基于cpDNA rps16序列分析兰考泡桐与白花泡桐和毛泡桐的遗传关系

【目的】通过测序法分析兰考泡桐与白花泡桐和毛泡桐在叶绿体rps16序列上的遗传差异,旨在分析三者之间在叶绿体基因上的变化特点和规律,探讨其种间的遗传关系。【方法】选取兰考泡桐、白花泡桐和毛泡桐各15个样本,对其提取的DNA用PCR扩增获得特异片段,并将其纯化与测序。利用软件Clustal X 2.0对所得序列进行排序;运行MEGA 4软件,进行多序列比对,分析其序列特征,并计算出K2P遗传距离。【结果】(1)对获得的rps16序列进行测定分析,得兰考泡桐序列长度分别为932 933 bp;白花泡桐序列长度为932 bp;毛泡桐序列长度分别为916918 bp。对所得rps16序列进行排序后的长度为938 bp,平均GC含量为34.31%。3个种所代表的个体之间共有10个变异位点,占整个序列长度的1.07%。其中有9个变异位点属于碱基插入或缺失类型,占变异位点总数的90%,占整个序列长度的0.96%。有1个变异位点属于碱基替换类型,占整个变异位点总数的10%,占整个序列长度的0.11%。(2)整个rps16片段的序列共有10个变异位点,其中兰考泡桐与白花泡桐在总的变异位点上,具有一致的碱基位点9个,占总变异的90%。而兰考泡桐与毛泡桐相比,没有相同的碱基。【结论】根据三种泡桐的rps16序列的序列特征和变异位点的分析,表明在叶绿体遗传方面,兰考泡桐具有与白花泡桐更多相似的遗传物质,其亲缘关系较近。综上所述,推测兰考泡桐与白花泡桐可能来自同一母系遗传。     

不同种源的三叶木通ITS序列分析及亲缘关系

对9份不同种源三叶木通样本的核糖体DNA ITS区序列进行测定与分析,同时分析遗传距离并构建NJ树。结果表明,参试的9份三叶木通样本的ITS区序列全长均为653bp,其中ITSl序列长度为269bp,ITS2序列长度为221bp;整个ITS序列区共有7个(1.07%)变异位点,其中ITS1、5.8S和ITS2的变异位点分别为4、0和3个,这些变异位点可作为三叶木通不同种源鉴别的信息位点;各序列间的遗传分化距离为0.002~0.008,聚类结果 9个样本构成2个分支,并显示出三叶木通的亲缘关系与其地理分布有一定关系。     

油桐尺蛾核型多角体病毒广西株全基因组序列

油桐尺蛾核型多角体病毒广西株基因组序列由Sanger测序的方法得到。拼接后获得了121 268 bp序列,GC含量为36.76%。以长度不小于50 aa的序列认定为功能基因,共预测到131个开放阅读框,通过Blast比对,其中87个能注释到功能基因。对基因组序列进重复序列分析,共发现SSR位点174个,同源重复序列1个。在SSR位点中,包含6种长度的重复基序,且以富含AT的重复基序为主。同源重复序列两端为一59 bp片段或其一部分组成的重复序列,两端分别重复12次和7次,中间则为一段与重复片段无关的236 bp片段。与武汉株相比,广西株病毒在37个核心基因中有4个存在蛋白序列长度上的差异,而在其他非核心基因中有6个基因仅存在于一个病毒株中,另有13个基因存在蛋白序列长度上的差异。     

基于叶绿体18S、CP12、CP15序列的西藏巨柏群体多态性遗传评价

为分析西藏巨柏群体的遗传多样性,利用3个叶绿体基因(18S、CP12、CP15)针对8个群体的67份巨柏材料的叶绿体序列进行了测序分析。结果表明:3个序列的长度分别为300 bp、396 bp、1 000 bp,共检测出单倍型(H_1-H_11) 11个,多态性位点4个,简约性信息位点4个。表明巨柏整体遗传多样性的水平较高。同时根据AMOVA分析,发现群体内的变异也较大(85. 8%),因此针对巨柏宜采用就地保护措施。本研究对巨柏遗传资源的保护与有效利用具有重要的理论意义。     

