竹子基因调查分析报告

竹子作为一种重要经济植物,具有经济、生态和文化价值。随着生物技术的快速发展,越来越多的以竹类植物为对象的基因序列得到克隆与验证,基于BPG(2012)更新系统,截至2014年底,已经有3913个竹子基因得到确证,这些基因覆盖了竹亚科的3个族,隶属19个属30个种。文章统计分析了已确认的基因描述、基因类型和参考序列情况,展望了竹子基因发展态势。     

巴西橡胶树CBF2基因的克隆和表达分析

分析植物CBF同源保守区序列设计简并引物,利用RT-PCR技术从橡胶树中克隆了CBF基因家族的保守区,并以SAFA-PCR法克隆了HbCBF2基因的5′端序列以及启动子序列。通过BLAST工具搜索Genbank数据库。结果表明,该序列同其他植物中的CFB家族基因高度同源,认为该序列就是橡胶树中的CBF基因。以此序列设计Northern Blot探针,从低温和干旱两个方面处理,探索该基因在巴西橡胶树中的表达情况。     

2个野扁桃自交不亲和SFB基因全长的克隆与序列分析

为给野扁桃的遗传改良和自交不亲和机制的进一步研究提供理论依据,以新疆野扁桃花药为试材,利用RT-PCR和RACE技术克隆野扁桃自交不亲和性花粉特异性决定因子编码基因SFB全长序列。采用BLAST进行序列比对,ORF Finder寻找开放阅读框,CDD分析蛋白保守结构域,Prot Param分析蛋白理化性质,TMHMM预测蛋白跨膜区,Signal P预测蛋白信号肽,Sub Loc预测蛋白亚细胞定位,SOPMA分析蛋白二级结构,DANMAN进行氨基酸多序列比对,MEGA6进行系统进化分析,Prot Fun预测蛋白功能。结果表明:克隆到的Pt SFB16基因和Pt SFB17基因属于F-box基因家族,与其它多种植物的SLF/SFB基因的序列相似度为88%,推导的氨基酸序列均具有F-box蛋白典型结构;Pt SFB16基因ORF长1 146 bp,编码381个氨基酸,Pt SFB17基因ORF长1 131 bp,编码376个氨基酸;预测2个SFB蛋白均为略显亲水性、不稳定的细胞质蛋白,二级结构均以α-螺旋,延伸链和无规则卷曲为主,SFB/SLF蛋白在蔷薇科李属植物中具有较高的系统进化一致性,种间同源性可能大于种内同源性,SFB蛋白可能的功能主要有辅助因子生物合成、能量代谢和裂合酶。     

Photosynthetic productivity of aspen clones varying in sensitivity to tropospheric ozone

Rooted cuttings from three aspen (Populus tremuloides Michx.) clones (216, 271 and 259, classified as high, intermediate and low in O(3) tolerance, respectively) were exposed to either diurnal O(3) profiles simulating those of Michigan's Lower Peninsula (episodic treatments), or diurnal square-wave O(3) treatments in open-top chambers in northern Michigan, USA. Ozone was dispensed in chambers ventilated with charcoal-filtered (CF) air. In addition, seedlings were compared to rooted cuttings in their response to episodic O(3) treatments. Early in the season, O(3) caused decreased photosynthetic rates in mature leaves of all clones, whereas only the photosynthetic rates of recently mature leaves of the O(3)-sensitive Clone 259 decreased in response to O(3) exposure. During midseason, O(3) caused decreased photosynthetic rates of both recently mature and mature leaves of the O(3)-sensitive Clone 259, but it had no effect on the photosynthetic rate of recently mature leaves of the O(3)-tolerant Clone 216. Late in the season, however, photosynthetic rates of both recently mature and mature leaves of Clone 216 were lower than those of the control plants maintained in CF air. Ozone decreased the photosynthetic rate of mature leaves of Clone 271, but it increased or had no effect on the photosynthetic rate of recently mature leaves. Photosynthetic response patterns of seedlings to O(3) treatment were similar to those of the clones, but total magnitude of the response was less, perhaps reflecting the diverse genotypes of the seedling population. Early leaf abscission was observed in all clones exposed to O(3); however, Clones 216 and 259 lost more leaf area than Clone 271. By late August, leaf area in the highest O(3) treatment had decreased relative to the controls by 26, 24 and 9% for Clones 216, 259 and 271, respectively. Ozone decreased whole-tree photosynthesis in all clones, and the decrease was consistently less in Clone 271 (23%) than in Clones 216 (56%) and 259 (56%), and was accompanied by declines in total biomass of 19, 28 and 47%, respectively. The relationship between biomass and whole-tree photosynthesis indicates that the negative impact of O(3) on biomass in the clones was determined largely by lower photosynthetic productivity of the foliage, rather than by potential changes in the carbon relations of other plant organs.     

