 15 species of yeasts was determined to obtain further clues to or supporting evidence for their taxonomic position. Species examined belonged to the genera Saccharomyces, Debaryomyces, Lodderomyces, Metschnikowia, and Candida. The range of moles per cent guanine plus cytosine (GC content) for all yeasts examined extended from 34.9 to 48.3%. The sporogenous species and the asporogenous yeasts spanned the range with 36.6 to 48.3% GC and 34.9 to 48% GC, respectively. Three Saccharomyces species (S. rosei and related species) exhibited significantly higher GC contents than S. cerevisiae, whereas the fermentative species D. globosus revealed a%GC more aligned to the S. rosei group than to the nonfermentative D. hansenii. Similar GC contents were demonstrated by L. elongasporus and its proposed imperfect form C. parapsilosis. The range of GC contents of various strains of three Metschnikowia species studied was 6.1%, with the type strain of M. pulcherrima having the highest GC content (48.3%) of all of the yeasts examined.     

基于28S rDNA D2基因片段与形态特征的矛茧蜂亚科系统发育研究（膜翅目：茧蜂科）

本研究选取矛茧蜂亚科Doryctinae（昆虫纲Insecta：膜翅目Hymenoptera：茧蜂科Braconidae）的6族15属18种做内群,茧蜂科其它7亚科11属11种做外群,首次结合同源核糖体28S rDNA D2基因序列片段和100个形态学和解剖学特征对该亚科进行了系统发育学研究。利用“非圆口类"的小腹茧蜂亚科Microgastrinae为根,以PAUP*4.0和MrBayes 3.0B4软件分别应用最大简约法（MP）和贝叶斯法对矛茧蜂亚科的分子数据和分子数据与非分子数据的结合体进行了运算分析;并以PAUP*4.0对矛茧蜂亚科的28S rDNA D2基因序列片段的碱基组成与碱基替代情况进行了分析。结果表明：矛茧蜂亚科的28S rDNA D2基因序列片段的GC含量在39.33%～48.28%之间变动,而对于碱基替代情况来讲,矛茧蜂亚科各成员间序列变异位点上颠换（transversion）大于转换（transition）。不同的分析算法所产生的系统发育树都表明矛茧蜂亚科是一个界限分明的单系群;在矛茧蜂亚科内,除了吉丁茧蜂族Siragrini为单系群外,其他族（矛茧蜂族Doryctini和方头茧蜂族Hecabolini）都是并系群。对于矛茧蜂亚科内各属之间的相互亲缘关系,不同算法所得的系统发育树的拓扑结构不完全一致,表明矛茧蜂亚科内（属及族）的系统发育关系还有待于进一步研究。     

Mechanisms of homology-facilitated illegitimate recombination for foreign DNA acquisition in transformable Pseudomonas stutzeri

Intra- and interspecific natural transformation has been observed in many prokaryotic species and is considered a fundamental mechanism for the generation of genetic variation. Recently, it has been described in detail how, in transformable Acinetobacter BD413 and Streptococcus pneumoniae, long stretches of nucleotides lacking homology were integrated into recipient genomes when they were linked on one side to a small piece of DNA with homology to resident DNA serving as a recA-dependent recombination anchor. Now, such homology-facilitated illegitimate recombination (HFIR) has also been detected in transformable Pseudomonas stutzeri. However, analysis of the recombinants revealed qualitative and quantitative differences in their generation compared with that in Acinetobacter BD413. In P. stutzeri, foreign DNA with an anchor sequence was integrated 105- to 106-fold less frequently than fully homologous DNA, but still at least 200-fold more frequently than without the anchor. The anchor sequence could be as small as 311 bp. Remarkably, in 98% of the events, the 3' end was integrated within the homologous anchor, whereas the 5' end underwent illegitimate fusion. Moreover, about one-third of the illegitimate fusion sites shared no or only a single identical basepair in foreign and resident DNA. The other fusions occurred within microhomologies of up to 6 bp with a higher GC content on average than the interacting nucleotide sequences. Foreign DNA of 69-1903 bp was integrated, and resident DNA of 22-2345 bp was lost. In a recA mutant, HFIR was not detectable. The findings suggest that genomic acquisition of foreign DNA by HFIR during transformation occurs widely in prokaryotes, but that details of the required recombination and strand fusion mechanisms may differ between organisms from different genera.     

Oxygen and Guanine–Cytosine Profiles in Marine Environments

One of the historic debates in molecular evolution concerns the strong variation in the genomic guanine–cytosine (GC) content of prokaryotes, which ranges from approximately 20–75%: Is this factor selectively neutral, or is it the result of natural selection? In a previous article published by our group, we showed that inside well-defined taxonomic groups of prokaryotes, strictly aerobic organisms tend to display higher genomic GC levels than strictly anaerobic species. In the present study, we examined the GC content of fragments of DNA obtained from microbial communities along a well-defined environmental gradient: a 4,000-m vertical profile in the North Pacific subtropical gyre. The patterns of GC distribution might be associated with oxygen concentrations in the seawater column. These results give further support to the link between a physiologic trait (aerobic respiration) and genomic GC content.