慈竹β-tubulin基因片段的克隆及序列分析

利用Trizol一步法提取慈竹幼笋总RNA,运用RT-PCR方法首次在慈竹中克隆到3条β-tubulin基因部分序列,命名为Na-βtub1、Naβ-tub2、Naβ-tub3,长度分别为958bp、958bp和959bp,分别编码318、318和319个氨基酸。核酸和氨基酸的序列比对分析结果表明,慈竹中3条β-tubulin基因核酸和推测的氨基酸序列之间相似性分别为92.46%和98.22%,与禾本科植物水稻、玉米、小麦的β-tubulin基因核酸和氨基酸序列相似性分别在89%和95%以上。     

基于ITS序列的杨柳树亲缘关系分析

该文以12个杨树无性系和4个柳树无性系为研究对象,利用MEGA5.0软件分析了16个无性系ITS序列平均总长度为663bp,其ITS序列区的各碱基含量为:A所占比例在17.14%~17.81%,T所占比例在16.79%~18.05%,G所占比例在31.93%~32.73%,C所占比例在31.89%~33.43%,G+C所占的比例在64.36%~65.66%,其中G+C含量最高的是小叶杨,最低的是窄冠。同时用邻接法构建了杨柳的系统进化树,其结果可以反映各无性系间的亲缘关系,表明ITS技术鉴定分析杨柳无性系植株是可行的。     

福木假尾孢菌Pseudocercospora elaeodendri的转录间隔区序列分析

PCR扩增福木假尾孢菌的转录间隔区序列(ITS)并测序,获得的基因序列长度为581bp,相似性分析发现其与假尾孢属不同种之间的ITS序列相似度极高。进一步对相似度高的不同种、属菌的ITS序列采用Neighbor-joining法构建系统进化树。遗传距离分析结果发现,试验菌株仅与同源性为100%的未知种名的假尾孢菌聚为一类。比较不同种的ITS碱基序列,结果表明,试验菌株与其它种之间的差异碱基分布于ITS1和ITS2区域,说明ITS能够体现假尾孢属的种间变异。     

几种野牡丹属植物系统发育关系的初步研究

采用nr ITS和叶绿体基因间隔区trnL-trnF的序列,初步研究分布于广东省的野牡丹属的6个物种,即展毛野牡丹(Melastoma normale)、野牡丹(M.candidum)、多花野牡丹(M.affine)、细叶野牡丹(M.in-termedium)、地稔(M.dodecandrum)、毛稔(M.sanguineum)和1个原产印度的印度野牡丹(M.malabathri-cum)及其白花变种(M.malabathricum var.alba)的遗传关系。结果表明,展毛野牡丹、野牡丹、多花野牡丹、细叶野牡丹和毛稔这5个物种具有完全一样的nr ITS和叶绿体基因间隔区trnL-trnF序列,表明它们之间存在非常近的亲缘关系。印度野牡丹在nr ITS序列上与前5个物种序列相同,但在叶绿体trnL-trnF序列上具有1个碱基的差异,表明它与这些物种之间存在非常近缘的关系。地稔与其他几个物种无论在nr ITS序列还是在叶绿体trnL-trnF序列上都差异甚大。     

中华大节竹耐盐基因Is SOS1的克隆与序列分析

通过RACE技术,从中华大节竹根中克隆出一个质膜型Na+/H+逆向转运蛋白基因,并命名为Is SOS1(基因登录号:KC113048)。Is SOS1序列分析结果显示,Is SOS1的全长为3 516 bp,其中开放读码框为3 105 bp,编码了1 035个氨基酸多肽。氨基酸同源性和聚类分析证实,Is SOS1氨基酸序列与拟南芥At SOS1和水稻Os SOS1的氨基酸序列同源性较高,分别为50. 3%和76. 63%,但是与液泡型的Na+/H+逆向转运蛋白氨基酸序列同源性较低。     

