Comparative Chloroplast Genomes of Camellia Species

Background

Camellia , comprising more than 200 species, is a valuable economic commodity due to its enormously popular commercial products: tea leaves, flowers, and high-quality edible oils. It is the largest and most important genus in the family Theaceae. However, phylogenetic resolution of the species has proven to be difficult. Consequently, the interspecies relationships of the genus Camellia are still hotly debated. Phylogenomics is an attractive avenue that can be used to reconstruct the tree of life, especially at low taxonomic levels.

Methodology/Principal Findings

Seven complete chloroplast (cp) genomes were sequenced from six species representing different subdivisions of the genus Camellia using Illumina sequencing technology. Four junctions between the single-copy segments and the inverted repeats were confirmed and genome assemblies were validated by PCR-based product sequencing using 123 pairs of primers covering preliminary cp genome assemblies. The length of the Camellia cp genome was found to be about 157kb, which contained 123 unique genes and 23 were duplicated in the IR regions. We determined that the complete Camellia cp genome was relatively well conserved, but contained enough genetic differences to provide useful phylogenetic information. Phylogenetic relationships were analyzed using seven complete cp genomes of six Camellia species. We also identified rapidly evolving regions of the cp genome that have the potential to be used for further species identification and phylogenetic resolution.

Conclusions/Significance

In this study, we wanted to determine if analyzing completely sequenced cp genomes could help settle these controversies of interspecies relationships in Camellia . The results demonstrate that cp genome data are beneficial in resolving species definition because they indicate that organelle-based “barcodes”, can be established for a species and then used to unmask interspecies phylogenetic relationships. It reveals that phylogenomics based on cp genomes is an effective approach for achieving phylogenetic resolution between Camellia species.     

野葛异黄酮合酶基因的分离与功能验证

异黄酮是野葛（Pueraria lobata）中的主要活性成分,而异黄酮合酶（IFS）是催化异黄酮生物合成的第一步关键酶,尽管野葛的IFS基因已被分离,但其功能还未得到任何验证。本研究以中国安徽省郎溪县的野葛为材料,利用RT-PCR技术成功克隆到野葛IFS基因,命名为PlIFS,PlIFS开放阅读框大小为1566 bp,编码521个氨基酸,将该基因克隆到GAL1启动子控制下的酵母表达载体pESC-TRP上,得到重组质粒pESC-TRP-PlIFS,通过LiAc/ssDNA/PEG方法将其转化进酿酒酵母（Saccharomyces cerevisiae）WAT11中进行异源表达,并在酵母体内对其活性进行验证,结果显示PlIFS能催化甘草素生成大豆苷元,表现出异黄酮合酶活性特征。荧光定量PCR分析显示,PlIFS基因主要在野葛的根中表达,这与活性物质异黄酮主要在野葛根中的积累模式一致。     

Mammal cells double their total RNAs against diabetes, ischemia reperfusion and malaria-induced oxidative stress

Total cellular RNA level is stable usually, although it may increase gradually during growth or decrease gradually under certain stressors. However, we found that mammal cell RNAs could be doubled within 24 h in response to free heme accumulation (ischemia reperfusion and malaria infection) or a high level of glucose treatment (diabetes). Clinical investigations in rats showed that pretreatment with heme (24 h for doubling total RNAs) alleviated oxidative damages caused by diabetes, and pretreatment with glucose (24 h for trebling total RNAs) alleviated oxidative damages caused by ischemia reperfusion or malaria infection. Therefore, this rapid RNA amplification may play an important role in mammal adaptation to diabetes, ischemia reperfusion and malaria infection-derived oxidative stress. This rapid RNA amplification is derived from glucose and heme, but not from their accompanying reactive oxygen species. Hexokinases endure glucose-derived reactive oxygen species accumulation but are not related glucose-derived RNA amplification. In contrast, the TATA box-binding protein (TBP) mediates all glucose- and heme-induced RNA amplification in mammal cells.     

Capillary electrophoretic determination of DNA damage markers: content of 8-hydroxy-2'-deoxyguanosine and 8-nitroguanine in urine

A sensitive and low-cost analytical method has been developed to determine 8-hydroxy-2'-deoxyguanosine (8-OHdG) and 8-nitroguanine (8-NO(2)Gua) based on capillary electrophoresis with amperometric detection (CE-AD) after solid phase extraction (SPE). Under optimized condition, these two markers were well separated from other components coexisting in urine, exhibiting a linear calibration over the concentration range of 0.1-50.0 μg/mL with the detection limits ranging from 0.02 to 0.06 μg/mL. The relative standard deviations (RSDs) were in the range of 0.1-2.1% for peak area, 0.1-1.5% for migration time, respectively. The average recovery and RSD were within the range of 100.0-108.0% and 0.1-1.7%, respectively. It was found that the urinary contents of 8-OHdG and 8-NO(2)Gua in cancer patients were significantly higher than those in healthy ones.     

