Saving Europe’s threatened flora: progress towards GSPC Target 8 in Europe

The European flora is of global significance but many species are facing an ever increasing range of threats, especially the growing impacts of climate change. While various estimates have been made for the number of threatened plant species in Europe, an up-to-date European plant Red List does not presently exist. Target 8 of the Global Strategy for Plant Conservation (GSPC) calls for 60% of threatened plant species to be conserved in ex situ collections by 2010. In the absence of a European plant Red List, it is difficult to monitor progress at the regional level towards this target. To address this gap Botanic Gardens Conservation International (BGCI) has developed a consolidated list of European threatened species as a step towards a formal Red List. The database consists of national Red List data from 28 European countries and includes records for over 11,000 taxa. National Red List data were supplemented by information on the critically endangered plants of Europe provided by the Museum National d’Histoire Naturelle/European Topic Centre on Biological Diversity and the Conservatoire Botanique National de Brest. A list of regionally threatened species was extracted from the database and screened against BGCI’s database of plants in cultivation in botanic gardens (PlantSearch) and ENSCONET’s (European Native Seed Conservation Network) database of plants conserved in European seed banks. This analysis revealed that 42% of European threatened species are currently included in ex situ conservation programmes in Europe.     

云南省第一批省级重点保护野生植物名录修订

保护植物名录是林政执法、科学研究、公众参与生物多样性保护等活动的重要工具。修订对于保持名录上植物名称准确性和使名录及时反映我省生物多样性保护成效具有重要意义。本文依据英文版《中国植物志》和植物名称数据库,对云南省政府1989年颁布的《云南省第一批省级重点保护野生植物名录》进行了修订。结果表明：名录上214种植物中有60种是异名或基名,28种原中文名称被改变了,9种原拉丁名称拼写错误,3种错误鉴定,5种是裸名,其他109种植物拉丁名和中文名都无变化。修订结果将为云南省重点保护野生植物管理提供参考。最后建议建立云南省重点保护野生植物名录修订标准和机制。     

Monitoring records of plant species in the Hakone region of Fuji-Hakone-Izu National Park, Japan, 2001–2010

The monitoring of species occurrences is a crucial aspect of biodiversity conservation, and regional volunteerism can serve as a powerful tool in such endeavors. The Fuji-Hakone-Izu National Park in the Hakone region of Kanagawa Prefecture, Japan, boasts a volunteer association of approximately 100 members. These volunteers have monitored plant species occurrences from 2001 to the present along several hiking trails in the region. In this paper, I present the annual observation records of plant occurrences in Hakone from 2001 to 2010. This data set includes 1,071 species of plants from 151 families. Scientific names follow the Y List, and this data set includes several threatened plant species. Data files are formatted based on the Darwin Core and Darwin Core Archives, which are defined by the Biodiversity Information Standards (BIS) or Biodiversity Information Standards Taxonomic Databases Working Group (TDWG). Data files filled on required and some additional item on Darwin Core. The data set can download from the author’s personal Web site as of July 2012. These data will soon be published for the Global Biodiversity Information Facility (GBIF) through GBIF Japan. All users can then access the data from the GBIF portal site.     

中国植物名称数据库的建设及若干问题的探讨

中国植物物种信息数据库是中国科学院科学数据库参考型数据库,中国植物名称数据库（CPNI）是中国植物物种信息数据库最重要的组成部分,是中国植物物种信息数据库收录植物的目录和索引,也是其他数据库的参考和联系的桥梁。以《中国植物志》和《Flora of China》为基础数据来源,加上少量参考数据作为补充,设计建设了中国植物名称数据库,并从现有已建成同类数据库的评价、数据来源和数据组成,以及建库策略实现对中国植物名称数据库建设进行了分析和探讨。中国植物名称数据库是植物名称的参考型数据库,能够辅助植物学相关学科研究中关于植物名称的研究和利用。     

