Comprehensive diversity assessment of walnut-associated xanthomonads reveal the occurrence of distinct Xanthomonas arboricola lineages and of a new species (Xanthomonas euroxanthea) within the same tree

Xanthomonas arboricola pv. juglandis (Xaj) is the aetiological agent of walnut diseases causing economic losses on walnut production worldwide. This phytopathogen is spread around the world where walnuts are produced and has a considerable genetic diversity. Using a comprehensive sampling methodology, focusing on factors that could influence the diversity of walnut-colonizing Xaj in Portugal, this work provides new insights on xanthomonad populations on walnut. Genetic diversity was assessed by multilocus sequence analysis (MLSA) and dot blot hybridization patterns on 131 Xanthomonas isolates obtained from 64 walnut trees considering epidemiological metadata such as year of isolation, distinct bioclimatic regions, production regimes, and host-related features. The results showed that the majority of isolates were split into 17 lineages of Xaj, while the other isolates clustered in four MLSA groups that did not include Xaj strains. These four groups were represented by three lineages of X. arboricola, and 11 lineages of Xanthomonas spp., including strains assigned to the recently proposed new species Xanthomonas euroxanthea. Furthermore, distinct Xaj, X. arboricola, and Xanthomonas spp. were isolated from the same walnut tree, suggesting possible genetic admixture within the same host. Phylogenetic analysis through geoBurst revealed the high diversity of these Xanthomonas spp. populations. Assessment of type III effector genes gave the indication that some Xanthomonas spp. strains were nonpathogenic on walnut, with the exception for X. euroxanthea CPBF 424. Altogether, these findings add to the thorough characterization of walnut-associated xanthomonads in Portugal, providing a comprehensive snapshot of the current diversity that could contribute to risk assessment analysis and improve phytosanitary control.     

The effect of salt stress on Arabidopsis thaliana and Phelipanche ramosa interaction

Salinity and Orobanche or Phelipanche spp. infection are important crop stress factors in agricultural areas. In this study, we investigated the effect of salt stress on Phelipanche ramosa seed germination and its attachment onto Arabidopsis thaliana roots. We also evaluated the effect of both stresses on the expression of genes regulated by abiotic and biotic stresses. According to our results, high concentration of NaCl delayed P. ramosa seed germination in the presence of a strigolactone analogue (GR24). A similar pattern was observed in the presence of A. thaliana plants. Furthermore, we found that salt‐treated A. thaliana seedlings were more sensitive to P. ramosa attachment compared with the untreated plants, indicating that there was a positive correlation between salt sensitivity and the ability of P. ramosa to infect A. thaliana plants. At the molecular level, a synergystic effect of both salt and P. ramosa stresses was observed on the cold‐regulated (COR) gene expression profile of treated A. thaliana seedlings. Our data clarify the interaction between parasitic plants and their hosts under abiotic stress conditions.     

向日葵3个谷胱甘肽-S-转移酶GST基因的克隆及表达模式分析

从向日葵转录组测序结果中获得了3个对盐胁迫有响应的谷胱甘肽-S-转移酶（GST，EC2.5.1.18）GST基因，构建了系统进化树并进行分析，得知这3个基因属于Tau型GST，并将它们命名为HaGSTU26（HanXRQChr04g0127901）、HaGSTU8（HanXRQChr06g0177581）、HaGSTU27（HanXRQChr10g0316331），然后以向日葵Sk02R为试验材料，克隆这3个基因，并进行了不同组织和不同胁迫条件下的表达分析。序列分析表明：HaGSTU26基因组为1674bp，CDS（编码蛋白序列）长666bp，编码221个氨基酸，由2个外显子和1个内含子组成；HaGSTU8基因组为2271bp，CDS长654bp，编码217个氨基酸，由2个外显子和1个内含子组成； HaGSTU27基因组为663bp，CDS长663bp，编码220个氨基酸,由1个外显子组成。实时荧光定量PCR分析表明：向日葵HaGSTU26、HaGSTU8、HaGSTU27基因在不同组织（根、幼叶、成熟叶、茎、幼茎、苞叶）中表达量不同，其中，HaGSTU26基因和HaGSTU27基因在根中表达量最高，而HaGSTU8基因在苞叶中表达量最高，但这3个基因均在成熟茎中的表达量最低。在不同胁迫条件下，测定这3个基因在向日葵幼苗中的表达量，结果表明在盐及ABA胁迫下，基因表达量均随着处理时间的增加而呈现先增加后下降的趋势。其中，在盐胁迫下，HaGSTU26基因在12 h后相对表达量最高，HaGSTU8及HaGSTU27基因表达量在3h后相对表达量最高。在ABA胁迫后，HaGSTU26及HaGSTU27基因表达量在12 h后相对表达量最高，HaGSTU8在24 h后相对表达量最高。在冷胁迫下，HaGSTU26和HaGSTU27基因上调表达,它们分别在3、24 h后相对表达量最高，HaGSTU8基因下调表达，其相对表达量随处理时间的延长呈现逐渐减少的趋势。在热胁迫条件下，这3个基因的相对表达量随着胁迫时间的延长而增加,均在24 h后表达量最高。以上结果说明这3个基因对不同非生物胁迫（盐、ABA、冷、热胁迫）均有响应。     