Prediction of carbohydrate binding sites on protein surfaces with 3-dimensional probability density distributions of interacting atoms

Non-covalent protein-carbohydrate interactions mediate molecular targeting in many biological processes. Prediction of non-covalent carbohydrate binding sites on protein surfaces not only provides insights into the functions of the query proteins; information on key carbohydrate-binding residues could suggest site-directed mutagenesis experiments, design therapeutics targeting carbohydrate-binding proteins, and provide guidance in engineering protein-carbohydrate interactions. In this work, we show that non-covalent carbohydrate binding sites on protein surfaces can be predicted with relatively high accuracy when the query protein structures are known. The prediction capabilities were based on a novel encoding scheme of the three-dimensional probability density maps describing the distributions of 36 non-covalent interacting atom types around protein surfaces. One machine learning model was trained for each of the 30 protein atom types. The machine learning algorithms predicted tentative carbohydrate binding sites on query proteins by recognizing the characteristic interacting atom distribution patterns specific for carbohydrate binding sites from known protein structures. The prediction results for all protein atom types were integrated into surface patches as tentative carbohydrate binding sites based on normalized prediction confidence level. The prediction capabilities of the predictors were benchmarked by a 10-fold cross validation on 497 non-redundant proteins with known carbohydrate binding sites. The predictors were further tested on an independent test set with 108 proteins. The residue-based Matthews correlation coefficient (MCC) for the independent test was 0.45, with prediction precision and sensitivity (or recall) of 0.45 and 0.49 respectively. In addition, 111 unbound carbohydrate-binding protein structures for which the structures were determined in the absence of the carbohydrate ligands were predicted with the trained predictors. The overall prediction MCC was 0.49. Independent tests on anti-carbohydrate antibodies showed that the carbohydrate antigen binding sites were predicted with comparable accuracy. These results demonstrate that the predictors are among the best in carbohydrate binding site predictions to date.     

关于iFlora创建工作框架的建议

iFlora是依据传统植物分类学及相关学科的研究基础,融入现代DNA测序技术,应用高速发展的信息、网络技术及云计算分析平台,收集、整合和管理植物物种相关信息,以建成智能物种鉴定和数据提取的开放应用系统（智能装备）。通过与该系统的双向交流,一方面,可以不断整合新的数据和技术充实iFlora的内容和功能;另一方面,可以通过该系统的多种鉴定途径实现快速、准确和方便的物种鉴定,获取所需物种的相关信息,满足专业机构和公众对物种和生物多样性的认知要求。本文重点介绍了构成iFlora的应用装置和支撑该装置的实物库（凭证标本、分子材料和DNA库）的建设及其重要性;阐述了构成iFlora各单元的高度整合和集成的特点,以及基于计算机技术的物种信息数字化和开放的云计算数据分析处理服务平台的枢纽作用;并讨论了iFlora创建过程所面临的困难和挑战,以及拟研发的智能装备的框架和应用前景。     

遗传信息及其获取技术与iFlora

随着世界主要国家和地区传统植物志的完成和即将完成,植物学进入后植物志时代。由于学科的积累和科技的发展,新一代植物志（iFlora）成为植物志发展的必然。本文概述了iFlora的特点、主要构件和应用范围;介绍了近三十年来遗传信息及其获取技术的发展概况,以及它们在iFlora中的重要作用;讨论了目前技术条件下各类遗传信息获取技术的优劣和整合提高的方法;提出了iFlora实施过程中的阶段性目标;以及随着数据信息的快速积累,相关技术特别是快速、简便测序技术和设备的发展与iFlora可能的最终发展目标。     

新一代植物志：iFlora

进入21世纪,随着分子生物学及计算机信息等技术的快速发展,人们认知自然的手段和方式发生了根本性的变化。在现有电子植物志（eFlora）的基础上,融入新一代测序技术、DNA条形码数据、地理信息数据和计算机信息技术等新元素的新一代植物志（iFlora）应运而生。iFlora是通过系列关键技术的集成和攻关,构建便捷、准确识别植物和掌握相关数字化信息的新一代植物志（或智能装备）,它将极大地促进植物分类学和系统发育、演化生物学、生态学、生物地理学和保护生物学等相关学科的发展,有效地服务于生物多样性保护和生物资源可持续利用、国家生态安全和社会公共教育等,并进一步提升公众对生物多样性的认识。iFlora的实施,将为培育和拓展物种识别圈（taxasphere）和生物文化圈（bioliterate world）做出应有的贡献,并可能成为引领国际植物学发展新的生长点。     

Camarosporium arezzoensis on Cytisus sp., an addition to sexual state of Camarosporium sensu stricto

During a study of saprobic fungi from Bagno di Cetica Province, Italy, we collected a pleosporoid ascomycete on stems of Cytisus sp. In morphology, our collection is similar to Cucurbitaria species, but molecular analysis of SSU, LSU and ITS genes reveals it can be referred to Camarosporium. In this study we compare all other Cucurbitaria species from Cytisus sp. and based on both morphology and molecular data, we introduce our collection as a new species in Camarosporium viz. C. arezzoensis.