Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome

AIM:To design and validate broad-range 16S rRNA primers for use in high throughput sequencing to classify bacteria isolated from the human foregut microbiome.METHODS:A foregut microbiome dataset was constructed using 16S rRNA gene sequences obtained from oral,esophageal,and gastric microbiomes produced by Sanger sequencing in previous studies represented by 219 bacterial species.Candidate primers evaluated were from the European rRNA database.To assess the effect of sequence length on accuracy of classification,16S rRNA genes of various lengths were created by trimming the full length sequences.Sequences spanning various hypervariable regions were selected to simulate the amplicons that would be obtained using possible primer pairs.The sequences were compared with full length 16S rRNA genes for accuracy in taxonomic classification using online software at the Ribosomal Database Project (RDP).The universality of the primer set was evaluated using the RDP 16S rRNA database which is comprised of 433 306 16S rRNA genes,represented by 36 phyla.RESULTS:Truncation to 100 nucleotides(nt)downstream from the position corresponding to base 28 in the Escherichia coli 16S rRNA gene caused misclassification of 87(39.7%)of the 219 sequences,compared with misclassification of only 29(13.2%)sequences with truncation to 350 nt.Among 350-nt sequence reads within various regions of the 16S rRNA gene,the reverse read of an amplicon generated using the 343F/798R primers had the least(8.2%)effect on classification.In comparison,truncation to 900 nt mimicking single pass Sanger reads misclassified 5.0%of the 219 sequences.The 343F/798R amplicon accurately assigned 91.8%of the 219 sequences at the species level.Weighted by abundance of the species in the esophageal dataset,the 343F/798R amplicon yielded similar classification accuracy without a significant loss in species coverage(92%).Modification of the 343F/798R primers to 347F/803R increased their universality among foregut species.Assuming that a typicalpolymerase chain reaction can tolerate 2 mismatches between a primer and a template,the modified 347F and 803R primers should be able to anneal 98%and 99.6%of all 16S rRNA genes in the RDP database.CONCLUSION:347F/803R is the most suitable pair of primers for classification of foregut 16S rRNA genes but also possess universality suitable for analyses of other complex microbiomes.

DNA sequencing by synthesis with degenerate primers

The degenerate primer-based sequencing was developed by a synthesis method （DP-SBS） for high-throughput DNA sequencing, in which a set of degenerate primers are hybridized on the arrayed DNA templates and extended by DNA polymerase on microarrays. In this method, a different set of degenerate primers containing a given number （n） of degenerate nucleotides at the 3＇-ends were annealed to the sequenced templates that were immobilized on the solid surface. The nucleotides （n＋1） on the template sequences were determined by detecting the incorporation of fluorescent labeled nucleotides. The fluorescent labeled nucleotide was incorporated into the primer in a base-specific manner after the enzymatic primer extension reactions and nine-base length were read out accurately. The main advantage of the DP-SBS is that the method only uses very conventional biochemical reagents and avoids the complicated special chemical reagents for removing the labeled nucleotides and reactivating the primer for further extension. From the present study, it is found that the DP-SBS method is reliable, simple, and cost-effective for laboratory-sequencing a large amount of short DNA fragments.

Next-generation sequencing in clinical virology: Discovery of new viruses

Viruses are a cause of significant health problem world-wide, especially in the developing nations. Due to different anthropological activities, human populations are exposed to different viral pathogens, many of which emerge as outbreaks. In such situations, discovery of novel viruses is utmost important for deciding prevention and treatment strategies. Since last century, a number of different virus discovery methods, based on cell culture inoculation, sequence-independent PCR have been used for identification of a variety of viruses. However, the recent emergence and commercial availability of nextgeneration sequencers(NGS) has entirely changed the field of virus discovery. These massively parallel sequencing platforms can sequence a mixture of genetic materials from a very heterogeneous mix, with high sensitivity. Moreover, these platforms work in a sequenceindependent manner, making them ideal tools for virus discovery. However, for their application in clinics, sample preparation or enrichment is necessary to detect low abundance virus populations. A number of techniques have also been developed for enrichment or viral nucleic acids. In this manuscript, we review the evolution of sequencing; NGS technologies available today as well as widely used virus enrichment technologies. We also discuss the challenges associated with their applications in the clinical virus discovery.