4个姬松茸菌株rDNA ITS序列比较

应用通用引物ITS1和ITS4从4个姬松茸(Agaricus blazei Murill.)菌株子实体中扩增出rDNA ITS序列(登录号分别为EF195648,EF471305,EF471306,EF471307),4菌株ITS序列长度分别为734bp、700bp、724bp和735bp。通过GenBank中BLAST,四个姬松茸菌株与A.brasiliensis(AJ884651)和A.blazei(AF161013)相似率最高,分别为:94%、99%、97%和98%。四个姬松茸菌株同源性较高,达93%以上,其中,ABM-B与ABM-D相似率最高,为97%;ABM-B与ABM-C相似率为96%,ABM-A与ABM-C、ABM-C与ABM-D相似率为94%,ABM-A与ABM-D相似率为93%。     

竹种内转录间隔区的核苷酸（ITS）序列分析

以慈竹、龙竹和紫竹3个竹种为研究对象,通过对竹子的新鲜叶片中的rDNA的ITS序列进行聚合酶PCR扩增,以及对其进行序列测定及分析。检测出目的片段ITS总长分别为慈竹390 bp、龙竹384 bp、紫竹380 bp。3种不同属的竹种之间的ITS序列有差异。同时在国家生物多样性保护信息系统（NCBI）上选取同属竹种ITS...     

Phylogenetic relationship of genus Lespedeza by ITS sequence data

ITS sequences of ten kinds of plants of Lespedeza and an out group were obtained by primer design PCR, sequencing and cluster analysis. The results show that ITS1 section length was 228–243 bp, 5.8S sequence length was 165 bp which was very conservative; ITS2 section lengths varied from 215 to 220 bp and the conservative sites occupied 88.1%. Phylogenetic analysis of ITS sequences using PAUP 4.0 software and their genetic relationship were discussed.     

美洲黑杨雄性花芽cDNA克隆测序及表达序列标签(ESTs)特性分析

采用SMART技术构建美洲黑杨雄性花芽cDNA文库.随机挑选4 200个克隆进行序列测定,获得原始序列3 092个ESTs,去除插入片段短于150 bp的序列和污染序列后,获得有效ESTs序列3 087个,平均长度515 bp.对聚类后的416个Clusters分别进行单独拼接,得到相应的Contigs和Singletons分别为451和1 104个,并通过与NCBI等核酸数据库进行比对、查询和注释,获得已知功能和未知功能的基因1 015个,无序列相似性的新基因540个.这些数据为进一步研究高等植物花发育提供了一个极有价值的资源.     

PCR‐based identification of Erysiphe pulchra and Phyllactinia guttata from Cornus florida using ITS‐specific primers

The internal transcribed spacer (ITS) regions of rDNA and the intervening 5.8S rRNA gene for the powdery mildew fungi Erysiphe (sect. Microsphaera) pulchra and Phyllactinia guttata were amplified using standard polymerase chain reaction (PCR) protocols and the universal primer pairs, ITS₁ and ITS₄. PCR products for ITS were analysed by electrophoresis in a 1.5% agarose gel and sequenced. The size of the amplified ITS products (approximately 650 bp) were not sufficiently different to allow reliable differentiation of E. pulchra and P. guttata; however, their sequences were distinct. Specific primers for E. pulchra and P. guttata were developed and evaluated for use as diagnostic tools. The diagnostic band size from E. pulchra‐specific primer pair was 568 bp while the P. guttata band was 597 bp; the two primer pairs were highly specific to E. pulchra and P. guttata. Comparison of ITS sequences with information in the GenBank showed a very close similarity between sequences of E. pulchra isolates from Cornus florida in the USA and isolates collected on Cornus kousa in Japan. BLAST analysis of the sequence of the 650‐bp band from P. guttata revealed a close alignment with sequences of P. moricola (92%), P. kakicola (94%), and P. fraxini (92%). The sequence of P. guttata in C. florida also had a 98% identity with P. guttata in Calycanthus occidentalis and 94% identity with P. guttata in Corylus cornuta.     

