Transposable elements in Coffea (Gentianales : Rubiacea) transcripts and their role in the origin of protein diversity in flowering plants

Transposable elements are major components of plant genomes and they influence their evolution, acting as recombination hot spots, acquiring specific cell functions or becoming part of protein-coding regions. The latter is the subject of the present analysis. This study is a report on the annotation of transposable elements (TEs) in expressed sequences of Coffea arabica, Coffea canephora and Coffea racemosa, showing the occurrence of 383 ESTs and 142 unigenes with TE fragments in these three Coffea species. Based on selected unigenes, it was possible to suggest 26 putative proteins with TE-cassette insertions, demonstrating a likely contribution to protein variability. The genes for two of those proteins, the fertility restorer (FR) and the pyrophosphate-dependent phosphofructokinase (PPi-PFKs) genes, were selected for evaluating the impact of TE-cassettes on host gene evolution of other plant genomes (Arabidopsis thaliana, Oryza sativa and populus trichocarpa). This survey allowed identifying a FR gene in O. sativa harboring multiple insertions of LTR retrotransposons that originated new exons, which however does not necessarily mean a case of molecular domestication. A possible transduction event of a fragment of the PPi-PFK beta-subunit gene mediated by Helitron ATREPX1 in Arabidopsis thaliana was also highlighted.

Fungal Planet description sheets: 320-370

Novel species of fungi described in the present study include the following from Malaysia: Castanediella eucalypti from Eucalyptus pellita, Codinaea acacia from Acacia mangium, Emarcea eucalyptigena from Eucalyptus brassiana, Myrtapenidiella eucalyptorum from Eucalyptus pellita, Pilidiella eucalyptigena from Eucalyptus brassiana and Strelitziana malaysiana from Acacia mangium. Furthermore, Stachybotrys sansevieriicola is described from Sansevieria ehrenbergii (Tanzania), Phacidium grevilleae from Grevillea robusta (Uganda), Graphium jumulu from Adansonia gregorii and Ophiostoma eucalyptigena from Eucalyptus marginata (Australia), Pleurophoma ossicola from bone and Plectosphaerella populi from Populus nigra (Germany), Colletotrichum neosansevieriae from Sansevieria trifasciata, Elsinoë othonnae from Othonna quinquedentata and Zeloasperisporium cliviae (Zeloasperisporiaceae fam. nov.) from Clivia sp. (South Africa), Neodevriesia pakbiae, Phaeophleospora hymenocallidis and Phaeophleospora hymenocallidicola on leaves of a fern (Thailand), Melanconium elaeidicola from Elaeis guineensis (Indonesia), Hormonema viticola from Vitis vinifera (Canary Islands), Chlorophyllum pseudoglobossum from a grassland (India), Triadelphia disseminata from an immunocompromised patient (Saudi Arabia), Colletotrichum abscissum from Citrus (Brazil), Polyschema sclerotigenum and Phialemonium limoniforme from human patients (USA), Cadophora vitícola from Vitis vinifera (Spain), Entoloma flavovelutinum and Bolbitius aurantiorugosus from soil (Vietnam), Rhizopogon granuloflavus from soil (Cape Verde Islands), Tulasnella eremophila from Euphorbia officinarum subsp. echinus (Morocco), Verrucostoma martinicensis from Danaea elliptica (French West Indies), Metschnikowia colchici from Colchicum autumnale (Bulgaria), Thelebolus microcarpus from soil (Argentina) and Ceratocystis adelpha from Theobroma cacao (Ecuador). Myrmecridium iridis (Myrmecridiales ord. nov., Myrmecridiaceae fam. nov.) is also described from Iris sp. (The Netherlands). Novel genera include (Ascomycetes): Budhanggurabania from Cynodon dactylon (Australia), Soloacrosporiella, Xenocamarosporium, Neostrelitziana and Castanediella from Acacia mangium and Sabahriopsis from Eucalyptus brassiana (Malaysia), Readerielliopsis from basidiomata of Fuscoporia wahlbergii (French Guyana), Neoplatysporoides from Aloe ferox (Tanzania), Wojnowiciella, Chrysofolia and Neoeriomycopsis from Eucalyptus (Colombia), Neophaeomoniella from Eucalyptus globulus (USA), Pseudophaeomoniella from Olea europaea (Italy), Paraphaeomoniella from Encephalartos altensteinii, Aequabiliella, Celerioriella and Minutiella from Prunus (South Africa). Tephrocybella (Basidiomycetes) represents a novel genus from wood (Italy). Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.

