A distinct small RNA pathway silences selfish genetic elements in the germline

In the Drosophila germline, repeat-associated small interfering RNAs (rasiRNAs) ensure genomic stability by silencing endogenous selfish genetic elements such as retrotransposons and repetitive sequences. Whereas small interfering RNAs (siRNAs) derive from both the sense and antisense strands of their double-stranded RNA precursors, rasiRNAs arise mainly from the antisense strand. rasiRNA production appears not to require Dicer-1, which makes microRNAs (miRNAs), or Dicer-2, which makes siRNAs, and rasiRNAs lack the 2',3' hydroxy termini characteristic of animal siRNA and miRNA. Unlike siRNAs and miRNAs, rasiRNAs function through the Piwi, rather than the Ago, Argonaute protein subfamily. Our data suggest that rasiRNAs protect the fly germline through a silencing mechanism distinct from both the miRNA and RNA interference pathways.     

Parasitoid wasps as effective biological control agents

Biological control (biocontrol) is a safe, sustainable approach that takes advantage of natural enemies such as predators, parasitic insects or pathogens to manage pests in agroecosystems. Parasitoid wasps, a very large evolutionary group of hymenopteran insects, are well-known biological control agents for arthropod pests in agricultural and forest ecosystems. Here, we summarize the recent progress on the application of parasitoid wasps in biocontrol in China for the last five years. These include species diversity of parasitoid wasps, identification of dominant parasitoid wasps associated with insect pests and biocontrol practices (three types of biological control, i.e., classical, augmentative and conservation biological control) in several Chinese agroecosystems. We then treat different mass-rearing and release technologies and the commercialization of several parasitoid wasp species. We also summarize other work that may have a potential use in biocontrol, including the effect of plant volatiles on parasitoids and recent advance in the molecular mechanisms underlying the host regulation by parasitoid wasps. Future research area and applied perspectives are also discussed, noting that advances in biocontrol technologies in Chinese agriculture informs research at the global level.     

A protein sensor for siRNA asymmetry

To act as guides in the RNA interference (RNAi) pathway, small interfering RNAs (siRNAs) must be unwound into their component strands, then assembled with proteins to form the RNA-induced silencing complex (RISC), which catalyzes target messenger RNA cleavage. Thermodynamic differences in the base-pairing stabilities of the 5' ends of the two approximately 21-nucleotide siRNA strands determine which siRNA strand is assembled into the RISC. We show that in Drosophila, the orientation of the Dicer-2/R2D2 protein heterodimer on the siRNA duplex determines which siRNA strand associates with the core RISC protein Argonaute 2. R2D2 binds the siRNA end with the greatest double-stranded character, thereby orienting the heterodimer on the siRNA duplex. Strong R2D2 binding requires a 5'-phosphate on the siRNA strand that is excluded from the RISC. Thus, R2D2 is both a protein sensor for siRNA thermodynamic asymmetry and a licensing factor for entry of authentic siRNAs into the RNAi pathway.     

高榕榕果内Eupristina属两种榕小蜂的遗传进化关系

对生长在福州地区的高榕进行长期追踪观察,发现高榕榕果内仅生活着Eupristina altissima和Eupristina sp.榕小蜂,前者为高榕的传粉小蜂,后者无传粉行为,两者雌蜂之间在体色、触角、花粉袋和花粉刷等部位存在细微的差异,而两者雄蜂之间无形态差异。通过克隆福建地区5个样地的高榕榕果内收集到的E. altissima和Eupristina sp.榕小蜂,以及细叶榕的传粉小蜂Eupristina verticillata(外群)的Cytb及COI基因,并进行碱基组成及遗传距离分析,用邻接法构建系统发育树,分析两榕小蜂群体之间的遗传进化关系,结果显示:(1)榕小蜂COI及Cytb序列碱基组成中A+T的含量(Cytb序列中A+T=75.3%,COI序列中A+T=75.5%)显著高于G+C,符合膜翅目昆虫线粒体基因碱基组成特征。(2)对两群体小蜂进行遗传距离分析显示,Cytb序列中E. altissima和Eupristina sp. 群体内各样本之间的平均遗传距离分别为0.0092和0.0030,而E. altissima与Eupristina sp. 群体间的平均距离为0.1588;COI序列中E. altissima 与Eupristina sp. 群体内各样本之间的平均遗传距离分别为0.0065和0.0205,而二者群体间的平均遗传距离为0.1043,表明两者群体间的遗传距离明显大于各自群体内各样本间的遗传距离。统计GenBank中下载的6个属34种榕小蜂Cytb序列的种间遗传距离为0.0811-0.1723,6个属28种榕小蜂COI序列的种间遗传距离为0.0939-0.1986。由此认为E. altissima和Eupristina sp.之间的遗传距离差异已经达到了种间水平,即E. altissima与Eupristina sp.为两个不同的种。(3)在形态上,两种小蜂的雌蜂之间有微小差异,而二者雄蜂之间无差异,但Cytb与COI序列分析结果一致表明:E. altissima与Eupristina sp.雄蜂之间,以及二者雌蜂之间的遗传距离均差异显著,表明形态变异滞后于基因变异。雌蜂在表型上进化快于雄蜂,可能是由于雌蜂羽化后从榕果出飞,受到外界环境因素的影响较大,且两种雌蜂在传粉功能上存在差异,故二者之间的形态差异较大,而雄蜂寿命短,又终生生活在黑暗封闭、环境变化相对恒定的榕果内,两种雄蜂在行为上不存在差异,故二者表型变异较为缓慢。E. altissima和Eupristina sp.小蜂对宿主的专一性不强,在榕-蜂协同进化过程中,可能发生过宿主转移事件。     

