大蒜根腐病根际土壤真菌群落结构及多样性分析

研究旨在解析根腐病发生时大蒜根际土壤真菌群落结构,明确大蒜根腐病与根际土壤真菌群落多样性变化的关系,探明根腐病发生的微生态机制,为病害的防控提供理论基础。以新疆连续3年的大蒜根腐病发病田的根际土壤为研究对象,采用高通量测序方法对大蒜根际土壤总DNA的真菌ITS区序列进行大规模测序分析。结果表明,与健康对照相比,在门的水平上,子囊菌门和接合菌门真菌是大蒜根腐病根际土壤的优势真菌类群,其中高水平的子囊菌门菌群与病害发生有着密切的关系。在属的水平上,注释获得137个属,其中19个属与大蒜根腐病有较大的相关性。镰刀菌属真菌数量在病土中高于健康对照。随着连作年限的延续,根腐病的发生愈发严重,土壤中真菌群落的Shannon指数、Simpson指数、真菌属的数量逐年降低,大蒜根腐病的发生与植株根际真菌群落组成及多样性密切相关,土壤真菌类群的平衡和多样性改变是根腐病发生的一大诱因。     

花椒茎尖节点转录组测序及基因注释

花椒茎枝有尖锐皮刺,在实际生产中增加采摘成本,并降低采摘效率。为培育品质优良的无刺品种,筛选皮刺分化的关键基因具有重要意义。使用二代高通量测序技术对花椒皮刺起始分化的茎尖节点组织转录组进行测序,使用生物学软件对原始数据进行拼装,最终获得45 057条转录本序列。使用比对工具将得到的转录本与Swiss-Prot,NR,Pfam,KEGG,KOG数据库比对后,80.34%的转录本序列至少被一个数据库注释。获取的大量的基因序列及注释信息为进一步探究花椒皮刺分化分子机理提供了良好的基础,为定位皮刺分化关键基因提供依据。     

连作、轮作对谷子根际细菌群落结构的影响

为探明谷子连作与轮作对土壤细菌群落组成的影响,利用高通量测序技术,结合土壤理化性质及酶活性,比较分析了撂荒地、玉米-谷子轮作、谷子连作2、3 a和5 a土壤细菌群落组成多样性。结果表明：谷子连作与轮作土壤均为碱性,pH为8.26~8.49,碱解氮、有机质、脲酶活性表现为轮作地最高,连作2 a开始降低,连作3 a达最低值,连作5 a又开始回升,速效钾、多酚氧化酶、过氧化氢酶以及蔗糖酶活性均是连作土壤高于轮作土壤。谷子连作与轮作土壤细菌在门水平上群落组成比较固定,但不同物种的丰度差异较大;菌群分析发现放线菌门、变形菌门以及酸杆菌门是谷子根际土壤优势菌群;菌群相对丰度在轮作土壤中高于连作土壤的有：变形菌门、酸杆菌门、拟杆菌门、厚壁菌门以及硝化螺旋菌门,低于连作土壤的有己科河菌门和绿弯菌门;Alpha多样性分析显示各组间菌群差异不显著,Beta多样性分析则显示连作、玉米-谷子轮作地和撂荒地土壤菌群分布差异较大;冗余分析（RDA）表明鞘氨醇单胞菌与pH、有效磷、碱解氮和有机质呈正相关,类诺卡氏菌与pH、有效磷、碱解氮、有机质、脲酶和过氧化氢酶呈正相关,轮作、连作、撂荒地组间根际土壤优势菌存在差异,LEfSe分析确定了谷子根际土壤特定标志物,其中轮作地的优势菌群为鞘氨醇单胞菌和类诺卡氏菌,3 a连作地的优势菌群为土壤红杆菌。综上所述,谷子连作土壤与轮作土壤相比,细菌的ASVs丰度减少,细菌群落分布差异较大;随着谷子连作年限增加,土壤养分呈先下降后上升趋势。     

DNA分子检测技术在节肢动物食物网结构解析中的应用

生态系统中节肢动物食物网结构错综复杂,通过观察和解剖等传统手段往往很难精准地获得物种种类及彼此之间食物关系的全面信息。近年来,DNA分子检测技术快速发展,显著促进了节肢动物食物网复杂结构的系统解析,有效实现了食物网结构分析由定性向定量的重要转变。该文介绍DNA分子检测的主要技术及其优缺点,列举其在节肢动物食物网结构分析中的应用实例,讨论DNA分子检测技术在应用中遇到的问题及挑战,旨在为节肢动物食物网结构分析提供科学依据和技术指导,有力推进农田等不同生态系统中节肢动物食物网结构及其生态功能的深入研究和挖掘利用。     

红螯光壳螯虾响应长期水体盐度胁迫的基因和代谢通路

为探究长期盐度胁迫条件下红螯光壳螯虾肠道基因表达和代谢通路的变化。实验采用Illumina Hiseq 2 500平台对0、5、10和15这4个盐度下养殖5周的红螯光壳螯虾的肠道组织进行了高通量测序。研究共获76 534个unigenes,通过与NR、NT、KO、Swissprot、PFAM、GO和KOG数据库进行比对,成功注释37 378个unigenes。通过引入FPKM(Fragments Per Kilo bases per Million fragments)来估算基因表达水平,基于NR和Pfam两个数据库的蛋白注释结果,448 362个unigenes在GO数据库得到注释。根据KO功能注释与Pathway的联系,9 483个unigenes在KEGG数据库被注释分类到34条通路途径。通过DEGseq进行基因表达差异分析,以盐度0为对照组,显著差异基因筛选条件设置为Q value<0.05且差异倍数|Fold Change|>2,盐度5、10和15组分别获得差异基因2 733、91和236个,其中盐度5组共有2 068个基因显著上调,665个基因显著下调。将所有差...     

