miRNA profiling in leaf and cork tissues of Quercus suber reveals novel miRNAs and tissue-specific expression patterns

The differentiation of cork (phellem) cells from the phellogen (cork cambium) is a secondary growth process observed in the cork oak tree conferring a unique ability to produce a thick layer of cork. At present, the molecular regulators of phellem differentiation are unknown. The previously documented involvement of microRNAs (miRNAs) in the regulation of developmental processes, including secondary growth, motivated the search for these regulators in cork oak tissues. We performed deep sequencing of the small RNA fraction obtained from cork oak leaves and differentiating phellem. RNA sequences with lengths of 19–25 nt derived from the two libraries were analysed, leading to the identification of 41 families of conserved miRNAs, of which the most abundant were miR167, miR165/166, miR396 and miR159. Thirty novel miRNA candidates were also unveiled, 11 of which were unique to leaves and 13 to phellem. Northern blot detection of a set of conserved and novel miRNAs confirmed their differential expression profile. Prediction and analysis of putative miRNA target genes provided clues regarding processes taking place in leaf and phellem tissues, but further experimental work will be needed for functional characterization. In conclusion, we here provide a first characterization of the miRNA population in a Fagacea species, and the comparative analysis of miRNA expression in leaf and phellem libraries represents an important step to uncovering specific regulatory networks controlling phellem differentiation.     

Buds buried in bark: the reason why <Emphasis Type="Italic">Quercus suber</Emphasis> (cork oak) is an excellent post-fire epicormic resprouter

Key message

Cork oak has buds protected by the full thickness of its substantial phellem, thus explaining why it is the only European tree that can epicormically resprout after higher intensity fire.

Abstract

Epicormic resprouting has various ecological advantages over basal resprouting. However, after higher intensity fires epicormic resprouting is rare as it is difficult for trees and shrubs to keep both their buds and vascular cambia alive. Quercus suber (cork oak) is the only European tree that can resprout epicormically after higher intensity fires. Q. suber develops very thick bark and it has been assumed, without anatomical evidence, that the bark protects the epicormic buds. We investigated if developmental anatomy could explain why Q. suber is an excellent post-fire epicormic resprouter. We examined buds from mature Q. suber trees, macroscopically using a stereo microscope and microscopically using semi-thin microtome sections. Q. suber produced buds in the foliage leaf axils and the bud scale axils. With the commencement of extensive phellem (cork) production the base of the epicormic buds remained at, or just below, the level of the phellogen and thus cork began to bury the buds, although a narrow tube connected each bud to the bark surface. Q. suber epicormic buds became deeply buried in the phellem and would be protected from heat by the full phellem thickness. With its rapid and substantial development of phellem Q. suber had well-protected epicormic buds even in relatively small diameter stems. These results provide the anatomical evidence to show why Q. suber is a noted epicormic resprouter after crown fire.

     

Phellogen Regeneration in Injured Peach Tree Bark

Injury to peach bark phellogen leads to the generation of newtissues and the re-establishment of meristematic continuity.Two types of tissue changes after wounding were identified andquantified in bark of seven peach clones: (1) cell wall modifications(lignification and suberization) of tissues present at the timeof wounding, and (2) generation of the new phellogen and itsderivatives. Tissue responses were quantified with a microscopephotometer using selective histochemistry and autofluorescenceto detect lignin and suberin deposition over time. Suberin continuitywas re-established via suberin deposition in a layer of cells,present at the time of wounding, approximately 800 µminternal to the wound surface. Phellogen continuity was re-establishedimmediately internal to and abutting the suberized tissue. Thenew phellogen gave rise to suberized phellem which, in its outwardexpansion, crushed the suberized boundary zone tissue formedearlier. All injured peach clones produced the same sequenceof tissue changes, although timing and degree of response variedwith clone and time of year. Differentiation, impervious tissue, lignin, Prunus persica (L.) Batsch, suberin, wounding     