Determination of the Population Structure of Fig Genotypes from Algeria and Turkey Using Inter Primer Binding Site-Retrotransposon and Simple Sequence Repeat Markers

In order to identify the variation and estimate the genetic diversity among the fig (Ficus carica L.) genotypes collected from Algeria and Turkey, the genetic relationships between 86 genotypes were investigated using 23 inter primer binding sites (iPBS)-retrotransposon and 16 simple sequence repeat (SSR) primers. A total of 63 polymorphic bands for the iPBS-retrotransposon markers and 25 alleles for the SSR markers were identified with an average of 2.7 and 1.6 per primer, respectively. The average value of polymorphism information content (PIC) for the iPBS markers (0.73) was higher than that for the SSR markers (0.69). Applying the neighbor-joining method to the combined iPBS-retrotransposon and SSR data, the fig genotypes were clustered into two groups. The STRUCTURE software was used to determine the population structure. Among the genotypes studied, two populations (K = 2) were identified indicating a low diversity between the Algerian and Turkish varieties. Both types of markers were able to differentiate all the fig genotypes and were efficient in discriminating the closely related genotypes. Our data also showed that as a universal marker, iPBS-retrotransposon is a useful tool for the molecular characterization of fig genotypes.

The application of sequence specific primer and RT-PCR to LRRK2 gene polymorphism typing

Objective:To establish a new detecting method for disease susceptibility loci R1628P and G2385R of Parkinson’s disease(PD)related gene LRRK2.Methods:Sequence specific primers were designed to make a genotyping of DNA markers with known genotypes by use of quantitative fluorescence real-time PCR(RT-PCR).100 cases of PD samples with unknown genotypes were tested,and verified by use of polymerase chain reaction linked restriction fragment length polymorphism(PCR-RLFP).Results:The genotyping results of DNA markers proved to be correct,and 100 cases of samples to be tested had a completely consistent genotyping result with PCR-RLFP genotyping result.Conclusions:Sequence specific primer and quantitative fluorescence RT-PCR can successfully make a genotyping for disease susceptibility loci R1628P and G2385R of LRRK2.

扩增子测序技术在牡蛎GⅡ型诺如病毒基因多样性研究中的评估

牡蛎中诺如病毒基因多样的研究对病毒的流行传播和疫情防控具有十分重要的意义,二代测序技术(next generation sequencing, NGS)的扩增子测序具有高通量、高准确性等优势,被广泛应用于基因组学、转录组学和表观基因组学等领域。为评估扩增子测序技术对牡蛎中诺如病毒多样性研究的可行性,采用经典的巢式反转录PCR(reverse transcription-PCR, RT-PCR)方法对人为污染诺如病毒的牡蛎样品进行检测并将产物进行扩增子测序,对病毒基因型覆盖度和灵敏度进行分析。结果显示,在覆盖度方面,扩增子测序技术能够检测出人为添加到牡蛎中的6种GⅡ型诺如病毒,覆盖率达到100%;在灵敏度方面,对人为污染有不同数量诺如病毒的牡蛎进行检测及测序分析,证实扩增子测序的灵敏性较高,低于50个病毒粒子也能检测出。综上,扩增子测序技术提高了牡蛎中诺如病毒检测的准确性以及基因型的丰富度。

