Transcriptome analysis of Verticillium lecanii based on RNA-Seq technology

[目的]蜡蚧轮枝菌是一种防治植物病原物和害虫的生防菌,弄清其致病的分子基础具有重要的意义。[方法]利用Illumina HiSeq技术测序蜡蚧轮枝菌的cDNA文库,并进行RNA-Seq序列拼接和功能注释。[结果]共获得1634670条高品质reads,碱基GC含量48.50%。14856条Unigene经组装拼接后,在Nr、Swiss-Prot、COG和KEGG数据库中分别比对得到1467、9379、6518和4188条Unigenes。采用GO分类工具将21403条Unigenes分成24个功能组,主要包含在细胞组成（1369）、分子功能（1679）和生物学过程（1928）3个大类里,在COG数据库注释的基础上,把6518条Unigenes分成38个功能组,通过GO和COG丰度识别分类,聚类的主要是一般功能预测、次生代谢产物的合成、运输和分解代谢以及信号转导机制起作用的独立基因。能与KEGG路径匹配的108条Unigenes中大部分和新陈代谢途径及次生代谢产物的合成有关。[结论]这些结果将有助于找寻蜡蚧轮枝菌的致病因子,从而丰富其致病机理。     

基于转录组的八角挥发油合成相关基因挖掘与分析

为更好地挖掘八角(Illicium verum)挥发油合成相关基因，该文对挥发油性状差异显著的优良无性系桂角69号及普通品种砧01号叶片进行了转录组测序及组装注释，并对差异表达基因进行了GO分类和KEGG通路分析。结果表明：(1)转录本经组装后获得84 182条序列，使用NR、NT、Swiss-Prot、KEGG、KOG、GO和Pfam数据库进行序列比对，共注释了59 161条序列，筛选出30 572个差异表达基因。与砧01号相比，桂角69号叶片中上调基因有15 025个，下调基因有15 547个。(2)GO分类结果显示共有20 287个差异基因被注释。KEGG分析结果表明，有21 600个差异基因被注释到133条KEGG通路上，其中挥发油合成相关的单萜生物合成通路、萜类骨架生物合成通路、苯丙素合成通路中的芳樟醇合酶、月桂烯合酶、香叶基香叶基焦磷酸合酶、肉桂酰辅酶A还原酶、咖啡酸3-O-甲基转移酶、肉桂醇脱氢酶等关键酶基因呈差异表达。(3)转录因子分析发现差异表达基因分布于31个转录因子家族，其中MYB家族序列数量最多。该文利用转录组测序技术分析八角优良无性系与普通品种叶片的差异基因及...     

Identification and characterization of Cucurbita gummy stem blight fungi in Northeast China

Cucurbita maxima (pumpkin) is a typical cucurbit that is susceptible to gummy stem blight. In recent years, this major fungal disease has decimated pumpkin yields in Northeast China (Heilongjiang Province) in increasingly numerous outbreaks with more rapid spread in recent years. After culturing fungi on potato dextrose agar medium, we conducted a systematic study of the growth and morphological characteristics of various purified strains of Cucurbita gummy stem blight (GSB) fungus from across Northeast China. Subsequently, DNA samples of 30 isolates with distinct hyphal variations were subjected to internal transcribed spacer (ITS) sequencing. Sequence analysis resulted in identification of the isolates as Stagonosporopsis cucurbitacearum and demonstrated that this is a dominant and widely distributed fungal species in this region. Subsequently, multi‐site phylogenetic analysis assigned the 30 aforementioned strains to two genotypes that aligned to seven phenotypic types of Cucurbita GSB fungi. By analysing ITS conserved sequences of these phenotypically diverse groups, we found that Cucurbita GSB pathogens broadly shared two motifs that contained sequence variations unique to two groups in addition to common identical motifs. Ultimately, this study provided useful data for rapid and accurate identification of S. cucurbitacearum and diagnosis in early symptoms of Cucurbita GSB. This work also provides tools to explore the distribution and regularity of GSB outbreaks spatially and temporally across Northeast China.     

2型猪链球菌脑膜炎小鼠模型的构建及其转录组学分析

【背景】2型猪链球菌(Streptococcus suis serotype 2, S. suis 2)可感染宿主引起严重的脑膜炎,对养猪业和人类公共卫生安全构成重大威胁。【目的】构建S. suis 2感染小鼠脑膜炎模型,并对其脑组织进行转录组学分析,为揭示S.suis2感染宿主后引起脑膜炎的分子机制和发现潜在的治疗靶点提供理论依据。【方法】采用S. suis 2感染小鼠,并对其脑组织进行病理组织学分析确认构建脑膜炎小鼠后,对其脑组织进行转录组学分析,对比S.suis2感染和未感染小鼠的差异表达基因,并对差异表达基因进行基因本体论(geneontology,GO)功能、京都基因和基因组百科全书(Kyoto encyclopedia of genes and genomes, KEGG)通路富集和韦恩分析。【结果】脑病理组织学分析结果显示,S. suis 2感染的小鼠脑膜中有大量的炎症细胞浸润,并且血管周围出现“袖套”现象,并能从感染小鼠的组织器官中再分离出攻毒的S. suis 2菌株,结果证明构建了S. suis 2感染脑膜炎小鼠模型。转录组学分析结果表明,感染S.suis2与未感染的...     