莲瓣王捧瓣与舌瓣SSH文库构建及EST序列分析

为了探索兰花舌瓣形成的分子机制,本研究利用消减抑制杂交技术构建了莲瓣王（Cymbidium lianpan Tang et Wang）捧瓣与舌瓣间的cDNA文库。对正向文库中随机挑选的147个阳性克隆测序,组装、拼接,找到37个唯一序列,其中包含25个单一序列和12个拼接序列。经同源性比对,这些EST分别归类于蛋白质折叠,结合、未知功能、应激反应、光合作用、转录调控、信号传导、生物合成、新陈代谢、MADS等10类。通过对MADS-box基因的系统进化树分析,可初步推测MADS-Contig1和MADS-Contig2属于A类基因中的SQUA-like亚家族基因。     

植物抗病虫SSH文库的EST分析

抑制差减杂交技术广泛应用于植物抗病虫(真菌、细菌和线虫)机理研究。本文在归纳出植物抗病虫SSH文库中ESTs的总体情况之基础上,重点分析了表达频率高的抗病、防御和信号转导基因,并展望了SSH的发展前景,有利于认识植物抗病虫分子机理的普遍规律和推广应用该技术。     

木栓质组成成分、组织化学特性及其生物合成研究进展

木栓质是一种植物次生代谢产物,是以甘油为基础的多聚脂类和多聚酚类物质的聚合物,定位于细胞壁和质膜之间,主要分布在根皮层和茎的次生边界组织中,可以降低细胞水分和营养物质的外流,限制病原体的入侵,阻碍有毒气体向内扩散。近年来,随着人们对果蔬贮藏和植物抗性的关注,对木栓质的研究越来越深入,尤其是代谢相关酶及基因功能研究。该文系统阐述木栓质组织化学、生物合成及其相关酶和基因的研究动态,介绍木栓质的生理功能,总结木栓质组成物质的转运、聚合及其堆积调控等,以期为木栓质的深入研究和开发利用提供参考。     

人参植物皂苷生物合成相关新基因的筛选与鉴定

人参植物根进行的特定发育过程在药用次生物———人参皂苷生物合成和累积中发挥重要作用。为从人参根中分离出人参皂苷生物合成相关基因 ,采用抑制差减杂交技术 ,构建四年和一年生人参根组织mRNA群体间正向差减cDNA文库。对从差减文库中筛选的 4 0个阳性cDNA克隆进行酶切、PCR与逆向Northern斑点杂交鉴定、DNA测序以及核苷酸序列同源性比较。结果表明 ,获得的 6个差减克隆在GenBank/DDBJ/BMBL无对应的同源基因 ,代表新基因序列。与此同时 ,使用Northern印迹杂交验证及半定量RT PCR进一步确认 ,6个转录本为根发育阶段差异性表达基因。因而提示 ,它们可能在人参皂苷生物合成中发挥了重要作用。此外 ,在人参茎、叶与种子中亦能检测到上述基因转录本的表达。目前 ,6个新基因已被命名 ,在GenBank注册并获登录号 ,为克隆上述新基因cDNA全长序列及深入鉴定其在人参皂苷生物合成中的功能提供了重要实验依据。     

A potato skin SSH library yields new candidate genes for suberin biosynthesis and periderm formation

Potato (Solanum tuberosum) tubers are underground storage organs covered by the skin or periderm, a suberized layer that protects inner flesh from dehydration and pathogens. Understanding the molecular processes associated with periderm formation is of great importance for a better knowledge of this protective tissue and for improving the storage life of tubers. Here, to isolate new candidate genes for potato periderm, a suppression subtractive hybridization library from potato skin was performed. This library yielded a comprehensive list of 108 candidate genes that were manually sorted in functional categories according to the main cellular and metabolic processes in periderm. As expected, the list contains Suberin and wax genes, including some genes with a demonstrated role in the biosynthesis of these cell wall aliphatic compounds. Moreover, Regulation and Stress and defence genes are highly abundant in the library in general agreement with previous potato skin proteomic studies. The putative function of the genes in periderm is discussed.     

