Expression of stress gene networks in tomato lines susceptible and resistant to Tomato yellow leaf curl virus in response to abiotic stresses.

The defense response to several abiotic stresses has been compared in two tomato inbred lines issued from the same breeding program, one susceptible and the other resistant to Tomato yellow leaf curl virus (TYLCV) infection. The level of oxidative burst and the amounts of key regulatory stress proteins: pathogenesis-related proteins (PRs), heat shock proteins (HSPs) and mitogen-activated protein kinases (MAPKs) were appraised following treatments with NaCl, H(2)O(2), and ethanol. Significant differences in the response of the two tomato genotypes to these stresses have been found for HSPs and MAPKs patterns at the level of down-regulation but not activation. The higher abundance of HSPs and MAPKs in tomatoes resistant to TYLCV could result in enhanced defense capacity against abiotic stresses.     

Tomato yellow leaf curl virus infection of a resistant tomato line with a silenced sucrose transporter gene LeHT1 results in inhibition of growth, enhanced virus spread, and necrosis

To identify genes involved in resistance of tomato to Tomato yellow leaf curl virus (TYLCV), cDNA libraries from lines resistant (R) and susceptible (S) to the virus were compared. The hexose transporter LeHT1 was found to be expressed preferentially in R tomato plants. The role of LeHT1 in the establishment of TYLCV resistance was studied in R plants where LeHT1 has been silenced using Tobacco rattle virus-induced gene silencing (TRV VIGS). Following TYLCV inoculation, LeHT1-silenced R plants showed inhibition of growth and enhanced virus accumulation and spread. In addition, a necrotic response was observed along the stem and petioles of infected LeHT1-silenced R plants, but not on infected not-silenced R plants. This response was specific of R plants since it was absent in infected LeHT1-silenced S plants. Necrosis had several characteristics of programmed cell death (PCD): DNA from necrotic tissues presented a PCD-characteristic ladder pattern, the amount of a JNK analogue increased, and production of reactive oxygen was identified by DAB staining. A similar necrotic reaction along stem and petioles was observed in LeHT1-silenced R plants infected with the DNA virus Bean dwarf mosaic virus and the RNA viruses Cucumber mosaic virus and Tobacco mosaic virus. These results constitute the first evidence for a necrotic response backing natural resistance to TYLCV in tomato, confirming that plant defense is organized in multiple layers. They demonstrate that the hexose transporter LeHT1 is essential for the expression of natural resistance against TYLCV and its expression correlates with inhibition of virus replication and movement.     

A developmentally regulated lipocalin-like gene is overexpressed in Tomato yellow leaf curl virus-resistant tomato plants upon virus inoculation, and its silencing abolishes resistance

To discover genes involved in tomato resistance to Tomato yellow leaf curl virus (TYLCV), we previously compared cDNA libraries from susceptible (S) and resistant (R) tomato lines. Among the genes preferentially expressed in R plants and upregulated by TYLCV infection was a gene encoding a lipocalin-like protein. This gene was termed Solanum lycopersicum virus resistant/susceptible lipocalin (SlVRSLip). The SlVRSLip structural gene sequence of R and S plants was identical. SlVRSLip was expressed in leaves during a 15-day window starting about 40?days after sowing (20?days after planting). SlVRSLip was upregulated by Bemisia tabaci (the TYLCV vector) feeding on R plant leaves, and even more strongly upregulated following whitefly-mediated TYLCV inoculation. Silencing of SlVRSLip in R plants led to the collapse of resistance upon TYLCV inoculation and to a necrotic response along the stem and petioles accompanied by ROS production. Contrary to previously identified tomato lipocalin gene DQ222981, SlVRSLip was not regulated by cold, nor was it regulated by heat or salt. The expression of SlVRSLip was inhibited in R plants in which the hexose transporter gene LeHT1 was silenced. In contrast, the expression of LeHT1 was not inhibited in SlVRSLip-silenced R plants. Hence, in the hierarchy of the gene network conferring TYLCV resistance, SlVRSLip is downstream of LeHT1. Silencing of another gene involved in resistance, a Permease-I like protein, did not affect the expression of SlVRSLip and LeHT1; expression of the Permease was not affected by silencing SlVRSLip or LeHT1, suggesting that it does not belong to the same network. The triple co-silencing of SlVRSLip, LeHT1 and Permease provoked an immediate cessation of growth of R plants upon infection and the accumulation of large amounts of virus. SlVRSLip is the first lipocalin-like gene shown to be involved in resistance to a plant virus.     

