小麦全基因组中YABBY基因家族的筛选与特征分析

YABBY家族是植物特有的转录因子,在植物侧生器官极性建立和发育过程中起重要的调控作用。从全基因组水平鉴定小麦YABBY家族并进行生物信息学和表达模式分析,为研究小麦YABBY家族基因的功能奠定基础。根据已经报道的拟南芥和水稻YABBY基因,在小麦基因组数据库中执行本地BLAST程序鉴定小麦基因组中的YABBY基因,采用MEGA、GSDS、MEME和PlantCARE等软件进行生物信息学分析,并利用已公开的RNA-seq数据绘制不同发育时期和不同组织的表达谱。结果表明,在小麦基因组范围内鉴定得到18个YABBY基因家族成员,分成5个亚家族。Motif分析表明小麦YABBY蛋白均具有C2C2锌指结构域及YABBY结构域; Ta YABBY启动子区检测到与植物生长发育、激素诱导和逆境胁迫有关的顺式作用元件。RNA-Seq表达谱发现小麦YABBY基因具有明显的组织表达特异性。     

拟南芥和大白菜YABBY蛋白家族的生物信息学分析

YABBY基因家族是一类含有C2C2锌指结构域和YABBY结构域的转录因子,在植物叶器官发育过程中起到重要的调控作用。本研究利用生物信息学的方法对拟南芥和大白菜YABBY基因家族的结构、系统进化、序列保守性以及顺式反应元件进行了分析。主要结果如下:YABBY基因在拟南芥和大白菜染色体上呈不均匀分布;基因的结构以含有6个内含子为主要形式;所有拟南芥和大白菜YABBY基因都具有保守的C2C2锌指结构域和YABBY结构域;YABBY蛋白家族在进化上可分为4个不同的亚组;YABBY基因的启动子序列中存在多个能够响应不同激素和逆境信号的顺式反应元件。本文为进一步研究YABBY基因在大白菜叶球发育中的调控作用和逆境响应中的功能奠定了基础。     

毛白杨PtYABBY基因家族3个成员的克隆与表达分析

  目的  YABBY是高等植物中特有的转录因子家族,在侧生器官发育和开花过程中发挥重要作用。本研究对毛白杨PtYABBY基因进行克隆和生物信息学分析,并对雌雄花芽8个关键发育时期和根茎叶等组织中PtYABBY基因表达模式进行探究,以期为阐明PtYABBY基因在毛白杨侧生器官发育过程中的功能奠定前期基础。  方法  以毛白杨为试材,采用同源基因克隆法从毛白杨中分离FILAMENTOUS FLOWER (FIL)/YABBY3 (YAB3)同源基因PtYABBY3、PtYABBY4和PtYABBY11的编码区序列,并开展生物信息学分析。通过qRT-PCR研究这3个基因在雌雄花芽8个发育时期及根、茎、幼叶、成熟叶片中的表达规律。  结果  PtYABBY3、PtYABBY4和PtYABBY11编码区长度分别为633、642、639 bp,分别编码210、213、212个氨基酸。所推测的氨基酸序列包含C₂C₂锌指结构域和YABBY结构域。系统进化分析进一步表明这3个基因属于FIL/YAB3亚家族成员。qRT-PCR结果显示这3个基因在根、茎、叶及8个时期雌雄花芽组织中均有表达,但PtYABBY基因间的表达水平存在明显差异。PtYABBY3表达水平在雌雄花芽发育初期下调,发育后期上调;花原基形成到休眠期内PtYABBY3在雌雄花芽中呈现相反的表达变化趋势。PtYABBY4和PtYABBY11基因在雌雄株成花诱导期表达水平最高,成花诱导到伸长期内呈现下降趋势,在雄花芽休眠期和小孢子发生期基因表达水平无明显变化。营养组织表达量测定结果显示这3个基因在幼叶和成熟叶片中表达水平相对较高,根系中表达量最低。  结论  YABBY基因家族成员PtYABBY3、PtYABBY4和PtYABBY11同属FIL/YAB3亚类,在毛白杨雌雄花芽发育的8个时期中表达水平存在较大差异,且在叶片和花芽中表达量较高,表明其可能与叶片和花芽发育相关。本研究为今后深入研究YABBY家族成员在杨树器官生长发育过程中的作用奠定基础。      

Usage of cold shock domain proteins for improvement of frost hardiness in plant biotechnology

We have discovered that overexpression of the gene TsCSDP3 that encodes the cold-shock domain protein from the extremophile plant Thellungiella salsuginea in the test plant A. thaliana considerably improves frost hardiness of the latter, which is promising for use of this gene and, perhaps, of other CDS protein genes in biotechnology of cultivated plants in order to enhance cold stress resistance.     