柑橘黄龙病菌亚洲种重复序列分析及其检测引物筛选

由柑橘黄龙病菌亚洲种(Candidatus Liberibacter asiaticus,CLas)引起的黄龙病(Huanglongbing,HLB)对柑橘产业危害严重,通过加强病原检测有利于减少病害传播。利用高拷贝重复序列位点设计引物,虽能提高黄龙病检测的灵敏度,但重复序列的多态性很难保障引物检测特征稳定。通过比较11个CLas全基因组的重复序列,以期获得保守的重复序列,利于开发通用型CLas检测引物。结果显示,CLas全基因组有4段长度>50 bp的高拷贝重复序列,其重复数量和序列在11个菌株中均具有保守性。基于4段重复序列开发了CLas特异的6对引物,均能稳定检测田间柑橘黄龙病样品,熔解曲线吸收峰单一,熔解温度稳定。比较6对引物的灵敏度,发现基于5个拷贝重复序列开发的IR16-fr灵敏度最高。使用IR16-fr和常规引物CQULas-FR对50份田间柑橘叶片样品进行检测,结果显示,CQULas-FR对CLas的检出率为20%,而IR16-fr的检出率为26%。新引物IR16-fr可为田间CLas高效率检测提供技术支撑。

应用Q-PCR定性检测KIR基因有无方法的建立

目的建立定性检测KIR基因有无的Q-PCR方法。方法根据高分辨水平中国人群KIR等位基因的多态性,并参考国际IPD-KIR数据库,针对16种KIR基因及2DS4-Normal、2DS4-Deleted两种亚型,设计KIR基因特异性引物用于Q-PCR扩增反应;同时设置一孔阴性对照、一孔阳性对照(特异性扩增人体生长激素HGH基因片段),以监控假阳性、假阴性的结果。为验证Q-PCR方法的可靠性,随机选择302份已采用KIR PCR-SSP商品化试剂盒检测的标本,采用Q-PCR方法盲检和对比。结果300人份的Q-PCR检测结果与已知的PCR-SSP检测结果相符,有2份标本结果不一致,其中1例标本的2DS5基因Q-PCR检测结果为阴性,而PCR-SSP检测结果为阳性;另一例标本2DS1基因Q-PCR检测结果为阳性,而PCR-SSP检测结果为阴性。对2份标本分别进行2DS5、2DS1基因测序分型,证实Q-PCR定性检测结果正确。结论本文建立的KIR Q-PCR方法结果准确、可靠,可用于KIR基因有无的定性检测。

根际促生菌对茄子、南瓜、辣椒穴盘苗胚轴和根际微生物多样性的影响

为探究根际促生菌对蔬菜幼苗胚轴和根际微生物群落多样性的影响,以茄子品种“京茄9号”、南瓜品种“超人”、辣椒品种“京旋1号”和解淀粉芽孢杆菌(L-S60、LPL-117、L-H15)为试验材料,利用Illumina NovaSeq高通量测序技术和生物信息学分析方法,分析了在根际接种解淀粉芽孢杆菌后蔬菜穴盘苗胚轴和根际微生物的多样性。结果表明:接种3个根际促生菌均能改变蔬菜幼苗胚轴和根际细菌特征序列的种类。α多样性分析表明,根际接种L-S60后降低了南瓜胚轴微生物Shannon指数和辣椒根际微生物的Chao1指数、Obserbed otus指数、Shannon指数;根际接种LPL-117后提高了茄子胚轴微生物的Chao1指数、Obserbed otus指数,降低了辣椒根际微生物的Chao1指数、Obserbed otus指数、Shannon指数;根际接种L-H15后降低了辣椒根际微生物的Chao1指数、Obserbed otus指数、Shannon指数。β多样性分析表明,在主成分1(PC1)上3种蔬菜接种3个根际促生菌后的胚轴和根际的细菌群落多样性均分别有明显区分。说明根际接种根际促生菌可影响蔬菜穴盘苗根际微生物群落的结构和组成,3株解淀粉芽胞杆菌可施用于蔬菜穴盘苗根际,用于改善幼苗根际的微生态环境。