Development of a maize molecular evolutionary genomic database

PANZEA is the first public database for studying maize genomic diversity. It was initiated as a repository of genomic diversity for an NSF Plant Genome project on 'Maize Evolutionary Genomics'. PANZEA is hosted at the Bioinformatics Research Center, North Carolina State University, and is open to the public (http://statgen.ncsu.edu/panzea). PANZEA is designed to capture the interrelationships between germplasm, molecular diversity, phenotypic diversity and genome structure. It has the ability to store, integrate and visualize DNA sequence, enzymatic, SSR (simple sequence repeat) marker, germplasm and phenotypic data. The relational data model is selected and implemented in Oracle. An automated DNA sequence data submission tool has been created that allows project researchers to remotely submit their DNA sequence data directly to PANZEA. On-line database search forms and reports have been created to allow users to search or download germplasm, DNA sequence, gene/locus data and much more, directly from the web.     

Drought-induced mortality of a foundation species (<Emphasis Type="Italic">Juniperus monosperma</Emphasis>) promotes positive afterlife effects in understory vegetation

Climate change-induced droughts have contributed to large-scale die-offs of dominant tree species throughout much of the southwestern United States. These mortality events provide ecologists with the opportunity to determine whether afterlife effects associated with the die-off occur and the potential implications for future ecosystem changes. We studied both the afterlife and interaction effects of condition (dead trees, living trees, and open areas) on understory vegetation in a Juniperus monosperma woodland of northern Arizona 7 years after a major mortality event. Five major findings resulted: (1) there was a positive afterlife effect on understory plants, in which vegetation under dead junipers contained almost double the amount of cover; (2) the competitive effect on understory plants was exemplified by a 1.3 times greater cover and 1.6 additional species in open areas compared to under living junipers; (3) plant community composition significantly differed by aspect and condition; (4) the highly invasive cheatgrass (Bromus tectorum) was 1.5 times greater under dead junipers compared to live junipers; and (5) litter depth and light availability were negatively and positively correlated with plant cover, respectively, but weakly correlated with afterlife effects. Our results indicate that mortality events can promote changes in understory vegetation through afterlife effects. In ecosystems where foundation species suffer high rates of mortality, changes in plant population dynamics and ecosystem function may promote an altered trajectory in community composition with the potential to increase the presence of invasive species. Continued species die-offs associated with climate change-induced drought may contribute to an increased occurrence and legacy of afterlife effects.     

Mendel, a database of nomenclature for sequenced plant genes

The Mendel database contains names for plant-wide families of sequenced plant genes. The names have either been approved by the Commission on Plant Gene Nomenclature (CPGN), an organization of the International Society for Plant Molecular Biology (ISPMB), or are identified as provisional or temporary names. Mendel also identifies the corresponding genes in individual species of plants. Mendel can be searched through the mirror sites at Cornell (http://genome. cornell.edu/cgi-bin/WebAce/webace?db=mendel) and Stanford (http://genome-www.stanford.edu/Mendel/). In addition, parts of Mendel can be downloaded from the CPGN Web site (http://mbclserver. rutgers.edu/CPGN/).     

The characterization of plant species using first‐derivative fluorescence spectra

Plants are one of the most important parts of the ecological system and demand a reliable method for accurate classification. In this study, the first‐derivative fluorescence spectral curves (FDFSCs) based on laser‐induced fluorescence technology were proposed for the characterization of plant species. The measurement system is mainly composed of a spectrometer, an excitation light source (the two excitation wavelengths are 460 and 556 nm, respectively), and an intensified charge‐coupled device camera. FDFSCs were calculated from the deviation between the fluorescence values at each wavelength, plus and minus one band, divided by the wavelength range. Principal component analysis was utilized to analyze the FDFSCs by extracting the main attributes and reducing the dimensionality of variables. A support vector machine was used to evaluate FDFSC performance for the identification of plant species. Plant species that are difficult to distinguished by the naked eye, can be identified effectively using the proposed FDFSCs. For the 556 nm and 460 nm excitation wavelengths, the overall identification rates of the six plant species evaluated were 93.3% and 91.7%, respectively. Experimental results demonstrated that the combination of the FDFSCs with multivariate analysis could provide a simple and reliable method for the characterization of plant species.     

