Molecular identification of species in Prunus sect.Persica (Rosaceae), with emphasis on evaluation of candidate barcodes for plants

Species of Prunus L. sect. Persica are not only important fruit trees, but also popular ornamental and medicinal plants. Correct identification of seedlings, barks, or fruit kernels is sometimes required, but no reliable morphological characters are available. Nowadays, the technique of DNA barcoding has the potential to meet such requirements. In this study, we evaluated the suitability of 11 DNA loci (atpB-rbcL, trnH-psbA, trnL-F, trnS-G, atpF-H, rbcL, matK, rpoB, rpoC1, nad1, and internal transcribed spa...     

DNA barcoding of Pedicularis L.(Orobanchaceae): Evaluating four universal barcode loci in a large and hemiparasitic genus

One application ofDNA barcoding is species identification based on sequences of a short and standardized DNA region.In plants,various DNA regions,alone or in combination,have been proposed and investigated,but consensus on a universal plant barcode remains elusive.In this study,we tested the utility of four candidate barcoding regions (rbcL,matK,trnH-psbA,and internal transcribed spacer (ITS)) as DNA barcodes for discriminating species in a large and hemiparasitic genus Pedicularis (Orobanchaceae).Amplification and sequencing was successful using single primer pairs for rbcL,trnH-psbA,and ITS,whereas two primer pairs were required for matK.Patterns of sequence divergence commonly showed a “barcoding gap”,that is,a bimodal frequency distribution of pairwise distances representing genetic diversity within and between species,respectively Considering primer universality,ease of amplification and sequencing,and performance in discriminating species,we found the most effective single-region barcode for Pedicularis to be ITS,and the most effective two-region barcode to be rbcL +ITS.Both discriminated at least 78％ of the 88 species and correctly identified at least 89％ of the sequences in our sample,and were effective in placing unidentified samples in known species groups.Our results suggest that DNA barcoding has the potential to aid taxonomic research in Pedicularis,a species-rich cosmopolitan clade much in need of revision,as well as ecological studies in its center of diversity,the Hengduan Mountains region of China.     

Evaluation of six candidate DNA barcoding loci in Ficus (Moraceae) of China

Ficus, with about 755 species, diverse habits and complicated co‐evolutionary history with fig wasps, is a notoriously difficult group in taxonomy. DNA barcoding is expected to bring light to the identification of Ficus but needs evaluation of candidate loci. Based on five plastid loci (rbcL, matK, trnH‐psbA, psbK‐psbI, atpF‐atpH) and a nuclear locus [internal transcribed spacer (ITS)], we calculated genetic distances and DNA barcoding gaps individually and in combination and constructed phylogenetic trees to test their ability to distinguish the species of the genus. A total of 228 samples representing 63 putative species in Ficus (Moraceae) of China were included in this study. The results demonstrated that ITS has the most variable sites, greater intra‐ and inter‐specific divergences, the highest species discrimination rate (72%) and higher primer universality among the single loci. It is followed by psbK‐psbI and trnH‐psbA with moderate variation and considerably lower species discrimination rates (about 19%), whereas matK, rbcL and atpF‐atpH could not effectively separate the species. Among the possible combinations of loci, ITS + trnH‐psbA performed best but only marginally improved species resolution over ITS alone (75% vs. 72%). Therefore, we recommend using ITS as a single DNA barcoding locus in Ficus.     

Assessment of loci for DNA barcoding in the genus Thrips (Thysanoptera:Thripidae)

Identification of the juveniles of economically important thrips species on imports by morphology alone can be challenging and culturing is usually required. In the case of EU quarantine species such as Thrips palmi, rapid and accurate identification is essential. DNA barcoding using the Cytochrome oxidase I (COI) gene has become a popular technique for species identification; however, in some invertebrate genera COI has been shown to provide insufficient variability for species discrimination. This study presents a comparison of five different loci to investigate their ability to discriminate a small number of Thrips species. All five loci discriminated the species by neighbour-joining tree and varying degrees of discrimination were determined upon further investigation of the intraspecific and interspecific distances. Two distinct COI clades were observed for T. Palmi and judged to be COI haplotypes when data from the other four additional loci and geographical collection data were taken into consideration. COI was shown to provide sufficient variation to be used in future DNA barcoding efforts within the genus Thrips.     