Report of the Poplar Working Group

Poplars consist of all species of the genus Populus, including cottonwoods, aspens, and the many interspecies hybrids in common use (Dickmann and Stuart 1983). Our working group focused on the fungal pathogens, arthropod herbivores, and weed competitors of Populus in the United States. However, bacterial and viral diseases of Populus are significant in Europe, and genetic engineering approaches toward their control or management are being studied. The key aspects of poplar biology important to understanding the use of pest resistance genes are described below.

Fire Frequency and the Vegetative Mosaic of a Spruce-Fir Forest in Northern Utah

Fire scar and vegetative analysis were used to construct a fire history for the Engelmann spruce/subalpine fir (Picea engelmannii/Abies lasiocarpa) vegetation type of the Utah State University (USU) T. W Daniel Experimental Forest. Three distinct periods of fire frequency were established-presettlement (1700-1855), settlement (1856-1909), and suppression (1910-1990). Mean fire interval (MFI) decreased during the settlement period and greatly increased during the suppression era. The difference was attributed to the influx of ignition sources during the settlement of nearby Cache Valley, located 40 km to the west. Logging and livestock grazing appear to have led to the reduced MFI, which in turn worked as a factor to create the vegetative mosaic now observed on the study area. The increase in MFI during the suppression era permitted the advancement of shade-tolerant species in the understory of the shade-intolerant lodgepole pine (Pinus contorta var. latifolia) and quaking aspen (Populus tremuloides). Continued suppression of disturbance from wildfire will allow the lodgepole pine cover type, which experienced the lowest MFI during the settlement period, to be further invaded by shade-tolerant species, decreasing spatial stand diversity and increasing the risk of more intense fires.

Biochemical, physicochemical and molecular characterization of a genuine 2-Cys-peroxiredoxin purified from cowpea [Vigna unguiculata (L.) Walpers] leaves

Background: Peroxiredoxins have diverse functions in cellular defense-signaling pathways. 2-Cys-peroxiredoxins (2-Cys-Prx) reduce H2O2 and alkyl-hydroperoxide. This study describes the purification and characterization of a genuine 2-Cys-Prx from Vigna unguiculata (Vu-2-Cys-Prx). Methods: Vu-2-Cys-Prx was purified from leaves by ammonium sulfate fractionation, chitin affinity and ion exchange chromatography. Results: Vu-2-Cys-Prx reduces H2O2 using NADPH and DTT. Vu-2-Cys-Prx is a 44 kDa (SDS-PAGE)/46 kDa (exclusion chromatography) protein that appears as a 22 kDa molecule under reducing conditions, indicating that it is a homodimer linked intermolecularly by disulfide bonds and has a pI range of 4.56-4.72; its NH2-terminal sequence was similar to 2-Cys-Prx from Phaseolus vulgaris (96%) and Populus tricocarpa (96%). Analysis by ESI-Q-TOF MS/MS showed a molecular mass/pI of 28.622 kDa/5.18. Vu-2-Cys-Prx has 8% alpha-helix, 39% beta-sheet, 22% of turns and 31% of unordered forms. Vu-2-Cys-Prx was heat stable, has optimal activity at pH 7.0, and prevented plasmid DNA degradation. Atomic force microscopy shows that Vu-2-Cys-Prx oligomerized in decamers which might be associated with its molecular chaperone activity that prevented denaturation of insulin and citrate synthase. Its cDNA analysis showed that the redox-active Cys(52) residue and the amino acids Pro(45), Thr(49) and Arg(128) are conserved as in other 2-Cys-Prx. General significance: The biochemical and molecular features of Vu-2-Cys-Prx are similar to other members of 2-Cys-Prx family. To date, only one publication reported on the purification of native 2-Cys-Prx from leaves and the subsequent analysis by N-terminal Edman sequencing, which is crucial for construction of stromal recombinant 2-Cys-Prx proteins. (C) 2012 Elsevier B.V. All rights reserved.

