ITS序列在酵母批量分子鉴定中的适用性

内部转录间隔区(internal transcribed spacer,ITS)序列是目前最常用的酵母分子鉴定标识之一。该文利用ITS序列同源性分析法对保藏于中国高校工业微生物资源与信息中心的623株酵母分离物进行了鉴定。实验结果显示:581株酵母分离物(93.3%)可通过ITS序列直接鉴定到种一级,40株分离物(6.4%)可鉴定至属一级,仅有2株酵母分离物无法通过ITS序列获得有效鉴定。上述结果表明,ITS序列在大多数酵母种属鉴定中具有很高的敏感性和特异性,可以作为第一分子标识用于大批量酵母分离物的分子鉴定。     

DNA条形码基因ITS和LSU在红曲菌分类鉴定中的比较分析

为评估DNA条形码基因核糖体内转录间隔区（ITS）和核糖体大亚基（LSU）在红曲菌分类鉴定中的有效性,从NCBI的GenBank数据库中下载现阶段红曲菌属所有物种的ITS和LSU基因序列,采用系统发育和遗传距离的方法对其进行分析,并用该研究所保存的部分红曲菌株的DNA序列进行验证。结果表明,同种红曲菌的不同菌株在基于ITS序列的邻接树中分别聚为单系;紫色红曲菌（Monascus purpureus）、佛罗里达红曲菌（Monascus floridanus）和蜂蜜红曲菌（Monascus mellicola）的同种不同菌株在基于LSU序列的邻接树中分别聚为单系。新月红曲菌（Monascus lunisporas）的ITS和LSU序列以及红色红曲菌（Monascus ruber）和累西腓红曲菌（Monascus recifensis）的LSU序列的条形码间隙不明显,其他红曲菌的ITS和LSU序列条形码间隙明显。同种红曲菌ITS序列的最小及最大种间遗传距离均高于LSU序列。研究表明ITS基因在红曲菌的分类鉴定中具有高效性,LSU基因在红曲菌分类鉴定中的分辨力有限。     

四川凉山地区烟草黑胫病菌的ITS序列分析

本研究利用真菌核糖体基因转录间隔区(ITS)通用引物,PCR扩增四川省凉山州不同地区的20株烟草黑胫病菌的ITS序列,并对PCR产物进行了克隆测序。结果表明,20个供试菌株的ITS1-5.8S-ITS2总长均为803 bp;各菌株之间的ITS序列同源性达到99.3%以上;与GenBank报道的寄生疫霉台湾烟草分离株Phytophthora parasitica(GU111675.1)的同源性在99.6%~100%之间;但各菌株ITS序列的个别位点存在突变,这些突变主要集中在ITS2区上,其中第468处的突变具有一定地域性,主要为德昌和西昌的菌株。利用MEGA6软件对20个供试菌株及GenBank中登陆的15个疫霉属菌株序列进行聚类分析,供试菌株与GenBank上登录的GU111675.1、KF010303.1、AJ854295.1、KC768775.1、L41383聚在同一聚类组上,均为Phytophthora parasitica(或Phytophthora nicotianae),其它疫霉种聚在不同的聚类组上,遗传关系较远,这表明来自四川凉山不同地区的20株烟草黑胫病分离菌株均为寄生疫霉(Phytophthora parasitica)。     

柽柳核纤孔菌分子鉴定及基于ITS序列的系统发育分析

在对形态特征进行初步鉴定的基础上,对河南省郑州市分离的柽柳核纤孔菌6-27菌株的rDNA ITS区段进行克隆测序,并对ITS序列进行核酸序列数据库GenBank同源性检索比对.将从GenBank检索获得的22个相关分类元真菌的ITS序列连同柽柳核纤孔菌6-27菌株ITS序列一起用于系统发育分析,结果表明:形态鉴定与ITS序列分析结果一致,测定菌株为柽柳核纤孔菌.供试的23份材料被聚为6个类群,其中7个核纤孔菌属菌株和1个纤孔菌属菌株被聚在类群A;另一个来自南半球阿根廷的Inocutis jamaicensis 4508与来自印度的Fomitiporella caryophylli CBS 448.76被聚类在类群B,与类群A为大姊妹类群,与类群C为小姊妹类群;类群C包括2个Fulvifomes真菌;纤孔菌属,木层孔菌属,Mensularia,Fuscoporia等不同属菌株被聚类在类群D,E和F.相关分类元系统发育分析支持核纤孔菌为独立的属分类单元,Fulvifomes属分类地位比较稳定,纤孔菌属与木层孔菌属真菌具有较大的异质性,其分类地位有待于进一步规范和统一.     