Climate response of cork growth in the Mediterranean oak (Quercus suber L.) woodlands of southwestern Portugal

In the Mediterranean climate regions, drought events are expected to affect the growth of forests ecosystems by changing trees growth rates and eventually inducing shifts in their growth patterns. Cork oak (Quercus suber L.) is a strictly western Mediterranean tree species periodically harvested for its bark, the cork. So far, cork oak has received limited attention for dendroclimatological studies due to its typical faint and erratic tree wood rings. Moreover, its distinct cork rings chronologies have been completely neglected. In this study we introduce an approach using cork ring chronologies dated back 9–10 years for climate response. Despite enhancing interannual variability and increasing statistical response to short-term climatic variability, still poorly understood, this study will possibly allow infer long-term climate response. We analyzed the cork ring chronologies of 55 cork samples collected in mature (under exploitation) trees in three distinct locations in southwestern Portugal. Cork growth recorded a high climate signal, with highly significant and coherent responses to the yearly climate-related sources of variation. We successfully assessed trends of cork growth via correlation analysis including selected climate variables among mean monthly temperature, monthly precipitation and, on an annual basis, eight precipitation indices. The high mean sensitivities and inter-series correlations found for cork ring chronologies combined with the significant variance explained by climate variables suggest that climate is likely one dominant signal that affects cork growth, but local environmental stresses can decisively affect this (climate) signal. Assuming cork growth as a proxy for cork oak growth, it seems conceivable that despite the trees being highly resistant to drought stress, cork oak woodlands in southwestern Portugal would have to face lesser growth in a global warming scenario.     

墨兰多舌奇花MADS特异表达基因筛选及分析

以墨兰‘南菊’为代表,用抑制消减杂交和基因芯片相结合技术构建墨兰多舌与正格花舌间的差异表达基因文库,筛选与花形态建成相关的MADS差异表达基因并构建系统进化树。结果表明:在多舌瓣中筛选出32个上调表达MADS基因,包括TM6、AG、AP1、DEF1、AP3及PI基因。其中有10个基因与AGL17、AGL29、FUI聚为一类,12个基因与其他的MADS基因归为一类。这些MADS基因参与了多舌瓣发生,并可能扮演了重要角色。该研究可为从兰花多舌变化的角度阐明墨兰奇花形成的分子机理及培育中国兰花新奇优良品种提供思路和理论依据。     

应用抑制性消减杂交技术克隆大鼠肝再生过程中特异表达基因

应用抑制性消减杂交技术成功地构建了高消减效率的正向消减cDNA文库,从随机挑取的50个克隆中有31个均检出了60~400bp插入片段,对这些插入cDNA片段进行测序后经Genbank同源性检索,表明其中7个片段为未知新序列。大鼠肝切除后肝再生cDNA正向消减文库的建立为进一步大批量筛选、克隆肝再生特异性表达的未知新基因奠定了基础,初步筛选出的特异性表达的序列标记为进一步研究肝再生中基因的功能提供了依据。 Abstract:The cDNA from rat regenerating liver tissue was used as the tester and that from normal liver was used as the driver.A highly efficient subtractive cDNA library was constructed by suppression subtractive hybridization(SSH).After screening,31 clones from 50 clones which were derived from the cDNA library were inserted by 60~400bp cDNA fragments.24 cDNA fragments corresponded to known genes and 7 cDNA fragments were unknown sequences(GenBank accession number:BG447490~447496).     