Silencing of a single gene in tomato plants resistant to Tomato yellow leaf curl virus renders them susceptible to the virus

A reverse-genetics approach was applied to identify genes involved in Tomato yellow leaf curl virus (TYLCV) resistance, taking advantage of two tomato inbred lines from the same breeding program—one susceptible (S), one resistant (R—that used Solanum habrochaites as the source of resistance. cDNA libraries from inoculated and non-inoculated R and S plants were compared, postulating that genes preferentially expressed in the R line may be part of the network sustaining resistance to TYLCV. Further, we assumed that silencing genes located at important nodes of the network would lead to collapse of resistance. Approximately 70 different cDNAs representing genes preferentially expressed in R plants were isolated and their genes identified by comparison with public databases. A Permease I-like protein gene encoding a transmembranal transporter was further studied: it was preferentially expressed in R plants and its expression was enhanced several-fold following TYLCV inoculation. Silencing of the Permease gene of R plants using Tobacco rattle virus-induced gene silencing led to loss of resistance, expressed as development of disease symptoms typical of infected susceptible plants and accumulation of large amounts of virus. Silencing of another membrane protein gene preferentially expressed in R plants, Pectin methylesterase, previously shown to be involved in Tobacco mosaic virus translocation, did not lead to collapse of resistance of R plants. Thus, silencing of a single gene can lead to collapse of resistance, but not every gene preferentially expressed in the R line has the same effect, upon silencing, on resistance.     

金针菇成熟期和伸长期菌盖的转录组与蛋白组比较分析

菌盖是大型真菌的重要组成部分,也是其产生有性孢子的部位,但是其发育机制仍不明确。本研究以金针菇Flammulina filiformis为材料,采用转录组和蛋白组联合分析的方法,比较分析了金针菇成熟期和伸长期菌盖的差异基因与蛋白,并对其进行GO (gene ontology)功能聚类分析、KEGG (Kyoto encyclopedia of genes and genomes)富集分析和蛋白互作网络分析。本研究筛选到差异表达基因有1 391个,差异表达蛋白147个,均以上调表达为主。GO功能聚类分析结果表明,催化活性(catalytic activity)条目富集基因最多,其次是细胞组分(cell part)、细胞过程(cellular process)和细胞器(organelle)。KEGG富集分析结果表明,差异表达基因和蛋白主要富集在碳水化合物代谢通路(carbohydrate metabolism)和氨基酸代谢通路(amino acid metabolism)等。本研究选取了9个关键的差异表达基因,使用实时荧光定量PCR (real-time quantitative PCR,RT-qPCR)对其表达量进行了验证。RT-qPCR验证结果与转录组测序结果相一致。蛋白互作网络分析表明,水解酶类、结构域类和转录调节类蛋白为互作网络的主要结点。本研究联合转录组、蛋白组测序数据,通过分析差异基因与蛋白,为深入了解金针菇菌盖发育机制提供数据参考。     

Within-Host Dynamics of the Emergence of Tomato Yellow Leaf Curl Virus Recombinants