The origin of the sporophyte shoot in land plants: a bryological perspective

Background

Land plants (embryophytes) are monophyletic and encompass four major clades: liverworts, mosses, hornworts and polysporangiophytes. The liverworts are resolved as the earliest divergent lineage and the mosses as sister to a crown clade formed by the hornworts and polysporangiophytes (lycophytes, monilophytes and seed plants). Alternative topologies resolving the hornworts as sister to mosses plus polysporangiophytes are less well supported. Sporophyte development in liverworts depends only on embryonic formative cell divisions. A transient basal meristem contributes part of the sporophyte in mosses. The sporophyte body in hornworts and polysporangiophytes develops predominantly by post-embryonic meristematic activity.

Scope

This paper explores the origin of the sporophyte shoot in terms of changes in embryo organization. Pressure towards amplification of the sporangium-associated photosynthetic apparatus was a major driver of sporophyte evolution. Starting from a putative ancestral condition in which a transient basal meristem produced a sporangium-supporting seta, we postulate that in the hornwort–polysporangiophyte lineage the basal meristem acquired indeterminate meristematic activity and ectopically expressed the sporangium morphogenetic programme. The resulting sporophyte body plan remained substantially unaltered in hornworts, whereas in polysporangiophytes the persistent meristem shifted from a mid-embryo to a superficial position and was converted into an ancestral shoot apical meristem with the evolution of sequential vegetative and reproductive growth.

Conclusions

The sporophyte shoot is interpreted as a sterilized sporangial axis interpolated between the embryo and the fertile sporangium. With reference to the putatively ancestral condition found in mosses, the sporophyte body plans in hornworts and polysporangiophytes are viewed as the product of opposite heterochronic events, i.e. an anticipation and a delay, respectively, in the development of the sporangium. In either case the result was a pedomorphic sporophyte permanently retaining juvenile characters.     

Phylogenetic species delimitation in ectomycorrhizal fungi and implications for barcoding: the case of the Tricholoma scalpturatum complex (Basidiomycota)

Population studies have revealed that the fungal ectomycorrhizal morphospecies Tricholoma scalpturatum consists of at least two genetically distinct groups that occur sympatrically in several geographical areas. This discovery prompted us to examine species boundaries and relationships between members formerly assigned to T. scalpturatum and allied taxa using phylogenetic analyses. Sequence data were obtained from three nuclear DNA regions [internal transcribed spacer (ITS), gpd and tef], from 101 carpophores collected over a large geographical range in Western Europe, and some reference sequences from public databases. The ITS was also tested for its applicability as DNA barcode for species delimitation. Four highly supported phylogenetic clades were detected. The two previously detected genetic groups of T. scalpturatum were assigned to the phylospecies Tricholoma argyraceum and T. scalpturatum. The two remaining clades were referred to as Tricholoma cingulatum and Tricholoma inocybeoides. Unexpectedly, T. cingulatum showed an accelerated rate of evolution that we attributed to narrow host specialization. This study also reveals recombinant ITS sequences in T. inocybeoides, suggesting a hybrid origin. The ITS was a useful tool for the determination of species boundaries: the mean value of intraspecific genetic distances in the entire ITS region (including 5.8S rDNA) was <0.2%, whereas interspecific divergence estimates ranged from 1.78% to 4.22%. Apart from giving insights into the evolution of the T. scalpturatum complex, this study contributes to the establishment of a library of taxonomically verified voucher specimens, an a posteriori correlation between phenotype and genotype, and DNA barcoding of ectomycorrhizal fungi.     

A large family with features of pseudoachondroplasia and multiple epiphyseal dysplasia: exclusion of seven candidate gene loci that encode proteins of the cartilage extracellular matrix

We have identified a large family with a dominantly inherited chondrodysplasia characterized by a waddling gait, short limbs, and early onset osteoarthritis. The radiographic presentation resembles pseudoachondroplasia in childhood and multiple epiphyseal dysplasia in adults. Electron microscopic examination of cartilage reveals accumulation of material within the rough endoplasmic reticulum similar to that seen in pseudoachondroplasia and the Fairbank type of multiple epiphyseal dysplasia. By linkage analysis, we have excluded the genes for aggrecan, decorin, hexabrachion (tenascin), type II procollagen, the 1 chain of type XI procollagen, the 1 chain of type IX procollagen, and link protein, candidate genes that encode structural components of the cartilage extracellular matrix, as the disease locus for this disorder.     