An integrated taxonomic study of Fusarium langsethiae, Fusarium poae and Fusarium sporotrichioides based on the use of composite datasets

An integrated systematic study was carried out to clarify the taxonomical position and relationship of Fusarium langsethiae to other taxa within the Fusarium section Sporotrichiella. Strains of this species were compared with strains of the closely related species Fusarium poae and Fusarium sporotrichioides using a composite dataset. This set consisted of DNA sequences derived from the ribosomal internal transcribed spacer (ITS) regions, partial sequences of the ribosomal intergenic spacer (IGS) region, the beta-tubulin and translation elongation factor-1 alpha (EF-1alpha) genes, AFLP fingerprints, chromatographic data on secondary metabolites and morphological data and growth characteristics. From these combined data, a consensus matrix was calculated by taking the mean of all pairwise distances between single isolates over all separate datasets. The consensus matrix was used as the basis for the construction of a UPGMA dendrogram and a multidimensional scaling, both of which revealed a clear separation of the three taxa. Partial IGS, EF-1alpha and beta-tubulin sequence-as well as chromatography-and AFLP-derived similarities turned out to be comparably consistent, while ITS sequence- and morphology-derived similarity matrices were rather divergent.     

Molecular identification of yeast species associated with 'Hamei'--a traditional starter used for rice wine production in Manipur, India

In Manipur state of North-Eastern India, wine from glutinous rice using traditional solid state starter called 'Hamei' is particularly interesting because of its unique flavour. A total of 163 yeast isolates were obtained from fifty four 'Hamei' samples collected from household rice wine preparations in tribal villages of Manipur. Molecular identification of yeast species was carried out by analysis of the restriction digestion pattern generated from PCR amplified internal transcribed spacer region along with 5.8S rRNA gene (ITS1-5.8S-ITS2). Seventeen different restriction profiles were obtained from the size of PCR products and the restriction analysis with three endonucleases (Hae III, Cfo I and Hinf I). Nine groups were identified as S. cerevisiae, Pichia anomala, Trichosporon sp., Candida tropicalis, Pichia guilliermondi, Candida parapsilosis, Torulaspora delbrueckii, Pichia fabianii and Candida montana by comparing this ITS-RFLP profile with type strains of common wine yeasts, published data and insilico analysis of ITS sequence data available in CBS yeast database. ITS-RFLP profile of eight groups was not matching with available database of 288 common wine yeast species. The most frequent yeast species associated with 'Hamei' were S. cerevisiae (32.5%), P. anomala (41.7%) and Trichosporon sp. (8%). The identity of major groups was confirmed by additional restriction digestion of ITS region with Hind III, EcoRI, Dde I and Msp I. The genetic diversity of industrially important S. cerevisiae group was investigated using Pulsed Field Gel Electrophoresis (PFGE). Although most of the 53 strains of S. cerevisiae examined were exhibited a common species specific pattern, a distinct degree of chromosomal length polymorphism and variable number of chromosomal DNA fragments were observed with in the species. Cluster analysis showed seven major karyotypes (K1-K7) with more than 83% similarity. The karyotype pattern K1 was the most frequent (67.9%) among the strains from different samples. Other karyotypes K2-K7 were very unique with less than 80% similarity. Finally using mitochondrial DNA restriction analysis (mt-DNA RFLP), S. cerevisiae strains belonging to the major karyotype K1 were distinctly differentiated with highly polymorphic bands by Hinf I and Hae III endonucleases.     

Differentiation of Staphylococci from Iberian dry fermented sausages by protein fingerprinting

The Staphylococci populations in different types of Iberian dry fermented sausages from central-west Spain were identified. A simple electrophoretic method of whole-cell proteins and extracellular protein profiling was evaluated for speed of identification. This study was correlated with a 16S rRNA gene sequence analysis and biochemical identification by API Staph. A total of 81 isolates were identified by SDS-PAGE of the whole-cell proteins. These showed stable profiles in the range 99-14kDa that were clearly different for the different species, and were grouped into clusters together with the profiles of the eight reference strains. SDS-PAGE of the extracellular protein extracts provided additional characteristic banding patterns for the characterization of the Staphylococcus species present. The whole-cell SDS-PAGE showed that the predominant species was Staphylococcus saprophyticus (61.7%) followed by Staphylococcus aureus (19.7%). The identifications were confirmed by the 16S rRNA gene sequencing and by a BLAST search of the GenBank database. However, the API Staph biochemical identifications were frequently erroneous at the species level. In sum, SDS-PAGE analysis showed itself to be rapid and accurate in identifying the most commonly encountered Staphylococcus isolates in dry fermented sausages.     