Tomato yellow leaf curl virus (TYLCV) is a highly damaging begomovirus native to the Middle East. TYLCV has recently spread worldwide, recombining with other begomoviruses. Recent analysis of mixed infections between TYLCV and Tomato leaf curl Comoros begomovirus (ToLCKMV) has shown that, although natural selection preserves certain co-evolved intra-genomic interactions, numerous and diverse recombinants are produced at 120 days post-inoculation (dpi), and recombinant populations from different tomato plants are very divergent. Here, we investigate the population dynamics that lead to such patterns in tomato plants co-infected with TYLCV and ToLCKMV either by agro-inoculation or using the natural whitefly vector Bemisia tabaci. We monitored the frequency of parental and recombinant genotypes independently in 35 plants between 18 and 330 dpi and identified 177 recombinants isolated at different times. Recombinants were detected from 18 dpi and their frequency increased over time to reach about 50% at 150 dpi regardless of the inoculation method. The distribution of breakpoints detected on 96 fully sequenced recombinants was consistent with a continuous generation of new recombinants as well as random and deterministic effects in their maintenance. A severe population bottleneck of around 10 genomes was estimated during early systemic infection–a phenomenon that could account partially for the heterogeneity in recombinant patterns observed among plants. The detection of the same recombinant genome in six of the thirteen plants analysed beyond 30 dpi supported the influence of selection on observed recombination patterns. Moreover, a highly virulent recombinant genotype dominating virus populations within one plant has, apparently, the potential to be maintained in the natural population according to its infectivity, within-host accumulation, and transmission efficiency - all of which were similar or intermediate to those of the parent genotypes. Our results anticipate the outcomes of natural encounters between TYLCV and ToLCKMV.     

Expression of stress-response proteins upon whitefly-mediated inoculation of Tomato yellow leaf curl virus in susceptible and resistant tomato plants

To better understand the nature of resistance of tomato to the whitefly (Bemisia tabaci, B biotype)-transmitted Tomato yellow leaf curl virus (TYLCV), whiteflies and TYLCV were considered as particular cases of biotic stresses and virus resistance as a particular case of successful response to these stresses. Two inbred tomato lines issued from the same breeding program that used Solanum habrochaites as a TYLCV resistance source, one susceptible and the other resistant, were used to compare the expression of key proteins involved at different stages of the plant response with stresses: mitogen-activated protein kinases (MAPKs), cellular heat shock proteins (HSPs, proteases), and pathogenesis-related (PR) proteins. The two biotic stresses-non-viruliferous whitefly feeding and virus infection with viruliferous insects--led to a slow decline in abundance of MAPKs, HSPs, and chloroplast protease FtsH (but not chloroplast protease ClpC), and induced the activities of the PR proteins, beta-1,3-glucanase, and peroxidase. This decline was less pronounced in virus-resistant than in virus-susceptible lines. Contrary to whitefly infestation and virus infection, inoculation with the fungus Sclerotinia sclerotiorum induced a rapid accumulation of the stress proteins studied, followed by a decline; the virus-susceptible and -resistant tomato lines behaved similarly in response to the fungus.     

flg22诱导的拟南芥转录组分析及芥子油苷代谢途径的变化

flg22是细菌鞭毛蛋白N端的一段保守性极高的区域,能够诱导植物天然的免疫反应,为全面了解植物在受到细菌性病原菌侵害后的系统响应,利用Illumina Hiseq2000对flg22处理和未处理的拟南芥幼苗进行转录组测序。对两组数据进行差异表达分析,共获得1 200个差异表达基因,包括290个下调基因和910个上调基因。对差异表达基因进行GO富集分析和KEGG pathway富集分析,结果显示,flg22处理后,拟南芥在能量代谢、氨基酸代谢及次生代谢产物的生物合成等方面产生了巨大变化。芥子油苷是一类在植物防御病原菌的天然免疫反应中起重要作用的次生代谢产物,因此对芥子油苷代谢途径的变化进行了深入分析。根据测序结果,Flg22处理后吲哚族芥子油苷合成途径的基因表达水平显著提高,而脂肪族芥子油苷代谢途径几乎没有变化,进一步对吲哚族芥子油苷合成途径的关键酶基因进行Real Time RT-PCR的分析,验证了测序结果的正确性,证明了吲哚族芥子油苷在植物抗病防御反应中的重要作用。这为深入理解病原菌诱导的植物防御性反应及吲哚族芥子油苷的抗病机制提供了大量参考数据。     