Characterization of transgene loci in plants using FISH: A picture is worth a thousand words

Transgenic plants are traditionally characterized using phenotypic and Southern analyses. Over the last several years, fluorescence in situ hybridization (FISH) has been efficiently used for visualization, chromosomal localization and estimation of numbers of transgene loci in transgenic plants. Recent results obtained in different plant species transformed using either Agrobacterium tumefaciens or microprojectile bombardment indicate that FISH is also a powerful tool for characterization of transgene locus structure that significantly augments conventional Southern analysis. The aim of this review is to document the usefulness of FISH for characterization of transgene loci in plants.     

Distribution of cell-wall xylans in bryophytes and tracheophytes: new insights into basal interrelationships of land plants

Xylans are known to be major cellulose-linking polysaccharides in secondary cell walls in higher plants. We used two monoclonal antibodies (LM10 and LM11) for a comparative immunocytochemical analysis of tissue and cell distribution of xylans in a number of taxa representative of all major tracheophyte and bryophyte lineages. The results show that xylans containing the epitopes recognized by LM10 and LM11 are ubiquitous components of secondary cell walls in vascular and mechanical tissues in all present-living tracheophytes. In contrast, among the three bryophyte lineages, LM11 binding was detected in specific cell-wall layers in pseudoelaters and spores in the sporophyte of hornworts, while no binding was observed with either antibody in the gametophyte or sporophyte of liverworts and mosses. The ubiquitous occurrence of xylans containing LM10 and LM11 epitopes in tracheophytes suggests that the appearance of these polysaccharides has been a pivotal event for the evolution of highly efficient vascular and mechanical tissues. LM11 binding in the sporophyte of hornworts, indicating the presence of relatively highly substituted xylans (possibly arabinoxylans), separates these from the other bryophytes and is consistent with recent molecular data indicating a sister relationship of the hornworts with tracheophytes.     

福建省海岸植物资源调查及园林应用综合评价

在查阅文献资料和标本的基础上,对位于福建省漳州市、厦门市、泉州市、福州市及宁德市的7个海岸样带的海岸植物组成、生活型及生态适应性进行了调查和分析;采用层次分析法构建了海岸植物园林应用综合评价体系,并据此筛选出适于福建海岸园林建设的原生植物种类。结果表明:7个海岸样带共包含74科229属323种海岸植物,其中原生种有278种、外来种有45种;含种数较多的科包括禾本科(Gramineae)、菊科(Compositae)、莎草科(Cyperaceae)、豆科(Leguminosae)和大戟科(Euphorbiaceae),共包含92属151种,分别占总属数和总种数的40.17%和46.75%。福建省海岸植物生活型大体分为乔木、灌木、草本、藤本及其他5类,其中草本占优势;草本、灌木、藤本和乔木的种数分别为204、64、31和14种,草本和灌木的种数分别占总种数的63.16%和19.81%。按照生态类群可将福建海岸植物分为陆岸沙生生态类群、盐生湿地生态类群、基岩海岸及海岸林生态类群、广生境生态类群4类。福建省海岸植物园林应用综合评价体系共包含5个一级因子和19个二级因子。一级因子中权重值排在前2位的因子为生理适应性和美学特性,权重值分别为0.276 2和0.218 9;二级因子中盐碱适应能力的权重值最高(0.082 7),栽培成本、养护成本、资源数量和植株形态观赏性的权重值也较高(均在0.070 0以上)。采用这一评价体系从福建海岸原生植物中共筛选出适于海岸园林建设的植物40种,这些植物的得分均在3.00以上且观赏性强、生态功能较佳。此外,还针对滨海滩涂地带、沙滩开阔地带和基岩质海岸带提出了几种人工植物群落景观营造的植物配置模式。     