Palaeoenvironment in North-Western Romania during the last 15 000 years

The objectives of this thesis are to establish a chronological framework for environmental changes during the last 15,000 years in northwest Romania, to reconstruct the vegetation development, and to evaluate the underlying processes for forest dynamics. Furthermore, an overview of earlier and ongoing pollenstratigraphic work in Romania is provided. Sediments from two former crater lakes, Preluca Tiganului and Steregoiu, situated in the Gutaiului Mountains, on the western extremity of the Eastern Carpathians at 730 m and 790 m a.s.l., respectively were obtained and analysed for high-resolution pollen, macrofossils, charcoal, mineral magnetic parameters and organic matter. The chronostratigraphic framework was provided by dense AMS 14C measurements. Cold and dry climatic conditions are indicated by the occurrence of open vegetation with shrubs and herbs, and cold lake water prior to 14,700 cal. yr BP. The climatic improvement at the beginning of the Lateglacial interstadial (around 14,700 cal. yr BP) is seen by the development of open forests. These were dominated by Pinus and Betula, but contained also new arriving tree taxa, such as Populus, Alnus and Prunus. The gradual establishment of forests may have led to a stabilization of the soils in the catchment. Between ca. 14,100 and 13,800 cal. yr BP the forest density became reduced to stands of Pinus, Betula, Alnus, Larix and Populus trees and grassland expanded, suggesting colder climatic conditions. Picea arrived as a new taxon at around 13,800 cal. yr BP, and between 13,800 and 12,900 cal. yr BP, the surroundings of the sites were predominantly covered by Picea forest. This forest included Betula, Pinus, Alnus, Larix and Populus and, from 13,200 cal. yr BP onwards also Ulmus. At ca. 12,900 cal. yr BP, the forest became significantly reduced and at 12,600 cal. yr BP, a recurrence of open vegetation with stands of Larix, Pinus, Betula, Salix and Alnus is documented, lasting until 11,500 cal. yr BP. This distinct change in vegetation may by taken as a strong decline in temperature and moisture availability. At the transition to the Holocene, at ca. 11,500 cal. yr BP, Pinus, Betula and Larix quickly expanded (from small local stands) and formed open forests, probably as a response to warmer and more humid climatic conditions. At 11,250 cal. yr BP Ulmus and Picea expanded and the landscape became completely forested. The rapid increase of Ulmus and Picea after 11,500 cal. yr BP may suggest the existence of small residual populations close to the study sites during the preceding cold interval. Ulmus was the first and most prominent deciduous taxa in the early Holocene in the Gutaiului Mountains. From ca. 10,750 cal. yr BP onwards Quercus, Tilia, Fraxinus and Acer expanded and Corylus arrived. A highly diverse, predominantly deciduous forest with Ulmus, Quercus, Tilia, Fraxinus, Acer, Corylus and Picea developed between 10,700 and 8200 cal. yr BP, which possibly signifies more continental climatic conditions. The development of a Picea-Corylus dominated forest between 8200 and 5700 cal. yr BP is likely connected to a more humid and cooler climate. The establishment of Carpinus and Fagus was dated to 5750 cal. yr BP and 5200 cal. yr BP, respectively. The dominance of Fagus during the late Holocene, from 4000 cal. yr BP onwards, may have been related to cooler and more humid climatic conditions. First signs of human activities are recorded around 2300 cal. yr BP, but only during the last 300 years did local human impact become significant. The vegetation development recorded in the Gutaiului Mountains during the Lateglacial is very similar to reconstructions based on lowland sites, whereas higher elevation sites seem not to have always experienced visible vegetation changes. The time of tree arrival and expansion during the past 11,500 cal. yr BP seems to have occurred almost synchronously across Romania. The composition of the forests during the Holocene in the Gutaiului Mountains is consistent with that reconstructed at mid-elevation sites, but differs from the forest composition at higher elevations. Important differences between the Gutaiului Mountains and other studied sites in Romania are a low representation of Carpinus and a late and weak human impact. The available data sets for Romania give evidence for the presence of coniferous and cold-tolerant deciduous trees before 14,700 cal. yr BP. Glacial refugia for Ulmus may have occurred in different parts of Romania, whereas the existence of Quercus, Tilia, Corylus and Fraxinus has not been corroborated.

