基于中麻黄萌发种子转录组的黄酮类化合物合成途径基因的挖掘

应用新一代高通量测序技术(Illumina Solexa),对中麻黄(Ephedra intermedin)同萌期的种子进行转录组测序,数据重头(denovo)组装后,共获得52 007条Unigene序列,总长为25 043 596 bp。COG功能注释、GO分类及KEGG代谢通路分析后,获得了64 751个GO功能注释,17 701个COG功能注释以及16 942个KEGG注释,并从KEGG通路中找到参与黄酮类化合物合成途径的关键基因片段283个,其中包含了查尔酮合酶基因、细胞色素相关基因和花青素还原酶等基因。中麻黄转录组测序工作的完成,极大地扩充了麻黄的基因资源,为麻黄属植物分子系统进化分析、抗性和药用功能基因的发掘与利用、遗传改良等研究奠定基础。     

不同封育年限下石灰岩山地植被 细根生物量及其动态

利用土钻法对不同封育年限下石灰岩山地植被细根生物量进行对比研究。结果表明院封育5 年林分细根 生物量为6.6287 t/hm2,封育10 年林分细根生物量为2.3063 t/hm2,封育20 年林分细根生物量为3.1316 t/hm2,封育 30 年林分细根生物量为2.8316 t/hm2;不同封育年限下细根生物量均随着土层深度的增加而降低,0~10 cm 土层的细 根生物量明显高于其他两个土层;不同封育年限细根生物量年动态变化均呈现双峰型。     

Evaluation of 'quick and dirty' DNA extraction methods for marker-assisted selection in rice (Oryza sativa L.)

Six simple methods for extracting DNA from rice seedlings were evaluated for marker‐assisted selection (MAS). The assessment of each method was based on PCR amplification of SSR markers, DNA yield and purity, time and cost. Based on these criteria, two methods were selected as being superior to other methods. The best two methods included the standard method developed at the International Rice Research Institute (IRRI), which utilizes a sodium dodecyl sulfate extraction buffer followed by chloroform/isoamyl alcohol extraction and a previously published method using sodium hydroxide and Tris. These two methods produced nearly identical PCR amplification results. The sodium hydroxide method is considerably simpler, quicker and cheaper than the standard IRRI method, and may be particularly useful for many applications of MAS or high‐resolution mapping. This method was also adapted into an effective high throughput method utilizing 96‐well plates emphasizing its versatility.     

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。     

连作与轮作下木薯产量及土壤微生物特征比较

本研究以木薯品种新选048为材料,利用高通量测序技术比较研究木薯连作与轮作的土壤微生物丰度、多样性、群落组成,并结合土壤三相比和木薯产量综合分析,探讨木薯连作障碍与土壤微生物的关系。结果表明：木薯连作土壤的细菌丰度、多样性高于轮作,连作细菌的OTU数目比轮作高23.05%,Chao1指数比轮作高463.2,香农指数比轮作高0.41;而连作真菌丰度、多样性低于轮作,轮作真菌的OTU数目比连作高19.57%,Chao1指数比连作高217.5,香农指数比连作高0.76;连作土壤容重比轮作高0.24 g/cm ³;土壤三相比,木薯连作的土壤固相比率比轮作高6.69%,液相比轮作高3.03%,而气相比率比轮作减少9.72%,差异显著（P<0.05）;轮作木薯产量比连作增产11.99 t/hm ²,差异显著（P<0.05）。由此可见,土壤微生物组和土壤三相比的变化与木薯连作障碍有密切关系,采取栽培管理措施调节土壤微物组成和土壤三相比,是克服木薯连作障碍的有效途径。     

基于DNA宏条形码的莼菜大田土壤真菌多样性研究

高通量测序与DNA条形码结合产生的DNA宏条形码技术(DNA-Metabarcoding),能快速鉴定混合样本中的物种,现已成为检测群类物种多样性和丰富度的常用方法.本试验采用这一方法分析了莼菜大田不同种植年限土壤真菌多样性,结果表明:10年生土壤中含有最多的真菌种类,多样性及丰富度最高;在属水平上表现为蛙粪霉属、裂梗霉属、酵母属等占优势;群类组成分析显示,种植年限的变化对土壤真菌群落组成有一定的影响;聚类分析中10年与15年生莼菜土壤物种多样性相似度较高.     

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.     

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.     

基于数字化植物表型平台（D3P）的田间小麦冠层光截获算法开发

冠层光截获能力是反映作物品种间差异的重要功能性状，高通量表型冠层光截获对提高作物改良效率具有重要意义。本研究以小麦为研究目标，利用数字化植物表型平台（D3P）模拟生成了100种冠层结构不同的小麦品种在5个生育期的三维冠层场景，记录了从原始冠层结构中提取的绿色叶面积指数（GAI）、平均倾角（AIA）和散射光截获率（FIPAR_dif）信息作为真实值,进一步利用上述三维小麦场景开展了虚拟的激光雷达（LiDAR）模拟实验，生成了对应的三维点云数据。基于模拟的点云数据提取了其高度分位数特征（H）和绿色分数特征（GF）。最后，利用人工神经网络（ANN）算法分别构建了从不同LiDAR点云特征（H、GF和H+GF）输入到FIPAR_dif、GAI和AIA的反演模型。结果表明，对于GAI、AIA和FIPAR_dif，预测精度从高到低对应的点云特征输入为GF+H > H > GF。由此可见，H特征对提高目标表型特性的估算精度起到了重要作用。输入GF + H特征，在中等测量噪音（10%）情况下，FIPAR_dif和GAI的估算均获得了满意精度，R²分别为0.95和0.98，而AIA的估算精度（R²=0.20）还有待进一步提升。本研究基于D3P模拟数据开展，算法的实际表现还有待通过田间数据进一步验证。尽管如此，本研究验证了D3P协助表型算法开发的能力，展示了高通量LiDAR数据在估算田间冠层光截获和冠层结构方面的较高潜力。     

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。