基于PCR-SSP技术的RhCE血型基因型检测方法

目的 基于序列特异性引物PCR(PCR-SSP)技术建立一种用于检测临床标本红细胞RhCE血型基因型的快速定型方法。方法 将2023年9至12月宁波大学附属第一医院收检的152例乙二胺四乙酸抗凝血样分别采用试管法、间接抗人球法和微柱凝胶卡法检测RhD血型和RhCE血型。采用硅基质柱法提取样本DNA。采用Sanger测序法选择RhCE基因标准品序列。采用PCR-SSP法确定检测RhC和Rhc、RhE和Rhe两对等位基因的4对序列特异性引物。采用TA克隆技术得到重组质粒并评估序列特异性引物的灵敏度和抗干扰性能。采用PCR-SSP法检测样本,并与血清学结果进行一致性评价。结果 用表型分别为CCee、CcEe、ccEE的3个标本成功确定不同RhCE基因型的标准品序列。4对序列特异性引物能有效区分RhC和Rhc、RhE和Rhe两对等位基因。序列特异性引物在对应等位基因1:128干扰下仍能检测出且灵敏度为10~4~10~5拷贝数/μL。临床样本RhE、Rhe和Rhc基因型检测结果与表型一致性为100.00%,但RhC基因型与表型一致性只有92.76%,其中RhD阳性背景人群中的一致率为98.39%,RhD阴性背景人群中一致率为88.89%。结论 PCR-SSP技术在红细胞RhCE血型基因型快速鉴定方面具有可行性,检测RhE、Rhe和Rhc基因型与表型具有较高的一致性,对RhC基因型的检测,需区分不同RhD血型背景,建议使用两种及以上的方法进行综合判断。

Optimization of Multiplex PCR and Multiplex Gel Electrophoresis in Sunflower SSR Analysis Using Infrared Fluorescence and Tailed Primers

In an effort to simplify the procedure and to reduce the cost of fluorescence SSR analysis, the conditions of the multiplex PCR and the multiplex gel electrophoresis were optimized in the genetic analysis of sunflower (Helianthus annuus L.) inbred lines. Results indicated that factors for a successful multiplex PCR assay were related to the cycling touchdown annealing temperature, the balance of primer concentration at the various loci, the concentration of PCR buffer and the Taq DNA polymerase. Based on the optimization, a tailed primer strategy was outlined, and the effective ways were proposed to overcome the troubleshootings commonly encountered in the multiplex PCR and the multiplex gel electrophoresis.

Analysis of Simple Sequence Repeats Information from Floral Expressed Sequence Tags Resources of Papaya (<i>Carica papaya</i>L.)

Papaya (Carica papaya L.) is one of the most economically, medicinally and nutritionally important tropical fruit crops. Expressed sequence tags (ESTs) derived simple sequence repeat (SSR) markers are more valuable as they are derived from conserved genic portion. Development of EST-SSRs markers through in silico approach is cheaper, less time consuming and labour-intensive. In this study, we aimed to mine SSRs and developed EST-SSR primers from papaya floral ESTs. A total of 75,846 papaya floral ESTs were downloaded from public database National Centre for Biotechnology Information (NCBI). A total of 26,039 floral unigenes (7961 contigs and 18,078 singletons) were generated after assembly of these ESTs. From these floral unigenes, 433,782 perfect SSRs, 204,968 compound SSRs and 6061 imperfect SSRs were mined, respectively. In perfect SSRs, mononucleotide repeats were most abundant (94.7%) followed by tri- (3.1%) and di-nucleotide repeats (1.7%). The frequencies of tetra-, hexa- and penta-nucleotide repeats accounted for only (0.17%), (0.04%) and (0.03%), respectively. In mononucleotide repeats, the most abundant motif was A/T (69.3%) and in di- and tri-nucleotide repeats were AG/CT (61%) and AAG/CTT (31%), respectively. In imperfect SSRs, mononucleotide repeats (56.5%) were most abundant. 176 different types of motifs were identified. A total of 3807 primer pairs for floral papaya ESTs were successfully designed. These developed EST-SSR primers are being used for the genetic improvement of papaya such as study of cross-transferability across genera/species, evaluation of genetic diversity, and identification of sex-specific markers. These EST derived SSRs can also be used in filling gaps in existing linkage maps in papaya.