Characterisation of microRNAs from apple (<Emphasis Type="Italic">Malus domestica</Emphasis>'Royal Gala') vascular tissue and phloem sap

Background  

Plant microRNAs (miRNAs) are a class of small, non-coding RNAs that play an important role in development and environmental responses. Hundreds of plant miRNAs have been identified to date, mainly from the model species for which there are available genome sequences. The current challenge is to characterise miRNAs from plant species with agricultural and horticultural importance, to aid our understanding of important regulatory mechanisms in crop species and enable improvement of crops and rootstocks.     

Micropropagation of the endangered Chilean tree, <Emphasis Type="Italic">Gomortega keule</Emphasis>

The endangered tree Gomortega keule remains only in small, isolated populations surrounded by timber plantations in the biodiversity hotspot of central Chile. This species, belonging to the monotypic family Gomortegaceae, produces edible fruit and high-quality wood, but its difficult propagation makes conservation essential. The percentage of seed germination is less than 40%, germination time exceeds 12 mo, and cuttings fail to root. These difficulties have stimulated efforts to explore in vitro approaches for propagation. Cultures were established from zygotic embryos; the optimum culture conditions for shoot proliferation were semi-solid Woody Plant Medium (WPM) with 20 g/l sucrose, 0.1 mg/l α-naphthaleneacetic acid and 1.0 mg/l 6-benzylaminopurine, at 18°C. Explants required about 12 mo in culture before stabilized growth resulted in consistent shoot production. Regenerated shoots excised from parental explants developed a normal morphology 1 mo after transfer to WPM with 2.0 g/l of activated charcoal, and lacking plant growth regulators. These normal shoots were rooted with a treatment of 7 d on WPM without activated charcoal, but containing 20 mg/l indole-3-butyric acid, followed by return to the same medium with 2.0 g/l activated charcoal, without growth regulators, for 1 mo. Regenerated plants were transferred to compost and covered with transparent plastic sleeves. The latter were opened gradually to decrease humidity and to establish plants under glasshouse conditions. There is an urgent requirement to extend this protocol to material collected from diverse sites and to introduce micropropagated specimens into the wild and living plant repositories to conserve this endangered species.     

Geographic distribution patterns and status assessment of threatened plants in China

Large scale heterogeneous distribution of biodiversity has become a hot topic for ecologists and conservationists. A threat status assessment combined with geographic distribution patterns of threatened plants in China has been conducted at a national scale in this study based upon a distribution database that refers to both specimen records and published references. Currently, 302 threatened plant species are cataloged in the “National Protected Key Wild Plants” in China belonging to 92 families and 194 genera. Results of the assessment according to the Categories and Criteria system of The World Conservation Union (IUCN) Red List indicate that three species have been assessed as Extinct in Wild (EW) while a further 79, 99 and 112 species have been assessed as Critically Endangered (CR), Endangered (EN), and Vulnerable (VU), respectively. Distribution patterns of threatened plants were analyzed with GIS to identify areas of high species diversity. It was found that threatened plant species occur unevenly within counties and are concentrated in the following eight hotspots: the central and southern Hengduanshan mountain area; the southeast regions of Yunnan as well as Xishuangbanna and southwestern Guangxi; the southern Hainan island; the border mountainous regions of Guizhou, Hunan and Guangxi provinces; the mountainous regions of southwestern Hubei and northern Hunan; southwestern Zhejiang and western Fujian; central Sichuan and southern Gansu; and the western mountains of Guangdong. Moreover, the 12 counties with the greatest number of threatened plant species represent cumulatively more than 50% of the total listed species and, therefore, are the regions in China that should be prioritized for conservation efforts. By overlapping the map of threatened plant species with the distribution of national nature reserves, a gap was identified in protected areas. This research will ultimately provide insights for prioritizing biodiversity conservation as well as processing the mechanisms of distribution patterns.     