基于DNA条形码技术鉴别有毒鹅膏菌属物种

收集27 个鹅膏菌属物种共38 份样本,提取样品基因组DNA,应用通用引物扩增其内转录间隔区（internal transcribed spacer,ITS）、核糖体大亚基（large ribosomal subunit,LSU）、RNA聚合酶的第二大亚基（the second largest subunit of RNA polymerase II,RPB2）、β-微管蛋白（β-tubulin）基因序列并进行Sanger双向测序,将得到的序列进行校对拼接后与NCBI的GenBank数据库中的参考序列进行比对鉴别物种来源;计算物种的种内、种间Kimura-2-Parameter（K2P）遗传距离并构建系统发育树。结果表明,β-tubulin、ITS基因序列鉴别能力优于RPB2、LSU基因序列,可将β-tubulin与ITS两者联合用于鹅膏菌属的物种鉴别,为有毒蘑菇诱发的食源性中毒风险进行预警。β-tubulin基因序列长度较LSU、ITS、RPB2等基因序列短,适合对深加工的蘑菇制品以及误食毒蘑菇后的呕吐物进行分析,可作为鹅膏菌属中毒事件中物种鉴定及溯源的优选条形码。     

虫草属真菌的ITS序列分析和系统发育研究

收集不同产地虫草属真菌,进行ITS(Internal Transcribed Spacer)区段克隆测序和序列特征比较分析,并对ITS序列进行核酸序列数据库GenBank同源性检索比对,并与检索获得的7个最相似物种的ITS序列构建系统发育树.结果表明,虫草属真菌的ITS序列长度为570～576bp,GC含量56.29～56.77%,系统发育分析显示,供试菌株中除C-6与九州虫草高度同源外,其他与蛹虫草均具有高度的亲缘关系.     

The use of tri5 gene sequences for PCR detection and taxonomy of trichothecene-producing species in the Fusarium section Sporotrichiella

Purified DNA from isolates of Fusarium poae, Fusarium sporotrichioides, Fusarium kyushuense and Fusarium langsethiae was used as a template to amplify a 658-bp fragment from the trichodiene synthase (tri5) gene of these fungi with the gene-specific PCR primer pair Tox5-1/Tox5-2. Fragments obtained were isolated and sequenced. DNA sequence alignments revealed high similarity between the sequences derived from F. sporotrichioides and F. langsethiae (98.7%) and less similarity between the latter species and F. poae (90.9%). Phylogenetic analysis of the aligned sequences using the tri5 sequence of Fusarium pseudograminearum as an outgroup revealed clear separation between one group consisting of F. poae and F. kyushuense and another consisting of F. sporotrichioides and F. langsethiae. The two latter species could not be distinguished phylogenetically on the basis of their tri5 sequences. Taxon-specific reverse primers were designed from the aligned sequences and combined with the tri5 gene-specific forward primer Tox5-1. The new reverse primers enabled specific amplification of a fragment of approximately 400 bp from DNA isolated from F. sporotrichioides, F. poae, F. langsethiae and F. kyushuense, respectively. All primers were tested for cross-reactivity with DNA from 26 fungal species potentially capable of producing trichothecenes. Only the primer designed for F. langsethiae cross-reacted with F. sporotrichioides. PCR assays were applied in analysis of artificially and naturally infected samples of barley and oats. On artificially infected barley, species were selectively detected by the corresponding primers. In naturally infected oats, F. langsethiae was identified by the combination of two PCR assays designed for detection of F. sporotrichioides and F. langsethiae, respectively.     

牦牛奶酪中乳酸菌的随机扩增多态性研究

目的：探讨随机扩增多态性(RAPD)技术在牦牛奶酪中乳酸菌基因型研究方面的应用价值。方法：采用M13引物,对退火温度、Mg2+浓度、引物用量、Taq酶用量、模板量进行单因素梯度试验,建立最佳反应条件,然后对分离自牦牛奶酪的39株乳酸菌进行扩增,用NTsys 2.10e软件分析扩增图谱,计算遗传相似系数,进行聚类分析,并与16S rRNA测序得到的菌种鉴定结果进行对比。结果：39株乳酸菌相互间的遗传相似系数在0.47～0.98之间,当相似系数为0.78时,菌株被分成10个组,除X23、Y36和Y37之外,其余菌株均按照不同的菌种聚类,与16S rRNA测序结果基本一致,聚类有较强的地域相关性。结论：RAPD技术可用于牦牛奶酪中乳酸菌的基因型研究,可用于菌种鉴定和遗传亲缘关系分析。     