植物微小RNA（microRNA）研究进展

真核细胞中存在大量的非编码RNA,～22nt的小RNA是其中一类非常重要的调控RNA,主要包括siRNA和miRNA两种类型,二者均由类似RNaseⅢ的核酸内切酶一Dicer加工产生,随后进入沉默复合体抑制靶基因表达。miRNA分子与siRNA类似,但miRNA的前体在基因组上具有独立的转录单位,可自身折叠成发卡结构,其靶基因主要是与器官发生及生长发育相关的转录因子以及调控蛋白。miRNA在生物生长发育的各个时期都扮演着重要的角色,调控许多重要的生物途径,处于基因调控网络的核心位置。     

捻转血矛线虫丙硫咪唑敏感虫株和耐药虫株miRNA-mRNA关联比较分析

旨在比较分析捻转血矛线虫敏感虫株和耐药虫株miRNA表达谱,探讨miRNA与捻转血矛线虫丙硫咪唑耐药性相关基因之间的调控机制。运用Illumina Hiseq2000平台进行测序并进行cDNA文库的构建,利用RNAhybrid、Miranda和TargetScan对测序得到的数据进行靶基因预测,并取交集作为miRNA的靶基因预测结果,使用Bowtie、RepeatMasker、MIREAP、Rfam、miRBase和DAVID等生物信息学分析软件和权威数据库系统,筛选出差异的miRNA以及与捻转血矛线虫耐药相关的miRNA并进行靶基因预测,同时对KEGG pathway和GO功能富集到的靶基因和可能参与调控的通路进行预测分析。结果表明,敏感虫株和耐药虫株共筛选显著差异表达的miRNA共294个,其中113个上调,181个下调。对miRNA和其靶向调节的mRNA进行关联分析,共关联到1 770个miRNA-mRNA对为负调控关系,其中涉及到274个差异的miRNA和603个差异的mRNA。显著差异表达的miRNA靶基因被注释到了1 430条GO terms和327条KEGG pathway,富集到FoxO信号通路(FoxO signaling pathway),mTOR信号通路(mTOR signaling pathway),PI3K-Akt信号通路(PI3K-Akt signaling pathway)等与耐药相关的一些抗性通路。综上,通过对miRNA表达谱分析以及miRNA-mRNA靶向分析,发现捻转血矛线虫敏感虫株和耐药虫株显著差异表达的miRNA和其对应的靶基因,并对部分耐药相关通路中存在的靶基因及显著差异的靶基因所在的通路进行筛选和分析,为后续进一步通过转录组学深层次挖掘捻转血矛线虫产生耐药性的关键基因及相关调控分子提供科学依据。     

植物内源小RNA及其介导的基因沉默途径

阐述了植物内源小RNA的种类及其介导的多种RNA基因沉默途径,RNA沉默途径中的主要效应蛋白及复合物的组成和功能,重点介绍了miRNA介导的基因沉默途径和siRNA介导的基因沉默途径的异同及其功能,为便于了解植物基因表达调控的多层次性和复杂性,进一步挖掘和利用植物内源信号途径提供一定的参考。     

捻转血矛线虫阿苯达唑耐药虫株给药前后miRNA差异表达谱及网络调控分析

旨在通过miRNA测序技术对捻转血矛线虫阿苯达唑给药前后的耐药虫株差异表达miRNA及网络调控分析,获取其转录本中全miRNA表达谱及耐药相关差异表达基因和miRNA,探究miRNA在捻转血矛线虫阿苯达唑耐药虫株给药前后的差异。采用Illumina Hiseq2 000平台对捻转血矛线虫阿苯达唑耐药虫株给药前和给药后的虫体进行Small RNA-seq测序,将Raw Data与参考基因组和miRBase数据库进行比对分析,使用RNAhybrid、Miranda和TargetScan对miRNA靶基因进行预测,筛选捻转血矛线虫耐药虫株给药前后表达量显著差异的miRNA并通过Stem-loop qRT-PCR验证,同时对差异显著的miRNA-mRNA调控关系采用Cytoscape软件进行可视化分析。将靶基因向KEGG和GO两大权威数据库映射,预测和分析靶基因功能注释情况和参与调控的通路情况。结果显示：1）捻转血矛线虫阿苯达唑耐药虫株给药前和给药后共筛选出显著差异表达的miRNA 188个,其中125个上调,63个下调,且qRT-PCR结果与转录组测序结果表达情况一致。2）显著差异表达的14...     