内蒙古珍稀濒危植物濒危现状及优先保护评估

以《中国珍稀濒危保护植物名录》、《中国植物红皮书》、《国家重点保护野生植物名录(第一批)》、《中国物种红色名录》、《中国生物多样性红色名录(高等植物卷)》、《内蒙古珍稀濒危保护植物名录》和《内蒙古珍稀濒危植物图谱》中127种内蒙古珍稀濒危植物为研究对象,通过资料收集及专家咨询,构建了内蒙古珍稀濒危植物受威胁等级、优先保护评估体系.建立了濒危系数、遗传价值系数、利用价值系数、生境系数、繁殖系数5项准则,准则下共设17个指标;运用层次分析法确定指标体系权重,计算出珍稀濒危植物濒危等级及优先保护级别.结果表明: 极危种2种、濒危种13种、易危种37种、近危种44种、无危种31种,分别占总数的1.6%、10.2%、29.1%、34.7%、24.4%.其中,受威胁种(极危、濒危和易危种)共52种,占总种数的40.9%.一级保护植物35种、二级保护植物72种、三级保护植物20种,分别占总数的27.6%、56.7%、15.8%.本评估结果与《中国生物多样性红色名录(高等植物卷)》、《内蒙古珍稀濒危保护植物名录》相比,有75种植物的濒危等级和62种植物的保护级别发生了变化.其中新增了9种植物的濒危等级评估和32种植物的保护级别.     

构建基于EBI数据库的本地SRS服务系统

为了建立基于EBI数据库的本地SRS服务系统,进而为生物医学研究人员提供方便、快速搜索EBI常用生物数据库的web服务,同时提供一套技术机制为其他生物医学研究机构建设自己的SRS服务系统提供参考。在Linux系统和Tomcat环境下安装调试EBI提供的SRS8.1学术版软件,并利用perl和shell程序设计语言开发EBI数据库的自动下载和定期更新模块。完成了本地SRS系统的安装和测试,实现了EBI数据库的自动下载和更新机制,目前系统已经正常运行。     

Food web associations and effect of trophic resources and environmental factors on parasitoids expanding their host range into non‐native hosts

Trophic interactions and environmental conditions determine the structure of food webs and the host expansion of parasitoids into novel insect hosts. In this study, we investigate plant–insect–parasitoid food web interactions, specifically the effect of trophic resources and environmental factors on the presence of the parasitoids expanding their host range after the invasion of Chrysodeixis chalcites (Esper) (Lepidoptera: Noctuidae). We also consider potential candidates for biological control of this non‐native pest. A survey of larval stages of Plusiinae (Lepidoptera: Noctuidae) and their larval parasitoids was conducted in field and vegetable greenhouse crops in 2009 and 2010 in various locations of Essex and Chatham‐Kent counties in Ontario, Canada. Twenty‐one plant–host insect–host parasitoid associations were observed among Trichoplusia ni (Hübner) (Lepidoptera: Noctuidae), C. chalcites, and larval parasitoids in three trophic levels of interaction. Chrysodeixis chalcites, an old‐world species that had just arrived in the region, was the most common in our samples. The larval parasitoids Campoletis sonorensis (Cameron) (Hymenoptera: Ichneumonidae), Cotesia vanessae (Reinhard), Cotesia sp., Microplitis alaskensis (Ashmead), and Meteorus rubens (Nees) (all Hymenoptera: Braconidae) expanded their host range into C. chalcites changing the structure of the food web. Copidosoma floridanum (Ashmead) (Hymenoptera: Encyrtidae) was the most common parasitoid of T. ni that was not found in the invasive species. Plant species, host abundance, and agro‐ecosystem were the most common predictors for the presence of the parasitoids expanding their host range into C. chalcites. Our results indicate that C. sonorensis, C. vanessae, and C. floridanum should be evaluated for their potential use in biological control of C. chalcites and T. ni.     

