Roses, which are one of the world’s most important ornamental plants, are often damaged by pathogens, resulting in serious economic losses. As a subclass of the disease resistance gene family of plant nucleotide-binding oligomerization domain (NOD)-like receptors, TIR-NBS-LRR (TNL) genes play a vital role in identifying pathogen effectors and activating defense responses. However, a systematic analysis of the TNL gene family is rarely reported in roses. Herein, 96 intact TNL genes were identified in Rosa chinensis. Their phylogenies, physicochemical characteristics, gene structures, conserved domains and motifs, promoter cis-elements, microRNA binding sites, and intra- and interspecific collinearity relationships were analyzed. An expression analysis using transcriptome data revealed that RcTNL genes were dominantly expressed in leaves. Some RcTNL genes responded to gibberellin, jasmonic acid, salicylic acid, Botrytis cinerea, Podosphaera pannosa, and Marssonina rosae (M. rosae); the RcTNL23 gene responded significantly to three hormones and three pathogens, and exhibited an upregulated expression. Furthermore, the black spot pathogen was identified as M. rosae. After inoculating rose leaves, an expression pattern analysis of the RcTNL genes suggested that they act during different periods of pathogen infection. The present study lays the foundations for an in-depth investigation of the TNL gene function and the mining of disease resistance genes in roses.

【目的】从‘月月粉’月季全基因组中鉴定NAC家族成员，并进行生物信息学和表达模式分析，为研究‘月月粉’NAC的潜在功能提供理论基础，筛选可能参与皮刺发育的候选基因。【方法】以拟南芥NAC氨基酸序列为参考，利用双向Blast及HMM结构域检索筛选RcNAC；对筛选成员进行理化性质、亚细胞定位、序列特征、顺式元件和系统进化分析；基于已释放转录组数据，分析RcNAC在不同组织器官，和不同逆境处理条件下的表达特性；同时通过‘月月粉’不同发育阶段皮刺组织转录组测序，筛选与皮刺发育可能相关的RcNAC。【结果】共鉴定得到116个RcNACs，均含有完整典型的NAM保守结构域，其编码蛋白包含69—713个氨基酸，等电点从4.43—9.54，分子质量从7.87—79.99 kD，81个RcNACs被预测定位于细胞核内；115个RcNACs在7条染色体上不均匀分布，1个RcNAC未明确位置信息；系统进化树分析将AtNACs、OsNACs和RcNACs聚为21类；在不同组织器官中，116个RcNACs表达模式各异，遭受水胁迫和感染灰霉病之后，31个RcNACs表达量发生变化；在衰老的花组织中，6个RcNACs表达量上升；皮刺转录组数据中检测到53个RcNACs，其中26个RcNACs为差异表达基因。【结论】基于已有转录组数据分析，RcNACs协同调控植物组织发育及逆境胁迫响应；结合皮刺转录组数据，部分成员可能参与皮刺细胞增殖、次生细胞壁生物合成及细胞程序性死亡等过程，可作为皮刺发育相关候选基因进行深入研究。

The degree of stigma exsertion has a major influence on self-pollination efficiency in tomato, and its improvement is essential for raising productivity and for fixing advantageous traits in cultivated tomato. To study the evolution of stigma exsertion degree in tomato, we searched for genes associated with this trait and other aspects of flower morphology, including the lengths of anthers, styles, and ovaries. We performed a genome-wide association on 277 tomato accessions and discovered a novel stigma exsertion gene (SE3.1). We reannotated the structure of the gene, which encodes a C2H2-type zinc finger transcription factor. A mutation of the lead single nucleotide polymorphism creates a premature termination codon in SE3.1 and an inserted stigma in cultivated tomatoes. SE3.1 is essential for the conversion of flush stigmas to inserted stigmas. This conversion has a major impact on the rate of self-fertilization. Intriguingly, we found that both SE3.1 and Style2.1 contribute to the transition from stigma exsertion to insertion during the domestication and improvement of tomato. Style2.1 controls the first step of exserted stigmas to flush stigmas, and SE3.1 controls the second step of flush stigmas to inserted stigmas. We provide molecular details for the two-step process that controls the transition from stigma exsertion to insertion, which is of great agronomic importance in tomato.

