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1.
To identify viruses in Henan tobacco-planting areas, from 2015 to 2017 and 2019, 288 symptomatic tobacco samples were collected and then subjected to small RNA sequencing. Results showed that at least 7 viruses were detected from these samples which including four previously reported viruses, cucumber mosaic virus (CMV), tobacco mosaic virus (TMV), potato virus Y (PVY) and tobacco vein banding mosaic virus (TVBMV). Other three viruses, wild tomato mosaic virus (WTMV), brassica yellows virus (BrYV), and cycas necrotic stunt virus (CNSV) were firstly detected in Henan province. However, tobacco etch virus (TEV) and tobacco ringspot virus (TRSV) were not detected from these samples. In addition, CMV, TMV, PVY, TVBMV, and BrYV were the dominant viruses infecting tobacco in Henan Province. 相似文献
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基于传统的酸性酚—异硫氰酸胍—氯仿一步提取法,比较分析多种优化操作步骤,摸索出一种高质量提取体质量为80~150 g草鱼肠系膜脂肪组织总RNA的改良方法。试验结果显示,相较于肝脏、脾脏、肠道等脏器组织,草鱼肠系膜脂肪组织RNA丰度低,且极易在样品前处理阶段出现顽固性降解问题。探索发现,将取样量增至约30 mg,可提升RNA产量以满足常规试验需求。针对降解难题,改良常规的样品前处理技术流程,采用鲜样液氮速冻,冻样直接放入TRIzol试剂中裂解,并即刻进行长时间机械匀浆,时长约3 min等核心操作步骤,可显著降低脂肪组织样品RNA的降解。Agilent生物分析仪检测结果显示,改良方法提取的草鱼肠系膜脂肪组织RNA完整度高,关键RIN值为8.7~9.0。研究推测,长时间机械匀浆所形成的持续剪切冲击力或许有助于TRIzol试剂中的异硫氰酸胍等成分突破油滴阻碍而有效抑制内源性RNA酶。本方法提取的草鱼脂肪组织总RNA质量可满足高通量转录组测序要求。 相似文献
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Cong HUANG Kun LANG Wan-qiang QIAN Shu-ping WANG Xiao-mei CAO Rui HE An-ran ZHAN Meng-yao CHEN Nian-wan YANG Fei LI 《农业科学学报》2021,20(1):191-200
Invasive alien species(IAS) are species whose introduction to areas outside of their native range cause harm to economics, biodiversity, and the environment. Understanding the genetic basis of invasiveness is critical for preventing invasion by an alien species and managing IAS with eco-friendly control methods. In addition, uncovering the genomic features of IAS is essential for accurately predicting invasiveness. However, even though increasing efforts have been devoted to sequencing the genomes of IAS, there is still not an integrated genome database for the invasive biology community. Here, we first determined a list of invasive plants and animals by mining references and databases. Then, we retrieved the genomic and gene data of these IAS, and constructed a database, Invasion DB. Invasion DB encompasses 131 IAS genomes, 76 annotated IAS assemblies, and links these data to conventional functions such as searching for gene coding sequences and Pfam, KEGG, NR annotations, BLAST server, JBrowse, and downloads services. Next, we analyzed 19 invasivenessrelated gene families which confer invasiveness in insects. To study the roles of noncoding RNA in invasiveness, we also annotated 135 494 mi RNAs, 89 294 r RNAs, and 2 671 941 t RNAs from these IAS. In summary, Invasion DB is useful for studying the invasiveness at the genomic level, and thus helps to develop novel management strategies to control IAS. 相似文献
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María P. Barrios Barón Verónica C. Delfosse Yamila C. Agrofoglio Vanesa Nahirñak Natalia I. Almasia Cecilia Vazquez Rovere Ana J. Distéfano 《Plant pathology》2021,70(2):259-274
The potato leafroll virus (PLRV) P0 protein (P0PL) is a suppressor of RNA silencing. In this study, we showed that P0 protein from an Argentinian isolate of PLRV (P0PL-Ar) has an additional activity not described for other PLRV or P0 proteins from poleroviruses. Besides reporting that P0PL-Ar displays both local and systemic silencing suppressor activity, we demonstrated, for the first time, that P0PL-Ar impedes accumulation of dsRNA-derived siRNAs. We also showed that P0PL-Ar interacts with Solanum tuberosum SKP1 orthologue (StSKP1) and triggers destabilization of ARGONAUTE 1 (AGO1) and that these actions are mediated by the F-box-like domain. A mutant in the GW/WG motif within the P0PL-Ar F-box-like motif lost the suppression activity, the interaction with StSKP1 and abolished AGO1 decay. Interestingly, a mutant in the L76/P77 residues within the P0PL-Ar F-box-like motif, which lost the suppression activity and the interaction with StSKP1, retained the capacity to enable AGO1 decay. Thus, unlike other P0 proteins of previously characterized poleroviruses, P0PL-Ar seems to have a dual activity, according to the findings of this study. This protein would act at both an upstream and a downstream step of the RNA silencing pathway: upstream of Dicer-like enzyme (DCL)-mediated primary siRNA production and downstream at the RNA-induced silencing complex (RISC) complex level. Our results contribute to the understanding of the different ways PLRV P0 proteins function as silencing suppressors. 相似文献