Isolation of genes up-regulated by copper in a copper-tolerant birch (Betula pendula) clone

Suppression subtractive hybridization (SSH) was used to isolate genes differentially expressed following exposure to copper (Cu) in a naturally selected Cu-tolerant birch (Betula pendula Roth.) clone originating from a disused lead/zinc smelter. Of the 352 cDNA fragments initially isolated, 108 were up-regulated by Cu, of which 55 showed over twofold induction by macroarray analysis. Searches against protein databases (Blastx) and sequence analysis provided the tentative identity of 21 genes. Three fragments lacked homology to any sequences in the databases. Most of the identified genes are involved in cellular transport, regulation or cell rescue and defense. Several genes have not previously been reported to be up-regulated by Cu, e.g., plasma intrinsic protein 2, glutamine synthetase and multi-drug resistance-associated protein (MRP4). The expression of MRP4, a vacuolar sorting receptor-like protein and an unidentified gene was studied in more detail by quantitative real-time PCR. These genes showed stronger up-regulation by Cu in the roots and shoots of the Cu-tolerant birch clone compared with a less tolerant clone. Clear clonal differences in gene expression were observed, e.g., for the regulator of chromosome condensation family protein, DnaJ protein homolog, vacuolar sorting receptor-like protein and MRP4. These findings contribute to our understanding of Cu tolerance in birch, a pioneer plant in metal-contaminated soils.     

PCR法克隆紫穗槐4-香豆酸:CoA连接酶全长cDNA

4 香豆酸 :CoA连接酶 (4CL)是木质素生物合成过程中重要的酶 .该文利用简并寡核苷酸PCR法结合cDNA末端快速扩增PCR法直接获得了紫穗槐 4CLAcDNA全长序列 ,避免了复杂的构建、筛选cDNA文库的过程 .先用简并PCR得到了 4CLA1片段 ,又据此片段设计反向嵌套引物 ,用RACE方法获得未知的 5′和 3′端序列 .所获得的全长 4CLAcDNA ,编码 5 40个氨基酸 .氨基酸序列同源性分析表明4CLA是典型的 4CL蛋白 ,含有预计的AMP binding位点、催化反应区和保守的Cys .     

毛竹漆酶基因启动子序列分析及基因表达模式

漆酶在细胞壁形成、逆境胁迫、花青素形成和酚类物质催化等过程中均发挥着重要作用，其基因表达受到多种外界因素的影响。为揭示竹子中漆酶基因的表达模式，以毛竹（Phyllostachys edulis）为对象，利用生物信息学手段分析了其中42个漆酶基因（PeLACs）启动子序列，利用已有的转录组数据分析了其中PeLACs的表达模式，克隆漆酶基因PeLAC20的启动子序列PeLACp，并构建了瞬时表达载体，在拟南芥（Arabidopsis thaliana）中瞬时表达。结果表明，在42个PeLACs启动子序列中包含多种与激素以及非生物胁迫相关的顺式作用元件，在GA₃处理以及低温和干旱胁迫下各基因表现为不同的表达模式，表明它们参与激素和非生物胁迫的应答，而且功能存在着一定的差异。PeLACs在毛竹不同生长阶段根和笋中的表达模式也证明了各基因功能的差异性。克隆的PeLACp序列为2 000 bp，利用GUS染色法检测启动子PeLACp的活性显示，PeLACp主要在转基因拟南芥的根中表达。研究结果为进一步揭示毛竹漆酶基因的生物学功能提供了参考依据。     