不同寄主上的蔗扁蛾ITS分析

蔗扁蛾(Opogona sacchari),隶属鳞翅目(Lepidoptera)辉蛾科(Hieroxestidae)扁蛾属(Opogona)(杨集昆等,1997),是近年来从境外传人我国的一种重要林业危险性有害生物(程桂芳等,1997).该虫寄主广泛,据资料报道(商晗武等,2003),目前已发现寄主植物28科87种8变种,其中,国外报道24科6种4变种,国内14科55种2变种,主要危害巴西木(Dracaena fragrans)、发财树(Pachira macrocarpa)、风梨(Ananas comosus)、一品红(Euphorbia pulcherrima)、朱顶兰(Amaryllis vittata)、木棉(Bombax malabaricum)、大王椰子(Roystonea regia)等观赏植物,我省新发现还能危害柳树(Salix sp.)、紫藤(Wisteria sinensis)、龙爪槐(Sophora japonica var.pendula)等本地绿化树种.它已对我国花卉苗木和林业生产造成严重威胁.为控制疫情扩散蔓延,国家林业局将其列入了林业检疫性有害生物名单.     

Molecular diagnosis of Phytophthora lateralis in trees,water, and foliage baits using multiplex polymerase chain reaction

A polymerase chain reaction (PCR)‐based protocol for detection of Phytophthora lateralis in plant tissues and water is described. Base‐pair (bp) deletions in both of the ribosomal DNA internal transcribed spacer (ITS) regions in P. lateralis were used to design complementary PCR primer sequences that amplify a 738 bp fragment only if P. lateralis DNA is present in the sample. Universal control primers based on conserved sequences of the nuclear ribosomal small subunit are included in a multiplexed reaction, providing an internal check on the procedure. The universal primers amplify an approximately 550 bp fragment that is common to plants, protists, and true fungi. The procedure reliably detects P. lateralis in cedar stem tissues and in roots. Positive reactions were obtained with as few as 200 P. lateralis zoospores in water.     

滨梅不同种源的遗传变异研究

用采自江苏省吴江苗圃收集的6个滨梅种源叶片样品(分别标记为7、9、10、11、12和13号),分析了ISSR、RAPD2种分子标记,以探讨各种源间的遗传变异及其亲缘关系.结果表明,ISSR标记的19个多态性较好的引物共产生了137条带,其中多态性条带91条,占总条带的66.42%.条带大小300～3030 bp;RAPD标记的15个多态性引物共产生99条带,其中多态性条带53条,占总条带的53.5%,条带大小为300～3000 bp.基于ISSR标记的6个种源间遗传距离为0.0680～0.9479:而基于RAPD标记的遗传距离为0.0412～0.6439.2种标记的聚类结果,7、9、10、11、12号可归为一类.另外13号单独归为一类,该分子标记结果与形态变异类型相一致.     

Analysis and characterization of the Salix suchowensis chloroplast genome

By screening sequence reads from the Salix suchowensis chloroplast(cp) genome that were generated by next-generation sequencing platforms, we assembled a complete circular pseudomolecule for the cp genome.This pseudomolecule is 155,508 bp long and has a typical quadripartite structure that contains two single copy regions, a large single copy region(LSC, 84,385 bp), and a small single copy region(SSC, 16,209 bp) separated by inverted repeat regions(IRs, 27,457 bp).Gene annotation revealed that the S.suchowensis cp genome encoded 119 unique genes, including four ribosome RNA genes, 30 transfer RNA genes, 82 protein-coding genes, and three pseudogenes.Analysis of the repetitive sequences revealed31 tandem repeats, 16 forward repeats, and five palindromic repeats.In addition, a total of 148 perfect microsatellites, which were characterized as A/T dominant in nucleotide composition, were detected.Significant shifting of the IR/SSC boundaries was revealed by comparing this cp genome with those of other rosid plants.We also constructed phylogenetic trees to demonstrate the phylogenetic position of S.suchowensis in Rosidae based on 66 orthologous protein-coding genes present in the cp genomes of 32 species.Sequencing 30 amplicons based on the pseudomolecule for experimental verification revealed99.88% accuracy for the S.suchowensis cp genome assembly.Therefore, we assembled a high-quality pseudomolecule of the S.suchowensis cp genome, which is a useful resource for facilitating development of this shrub willow into a more productive bioenergy crop.