氯虫苯甲酰胺和氟虫腈对黏虫细胞色素P450基因表达的影响

为筛选出黏虫Mythimna separata参与杀虫剂解毒代谢的主效细胞色素P450基因,采用叶片浸渍法测定了用于处理黏虫3龄幼虫的亚致死浓度,通过构建转录组测序文库并结合数字基因表达(digital gene expression,DGE)对不同处理的黏虫进行测序,并运用实时荧光定量PCR(realtime quantitative polymerase chain reaction,RT-qPCR)技术验证12个P450基因的表达情况。结果表明,用于处理黏虫的氯虫苯甲酰胺和氟虫腈亚致死浓度LC_(10)分别为0.15、13.66 mg/L;对照样品、氟虫腈处理样品和氯虫苯甲酰胺处理样品分别获得59 521 504、64 838 148和41 722 990个原始序列数据,分别获得57 441 216、62 368 912和40 285 164个过滤后的序列数据;过滤后的序列长度分别为8.62、9.36和6.04 G;碱基错误率均为0.02%;Phred数值大于20、30的碱基占总碱基的百分比均高于90.59%;鸟嘌呤+胞嘧啶(guanine cytosine,GC)含量分别为47.16%、48.94%和47.55%,表明转录组测序质量较高;黏虫受氯虫苯甲酰胺胁迫后,29个P450基因表达量上调,27个P450基因表达量下调;黏虫受氟虫腈胁迫后,23个P450基因表达量上调,26个P450基因表达量下调;12个P450基因表达量的RT-qPCR技术检测结果与DGE测序文库显示的结果基本一致。     

水稻黑条矮缩病毒和水稻条纹叶枯病毒侵染下水稻qRT\|PCR内参基因的筛选

 病毒侵染通常会干扰寄主细胞的生理代谢过程,分析病毒侵染后寄主基因的表达差异,将为病毒与寄主之间的互作研究提供重要的分子基础。实时荧光定量PCR(qRT\|PCR)是目前基因表达分析中应用最广泛的方法之一,选择合适的内参基因对实验进行校正和标准化至关重要。但是,一些常用作内参的看家基因会受到病毒侵染的影响。本研究中,以感染水稻黑条矮缩病毒(Rice black\|streaked dwarf virus,RBSDV)和水稻条纹叶枯病毒(Rice stripe virus,RSV)的水稻总RNA为材料,利用qRT\|PCR技术和3个统计学软件探讨了10个常用内参基因在病毒侵染下的稳定性。结果显示,感染RBSDV和RSV水稻中表达最稳定的都是UBC和β\|TUB。因此,可选用UBC和β\|TUB组合作为分析RBSDV和RSV侵染过程的水稻内参基因。     

玉米NF-YC亚基基因的鉴定与表达规律分析

0 引言 NF-Y(nuclear factor-Y,NF-Y)是一类与CCAAT基序结合的转录因子,由NF-YA、NF-YB和NF-YC 3个亚基组成[1-2].NF-YC参与并调控植物生长发育的进程以及在生物和非生物胁迫响应过程中起作用[3].AtNF-YC1通过与AtXTH21基因启动子区的CCAAT-box结合...     

三个水稻逆转座子相关基因的逆境响应特征

 逆转座子是植物基因组的重要成分, 对基因组的大小、结构、功能和进化都有重要影响。研究表明多种生物和非生物逆境胁迫可以激活植物逆转座子的转录, 但其调控机制和功能还属未知。本研究从稻瘟菌侵染后云南地方水稻品种月亮谷的基因转录谱中筛选出3个逆转座子相关基因, 通过RT PCR分析了逆境胁迫处理对其表达水平的影响。结果表明, 稻瘟病菌、水杨酸、2, 4 D和NaCl处理水稻苗都能诱导这3个基因的快速转录, 表明这3个基因能够同时响应生物逆境和非生物逆境, 是研究该类逆转座子表达调控的良好候选基因。通过生物信息学分析还发现, 它们在月亮谷基因组中没有发生大的结构变异;且在水稻基因组中都具有与植物抗病相关的旁系同源物, 意味着其表达后可能对抗性产生影响, 因此, 这些基因在逆境和非生物逆境中的表达模式和功能值得关注。     