C2H2型锌指蛋白是最常见的锌指蛋白之一，广泛存在于真核生物中，在植物的生长发育、盐、低温、干旱胁迫等非生物胁迫响应中扮演重要作用。本研究以拟南芥C2H2氨基酸序列作为探针，在油棕基因组数据库中进行本地BLASTP比对和保守结构域预测分析，筛选出油棕C2H2型锌指蛋白家族成员，利用生物信息学手段对基因家族成员的理化性质、进化关系、染色体位置、基因结构、保守基序和启动子顺式元件进行分析，并利用转录组数据和荧光定量PCR方法分析EgC2H2基因家族成员在低温胁迫下的表达情况。结果显示：从油棕基因组中共鉴定出73个C2H2型锌指蛋白家族成员，EgC2H2家族成员氨基酸的数目为128~556个，分子量为14 176.73~58 983.30 Da，等电点为4.99~9.62，不稳定系数为38.84~86.01，亲水性为-1.154~-0.226，亚细胞定位显示C2H2基因家族所有成员均定位于细胞核；系统进化树分析显示EgC2H2家族成员可以分为4个亚家族，EgC2H2家族成员多数归类于第Ⅰ亚家族和第Ⅱ亚家族，且同一亚家族成员的结构域具有较高的一致性；染色体定位结果显示，EgC2H2家族成员不均匀地分布于油棕的16条染色体上；启动子顺式元件分析显示，EgC2H2家族包含许多光响应元件、植物激素响应元件和逆境胁迫响应元件；转录组数据分析显示，大部分EgC2H2基因响应低温胁迫，且大多数EgC2H2基因在耐寒材料中高表达，在冷敏感材料中低表达；荧光定量PCR分析显示，EgC2H2-23、EgC2H2-11、EgC2H2-19、EgC2H2-17和EgC2H2-21显著上调表达，且在耐寒材料中的表达量显著高于冷敏感材料，推测这些基因可能在油棕低温响应中发挥关键作用，可以作为候选基因进一步深入研究。本研究为深入研究油棕C2H2基因家族功能提供理论参考。

  已知植物TFIIIA型锌指蛋白的锌指区含有保守的QALGGH区，属于C2H2型转录因子，参与调控植物生长发育和逆境胁迫应答。为详细了解甘蓝型油菜的同源基因，参照拟南芥AtZFP基因C2H2结构域氨基酸序列，采用生物信息学分析方法鉴定了46个甘蓝型油菜TFIIIA型锌指蛋白基因，分析了基因结构、生化特性、进化关系和基因表达模式。结果表明：42个基因为单锌指蛋白基因，4个为多锌指蛋白基因；40个基因不含内含子，6个基因含内含子；氨基酸序列同源性变幅为9.0%~99.2%，氨基酸序列保守性差异明显，亚类成员间包含相同的保守基序，亚类间的保守基序不同；PlantCARE分析发现其启动子区富含激素、非生物胁迫及特定生理过程响应的顺式作用元件；甘蓝型油菜品种中双11号12种组织RNA-seq分析表明，部分基因在角果、根、初花期雌蕊中特异性表达。

C2H2-type zinc finger proteins (C2H2-ZFPs) play a key role in various plant biological processes and responses to environmental stresses. In Arabidopsisthaliana, C2H2-ZFP members with two zinc finger domains have been well-characterized in response to abiotic stresses. To date, the functions of these genes in strawberries are still uncharacterized. Here, 126 C2H2-ZFPs in cultivated strawberry were firstly identified using the recently sequenced Fragaria × ananassa genome. Among these C2H2-ZFPs, 46 members containing two zinc finger domains in cultivated strawberry were further identified as the C1-2i subclass. These genes were unevenly distributed on 21 chromosomes and classified into five groups according to the phylogenetic relationship, with similar physicochemical properties and motif compositions in the same group. Analyses of conserved domains and gene structures indicated the evolutionary conservation of the C1-2i subclass. A Ka/Ks analysis indicated that the C1-2i members were subjected to purifying selection during evolution. Furthermore, FaZAT10, a typical C2H2-ZFP, was isolated. FaZAT10 was expressed the highest in roots, and it was induced by drought, salt, low-temperature, ABA, and MeJA treatments. It was localized in the nucleus and showed no transactivation activity in yeast cells. Overall, these results provide useful information for enriching the analysis of the ZFPs gene family in strawberry, and they provide support for revealing the mechanism of FaZAT10 in the regulatory network of abiotic stress.

C2H2-type zinc finger proteins (ZFPs) have been shown to play important roles in the responses of plants to oxidative and abiotic stresses, and different members of this family might have different roles during stresses. Here a novel abscisic acid (ABA)- and hydrogen peroxide (H₂O₂)-responsive C2H2-type ZFP gene, ZFP36, is identified in rice. The analyses of ZFP36-overexpressing and silenced transgenic rice plants showed that ZFP36 is involved in ABA-induced up-regulation of the expression and the activities of superoxide dismutase (SOD) and ascorbate peroxidase (APX). Overexpression of ZFP36 in rice plants was found to elevate the activities of antioxidant enzymes and to enhance the tolerance of rice plants to water stress and oxidative stress. In contrast, an RNA interference (RNAi) mutant of ZFP36 had lower activities of antioxidant enzymes and was more sensitive to water stress and oxidative stress. ABA-induced H₂O₂ production and ABA-activated mitogen-activated protein kinases (MAPKs) were shown to regulate the expression of ZFP36 in ABA signalling. On the other hand, ZFP36 also regulated the expression of NADPH oxidase genes, the production of H₂O₂, and the expression of OsMPK genes in ABA signalling. These results indicate that ZFP36 is required for ABA-induced antioxidant defence, for the tolerance of rice plants to water stress and oxidative stress, and for the regulation of the cross-talk between NADPH oxidase, H₂O₂, and MAPK in ABA signalling.© The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.