番茄YABBY基因家族的生物信息学分析

YABBY基因家族是植物特有转录因子,与植物形态有关,在植物叶和花器官发育过程中起重要调控作用。试验在番茄基因组范围内鉴定出9个YABBY基因家族成员,分别位于第1、5、6、7、8、11和12号染色体。利用MEGA程序对番茄、拟南芥、大白菜和玉米YABBY基因家族作进化分析,进化树可分为四个亚组;利用GSDS程序分析基因结构保守性,显示Sl YABBY基因内含子保守5~6个;MEME程序作基序分析,显示Sl YABBY基序保守,经鉴定所有Sl YABBYs均具有C2C2锌指结构域及YABBY结构域。运用plant CARE软件分析顺势作用元件发现,在番茄YABBY基因上游1 000 bp序列中存在多个应答不同生物和非生物胁迫的顺式作用元件,且种类和数目不同,表明其作用于番茄生长发育和逆境胁迫过程。基因功能预测和蛋白-蛋白网络分析表明,番茄YABBY家族对根、茎、叶、花、蜜腺、心皮、胚珠等部位发育具有重要调控作用。番茄YABBY基因家族表达分析发现Sl YABBY1、Sl YABBY3和Sl YABBY4在根、茎、花、叶及果实中均无表达,Sl YABBY2和Sl YABBY9表达具有较强组织特异性,为番茄YABBY基因功能研究提供参考。     

谷子GATA基因家族的鉴定及表达分析

本研究从谷子基因组水平鉴定出33个SiGATA成员,命名为 SiGATA1～ SiGATA33。利用生物信息学方法对谷子SiGATA家族的系统发育、基因结构、染色体分布、保守基序、蛋白三级结构和顺式调控元件进行预测和分析。结果表明,33个SiGATA转录因子被划分为3组,不均匀的分布在8条染色体上,多数含有CX_2CX_(18)CX_2C保守结构域;谷子GATA蛋白与单子叶植物水稻的同源性大于其他两种单子叶植物;蛋白三级结构分析表明,整体结构相似度存在差异,同组进化序列基因的结构相似度较高;顺式作用元件分析表明,SiGATAs启动子序列中存在调控生长发育、激素信号传导和逆境胁迫响应元件,其中 SiGATA15、 SiGATA22、 SiGATA31在干旱、厌氧诱导及脱落酸响应等元件中表达量较高,其在谷子生长发育及逆境响应过程中可能发挥了重要生物学功能。这些逆境响应及生长发育相关转录因子的挖掘,将为作物育种提供一定理论参考。     

Cloning and structure analysis of an NBS-LRR disease-resistant gene from Setaria italica Beauv

Degenerate PCR primers targeting conserved motifs of most NBS-LRR disease-resistant genes in plants were tested in Setaria italica Beauv. cultivar Shilixiang, which is resistant to Uromyces setariae-italicae. A sequence with a length of 2673 bp has been obtained by using Genomic Walking technology. The nucleotide sequence contained an open reading frame that encoded 891 amino acid residues with a calculated molecular mass of 101.44 kDa. It was named RUS1 (Resistance against Uromyces setariae-italicae, GenBank No. FJ467296). It contained an NB-ARC domain and three conserved motifs P-loop, kinase 2, and kinase 3, which had the characteristics of NBS-LRR type resistant gene of plant. Phylogenetic analysis indicated that it was similar to RPM1 and might belong to LZ-NBS-LRR type disease resistance gene. Southern blotting result displayed that there were at least three copies of RUS1 in the foxtail millet genome.     