西双版纳三种药用植物的民间利用及抗菌活性

结合民族植物学和药理学的研究方法,对西双版纳地区傣族、哈尼族和基诺族等3个少数民族民间利用番石榴(Psidium guajava)、余甘子(Phyllanthus emblica)和水柳(Homonoia riparia)的传统知识进行调查研究及体外抗菌活性实验。结果表明:番石榴和余甘子在村寨中较为常见,当地少数民族将其种植于庭院中,常作为果蔬食用,食用番石榴嫩叶可缓解拉肚子的症状,治疗腹痛、腹泻。水柳生长在水边,傣族会将其叶作为腌酸鱼的配料之一。根据文献记载,番石榴、余甘子和水柳的叶部位作为药使用时,常煎水外洗,治疗皮肤瘙痒。对这3种药用植物叶部位采用80%乙醇浸泡制备的提取物进行体外抗菌实验,结果显示番石榴、余甘子和水柳3种药用植物对金黄色葡萄球菌和大肠埃希菌均有较好的抑菌和杀菌活性,其最小抑菌浓度MIC在98~390μg·mL~(-1)之间,最小杀菌浓度MBC在98~781μg·mL~(-1)之间。番石榴和水柳叶对铜绿假单胞菌有一定抑菌和杀菌活性,其MIC和MBC范围均为6 250~12 500μg·mL~(-1)。由此可见,这3种药用植物的民间利用具有一定的合理性和药用开发价值。     

Bacterial endophytes from arid land plants regulate endogenous hormone content and promote growth in crop plants: an example of Sphingomonas sp. and Serratia marcescens

The objective of the present study was to determine the potential plant growth-promoting action of bacterial endophytes isolated from arid land-dwelling plants under normal conditions. Overall, five bacterial endophytes LK11 (Sphingomonas sp. LK11), TP5 (Bacillus subtilis), MPB5.3 (B. subtilis subsp. Subtilis), S9 (B. subtilis subsp. Subtilis), and TP1 (Serratia marcescens) were evaluated based on morphological characteristics after isolation and purification. Phytohormonal analysis of these endophytes predicted indole acetic acid (IAA) production 12.31?±?0.45?, 6.8?±?0.59, and 10.5?±?1.02?μM/mL in the culture broths of LK11, MPB5.3, and TP1, respectively. Under controlled greenhouse conditions, these endophytes were inoculated into soybean, and their growth-promoting characteristics were compared with those of non-phytohormone-producing endophytes. In terms of plant growth promotion, among IAA-producing endophytes, LK11 and TP1 greatly improved physiological characteristics such as shoot/root length, fresh/dry weight, and chlorophyll contents. However, the non-phytohormone-producing endophytes TP5 and S9 did not show a growth-promoting effect. Based on these results, plants inoculated with LK11 and TP1 along with a control were subjected to endogenous hormonal analysis and showed a significant increase in abscisic acid (457.30–398.55 vs. 205.93 ng/g D.W.) and a decrease in jasmonic acid content (50.07–85.07 vs. 93.90 ng/g D.W.), respectively. Total gibberellin content was found to significantly increase in endophyte-inoculated plants (155.43–146.94?ng/g D.W.) as compared to that in controls (113.76 ng/g D.W.). In summary, bacterial endophytes might be used to enhance crop plant physiological characteristics isolated from arid land-inhabiting plants under normal conditions.     

The mitochondrial genome of the moss Physcomitrella patens sheds new light on mitochondrial evolution in land plants

The phylogenetic positions of bryophytes and charophytes, together with their genome features, are important for understanding early land plant evolution. Here we report the complete nucleotide sequence (105,340 bp) of the circular-mapping mitochondrial DNA of the moss Physcomitrella patens. Available evidence suggests that the multipartite structure of the mitochondrial genome in flowering plants does not occur in Physcomitrella. It contains genes for 3 rRNAs (rnl, rns, and rrn5), 24 tRNAs, and 42 conserved mitochondrial proteins (14 ribosomal proteins, 4 ccm proteins, 9 nicotinamide adenine dinucleotide dehydrogenase subunits, 5 ATPase subunits, 2 succinate dehydrogenase subunits, apocytochrome b, 3 cytochrome oxidase subunits, and 4 other proteins). We estimate that 5 tRNA genes are missing that might be encoded by the nuclear genome. The overall mitochondrial genome structure is similar in Physcomitrella, Chara vulgaris, Chaetosphaeridium globosum, and Marchantia polymorpha, with easily identifiable inversions and translocations. Significant synteny with angiosperm and chlorophyte mitochondrial genomes was not detected. Phylogenetic analysis of 18 conserved proteins suggests that the moss-liverwort clade is sister to angiosperms, which is consistent with a previous analysis of chloroplast genes but is not consistent with some analyses using mitochondrial sequences. In Physcomitrella, 27 introns are present within 16 genes. Nine of its intron positions are shared with angiosperms and 4 with Marchantia, which in turn shares only one intron position with angiosperms. The phylogenetic analysis as well as the syntenic structure suggest that the mitochondrial genomes of Physcomitrella and Marchantia retain prototype features among land plant mitochondrial genomes.     