mRNA差异显示法研究杉木木材形成相关cDNA

利用差异显示法(DDRT-PCR)研究杉木的2个自然变异类型(句容0号及独干杉)木材形成过程中基因表达差异.通过银染后切割回收54个差异条带,经2次扩增和纯化、克隆转化及反向Northern杂交验证后共获得29个阳性克隆.测序后进行比对分析,结果表明:1)Blastn比对(分值＞60)有9个cDNA克隆在GeneBank中找到了相似的功能,分别与核糖体蛋白基因、信号传导功能、泛素蛋白基因、抗性功能、组氨酸磷酸转移蛋白、细胞发生功能及能量代谢相关;2)Blastx比对有12个序列可进行功能推测;3)还有8个cDNA在数据库中未发现匹配信息.这些信息可为杉木木材形成相关基因的分离和克隆提供研究基础.     

Overexpression of the ThTPS gene enhanced salt and osmotic stress tolerance in Tamarix hispida

Trehalose is a non-reducing disaccharide with high stability and strong water absorption properties that can improve the resistance of organisms to various abi-otic stresses.Trehalose-6-phosphate synthase (TPS) plays important roles in trehalose metabolism and signaling.In this study,the full-length cDNA of ThTPS was cloned from Tamarix hispida Willd.A phylogenetic tree includ-ing ThTPS and 11 AtTPS genes from Arabidopsis indicated that the ThTPS protein had a close evolutionary relationship with AtTPS7.However,the function of AtTPS7 has not been determined.To analyze the abiotic stress tolerance function of ThTPS,the expression of ThTPS in T.hispida under salt and drought stress and JA,ABA and GA3 hormone stimu-lation was monitored by qRT-PCR.The results show that ThTPS expression was clearly induced by all five of these treatments at one or more times,and salt stress caused par-ticularly strong induction of ThTPS in the roots of T.hispida.The ThTPS gene was transiently overexpressed in T.his-pida.Both physiological indexes and staining results showed that ThTPS gene overexpression increased salt and osmotic stress tolerance in T.hispida.Overall,the ThTPS gene can respond to abiotic stresses such as salt and drought,and its overexpression can significantly improve salt and osmotic tolerance.These findings establish a foundation to better understand the responses of TPS genes to abiotic stress in plants.     

Carbon allocation and partitioning in aspen clones varying in sensitivity to tropospheric ozone

Clones of aspen (Populus tremuloides Michx.) were identified that differ in biomass production in response to O(3) exposure. (14)Carbon tracer studies were used to determine if the differences in biomass response were linked to shifts in carbon allocation and carbon partitioning patterns. Rooted cuttings from three aspen Clones (216, O(3) tolerant; 271, intermediate; and 259, O(3) sensitive) were exposed to either charcoal-filtered air (CF) or an episodic, two-times-ambient O(3) profile (2x) in open-top chambers. Either recently mature or mature leaves were exposed to a 30-min (14)C pulse and returned to the treatment chambers for a 48-h chase period before harvest. Allocation of (14)C to different plant parts, partitioning of (14)C into various chemical fractions, and the concentration of various chemical fractions in plant tissue were determined. The percent of (14)C retained in recently mature source leaves was not affected by O(3) treatment, but that retained in mature source leaves was greater in O(3)-treated plants than in CF-treated plants. Carbon allocation from source leaves was affected by leaf position, season, clone and O(3) exposure. Recently mature source leaves of CF-treated plants translocated about equal percentages of (14)C acropetally to growing shoots and basipetally to stem and roots early in the season. When shoot growth ceased (August 16), most (14)C from all source leaves was translocated basipetally to stem and roots. At no time did mature source leaves allocate more than 6% of (14)C translocated within the plant to the shoot above. Ozone effects were most apparent late in the season. Ozone decreased the percent (14)C translocated from mature source leaves to roots and increased the percent (14)C translocated to the lower stem. In contrast, allocation from recently mature leaves to roots increased. Partitioning of (14)C among chemical fractions was affected by O(3) more in source leaves than in sink tissue. In source leaves, more (14)C was incorporated into the sugar, organic acid and lipids + pigments fractions, and less (14)C was incorporated into starch and protein fractions in O(3)-treated plants than in CF-treated plants. In addition, there were O(3) treatment interactions between leaf position and clones for (14)C incorporation into different chemical fractions. When photosynthetic data were used to convert percent (14)C transported to the total amount of carbon transported on a mass basis, it was found that carbon transport was controlled more by photosynthesis in the source leaves than proportional changes in allocation to the sinks. Ozone decreased the total amount of carbon translocated to all sink tissue in the O(3)-sensitive Clone 259 because of decreases in photosynthesis in both recently mature and mature source leaves. In contrast, O(3) had no effect on carbon transport from recently mature leaves to lower shoots of either Clone 216 or 271, had no significant effect on transport to roots of Clone 216, and increased transport to roots of Clone 271. The O(3)-induced increase in transport to roots of Clone 271 was the result of a compensatory increase in upper leaf photosynthesis and a relatively greater shift in the percent of carbon allocated to roots. In contrast to those of Clone 271, recently mature leaves of Clone 216 maintained similar photosynthetic rates and allocation patterns in both the CF and O(3) treatments. We conclude that Clone 271 was more tolerant to O(3) exposure than Clone 216 or 259. Tolerance to chronic O(3) exposure was directly related to maintenance of high photosynthetic rates in recently mature leaves and retention of lower leaves.     