Genome-wide identification and analysis of the regulation wheat DnaJ family genes following wheat yellow mosaic virus infection

The co-chaperone DnaJ plays an important role in protein folding and regulation of various physiological activities, and participates in several pathological processes. DnaJ has been extensively studied in many species including humans, drosophila, mushrooms, tomatoes, and Arabidopsis. However, few studies have examined the role of DnaJ in wheat (Triticum aestivum), and the interaction mechanism between TaDnaJs and plant viruses. Here, we identified 236 TaDnaJs and performed a comprehensive genome-wide analysis of conserved domains, gene structure and protein motifs, chromosomal positions and duplication relationships, and cis-acting elements. We grouped these TaDnaJs according to their domains, and randomly selected six genes from the groups for tissue-specific analysis, and expression profiles analysis under hormone stress, and 17 genes for plant virus infection stress. In qRT-PCR, we found that among the 17 TaDnaJ genes tested, 16 genes were up-regulated after wheat yellow mosaic virus (WYMV) infection, indicating that the TaDnaJ family is involved in plant defense response. Subsequent yeast two-hybrid assays verified the WYMV NIa, NIb and 7KD proteins interacted with TaDJC (TraesCS7A02G506000), which had the most significant changes in gene expression levels after WYMV infection. Insights into the molecular mechanisms of TaDnaJ-mediated stress tolerance and sensitivity could inform different strategies designed to improve crop resistance to abiotic and biotic stress. This study provides a basis for future investigation of the TaDnaJ family and plant defense mechanisms.     

Genome-wide identification,molecular evolution,and expression divergence of the hexokinase gene family in apple

Hexokinase(HXK) is the first irreversible catalytic enzyme in the glycolytic pathway, which not only provides energy for plant growth and development but also serves as a signaling molecule in response to environmental changes. However, the evolutionary pattern of the HXK gene family in apple remains unknown. In this study, a total of nine HXK genes were identified in the Malus×domestica genome GDDH13 v1.1. The physiological and biochemical properties, exonintron structures, conserved motifs, and cis-elements of the MdHXK genes were determined. Predicted subcellular localization indicated that the MdHXK genes were mainly distributed in the mitochondria, cytoplasm, and nucleus. Gene duplication revealed that whole-genome duplication(WGD) and segmental duplication played vital roles in MdHXK gene family expansion. The ω values of pairwise MdHXK genes indicated that this family was subjected to strong purifying selection during apple domestication. Additionally, five subfamilies were classified, and recent/old duplication events were identified based on phylogenetic tree analysis. Different evolutionary rates were estimated among the various HXK subfamilies. Moreover, divergent expression patterns of the Md HXK genes in four source-sink tissues and at five different apple fruit developmental stages indicated that they play vital roles in apple fruit development and sugar accumulation. Our study provides a theoretical basis for future elucidation of the biological functions of the MdHXK genes during apple fruit development.     

Knockdown of ACS9 expression in Arabidopsis decreases the tolerance to salt and osmotic stress

Based on the DNA sequence of ACS9, two produced fragments were subcloned into binary vector pCAMBIA1300 in antisense and sense orientations, and the generated RNA interference (RNAi) vector was then transformed into Arabidopsis thaliana. The stress resistance function of ACS9 gene in Arabidopsis thaliana was researched by determination of stress resistance physiologic indexes, NaCl and PEG6000 resistance. The results showed that the inhibition of ACS9 expression enhanced the sensitivity to high concentration NaCl (150 mmol/L) and PEG6000 (7%) in Arabidopsis thaliana seeding stage. The proline contents and water loss rates in transgenic plants were 0.68 and 1.4 times higher than those in the wild-type leaves, respectively, indicating that the inhibition of ACS9 expression due to salt and drought resistant was reduced and suggested that ACS9 gene played important roles in plant salt and drought tolerance.     

植物表皮形态建成的分子调控机制

植物表皮细胞在组织器官的生长发育和形态建成中发挥非常重要的作用。植物的表皮是由原表皮发育来的,表皮包括表皮(扁平)细胞、气孔器和表皮毛等。双子叶植物的表皮由不规则的表皮细胞、气孔器和表皮毛组成;单子叶植物的表皮由长形的表皮细胞、短形的硅化和栓化表皮细胞、泡状细胞、气孔器和表皮毛等组成。近年来,随着生物技术的不断提高,人们对全球淡水资源紧缺的认识加强,对培育农业抗旱品种的渴求,因此,对植物表皮形态建成的研究已经成为一大热点。本文综述了目前有关双子叶模式植物拟南芥中气孔及扁平细胞的图式发育及参与调控的分子遗传调控网络,以及单子叶植物水稻、玉米中参与气孔及表皮细胞图式发育的功能基因。旨在阐明单双子叶模式植物表皮发育调控的分子机制。     