Specific identification of Candida albicans by hybridization with oligonucleotides derived from ribosomal DNA internal spacers

In order to develop DNA probes for rapid, sensitive and specific detection of the pathogenic yeast species Candida albicans, we carried out comparative sequence analysis of the two internal transcribed spacer regions (ITS1 and ITS2) of the ribosomal DNA (rDNA) units of C. albicans and the closely related pathogenic species C. tropicalis. While overall sequence similarity between the two species was considerable (65–75%), both ITS1 and ITS2 were found to contain distinct regions with sufficient sequence divergence to make them suitable as specific target sites for the identification of C. albicans. On the basis of these results one ITS1-derived ( ANAB1 ) and two ITS2-derived ( ANAB2 and ANAB3 ) oligonucleotides were selected, chemically synthesized, and used as hybridization probes. Their specificity and reliability were evaluated in dot-blot hybridization experiments with total genomic DNA from 13 strains of medically important Candida species, six strains of other yeast genera associated with man and animals, and ten strains previously identified as C. albicans by phenotypic criteria. Under well-defined hybridization conditions the three probes hybridized exclusively with DNA derived from strains belonging to the species C. albicans, thus demonstrating their potential clinical usefulness. The failure of four of the (presumed) C. albicans strains to show hybridization to the ITS probes sheds doubt upon their taxonomic classification, which is reinforced by other phenotypic aspects of these strains.     

梨果棒曲霉素产生菌的分离及ITS区鉴定

以莱阳仕梨、阳信鸭梨腐败果为材料,分离棒曲霉素产生菌并对其进行形态及ITS区鉴定。试验采用高效液相色谱法(HPLC)检测棒曲霉素含量,确定所分离菌株产毒能力,通过对产毒菌株保守区域ITS扩增测序,得到的序列号与GenBank中核酸数据库进行对比,初步确定了各菌株的亲缘菌,建立系统发育树。结果表明:分离得到10株不同能力的棒曲霉素产生菌,7株为青霉属,2株为曲霉属,1株为镰刀菌属;进化发育关系为:P-9菌为一类群,其他9株菌为另一类群,彼此之间存在不同程度的进化关系。易污染梨果的产毒霉菌主要为青霉菌,分离得到P-1菌株的产毒能力最强。     

Species-specific PCR-based assays for the detection of Fusarium species and a comparison with the whole seed agar plate method and trichothecene analysis

Species-specific PCR was used for the identification of nine Fusarium species in pure mycelial culture. A PCR-based method was compared with the whole seed agar plate method and trichothecene analysis for three toxin-producing Fusarium species using 85 grain samples of wheat, barley, oat, corn and rye. A simple SDS-based DNA extraction system followed by potassium acetate precipitation resulted in consistent PCR amplification of DNA fragments from cultures and grain samples. The species-specific PCR assays correctly identified pure cultures of Fusarium avenaceum ssp. avenaceum (9 isolates), Fusarium acuminatum ssp. acuminatum (12 isolates), Fusarium crookwellense (7 isolates), Fusarium culmorum (12 isolates), Fusarium equiseti (11 isolates), Fusarium graminearum (77 isolates), Fusarium poae (10 isolates), Fusarium pseudograminearum (23 isolates), and Fusarium sporotrichioides (10 isolates). Multiplex PCR was developed for the simultaneous detection of F. culmorum, F. graminearum and F. sporotrichioides, the three most important trichothecene producing species in Canada. In grain samples, results of PCR assays for these same three species related well with whole seed agar plate method results and determination of Fusarium trichothecenes. The PCR assay described in this study can be used for routine detection and identification of Fusarium spp. in Canada.     

Rapid differentiation of lactic acid bacteria from autochthonous fermentation of Iberian dry-fermented sausages

The populations of lactic acid bacteria (LAB) in different types of Iberian dry-fermented sausages from central-west Spain were identified. A simple and rapid electrophoretic method of whole-cell protein profiles was evaluated, correlating it with 16S rRNA gene sequence analysis and biochemical identification by API 50 CHL. A total of 96 isolates were identified by SDS-PAGE showing stable profiles corresponding to 30-45 polypeptides in the range 95-8kDa that were clearly different for the different species and were grouped with those of the 9 reference strains used in this study. The SDS-PAGE method showed that the predominant species were Pediococcus acidilactici (48%) followed by Lactobacillus plantarum (23%) and Lactobacillus brevis (18%). The identifications obtained by this approach were confirmed by sequencing the V2-V3 region of the 16S rRNA gene and by a BLAST search of the GenBank database. However, biochemical identifications by API 50 CHL showed different errors at the genus and species level. In sum, the SDS-PAGE analysis showed itself to be a rapid and accurate differentiation method for the most commonly encountered LAB isolates in dry-fermented sausages.     