Full screening and accurate subtyping of HLA-A＊02 alleles through group-specific amplification and mono-allelic sequencing

HLA-A＊02 is the most prevalent and polymorphic major histocompatibility complex （MHC） allele family in humans. Functional differences have been revealed among subtypes, demanding further subtyping of HLA-A＊02 in basic and clinical settings. However, the fast growing polymorphisms render traditional primeror probe-based typing methods impractical and result in increasing ambiguities in direct sequence-based typing. In this study, we combined group-specific amplification and mono-allelic sequencing to design and validate a simple scheme for the complete screening and accurate subtyping of all 540 reported HLA-A＊02 alleles. This scheme could be performed in routine labs to facilitate studies with an interest in HLA-A＊02.

Molecular Marker Techniques Using Single Primers and Their Advances

Molecular marker techniques have been widely applied in the fields of genetic diversity analysis,germplasm resources identification,molecular fingerprint and genetic linkage map construction,QTL mapping and molecular assisted breeding.On the basis of stating the concept of molecular marker techniques based on single primer amplification reactions,this study focused on the sorting and induction of single-primer molecular marker techniques,and expounded their derivative development.Finally,the application prospect and future expectation of single-primer molecular marker techniques were described in detail.The purpose of this study was to clarify the types of molecular marker techniques based on single primer amplification reactions,so that researchers can quickly and conveniently select molecular marker techniques according to their own specific scientific research conditions.

石斛基因组保守序列特性的生物信息学分析

为了探明石斛属植物基因组保守序列的种类和特性,从44096条石斛基因组序列中优选出4320条用作分析材料,分析方法采用本实验室编写的VBA程序。结果表明,保守序列出现频率越高,种类数越少,序列保守性越强,序列之间保守性差距越大;分布频率较高的保守序列可以演变为序列更长的保守序列;15.4%的基因组序列具有SSR,其中GC或CG为基元的SSR最少,TC、CT、GA、AG为基元的SSR最为丰富,随着基元重复次数的增加,SSR的频率逐渐下降。此VBA程序可以用于其他任何基因组分析,分析结果将有助于分子标记引物设计、相关基因克隆和遗传多样性研究,也为进一步探索基因组作用机理提供了依据。

白三叶转录组SSR位点特征分析及引物开发

本研究旨在了解白三叶(Trifoliumrepens)SSR位点信息和序列特征,开发多态性SSR引物,区分20份白三叶材料。对白三叶不同颜色的花瓣进行转录组(RNA-seq)测序,并根据转录组测序结果中的SSR位点批量设计引物,随机选择60对引物进行多态性验证,选择多态性高的引物指纹图谱构建。结果表明,白三叶转录组中含有SSR位点的序列有24960个,出现频率为13.25%,平均约5.29 kb出现1个SSR位点;白三叶转录组SSR重复碱基类型有6种,其中三碱基重复占比最高(33.70%),其次为双碱基(28.26%)和单碱基重复(25.02%),其他碱基重复类型较低,仅占总SSR的9.01%。A/T(24.85%)、AG/CT(16.48%)和AAG/CTT(8.89%)分别为单碱基到三碱基的优势重复单元;单碱基至六碱基各基元重复次数集中在4~21次,占总数量的98.11%;序列长度变化在12~35 bp,占总数的96.43%;根据SSR位点序列设计出18594对引物,占总SSR的74.50%;60对随机引物中能扩增出条带的有52对,多态性引物17对,分别占86.7%和32.7%;以多态性较高的5对引物构建的白三叶指纹图谱,能够有效地将20个不同白三叶品种区分开。本研究中白三叶转录组SSR位点分布频率高,类型丰富,具有较高的多态性,在白三叶遗传多样性分析、分子标记辅助育种和指纹图谱构建中具有较大的应用潜力。