The Plant PTM Viewer,a central resource for exploring plant protein modifications

Post‐translational modifications (PTMs) of proteins are central in any kind of cellular signaling. Modern mass spectrometry technologies enable comprehensive identification and quantification of various PTMs. Given the increased numbers and types of mapped protein modifications, a database is necessary that simultaneously integrates and compares site‐specific information for different PTMs, especially in plants for which the available PTM data are poorly catalogued. Here, we present the Plant PTM Viewer (http://www.psb.ugent.be/PlantPTMViewer), an integrative PTM resource that comprises approximately 370 000 PTM sites for 19 types of protein modifications in plant proteins from five different species. The Plant PTM Viewer provides the user with a protein sequence overview in which the experimentally evidenced PTMs are highlighted together with an estimate of the confidence by which the modified peptides and, if possible, the actual modification sites were identified and with functional protein domains or active site residues. The PTM sequence search tool can query PTM combinations in specific protein sequences, whereas the PTM BLAST tool searches for modified protein sequences to detect conserved PTMs in homologous sequences. Taken together, these tools help to assume the role and potential interplay of PTMs in specific proteins or within a broader systems biology context. The Plant PTM Viewer is an open repository that allows the submission of mass spectrometry‐based PTM data to remain at pace with future PTM plant studies.     

Expression of a KDEL-tagged dengue virus protein in cell suspension cultures of <Emphasis Type="Italic">Nicotiana tabacum</Emphasis> and <Emphasis Type="Italic">Morinda citrifolia</Emphasis>

Hypericum perforatum L. (St. John’s wort) produces a number of phytochemicals having medicinal, anti-microbial, anti-viral and anti-oxidative properties. Plant extracts are generally used for treatment of mild to medium cases of depression. Plant regeneration can be achieved in this species by in vitro culture of a variety of explants. However, there are no reports of regeneration from petal explants. In this report plant regeneration from petal explants of St. John’s wort was evaluated. Petals of various ages were cultured on agarized Murashige and Skoog 1962 (MS) medium supplemented with auxin and cytokinin (kinetin), maintained in the dark and callus and shoot regeneration determined after 28 days. At an auxin to cytokinin ratio of 10:1, callus and shoot formation were induced by all levels of indole-3-acetic acid (IAA), indole-3-butyric acid (IBA) and 1-naphthaleneacetic acid (NAA), while 2,4-dichlorophenoxyacetic acid (2,4-D) induced only callus formation. The optimum level of auxin for shoot regeneration was 1.0 and 0.1 mg/l kinetin, where the regeneration frequency was 100 percent for all three auxins. The highest number of shoots per explant (57.4 and 53.4) was obtained with IAA and IBA, respectively. In the absence of auxin, kinetin levels of 0.1 and 0.25 mg/l induce callus and shoot formation at low frequency but not at lower levels. Callus and shoot formation did not occur in the absence of growth regulators. Petal-derived shoots were successfully rooted on half-strength MS medium without a requirement for exogenous auxin and flowering plants were established under greenhouse conditions. From these results it can be concluded that auxin type is a critical factor for plant regeneration from petal explants of Hypericum perforatum and there is no absolute requirement for high levels of cytokinin.     

An efficient method for <Emphasis Type="Italic">in vitro</Emphasis> regeneration of leafy spurge (<Emphasis Type="Italic">Euphorbia esula</Emphasis> L.)

Leafy spurge (Euphorbia esula L.) is a perennial, invasive weed used as a model to study invasive plant behavior, because molecular tools (such as a deep expressed sequence tag database and deoxyribonucleic acid microarrays) have been developed for this species. However, the lack of effective in vitro regeneration and genetic transformation systems has hampered molecular approaches to study leafy spurge. In this study, we describe an efficient in vitro regeneration system. Three highly regenerative lines were selected by screening the in vitro regeneration capabilities of stem explants of 162 seedlings. The effects of various culture conditions on in vitro regeneration were then evaluated based on explant competence to form calluses and shoots. High rates of shoot regeneration can be obtained using a growth medium containing 1× woody plant basal medium and 1× Murashige and Skoog (MS) basal salts, 1× MS vitamins, 1.11 μM 6-benzylaminopurine, 1.97 μM indole-3-butyric acid, and 3% sucrose, pH 5.6–5.8. After 30 d culture, multiple shoots formed either directly from the stem or indirectly from the callus. This method is a requisite for the development of genetic transformation systems for leafy spurge and may be used to develop in vitro regeneration techniques for other species in the Euphorbiaceae.