玉米SPXs家族基因的鉴定与表达规律分析

 SPXs(SPX-domain-containing proteins)家族基因在真核生物无机磷酸盐(Pi)的传感、信号转导和转运中发挥着重要作用,但玉米SPXs家族基因的相关研究未见报道。本研究利用生物信息学手段鉴定了15个玉米SPXs家族基因,通过系统进化和保守结构域分析将其分为SPX-EXS、SPX、SPX-Zinc finger和SPX-MFS 4个亚家族。通过表达谱数据分析,发现ZmSPXs家族基因具有明显的组织特异性表达。同时,我们还发现ZmSPXs家族基因在生物胁迫和非生物胁迫过程中表达模式也具有很大差异,说明这些基因可能在不同的生物过程中发挥重要作用。最后,利用荧光实时定量PCR技术,对玉米SPXs家族基因在磷胁迫处理下的表达规律进行分析,结果发现大部分基因在磷胁迫处理下呈现高水平表达。本研究鉴定了玉米SPXs家族基因,明确了该家族基因的系统进化关系、保守结构域、组织表达特性以及在生物和非生物胁迫条件下的表达规律,为阐明玉米SPXs家族基因的功能及其机制奠定了理论基础。     

Evaluation of six commonly used reference genes for gene expression studies in herbicide‐resistant Avena fatua biotypes

Avena fatua of the family Poaceae is one of the most common and economically damaging grass weeds. Resistance to herbicides that inhibit acetyl‐coenzyme A carboxylase and acetolactate synthase activities has recently been detected in A. fatua. The resistance may be due to mutations in the herbicide targets and/or enhanced herbicide metabolism resulting from changes in gene expression, including in genes involved in detoxifying herbicide active ingredients. To analyse gene expression, stable housekeeping genes must be experimentally determined and used for data normalisation. In this study, A. fatua plants were treated with different herbicide types and plant materials were harvested at three time points following treatment. Six candidate reference genes (18S rRNA, ACT, EF1α, GAPDH, TBP, and TUB) were selected, sequenced and analysed by RT‐qPCR. The resulting data were assessed using four algorithms from the RefFinder software to determine gene expression stability. We identified TBP and GAPDH as the most stably expressed A. fatua reference genes following herbicide treatment.     

Expression of genes related to Parkinson’s disease after paraquat treatment in Drosophila melanogaster

This study was designed to determine the minimum effective concentration of paraquat that modulated the expression of PKD-related genes in Drosophila. We first studied the viability of Drosophila and then tested the expression of the PKD-related genes—Parkin, UCH, and tau—in various concentrations of paraquat in the water sucked by Drosophila. The lowest effective concentration of paraquat was approximately 20 μM and the gene expression was induced at paraquat doses between 20 mM and 20 μM. Parkin and tau expression was inhibited, while that of UCH was significantly increased.Next, we examined the expression of the Parkin and UCH genes in the neurons of SOD-reduced mutants under oxidative stress conditions and found that Parkin was up regulated, while UCH was down regulated. We also found that the expression of Parkin was regulated by JNK. This study revealed that paraquat affects the expression of PKD-related genes via oxidative stress.In conclusion, our results showed that paraquat in the water sucked by Drosophila altered the gene expression at a minimum concentration of 20 μM, and that it not only promoted but also inhibited PKD-related gene expression via signal transduction mediated by oxidative stress. In order to confirm whether paraquat is a causal factor of PKD, more balanced and in-depth tests seem to be done looking into multiple aspects.     