Two new IncRNAs regulate the key immune factor NOD1 and TRAF5 in chicken lymphocyte

Reticuloendotheliosis virus (REV) causes the atrophy of immune organs and immuno-suppression in chickens, but the underlying molecular mechanism of the immune response after infection by REV is not well understood. Presently, the RNA-seq was used to analyze the regulation of immune response to REV in chicken lymphocytes from peripheral blood. Overall, 134 differentially expressed long non-coding RNAs (lncRNAs) between cells with REV infection or without in vitro were screened. Based on the differentially expressed protein-coding genes, the nucleotide-binding oligomerization domain (NOD)-like receptor pathway related to immune regulation was enriched. Two lncRNAs (L11530 and L09863) were predicted to target the NOD1 and tumor necrosis factor receptor-associated factor 5 (TRAF5) gene, respectively, which are involved in the NOD-like receptor pathway with cis-regulation way. The in vitro results revealed the significantly up-regulated (P<0.01) levels of lncRNA-L11530 and its target gene, NOD1, and the significantly down-regulated (P<0.05) levels of lncRNA-L09863 and its target gene, TRAF5, in lymphocytes after REV infection. These changes also occurred in vivo in blood lymphocytes of chickens infected with REV. Further, L09863 and L11530 were respectively interfered, the expression levels of their target genes NOD1 or TRAF5 were significantly down-regulated, accompanied by the change of IL-8 and IL-18 secretions in lymphocytes. The NOD-like receptor pathway appears to be important in the immune response to REV, LncRNA-11530 and IncRNA-09863 might involve in the immune regulation on REV infection by targeting NOD1 or TRAF5 in blood lymphocytes of chickens. Our findings reveal a new regulation of lncRNAs (L11530 and L09863) on immunity in chicken peripheral blood lymphocytes for REV infection by changing the expression of the target genes via the NOD-like receptor pathway.     

Isolation and Expression Analysis of Two Genes Encoding Cinnamate 4-Hydroxylase from Cotton （Gossypium hirsutum）

Two genes （GhC4H1 and GhC4H2） that encode putative cotton cinnamate 4-hydroxylases that catalyze the second step in the phenylpropanoid pathway were isolated from developing cotton fibers. GhC4H1 and GhC4H2 each contain open reading frames of 1 518 base pairs （bp） in length and both encode proteins consisting of 505 amino acid residues. They are 90.89% identical to each other at the amino acid sequence level and belong to class I of plant C4Hs. GhC4H1 and GhC4H2 genomic DNA are 2 247 and 2 161 bp long, respectively, and contain two introns located at conserved positions relative to the coding sequence. GhC4HI and GhC4H2 promoters were isolated and found to contain many cis-elements （boxes P, L and AC-1 element） previously identified in the promoters of other phenylpropanoid pathway genes. Histochemical staining showed GUS expression driven by the GhC4H1 and GhC4H2 promoters in ovules and fibers tissues. GhC4H1 and GhC4H2 were also widely expressed in other cotton tissues. GhC4H2 expression reached its highest level during the elongation stage of fiber development, whereas GhC4H1 expression increased during the secondary wall development period in cotton fibers. Our results contribute to a better understanding of the biochemical role of GhC4H1 and GhC4H2 in cotton fiber development.     

RNA干扰研究现状

RNA干扰(RNAi)是指生物体内利用双链RNA(dsRNA)诱导同源靶基因的mRNA特异性降解,从而导致转录后基因沉默的现象。其在抵抗病毒感染、抑制转座子活动、调控内源性基因表达等方面发挥重要作用。RNAi以其高特异性、高效性等显著优势将成为研究基因功能的全新手段。简要概括RNAi作用机制和siRNA技术的原理,同时也讨论了RNAi技术在其他领域,如在基因信号通路研究、高通量研究基因功能、基因治疗如肿瘤研究和疾病治疗等方面的应用。     

初情期山羊胸腺microRNAs的筛选

为分析初情期前和初情期雌性山羊胸腺中MicroRNA的差异表达情况,并探讨其在山羊初情期启动过程中所起的作用.对初情期前(n = 3)和初情期(n = 3)山羊的胸腺组织进行了 Solexa测序,采用GO富集和KEGG分析评估差异miRNA靶基因.在初情期前和初情期的山羊胸腺组织中检测到538个miRNA,其中64个miRNA显著差异表达.与初情期前的山羊胸腺样本相比,初情期胸腺样本中存在19个上调基因和45个下调基因.KEGG通路富集分析显示,差异miRNA靶基因主要富集在苯丙氨酸,酪氨酸和色氨酸的生物合成,丁螺菌素和新霉素的生物合成等通路以及胆碱能突触和过氧化物酶体增殖物激活受体(PPAR)等与初情期启动相关信号途径.结果提示胸腺中miRNA参与山羊初情期启动.     