谷子 SWI3基因鉴定及其在盐和干旱胁迫下的表达分析

SWI/SNF染色质重塑因子在植物的生长发育及逆境应答过程中起重要作用。本研究首先通过序列比对，从谷子基因组中鉴定出6个候选SiSWI3基因，分别命名为SiSWI3A、SiSWI3B、SiSWI3C1、SiSWI3C2、SiSWI3D1和SiSWI3D2。然后对上述基因的结构、编码蛋白、启动子元件、亚细胞定位等进行生物信息学分析和预测，结果表明：SiSWI3蛋白都含有SANT Motif，且亚细胞定位预测显示SiSWI3成员主要被定位在细胞核中；SiSWI3基因启动子区域含有大量与光响应、激素类应答、逆境应答、代谢调控等相关的顺式作用元件。最后采用实时荧光定量PCR（qRT-PCR）检测这些基因在谷子苗期盐胁迫和干旱胁迫下的表达量变化，检测结果表明：SiSWI3基因受盐和干旱不同程度的诱导，说明SiSWI3基因参与谷子苗期盐胁迫和干旱胁迫应答。本研究所得结论为进一步探究SiSWI3染色质重塑因子在抗逆作物谷子的逆境响应中的功能和机制奠定了基础。     

Genome-wide identification and expression analysis of StPP2C gene family in response to multiple stresses in potato(Solanum tuberosum L.)

The plant protein phosphatase 2Cs(PP2Cs) play an essential role in response to stress and abscisic acid(ABA) signaling pathway. However, to date, no systemic characterization of the PP2Cs has yet been conducted in potato(Solanum tuberosum L.). In the study, a comprehensive research was performed on genome-wide identification and expression analysis of StPP2C genes in potato. A total of 78 potato StPP2C genes were identified based on specific structure of PP2C domain, which were distributed across 11 out of 12 potato chromosomes and divided into 12(A–L) phylogenetic branches. The result from gene duplication analysis showed that 14 StPP2Cs were involved in gene tandem duplication and 8 genes formed fragment duplication events, which indicated that both tandem and fragment duplication contributed to the expansion of the gene family in evolution. Exon–intron structural analysis showed that they had a wide range of exon numbers. Analysis of protein conservative motif demonstrated that StPP2Cs contained more similar motif structures in the same phylogenetic branches. The cis-elements in StPP2C gene promoter regions were mainly responded to light, phytohormone and abiotic stress. Most of them exhibited tissue-specific expression patterns, and some members could differentially express under abiotic stress. The evidence suggested that StPP2C genes may contribute to different functions in several physiological stress and environmental stress conditions. This study could provide new insights to further investigate StPP2C functional characteristics responding to various stresses in potato.     

Genome-wide analysis of the SCPL gene family in grape(Vitis vinifera L.)

Serine carboxypeptidase-like(SCPL) proteins are a group of acyltransferase enzymes that have important roles in plant growth, development, and stress responses. Although SCPL proteins have been studied in many plants, the biological functions of SCPL genes in grape are still unknown. In this study, 59 putative SCPL proteins were identified from the grape genome. A bioinformatics analysis, including chromosomal locations, exon/intron structures, phylogeny, ciselements, and conserved motifs, was performed for the gene family. The phylogenetic analysis revealed that VvSCPL proteins could be classified into three groups, with the gene motifs in each group showing high similarity levels. The number of exons in the VvSCPL genes ranged from 1 to 19, suggesting significant variations among grape SCPL genes. The expression of the VvSCPL genes, as assessed by RNA sequencing(RNA-seq) and quantitative real-time PCR, showed that most VvSCPL genes responded to drought-and waterlogging-stress treatments, which indicated their roles in abiotic stress responses. The results provide useful information for further study of SCPL genes in grape.     

短柄草Hsf家族全基因组鉴定、分类和高温响应

分析短柄草Hsf家族成员的进化关系,并进行分类;利用多种软件和在线工具分析短柄草Hsf的蛋白结构功能域和基因启动子区域的顺式作用元件;分析基因组信息,进行基因的染色体定位;利用荧光实时定量技术(qRT-PCR),分析短柄草Hsf基因在高温胁迫下的表达模式,鉴定出一些高温诱导表达的Hsf基因。     