饥饿胁迫下黑肩绿盲蝽转录组分析及S6K基因功能分析

为扩大黑肩绿盲蝽Cyrtorhinus lividipennis的人工繁殖规模,利用RNA-seq技术对饥饿胁迫2 d的黑肩绿盲蝽雌成虫进行转录组测序分析,筛选参与生殖调控的相关信号通路,挖掘直接或者间接影响生殖的相关基因,采用实时荧光定量PCR（real-time fluorescence quantification PCR,qRT-PCR）对筛选的相关基因进行验证,并通过试验分析沉默S6K基因和饥饿处理对黑肩绿盲蝽生殖的影响。结果显示,与取食褐飞虱Nilaparvata lugens卵（CK）的黑肩绿盲蝽相比,饥饿处理2 d的黑肩绿盲蝽雌成虫有11 675个基因差异表达,其中有4 264个基因表达量上调,7 411个基因表达量下调。共筛选到7条与生殖调控相关的信号通路和6个与生殖调控相关的基因,除TSC2基因表达量上调外,其他S6K、INSR、Akt、HSP70-1、HSP70-2五个与生殖相关基因的表达量在7条生殖相关信号通路中均下调。qRT-PCR检测结果与转录组测序结果一致,说明转录组分析结果可靠。沉默S6K基因后,黑肩绿盲蝽雌成虫脂肪体和卵巢蛋白质含量、Vg基因表达量、雌成虫产卵量和Vg含量较对照显著降低。此外,饥饿处理2 d后黑肩绿盲蝽雌成虫产卵量也较对照显著减少。表明饥饿胁迫后黑肩绿盲蝽雌成虫的生殖相关通路可能受多个信号通路调控,S6K表达量下降显著影响黑肩绿盲蝽的生殖。     

有翅型和无翅型小麦禾谷缢管蚜转录组差异分析

为有效防控有翅型小麦禾谷缢管蚜Rhopalosiphum padi,以浙江省小麦主要害虫禾谷缢管蚜为研究对象,比较分析其有翅型和无翅型转录组之间的差异,筛选差异表达基因,并对差异表达基因进行功能注释和代谢通路分析,采用实时荧光定量PCR（real-time fluorescence quantification PCR,RT-qPCR）技术对转录组测序结果进行验证。结果显示,经过StringTie软件组装,共获得39 699条unigenes。注释到NCBI-NR、GO、KEGG、Pfam、Swiss-Prot和eggNOG六个数据库中unigenes数量分别为24 120、17 351、17 137、17 532、15 494和23 128条,分别占unigenes总数量的60.76%、43.71%、43.17%、44.16%、39.03%和58.26%。有翅型和无翅型禾谷缢管蚜之间共筛选到6 747个基因差异表达显著,其中289个基因上调表达,其他6 458个基因下调表达,大多数差异表达基因集中在糖代谢及氨基酸代谢等信号通路上,表明禾谷缢管蚜翅型分化可能与能量分配有关。UGT、MME、GST和ABCG14四个基因的RT-qPCR测定结果与转录组测定结果一致,表明转录组测序数据准确可信。     

A PAL1 Gene Promoter–Green Fluorescent Protein Reporter System to Analyse Defence Responses in Live Cells of Arabidopsis thaliana

Arabidopsis thaliana ecotype Columbia-0 was transformed with a green fluorescent protein (GFP) gene under control of a phenylalanine ammonia-lyase (PAL) promoter. PAL is a key enzyme of the phenylpropanoid pathway and is induced to high levels during plant stress. Constitutive expression of PAL1 promoter-controlled GFP occurred in vascular tissues within stems, leaves and roots and in developing flowers. PAL1 promoter–GFP expression was examined in leaves of transgenic plants subjected to an abiotic elicitor, mechanical wounding or to inoculation with the pathogens Pseudomonas syringae pv. tomato or Peronospora parasitica. Wounding of leaves and treatment with an abiotic elicitor and compatible interactions produced low to moderate levels of GFP. However, in incompatible interactions there were high levels of GFP produced. In incompatible interactions, the intensity of GFP fluorescence was similar to that produced in transgenic plants expressing GFP driven by the CaMV promoter. The bright green fluorescence produced in live cells and tissues was readily visualised using conventional fluorescence microscopy and was quantified using spectroflourometry. This is the first report of the use of GFP as a reporter of defence gene activation against pathogens. It has several advantages over other reporter genes including real time analysis of gene expression and visualisation of defence gene activation in a non-invasive manner.     

Erwinia carotovora Infection Enhances the Expression of Two Novel Abiotic Stress-inducible Genes in Potato

In this study, cDNAs of two Erwinia carotovora-induced potato genes, designated Solanum tuberosum–Erwinia-induced-1 and 2 (Stei1 and Stei2) were isolated by differential display technique. Stei1 and Stei2 were detected in low copy number in the potato genome and found to encode putative proteins with no significant homology to any genes with known function. Treatment of the leaves with salicylic acid, methyl jasmonate and ethylene elevated neither Stei1 nor Stei2 mRNA levels. However, Stei1 and Stei2 expression were induced not only by E. carotovora but also by infiltration of water in leaves, albeit to a lesser extent. In addition, Stei2 was up-regulated by NaCl, wounding, dehydration and abscisic acid. Thus Stei1 and Stei2 define novel genes belonging to the family of those pathogenesis-related genes whose expression can be induced both by biotic and abiotic stresses.