Speciation in Passerina buntings: introgression patterns of sex-linked loci identify a candidate gene region for reproductive isolation

Sex-chromosomes are thought to play an important role in speciation, but few studies of non-model organisms have investigated the relative influence of multiple sex-linked markers on reproductive isolation. We collected 222 individuals along a geographical transect spanning the hybrid zone between Passerina amoena and P. cyanea (Aves: Cardinalidae). Using maximum-likelihood cline fitting methods, we estimated locus-specific introgression rates for 10 z-linked markers. Although the cline width estimates ranged from 2.8 to 584 km, eight of 10 loci had cline widths between 224 and 271 km. We also used coalescent-based estimates of locus-specific divergence times between P. amoena and P. cyanea to test a recently proposed hypothesis of an inverse relationship between divergence time and cline width but did not find a significant association. The narrow width (2.8 km) of the cline estimated from the VLDLR9 locus indicates strong selection retarding introgression of alleles at this locus across the hybrid zone. Interestingly, a mutation in the very low density lipoprotein receptor ( VLDLR ) gene, in which VLDLR9 is an intron, is known to reduce the egg-laying ability of some chickens, suggesting a possible link between this gene region and reproductive isolation between P. amoena and P. cyanea . These results underscore the importance of sampling multiple loci to investigate introgression patterns across a chromosome or genome and support previous findings of the importance of sex-linked genes in speciation.     

Health risk assessment of arsenic in soils from three thermal power plants in Southwest China

Abstract

High levels of arsenic (As) contamination in soils from thermal power plants pose a great threat to human health. This study aimed to evaluate the As contamination levels and assess the possible health risk of As in soils from three typical thermal power plants in Southwest China. The concentration of As was detected by using novel collision/reaction cell technology (CCT) with inductively coupled plasma mass spectrometry (ICP-MS, collectively ICP-CCT-MS) after aseptic digestion of soil samples. The carcinogenic risk and hazard quotient were estimated for health risk to workers in the study area by using “Chinese Technical Guidelines for Risk Assessment of Contaminated Sites (HJ 25.3-2014)”. Results showed that the concentration of As was between 3.65 and 33.80?mg/kg, and the comprehensive carcinogenic risk level of As was 3–28 times over the maximum acceptable level (10^?6), indicating that workers in the study area are facing serious threat of As. Oral ingestion (76.65%) was the main exposure pathway to carcinogenic risk, followed by skin contact (13.15%) and inhalation of soil particles (10.20%). After calculating the safety threshold values under three different exposure pathways (oral ingestion, skin contact and inhalation of soil particles), the minimum safety threshold value (1.59?mg/kg) was selected as the reference safety threshold value of As in the study area. These results provide basic information of health risk assessment of As and environmental management in thermal power plant areas.     

Effects of physico-chemistry, land use and hydromorphology on three riverine organism groups: a comparative analysis with monitoring data from Germany and Austria

The majority of studies comparing the response of biotic metrics to environmental stress in rivers are based on relatively small, homogeneous datasets resulting from research projects. Here, we used a large dataset from Austrian and German national river monitoring programmes (2,302 sites) to analyse the response of fish, diatom and macroinvertebrate metrics to four stressors acting at different scales (hydromorphology, physico-chemistry, riparian and catchment land use). Nutrient enrichment and catchment land use were the main discriminating stressors for all organism groups, over-ruling the effects of hydromorphological stress on the site scale. The response of fish metrics to stress was generally low, while macroinvertebrate metrics performed best. The Trophic Diatom Index (TDI) responded most strongly to all stressors in the mountain streams, while different metrics were responsive in the lowlands. Our results suggest that many rivers are still considerably affected by nutrient enrichment (eutrophication), which might directly point at implications of catchment land use. We conclude that monitoring datasets are well-suited to detect major broad-scale trends of degradation and their impact on riverine assemblages, while the more subtle effects of local-scale stressors require stream type-specific approaches.     