大豆LIM转录因子家族鉴定及盐胁迫响应分析

为探究大豆LIM转录因子家族基因在应答盐胁迫中的功能,利用生物信息学方法,根据大豆全基因组数据,共鉴定出21个LIM基因,命名为GmLIM01～GmLIM21,分析大豆LIM基因家族的染色体位置、蛋白质的理化性质、进化关系、保守基序以及对非生物逆境胁迫的响应。结果表明,这些GmLIM基因在大豆20条染色体中的14条染色体上分布不均,片段重复是大豆LIM家族扩大的主要原因。根据系统发育进化分析,大豆21个LIM基因可分为5个亚家族,与其他9个物种的LIM基因一起构建进化树,也可分为5个亚家族。大豆的21个GmLIM基因共包含10个基序,大部分LIM蛋白含有motif 1、motif 2和motif 4这3个保守基序。此外,顺式调控元件的分析表明,在GmLIM基因的启动子序列中,与光响应、生长发育、植物激素和非生物逆境胁迫应答相关的调控元件非常丰富。定量PCR结果表明,在盐胁迫处理后大豆叶和根中GmLIM07、GmLIM17基因的表达量分别在3和6 h达到峰值,后随着处理时间的加长表达量下降。综上GmLIM基因在大豆的盐胁迫应答过程中具有重要的调控作用。     

Genome-wide identification and function analysis of the sucrose phosphate synthase MdSPS gene family in apple

Sucrose phosphate synthase (SPS) is a rate-limiting enzyme that works in conjunction with sucrose-6-phosphate phosphatase (SPP) for sucrose synthesis, and it plays an essential role in energy provisioning during growth and development in plants as well as improving fruit quality. However, studies on the systematic analysis and evolutionary pattern of the SPS gene family in apple are still lacking. In the present study, a total of seven MdSPS and four MdSPP genes were identified from the Malus domestica genome GDDH13 v1.1. The gene structures and their promoter cis-elements, protein conserved motifs, subcellular localizations, physiological functions and biochemical properties were analyzed. A chromosomal location and gene-duplication analysis demonstrated that whole-genome duplication (WGD) and segmental duplication played vital roles in MdSPS gene family expansion. The Ka/Ks ratio of pairwise MdSPS genes indicated that the members of this family have undergone strong purifying selection during domestication. Furthermore, three SPS gene subfamilies were classified based on phylogenetic relationships, and old gene duplications and significantly divergent evolutionary rates were observed among the SPS gene subfamilies. In addition, a major gene related to sucrose accumulation (MdSPSA2.3) was identified according to the highly consistent trends in the changes of its expression in four apple varieties (‘Golden Delicious’, ‘Fuji’, ‘Qinguan’ and ‘Honeycrisp’) and the correlation between gene expression and soluble sugar content during fruit development. Furthermore, the virus-induced silencing of MdSPSA2.3 confirmed its function in sucrose accumulation in apple fruit. The present study lays a theoretical foundation for better clarifying the biological functions of the MdSPS genes during apple fruit development.     

Functional characterization of the catalytic and bromodomain of FgGCN5 in development,DON production and virulence of Fusarium graminearum

FgGCN5, a GCN5 homolog in Fusarium graminearum, plays a critical role in hyphal vegetative growth, asexual and sexual reproduction, deoxynivalenol(DON) biosynthesis and plant infection. For nuclear localized GCN5, four conserved sequence motifs(I–IV) are presented in the catalytic domain and a bromodomain in the carboxy-terminus. As a lysine acetyltransferase, conserved negatively charged residues are present to neutralize the protons from lysine substrates. However, the role of conserved motifs/domains and residues in FgGCN5 are unclear. Here, we generated deletion mutant strains for each the conserved motifs/domains and a glutamate residue 130(E130) replacement mutant. Deletion of each conserved motif in the catalytic domain and replacement of E130 site resulted in manifold defects in hyphae growth, asexual and sexual development, DON biosynthesis, and plant infection. Phenotypic defects in the mutant strains were similar to deletion mutants. The deletion of the bromodomain led a significant reduction in DON production and virulence, with no effects on hyphae growth, asexual or sexual reproduction. FgGCN5 was further found to localize to the nucleus in conidia and hyphae cells. In conclusion, FgGCN5 encodes a nuclear localized acetyltransferase. The conserved motifs in the catalytic domain and E130 are essential for correct functions of the gene. The conserved bromodomain is important for DON production and pathogen virulence. This was the first report to identify the functions of conserved motifs/domains in FgGCN5, which will contribute to our understanding of the mechanism(s) by which FgGCN5 regulates F. graminearum.