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Peritrophic matrix/membrane (PM) critically prevents the midgut of insects from external invasion by microbes. The proteins in the peritrophic membrane are its major structural components. Additionally, they determine the formation and function of this membrane. However, the role of PM proteins in immune regulation is unclear. Herein, we isolated a novel PM protein (MdPM-17) from Musca domestica larvae. Further, the function of MdPM-17 in regulating host innate immunity was identified. Results showed that the cDNA of MdPM-17 full is 635 bp in length. Moreover, it consists of a 477-bp open reading frame encoding 158 amino acid residues. These amino acid residues are composed of two Chitin-binding type-2 domain (ChtBD2) and 19 amino acids as a signal peptide. Moreover, tissue distribution analysis indicates that MdPM-17 was enriched expressed in midgut, and moderate levels in the fat body, foregut, and malpighian tubule. Notably, MdPM-17 recombinant protein showed high chitin-binding capacity, thus belongs to the Class III PM protein group. MdPM-17 protein silencing via RNA interference resulted in the expression of antimicrobial peptide (defensin, cecropins, and diptericin) genes, and this occurred after oral inoculation with exogenous microbes Escherichia coli (Enterobacteriales:Enterobacteriaceae), Staphylococcus aureus (Bacillales:Staphylococcaceae), and Candida albicans (Endomycetales:Saccharomycetaceae)). Therefore, all the antimicrobial peptide (AMP) gene expression levels are high in MdPM-17-depleted larvae during microbial infection compared to controls. Consequently, these findings indicate that MdPM-17 protein is associated with the antibacterial response from the housefly. 相似文献
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Kelsey T. Young Kevin K. Lahmers Holly S. Sellers David E. Stallknecht Rebecca L. Poulson Jerry T. Saliki Stephen Mark Tompkins Ian Padykula Chris Siepker Elizabeth W. Howerth Michelle Todd James B. Stanton 《Journal of veterinary diagnostic investigation》2021,33(2):202
RNA viruses rapidly mutate, which can result in increased virulence, increased escape from vaccine protection, and false-negative detection results. Targeted detection methods have a limited ability to detect unknown viruses and often provide insufficient data to detect coinfections or identify antigenic variants. Random, deep sequencing is a method that can more fully detect and characterize RNA viruses and is often coupled with molecular techniques or culture methods for viral enrichment. We tested viral culture coupled with third-generation sequencing for the ability to detect and characterize RNA viruses. Cultures of bovine viral diarrhea virus, canine distemper virus (CDV), epizootic hemorrhagic disease virus, infectious bronchitis virus, 2 influenza A viruses, and porcine respiratory and reproductive syndrome virus were sequenced on the MinION platform using a random, reverse primer in a strand-switching reaction, coupled with PCR-based barcoding. Reads were taxonomically classified and used for reference-based sequence building using a stock personal computer. This method accurately detected and identified complete coding sequence genomes with a minimum of 20× coverage depth for all 7 viruses, including a sample containing 2 viruses. Each lineage-typing region had at least 26× coverage depth for all viruses. Furthermore, analyzing the CDV sample through a pipeline devoid of CDV reference sequences modeled the ability of this protocol to detect unknown viruses. Our results show the ability of this technique to detect and characterize dsRNA, negative- and positive-sense ssRNA, and nonsegmented and segmented RNA viruses. 相似文献
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以已公布的棉铃虫线粒体DNA序列对来自4头棉铃虫雄蛹的DNA的三代测序数据进行筛选,获得了11条与线粒体DNA有同源性的三代read序列,并根据其中的read 66003鉴定出了一种膨胀的线粒体基因组。该线粒体基因组大小为27 113 bp,其保守区域包含13个蛋白编码基因、2个rRNA基因、22个tRNA基因以及1个AT富集区,与已公布的棉铃虫线粒体基因组的结构相似。膨胀区域位于cox1基因编码区内部,大小为11 467 bp,经预测含有一个完整的真核基因(依赖ATP的RNA解旋酶)以及多种转座元件的片段,但与线粒体DNA无同源性,也无I类或Ⅱ类内含子存在的证据。对田间和室内棉铃虫DNA样品的PCR扩增未能检测到膨胀线粒体基因组的存在。以上结果表明膨胀片段可能是细胞核DNA序列通过偶然的水平转移事件而整合到线粒体基因组中的,且该种膨胀方式的发生概率极低。本文报道的膨胀线粒体基因组为日后动物线粒体基因组学的研究提示了一种独特的变异方式。 相似文献
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