版纳龙竹CONSTANS同源基因的克隆与序列分析

以版纳龙竹基因组DNA为模板,采用前人基于水稻CO同源基因Hd1序列的保守区所设计的特异引物COS1和COA1,运用PCR方法扩增出一条1 520 bp的DNA片段,并克隆到pGEM-T载体。测序和序列分析结果显示:该片段含有1个590 bp的内含子,编码区930 bp共编码310个氨基酸;该基因被命名为DxCO1,其DNA序列在G enB ank中的注册号为GQ358925。在G enB ank中进行同源性检索的结果显示:其核苷酸序列与其它禾本科植物CO同源基因的氨基酸序列同源性高达81%~91%;推测的DxCO1蛋白质序列与其它种子植物CO同源基因蛋白质序列的系统发育分析结果显示:DxCO1与小麦Hd1-like等5个基因聚成了一个强烈支持的分支;另外,在该片段推测的蛋白质序列的氨基端含有一个类似锌指蛋白的B-box(Cx2Cx8Cx7Cx2Cx4Hx8H)结构域,羧基端含有一个CCT(CO,CO-like,TOC1)结构域。序列和结构的高度同源性表明:DxCO1是版纳龙竹的1个CO-like基因,可能对其开花调控有着重要作用。     

基于ITS和ycf1序列的白及遗传多样性分析

在白及资源调查和收集过程中,发现白及花型、花色、花期、叶片形态等多个性状变异程度较大.本研究收集了来源于四川和云南的白及资源30份,克隆并分析其nrDNA ITS和叶绿体ycf1基因差异,发现ycf1基因差异小,ITS基因差异较大,根据ITS序列差异,将白及聚类为3个支系,结合白及的表观性状,发现白及ITS序列与其花期...     

马尾松肉桂酰辅酶A还原酶基因(CCR)克隆及分析

对马尾松肉桂酰辅酶A还原酶基因(CCR)进行扩增、克隆和测序(GenBank登录号:EU753854).应用MEGA4.0.2软件对不同树种CCR基因的核苷酸和氨基酸序列进行比对,结果表明:马尾松CCR基因的外显子和内含子数目与火炬松、杨树、银合欢、光皮桦、冈尼桉、柳桉、蓝桉的外显子和内含子数目相同,都有5个外显子和4个内含子.马尾松CCR基因编码区975 bp,编码324个氨基酸.马尾松外显子Ⅰ,Ⅱ,Ⅲ,Ⅳ,Ⅴ分别为133,155,186,353,148 bp,而内含子Ⅰ,Ⅱ,Ⅲ,Ⅳ分别为1 450,216,737,941 bp.马尾松CCR外显子和内含子连接处序列除内含子Ⅱ/外显子Ⅲ出现CTPuCG/外显子Ⅲ,其余遵循外显子/GTPuAG/外显子组成规律.马尾松外显子Ⅱ,Ⅲ,Ⅳ核苷酸数目与桉属、杨属、桦木属和松属树种相同,但外显子Ⅰ和外显子Ⅴ不尽相同.比对的树种间在该基因编码区核苷酸序列和氨基酸序列上相对保守,也存在一定差异.马尾松与火炬松、光皮桦、银合欢、杨树、冈尼桉、柳桉、蓝桉各物种间编码区核苷酸序列相似性大小分别为99.2%,67.8%,68.0%,68.9%,69.5%,69.3%,69.9%,而相应的氨基酸序列间相似性大小分别为99.1%,73.5%,72.5%,74.4%,75.0%,74.4%,75.0%.马尾松与其他13个树种CCR序列构建的系统进化树表明:3个针叶树种形成1个独立分支,而且最早进化.     