东乡野生稻苗期响应低温胁迫的转录组分析

为了解东乡野生稻（Oryza rufipogon）对低温胁迫的响应机制,对苗期的RNA-seq转录表达谱进行了研究。结果表明,与对照相比,共检测到10 200个差异表达基因（DEGs）,其中5 201个上调表达,4 999个下调表达,其中有426个DEGs位于已报道的水稻耐冷QTL区间,且37个为耐冷调控相关的家族基因。GO功能分类和KEGG代谢路径分析表明,核酸结合转录因子活性、氨基酸生物合成以及光合作用代谢等均参与响应低温胁迫过程。实时荧光定量分析表明,ABA响应蛋白基因、MYB转录因子和40S核糖体蛋白SA基因等12个可能与低温胁迫响应相关的DEGs表达模式与RNA-seq的一致。可见,植物激素传导途径和转录因子相关调控基因在东乡野生稻苗期响应低温胁迫过程中起重要作用。     

基于转录组的不同火龙果品种抗性差异分析

不同的品种抗性不同,为进一步探究不同火龙果品种之间的抗性差异,为后续火龙果抗性育种提供参考,该研究利用Illumina HiSeq 2000测序平台对'普通白肉'(BR)和'厄瓜多尔黄龙'(EY)两个品种进行转录组测序分析,并参考GO Ontology、KEGG等公共数据库对差异表达基因进行功能分类与富集分析.结果表明...     

Global changes in gene expression during compatible and incompatible interactions of cowpea (Vigna unguiculata L.) with the root parasitic angiosperm Striga gesnerioides

ABSTRACT: BACKGROUND: Cowpea, Vigna unguiculata L. Walp., is one of the most important food and forage legumesin the semi-arid tropics. While most domesticated forms of cowpea are susceptible to the rootparasitic weed Striga gesnerioides, several cultivars have been identified that show racespecificresistance. Cowpea cultivar B301 contains the RSG3-301 gene for resistance to S.gesnerioides race SG3, but is susceptible to race SG4z. When challenged by SG3, roots ofcultivar B301 develop a strong resistance response characterized by a hypersensitive reactionand cell death at the site of parasite attachment. In contrast, no visible response occurs inB301 roots parasitized by SG4z. RESULTS: Gene expression in the roots of the cowpea cultivar B301 during compatible (susceptible) andincompatible (resistant) interactions with S. gesnerioides races SG4z and SG3, respectively,were investigated at the early (6 days post-inoculation (dpi)) and late (13 dpi) stages of theresistance response using a Nimblegen custom design cowpea microarray. A total of 111genes were differentially expressed in B301 roots at 6 dpi; this number increased to 2102genes at 13 dpi. At 13 dpi, a total of 1944 genes were differentially expressed duringcompatible (susceptible) interactions of B301 with SG4z . Genes and pathways involved insignal transduction, programmed cell death and apoptosis, and defense response to biotic andbiotic stress were differentially expressed in the early resistance response; at the later timepoint, enrichment was primarily for defense-related gene expression, and genes encodingcomponents of lignifications and secondary wall formation. In compatible interactions (B301- SG4z), multiple defense pathways were repressed, including those involved in ligninbiosynthesis and secondary cell wall modifications, while cellular transport processes fornitrogen and sulfur were increased. CONCLUSION: Distinct changes in global gene expression profiles occur in host roots following successfuland unsuccessful attempted parasitism by Striga. Induction of specific defense related genesand pathways defines components of a unique resistance mechanism. Some genes andpathways up-regulated in the host resistance response to SG3 are repressed in the susceptibleinteractions, suggesting that the parasite is targeting specific components of the host'sdefense. These results add to our understanding of plant-parasite interactions and theevolution of resistance to parasitic weeds.