An evaluation of artificial substrates for sampling macrobenthos in reservoirs

Artificial substrates were compared with a Ponar grab for sampling benthic macroinvertebrates in Lake Anna, Louisa Co., Virginia. The objective was t0 find which technique was best for assessment 0f thermal effluent effects using the following criteria: 1) provide reliable data on density and composition 0f the macrobenthos with a reasonable number 0f replicates; 2) collect the most taxa; and, 3) require the least amount 0f time. Leaves, 3M Corporation's #200 conservation web, and limestone rocks were compared. Each material was tested separately in chicken wire baskets placed 0n the bottom at several depths. Three replicates of each type were retrieved monthly from each depth using SCUBA and cloth flour sacks and compared with grab samples taken from the same depths. Lesser amounts of these materials were tested separately in smaller plastic containers. All large artificial substrate samplers collected significantly more individuals (P = 0.05) and taxa than the Ponar grab. Small web and leaf samplers best met all three 0f the established criteria. The SCUBA system developed in the study is a fast and reliable sampling method.     

Identification of quantitative trait loci and associated candidate genes for low-temperature tolerance in cold-hardy winter wheat

Low-temperature (LT) tolerance is an important economic trait in winter wheat (Triticum aestivum L.) that determines the plants’ ability to cope with below freezing temperatures. Essential elements of the LT tolerance mechanism are associated with the winter growth habit controlled by the vernalization loci (Vrn-1) on the group 5 chromosomes. To identify genomic regions, which in addition to vrn-1 determine the level of LT tolerance in hexaploid wheat, two doubled haploid (DH) mapping populations were produced using parents with winter growth habit (vrn-A1, vrn-B1, and vrn-D1) but showing different LT tolerance levels. A total of 107 DH lines were analyzed by genetic mapping to produce a consensus map of 2,873 cM. The LT tolerance levels for the Norstar (LT₅₀=−20.7°C) × Winter Manitou (LT₅₀=−14.3°C) mapping population ranged from −12.0 to −22.0°C. Single marker analysis and interval mapping of phenotyped lines revealed a major quantitative trait locus (QTL) on chromosome 5A and a weaker QTL on chromosome 1D. The 5A QTL located 46 cM proximal to the vrn-A1 locus explained 40% of the LT tolerance variance. Two C-repeat Binding Factor (CBF) genes expressed during cold acclimation in Norstar were located at the peak of the 5A QTL.     

Assessing extinction risk in the absence of species-level data: quantitative criteria for terrestrial ecosystems

The conservation of individual plant and animal species has been advanced greatly by the World Conservation Union’s (IUCN) development of objective, repeatable, and transparent criteria for assessing extinction risk, which explicitly separate the process of risk assessment from priority-setting. Here we present an analogous procedure for assessing the extinction risk of terrestrial ecosystems, which may complement traditional species-specific risk assessments, or may provide an alternative when only landscape-level data are available. We developed four quantitative risk criteria, derived primarily from remotely sensed spatial data, information on one of which must be available to permit classification. Using a naming system analogous to the present IUCN species-specific system, our four criteria were: (A) reduction of land cover and continuing threat, (B) rapid rate of land cover change, (C) increased fragmentation, and (D) highly restricted geographical distribution. We applied these criteria to five ecosystems covering a range of spatial and temporal scales, regions of the world, and ecosystem types, and found that Indonesian Borneo’s lowland tropical forests and the Brazilian Atlantic rainforest were Critically Endangered, while South Africa’s grasslands and Brazil’s Mato Grosso were Vulnerable. Furthermore, at a finer grain of analysis, one region of Venezuela’s coastal dry forests (Margarita Island) qualified as Vulnerable, while another (the Guasare River watershed) was Critically Endangered. In northern Venezuela, deciduous forests were classified as Endangered, semi-deciduous forests Vulnerable, and evergreen forests of Least Concern. We conclude that adoption of such a standardized system will facilitate globally comparable, repeatable geographic analyses that clearly separate risk assessment (a fundamentally scientific process), from the definition of conservation priorities, which should take into account additional factors, such as ecological distinctiveness, costs, logistics, likelihood of success, and societal preferences. Jon Paul Rodríguez and Jennifer K. Balch are contributed equally to this work