The Arabidopsis cytochrome P450 CYP86A1 encodes a fatty acid omega-hydroxylase involved in suberin monomer biosynthesis

The lipophilic biopolyester suberin forms important boundaries to protect the plant from its surrounding environment or to separate different tissues within the plant. In roots, suberin can be found in the cell walls of the endodermis and the hypodermis or periderm. Apoplastic barriers composed of suberin accomplish the challenge to restrict water and nutrient loss and prevent the invasion of pathogens. Despite the physiological importance of suberin and the knowledge of the suberin composition of many plants, very little is known about its biosynthesis and the genes involved. Here, a detailed analysis of the Arabidopsis aliphatic suberin in roots at different developmental stages is presented. This study demonstrates some variability in suberin amount and composition along the root axis and indicates the importance of omega-hydroxylation for suberin biosynthesis. Using reverse genetics, the cytochrome P450 fatty acid omega-hydroxylase CYP86A1 (At5g58860) has been identified as a key enzyme for aliphatic root suberin biosynthesis in Arabidopsis. The corresponding horst mutants show a substantial reduction in omega-hydroxyacids with a chain length 相似文献   

Variability of cork from Portuguese Quercus suber studied by solid-state (13)C-NMR and FTIR spectroscopies.

A new approach is presented for the study of the variability of Portuguese reproduction cork using solid-state (13)C-NMR spectroscopy and photoacoustic (PAS) FTIR (FTIR-PAS) spectroscopy combined with chemometrics. Cork samples were collected from 12 different geographical sites, and their (13)C-cross-polarization with magic angle spinning (CP/MAS) and FTIR spectra were registered. A large spectral variability among the cork samples was detected by principal component analysis and found to relate to the suberin and carbohydrate contents. This variability was independent of the sample geographical origin but significantly dependent on the cork quality, thus enabling the distinction of cork samples according to the latter property. The suberin content of the cork samples was predicted using multivariate regression models based on the (13)C-NMR and FTIR spectra of the samples as reported previously. Finally, the relationship between the variability of the (13)C-CP/MAS spectra with that of the FTIR-PAS spectra was studied by outer product analysis. This type of multivariate analysis enabled a clear correlation to be established between the peaks assigned to suberin and carbohydrate in the FTIR spectrum and those appearing in the (13)C-CP/MAS spectra.     

Identification and analysis of genes present in Leptospira interrogans serovar lai but absent in L. biflexa serovar monvalerio

Genes present in virulent bacterial strains but absent in avirulent close relatives can be of great biologic and clinical interest. This project aimed to identify strain specific DNA sequences of Leptospira interrogens serovar lai, which is absent in the saprophytic L. biflexa serovar monvalerio, via suppression subtractive hybridization with the former as the tester while the latter as the driver. The mixture of PCR amplified DNA fragments from two subtractive hybridization experiments were cloned into pMD 18-T vector and the positive clones were identified by dot blotting against the chromosome DNA of the two strains individually. After DNA sequencing and analysis, the distribution of these genomic fragment sequences in a panel of pathogenic and nonpathogenic leptospires was investigated employing dot blot analysis. Among the 188 positive clones randomly chosen, 24 contained the tester strain specific genomic regions, of which, 5 were non-coding fragments while the others contained 23 distinct protein coding sequences. Besides 9 genes encoding functional proteins, 12 genes encode unknown proteins and the rest two genes encode proteins with recognizable domain structures, one for a putative leucine-rich repeats (LRR) family protein while the other as an outer-membrane protein. Our experiment results indicated that suppression subtractive hybridization is effective for screening specific DNA sequences between two leptospiral strains, and some of these sequences might be responsible for virulence determination. Further analysis of these DNA sequences will provide important information on the pathogenesis of Leptospira.     

罗汉果果实不同发育时期SSH文库的构建

以罗汉果授粉后50 d和70 d果实为材料,利用抑制消减杂交技术构建了罗汉果果实在不同生育时期皂苷生物合成相关基因的差减cDNA文库.在正向差减文库(70 d为tester,50 d果实为driver)中随机挑选了641个cDNA阳性克隆测序,得到622条有效序列,重组率在96%以上.外源片段的长度分布在101～934...