基于28S, COI和Cytb基因序列的薜荔和爱玉子传粉小蜂分子遗传关系研究

薜荔和爱玉子均属于桑科榕属植物,二者为同一物种的原变种与变种的关系,早期研究认为这两种榕树与同一种传粉榕小蜂(Wiebesia pumilae (Hill))建立了稳定的互利共生关系,但近期在形态学、生态学、传粉生物学等方面对二者的研究结果表明,薜荔传粉小蜂和爱玉子传粉小蜂之间可能发生了遗传分化。实验用核糖体28SrDNAD1-D3区、线粒体Cytb及COI基因部分序列,对采自福建3个不同样地的薜荔传粉小蜂和3个不同品系的栽培爱玉子的传粉小蜂进行分析,结果表明:(1)薜荔传粉小蜂和爱玉子传粉小蜂的核糖体28S序列的碱基组成中A,T,G,C 4种含量较平均,C+G的平均含量(56%)稍高于A+T的含量(44%)。线粒体Cytb序列中A+T的含量(76.1%)明显高于C+G的含量(23.9%),COI序列中A+T的含量(71.9%)也明显高于G+C的含量(28.1%),这是膜翅目昆虫线粒体基因的普遍特征。在薜荔和爱玉子传粉小蜂的线粒体Cytb及COI基因中,密码子第三位点A+T的含量最高。(2)比较薜荔和爱玉子传粉小蜂的3种分子标记的变异范围显示,28S进化速度较Cytb及COI序列慢,比较保守,更适合科、亚科等较高分类单元的研究。薜荔传粉小蜂与爱玉子传粉小蜂之间的亲缘关系较近,采用Cytb与COI序列进行分析更为精确。(3)用Cytb及COI序列对薜荔传粉小蜂与爱玉子传粉小蜂之间的遗传距离进行分析显示,薜荔传粉榕小蜂个体间Cytb序列平均遗传距离为0.0054,爱玉子传粉小蜂个体间的Cytb遗传距离为0.0164;薜荔传粉小蜂与爱玉子传粉小蜂群体之间的Cytb序列平均遗传距离为0.1385;COI序列的薜荔传粉榕小蜂个体间遗传距离为0.0048,爱玉子传粉小蜂各样本间平均遗传距离为0.0102;薜荔传粉小蜂与爱玉子传粉小蜂群体间COI序列平均遗传距离为0.1896,两群体间的遗传距离(差异大于10%以上)明显大于群体内各样本之间的遗传距离,表明薜荔传粉小蜂与爱玉子传粉小蜂之间已经发生了很大的遗传分化,其变异水平达到了种间分化水平,即薜荔传粉小蜂与爱玉子传粉小蜂为两个不同的种。     

R2D2, a bridge between the initiation and effector steps of the Drosophila RNAi pathway

The RNA interference (RNAi) pathway is initiated by processing long double-stranded RNA into small interfering RNA (siRNA). The siRNA-generating enzyme was purified from Drosophila S2cells and consists of two stoichiometric subunits: Dicer-2(DCR-2) and a previously unknown protein that we named R2D2. R2D2 is homologous to the Caenorhabditis elegans RNAi protein RDE-4. Association with R2D2 does not affect the enzymatic activity of DCR-2. Rather, the DCR-2/R2D2 complex, but not DCR-2 alone, binds to siRNA and enhances sequence-specific messenger RNA degradation mediated by the RNA-initiated silencing complex (RISC). These results indicate that R2D2 bridges the initiation and effector steps of the Drosophila RNAi pathway by facilitating siRNA passage from Dicer to RISC.     

Genome-wide association study and metabolic pathway prediction of barrenness in maize as a response to high planting density

Increasing the planting density is one way to enhance grain production in maize.However,high planting density brings about growth and developmental defects such as barrenness,which is the major factor limiting grain yield.In this study,the barrenness was characterized in an association panel comprising 280 inbred lines under normal (67 500 plants ha^–1,ND) and high (120 000 plants ha^–1,HD) planting densities in 2017 and 2018.The population was genotyped using 776 254single n...