草地贪夜蛾雄性成虫和5龄幼虫的转录组比较分析

【目的】草地贪夜蛾Spodoptera frugiperda是一种新近入侵我国的重要害虫。本研究旨在对草地贪夜蛾雄性成虫和5龄幼虫两个不同发育阶段的转录组进行比较分析。【方法】利用高通量测序技术对草地贪夜蛾雄性成虫和5龄幼虫进行转录组测序和数据组装,并对转录组数据进行功能注释和比较分析。【结果】经de novo组装共获得209 002条转录本,平均长度为687.55 bp,N50为982 bp。共有46 198条(57.43%) unigene在至少一个数据库中获得功能注释,其中1 713条(2.13%) unigene在所有数据库中均能获得注释。在GO数据库中获得205 269条unigene的注释,主要包括68个功能分类;在KEGG数据库中共有3 408条unigene得到注释,涉及277个代谢通路。共鉴定到424个嗅觉相关的基因,并且在雄性成虫和5龄幼虫之间的表达存在差异。通过比较转录组分析,在雄性成虫中鉴定到9 162个上调和6 399个下调差异表达基因(DEGs);功能富集分析发现在上调DEGs中涉及信息素以及信号转导的代谢通路显著富集,而下调DEGs中涉及解毒相关的通路显著富集。【结论】这些转录组数据为探究草地贪夜蛾的生长发育、嗅觉相关功能基因以及候选分子靶标提供资源信息。     

球囊菌胁迫中华蜜蜂幼虫肠道过程中病原的转录组学研究

【目的】本研究利用RNA-seq技术对球囊菌胁迫的中华蜜蜂(中蜂)幼虫肠道进行深度测序,经趋势分析得到差异表达基因(DEGs)的显著表达模式,进而对胁迫过程中的球囊菌进行转录组学分析。【方法】利用Illumina HiSeq 2500平台对球囊菌胁迫的中蜂幼虫肠道进行深度测序,并利用相关软件进行了深入分析。最后,通过RT-qPCR对RNA-seq数据进行了验证。【结果】本研究共得到球囊菌的41133932条高质量clean reads。22865个DEGs共聚类为8个基因表达模式,其中,16769个DEGs聚类为2个显著上调趋势与2个显著下调趋势。GO富集分析结果显示,显著上调与显著下调趋势中的DEGs分别富集于40与37个GO term,基因富集数最多的为细胞进程(2486 unigenes)。KEGG代谢通路(pathway)富集分析结果显示,显著上调与显著下调趋势中的DEGs分别富集于119和112个pathway,基因富集数最多的分别是氨基酸生物合成(127 unigenes)与核糖体(98 unigenes)。进一步分析表明球囊菌在胁迫中蜂幼虫肠道的过程中通过提高物质合成促进其增殖,而宿主通过抑制球囊菌的蛋白合成抵御病原入侵。富集在MAPK信号通路的11个DEGs的表达水平随着胁迫时间的延长而逐渐下降,推测中蜂幼虫通过抑制该通路而阻遏球囊菌增殖。【结论】本研究不仅为揭示白垩病过程中的球囊菌-中蜂幼虫互作提供了重要信息,也为阐明不同抗性蜂种的球囊菌抗性差异奠定了基础。     

Identification of Genes Involved in Flavonoid Biosynthesis in Sophora japonica Through Transcriptome Sequencing

Sophora japonica is a traditional Chinese medicinal ingredient that is widely used in the medicine, food, and industrial dye industries. Since flavonoids are the main components of S. japonica, studying the flavonoid composition and content of this plant is important. This study aimed to identify molecules involved in the flavonoid biosynthetic pathways in S. japonica. Deep sequencing was performed, and 85,877,352 clean reads were filtered from 86,095,152 raw reads. The clean reads were spliced to obtain 111,382 unigenes, which were then annotated with NR, GO, KEGG, eggNOG. Differential expression analysis and NR function prediction revealed 18 differentially expressed unigenes associated with 13 enzymes in flavonoid biosynthetic pathways. Our results reveal new insights on secondary metabolite biosynthesis‐related genes in S. japonica and enhance the potential applications of S. japonica in genetic engineering.