杨树抗黑斑病相关基因表达谱分析

利用黑斑病的高抗无性系美洲黑杨I-69及黑斑病的高感无性系欧美杨I-45为材料建立的2个cDNA文库,随机挑取cDNA克隆进行5'端EST序列测序,共获得有效序列20 023条.序列经聚类分析和拼接后,共获得10 816个Unigene,其中包括3 734个Contig,7 082个独立的Singleton.被注释的8 853个具有同源性匹配序列基因中,按照GO的分子功能、生物过程和细胞组分3个不同分类角度进行分类.在具有功能注释的8 853个Unigene中,选出330个与完成全基因组测序的毛果杨序列进行BLAST分析,结果发现有177个抗病相关候选基因出现在282个Unigene中,其中135个分布于杨树的18个不同连锁群上,其他42个基因位于还没定位的scaffolds上.所测定的这些EST序列为后期在基因组水平上研究杨树黑斑病的水平抗性遗传机制及进一步的相关基因发现奠定基础.

Abstract：

In an attempt to elucidate the molecular mechanism for resistance of black spot disease in poplar,gene expression profiles in leaves of Populus deltoides'Lus'(I-69/55)and P.euramericana'I-45/51',which were inoculated with the pathogen Marssonina brunnea f.sp.brunnea,were analyzed based on expressed sequence tags (ESTs).A total of 20 023 valid ESTs from the 5'terminal ends derived from corresponding cDNA libraries of the two poplar species were sequenced.Cluster analysis of the 20 023 sequences yielded 10 816 tentative unigenes,including 3 734 contigs and 7 082 singletons.All tentative unigenes were classified by Gene Ontology functional categories.To find resistance-associated candidate genes and locate them on poplar genome,330 unigenes was chosen from 8 853 annotated tentative unigenes,and their BLAST alignment was conducted with Populus trichocarpa assembly,1 77 related candidate resistant genes were found,and they presented in 282 unigenes.Among these genes,there were 1 35 genes located on 18 different linkage groups of poplar genome,and 42 genes located on the different scaffolds.This study supplied a resource of candidate genes for further exploring the genetic mechanism for the host horizontal resistance to the pathogen Marssonina brunnea at the whole genome range,and provided important information for further gene discovery.     

Nighttime exposure to ozone reduces whole-plant production in Betula pendula

For 20 weeks during the growing season, cuttings of one birch clone (Betula pendula Roth.) were exposed in the Birmensdorf fumigation chambers to O(3)-free air (control) or 75 nl O(3) l(-1). Ozone was supplied either from 1900 until 0700 h (nighttime regime), from 0700 until 1900 h (daylight regime), or all day (24-h regime). By autumn, reductions in whole-plant biomass production, root/shoot biomass and stem weight/length ratios were evident in all three O(3) regimes. The reductions in cuttings receiving the 24-h O(3) treatment were about twofold larger than in cuttings receiving the daylight O(3) treatment. Stomata were open at night, and stomatal conductance was about 50% of its maximum daytime value. We calculated that the rate of O(3) uptake into leaves in the dark approached 4 nmol m(-2) s(-1). Whole-plant production and carbon allocation were more sensitive to O(3) during the night than during the day; however, O(3) exposure caused similar visible leaf injury in both of the 12-h regimes, although the leaves exposed to O(3) at night exhibited delayed O(3)-induced shedding. Overall, changes in production and carbon allocation were determined by the external O(3) dose rather than by the kind of O(3) exposure, indicating that, at the seasonal scale, the internal dose of ozone that was physiologically effective was a constant fraction of the external O(3) dose. We conclude that nighttime O(3) exposures should be included in the daily time period for determining critical concentrations of O(3) causing injury in trees.