草菇有性世代间rDNA序列变异分析及RAPD分析

草菇的遗传与有性生殖过程存在很多的特殊性和不确定性,本研究以草菇V23菌株的成熟子实体弹射孢子,单孢分离后得13个单株,分别摇瓶培养、收集菌丝,提取总DNA,用通用引物ITS4、ITS5进行PCR扩增后连接、转化并测序,将单孢间和单孢与亲本间的ITS序列进行比对,分析草菇ITS序列多样性及变异性;同时以相应单孢菌株DNA为模板,用20条随机引物进行RAPD扩增。结果表明:草菇单孢间和单孢与亲本间的ITS序列相似度均在99%以上,相较于亲本的ITS序列,单孢序列中发现了有5个位点出现碱基转换,但没有两个以上的单孢发生同一转换;20条随机引物分别与14个样本进行RAPD扩增,其中3个引物出现多态性条带,带型结果发现单孢菌株间的带型差异呈现一定规律。草菇ITS序列变异较少,不适于单孢间的变异分析,而RAPD方法对摸索草菇有性世代间的遗传分离规律有重要价值。     

DNA-based identification of fish species implicated in Puffer fish poisoning

A method for identification of fish species using three different mitochondrial DNA regions, 16S rRNA, cytochrome b and cytochrome c gene fragments, was investigated. The combined use of all three regions enabled reliable species identification in not only raw fish, but also dried, seasoned and boiled fish, products. Furthermore, the method was applicable even to vomitus from a patient involved in a puffer fish poisoning incident. However, further improvement is necessary to discriminate between closely related species such as Takifugu rubripes and T. chinensis, because they showed close similarity in the nucleotide sequences in the three gene fragments analyzed in this study.     

黑龙江、吉林地区松茸ITS序列遗传多样性分析

提取黑龙江省5个不同产地和吉林省汪清地区不同产地松茸子实体的基因组DNA,利用ITS序列分析技术研究其遗传多样性。测序后通过和GenBank中序列比对,采用最大简约法(Maximum Parsimony,MP)、最小进化法(Minimum Evolution,ML)和邻位相接法(Neighbor Joining,NJ)构建系统发育树。结果表明,6个样品的ITS序列被分成了两大组,鸡东,汪清,东京城,东宁由于序列比较相似被分为一组,穆棱和海林被分为另一组。每组的ITS序列变化较小,相似度较高。同时,多个位点存在着差异,有转换、颠换和缺失。     

基于rDNA ITS序列分析的桑黄真菌菌株分子鉴定

对6份桑黄真菌菌株的rDNA ITS区段进行克隆测序和序列特征比较分析,并与GenBank中获得的桑黄基源物种相关序列进行同源性比对,进一步将从GenBank检索获得的桑黄基源物种的ITS序列、复合外组ITS序列连同6份桑黄菌ITS序列一起作系统发育分析。结果表明:Sh-03、04、05、06与Phellinus linteus亲缘关系最近,Sh-01与Phellinus baumii亲缘关系最近,Sh-02与Phellinus baumii、Phellinus linteus、Phellinus igniarius的亲缘关系相差甚远,为一错误菌种。本实验的研究结果可以提供一种准确可靠且简单易行的桑黄真菌分子鉴定技术。     

基于DNA条形码技术对常见石首鱼科鱼胶的物种鉴定

摘　要：目的　运用DNA条形码技术对常见石首鱼鱼胶进行物种鉴定。方法　通过对26份鱼胶样品基因组DNA提取，PCR扩增COI基因、测序，用BOLD物种鉴定系统，与数据库中已有鱼类序列进行比对分析，鉴定出各鱼胶的物种；根据Kimura双参数模型计算样品序列遗传距离，并将所得序列构建NJ和MP系统发育树，进行聚类分析。结果　26份鱼胶样品通过鉴定引物“Fish-F”、“Fish-R”均可实现扩增，条带清晰单一，扩增和测序成功率均为100%；BOLD鉴定结果显示，26份鱼胶样品中23份能够确定物种来源（相似性达98%以上），包括石首鱼科12属15种鱼类，且多数为外来物种，另外3份鱼胶可推测其近缘物种。此外，系统发育树聚类分析结果与物种鉴定结果一致。结论　目前石首鱼类鱼胶来源物种较多，且多为外来基原鱼种。DNA条形码技术与BOLD鉴定系统相结合，可对大部分鱼胶进行准确的物种鉴定。