高通量测序技术及其在生命科学中的应用

Sanger法第1代测序技术给人类破译遗传密码提供了强有力的工具,经过30多年的不断改善,现已发展到以高通量、速度快、低成本为主要特征的第二代测序技术,给生命科学领域带来了革命性的变化。比较了第2代测序方法与Sanger测序方法的差异,并阐述了其在生命科学中的应用。     

基于高通量测序的技术检测梨树病毒

【目的】 研究运用基于高通量测序的技术检测梨树病毒,为梨树病毒的检测提供新方法。【方法】 于2014年、2017年、2018年4月中旬采集库尔勒香梨花朵若干,分别进行转录组测序,将得到的序列经过转录本拼接、层次聚类和基因功能注释,筛选出注释为植物病毒的序列作为候选病毒序列。利用RT-PCR方法检测随机采集的香梨枝条样品,验证高通量测序结果的可靠性。【结果】 根据3组转录组测序数据的生物信息学分析结果,分别对注释为来源于植物病毒的66、202和921条基因序列进行分析。3种梨树中已报道的病毒,分别是苹果茎痘病毒、苹果茎沟病毒和苹果褪绿叶斑病毒,以及梨树中未报道的芸薹黄化病毒。采用设计的特异性引物,通过RT-PCR技术对筛选出的4种病毒进行扩增验证,结果扩增出苹果茎痘病毒和苹果茎沟病毒的目的片段。【结论】 高通量测序技术可作为检测梨树病毒的一种快速、有效手段。     

Improvement,identification, and target prediction for miRNAs in the porcine genome by using massive,public high-throughput sequencing data

Despite the broad variety of available microRNA (miRNA) research tools and methods, their application to the identification, annotation, and target prediction of miRNAs in nonmodel organisms is still limited. In this study, we collected nearly all public sRNA-seq data to improve the annotation for known miRNAs and identify novel miRNAs that have not been annotated in pigs (Sus scrofa). We newly annotated 210 mature sequences in known miRNAs and found that 43 of the known miRNA precursors were problematic due to redundant/missing annotations or incorrect sequences. We also predicted 811 novel miRNAs with high confidence, which was twice the current number of known miRNAs for pigs in miRBase. In addition, we proposed a correlation-based strategy to predict target genes for miRNAs by using a large amount of sRNA-seq and RNA-seq data. We found that the correlation-based strategy provided additional evidence of expression compared with traditional target prediction methods. The correlation-based strategy also identified the regulatory pairs that were controlled by nonbinding sites with a particular pattern, which provided abundant complementarity for studying the mechanism of miRNAs that regulate gene expression. In summary, our study improved the annotation of known miRNAs, identified a large number of novel miRNAs, and predicted target genes for all pig miRNAs by using massive public data. This large data-based strategy is also applicable for other nonmodel organisms with incomplete annotation information.     

Identification of novel juvenile-hormone signaling activators via high-throughput screening with a chemical library

Juvenile hormone (JH) is an insect-specific hormone that regulates molting and metamorphosis. Hence, JH signaling inhibitors (JHSIs) and activators (JHSAs) can be used as effective insect growth regulators (IGRs) for pest management. In our previous study, we established a high-throughput screening (HTS) system for exploration of novel JHSIs and JHSAs using a Bombyx mori cell line (BmN_JF&AR cells) and succeeded in identifying novel JHSIs from a chemical library. Here, we searched for novel JHSAs using this system. The four-step HTS yielded 10 compounds as candidate JHSAs; some of these compounds showed novel basic structures, whereas the others were composed of a 4-phenoxyphenoxymethyl skeleton, the basic structure of several existing JH analogs (pyriproxyfen and fenoxycarb). Topical application of seven compounds to B. mori larvae significantly prolonged the larval period, suggesting that the identified JHSAs may be promising IGRs targeting the JH signaling pathway.     

Element interconnections in Lotus japonicus: A systematic study of the effects of element additions on different natural variants

Lotus japonicus was used to study the distribution and interconnections of 15 elements in plant tissues, including essential and non-essential elements: boron (B), sodium (Na), magnesium (Mg), potassium (K), calcium (Ca), manganese (Mn), iron (Fe), nickel (Ni), copper (Cu), zinc (Zn), arsenic (As), strontium (Sr), molybdenum (Mo), cadmium (Cd) and cesium (Cs). Large amounts of B and Ca accumulated in plant leaves, while Fe, Na, Ni, As and Cd tended to mainly occur in the roots, and Mo was the only element to accumulate in the stems. The elemental compositions within plants were severely disturbed by treatment with toxic elements. Competition between element pairs in the same group (e.g. K and Cs; Ca and Sr) was not found. Iron, Cu and Zn accumulation were induced by Cd and Ni addition. When natural variants grew in a nutrition solution with subtoxic levels of As, Cd, Cs, Ni, Mo and Sr, intriguing relationships between the elements (such as Fe, As and K; Mg and Ni; Mn and Ca) were revealed using principal-component analysis. This study on the plant ionome offers detailed information of element interactions and indicates that chemically different elements might be closely linked in uptake or translocation systems.