利用重测序技术开发高粱InDel分子标记

高粱是重要的禾谷类作物,其测序品种BTx623的全基因组序列已经公布,为高粱InDel标记的开发提供了研究基础。插入与缺失(insertion/deletion,InDel)标记作为高通量分子标记,在植物基因组中具有遗传稳定性高、分布广、多态性强、通用性强等优点,目前已在水稻、玉米、棉花等主要作物中得到广泛应用,然而在高粱中的研究尚不多见。以高粱品种JIUTIAN1基因组DNA为研究对象,利用Illumina平台进行重测序,进一步利用Trimmomatic软件对测序原始数据进行质量控制,剔除低质量数据,使用BWA软件将获得的高质量有效数据与测序品种BTx623参考基因组进行序列比对,从中检测出大量InDel位点。利用这些InDel位点在全基因组范围内设计均匀分布的205个标记,通过PCR验证后筛选出87个多态性标记,多态性为42.44%。高粱Indel标记的开发有望为高粱遗传连锁图谱的构建、遗传多样性分析、杂交种纯度鉴定、高粱重要农艺性状相关基因的定位和分子标记辅助选择育种等研究奠定基础。

应用分子生物学技术检测及蛋白质模型预测1例弱D型54

目的对1例血型血清学检测为RHD变异型的样本进行基因分型,并进行家系调查分析。方法运用血型血清学检测方法对先证者及其家系样本进行RHD确认及RH血型抗原表位检测,用序列特异性引物PCR(sequence specific primer PCR,PCR-SSP)法分析RHD基因外显子的表达,运用Sanger和SMRT(single molecule real-timesequencing)测序法对先证者及其家系样本进行RHD基因的1~10外显子测序分析。通过AlphaFold模拟构建蛋白质三级结构,将突变前后的蛋白质结构进行叠合以观察结构内分子间相互作用力的改变。结果先证者为RHD弱表型,其他抗原为Ccee,直接抗人球蛋白试验、抗体筛查、抗体鉴定试验均为阴性,PCR-SSP初步分型为RHD阳性。其父母血型血清学及PCR-SSP结果均为RHD阳性。SMRT测序结果显示先证者母亲为RHD^(+)/RHD^(-)杂合子。Sanger测序结果显示,先证者父亲携带弱D型54等位基因。AlphaFold建模预测揭示,p.Ser122Leu突变不能与146位GLU形成氢键相互作用。结论该样本为弱D型54,p.Ser122Leu突变导致氨基酸内部分子间作用力发生改变,从而引起突变后蛋白质结构和功能的部分改变。

细菌高通量数据荟萃分析的可行性研究

细菌作为重要的分解者,对于生态系统功能至关重要,其群落多样性一直是生态研究的热点。通过荟萃分析,整理已发表的细菌高通量数据,已经取得一些重要的全球性研究结果。这些荟萃分析的核心是将不同引物来源序列提取统一区段,进行细菌群落分析,但该方法的可行性和准确性还一直未被探究。本研究使用了含有三种引物扩增的同一细菌16S rRNA高通量数据,分析了不同引物和提取统一区段后细菌群落情况。结果显示,不同引物以及提取统一区段后,得到细菌群落组成和多样性显著不同,且提取同一区段后的群落主要受原始引物的影响较大。该研究表明,细菌高通量数据荟萃分析中,引物差异会影响其统一分析的群落结果,荟萃方法需要慎重使用。

序列特异引物引导的聚合酶链式反应(PCR-SSP)结合血清学在疑难血型鉴定中的应用

目的 探讨血型血清学与序列特异引物引导的聚合酶链式反应(PCR-SSP)基因分型在ABO疑难血型鉴定中的作用。方法 用血清学分析鉴定的ABO疑难血型标本80例,同时采用PCR-SSP法进行基因分型,结合两种方法学结果,确定血型及制定输血策略。结果 血清学鉴定亚型40例,其他原因引起的抗原抗体缺失或减弱正常血型40例;PCR-SSP法基因分型亚型41例(3例二者结果不一致:血清学Ael型1例,基因分型O2O2;血清学O型1例,基因分型BO1;血清学A型1例,基因分型AB),正常血型39例。结论 使用血清学结合基因分型鉴定ABO疑难血型具有重要意义。