Uso sostenibile dei suoli forestali di ambiente costiero in relazione ai fattori di pressione esistenti

Oggetto di studio del dottorato sono stati i suoli forestali in ambiente litoraneo della Regione Emilia-Romagna. In particolare sono state considerate quattro zone di studio in Provincia di Ravenna: Pineta di San Vitale, aree boscate di Bellocchio, Pineta di Classe e Pineta di Pinarella di Cervia. Lo studio in una prima fase si è articolato nella definizione dello stato del sistema suolo, mediante la caratterizzazione pedologica delle zone di studio. A tale scopo è stata messa a punto un’adeguata metodologia d’indagine costituita da un’indagine ambientale e successivamente da un’indagine pedologica. L’indagine ambientale, mediante fotointerpretazione ed elaborazione di livelli informativi in ambito GIS, ha permesso di individuare ambiti pedogenetici omogenei. L’indagine pedologica in campo ha messo in luce l’elevata variabilità spaziale di alcuni fattori della pedogenesi, in particolar modo l’andamento microtopografico tipico dei sistemi dunali costieri e la profondità della falda freatica del piano campagna. Complessivamente sono stati aperti descritti e campionati 40 profili pedologici. Sugli orizzonti diagnostici di questi sono state eseguite le seguenti analisi: tessitura, pH, calcare totale, carbonio organico, azoto kjeldahl, conduttività elettrica (CE), capacità di scambio cationico (CSC) e calcare attivo. I suoli presentano, ad eccezione della tessitura (generalmente grossolana), un’elevata variabilità delle proprietà chimico fisiche in funzione della morfologia, della profondità e della vicinanza della falda freatica. Sono state riscontrate diverse correlazioni, tra le più significative quelle tra carbonio organico e calcare totale (coeff. di correlazione R = -0.805 per Pineta di Classe) e tra calcare totale e pH (R = 0.736), dalle quali si è compreso in che misura l’effetto della decarbonatazione agisce nei diversi ambiti pedogenetici e tra suoli con diversa età di formazione. Il calcare totale varia da 0 a oltre 400 g.kg-1 e aumenta dalla superficie in profondità, dall’entroterra verso la costa e da nord verso sud. Il carbonio organico, estremamente variabile (0.1 - 107 g.kg-1), è concentrato soprattutto nel primo orizzonte superficiale. Il rapporto C/N (>10 in superficie e molto variabile in profondità) evidenzia una efficienza di umificazione non sempre ottimale specialmente negli orizzonti prossimi alla falda freatica. I tipi di suoli presenti, classificati secondo la Soil Taxonomy, sono risultati essere Mollic/Sodic/Typic Psammaquents nelle zone interdunali, Typic Ustipsamments sulle sommità dunali e Oxiaquic/Aquic Ustipsamments negli ambienti morfologici intermedi. Come sintesi della caratterizzazione pedologica sono state prodotte due carte dei suoli, rispettivamente per Pineta di San Vitale (scala 1:20000) e per le aree boscate di Bellocchio (scala 1:10000), rappresentanti la distribuzione dei pedotipi osservati. In una seconda fase si è focalizzata l’attenzione sugli impatti che le principali pressioni naturali ed antropiche, possono esercitare sul suolo, condizionandone la qualità in virtù delle esigenze del soprasuolo forestale. Si è scelta la zona sud di Pineta San Vitale come area campione per monitorarne mensilmente, su quattro siti rappresentativi, le principali caratteristiche chimico-fisiche dei suoli e delle acque di falda, onde evidenziare possibili correlazioni. Le principali determinazioni svolte sia nel suolo in pasta satura che nelle acque di falda hanno riguardato CE, Ca2+, Mg2+, K+, Na+, Cl-, SO4 2-, HCO3 - e SAR (Sodium Adsorption Ratio). Per ogni sito indagato sono emersi andamenti diversi dei vari parametri lungo i profili, correlabili in diversa misura tra di loro. Si sono osservati forti trend di aumento di CE e degli ioni solubili verso gli orizzonti profondi in profili con acqua di falda più salina (19 – 28 dS.m-1) e profonda (1 – 1.6 m dalla superficie), mentre molto significativi sono apparsi gli accumuli di sali in superficie nei mesi estivi (CE in pasta satura da 17.6 a 28.2 dS.m-1) nei profili con falda a meno di 50 cm dalla superficie. Si è messo successivamente in relazione la CE nel suolo con diversi parametri ambientali più facilmente monitorabili quali profondità e CE di falda, temperatura e precipitazioni, onde trovarne una relazione statistica. Dai dati di tre dei quattro siti monitorati è stato possibile definire tali relazioni con equazioni di regressione lineare a più variabili. Si è cercato poi di estendere l’estrapolabilità della CE del suolo per tutte le altre casistiche possibili di Pineta San Vitale mediante la formulazione di un modello empirico. I dati relativi alla CE nel suolo sia reali che estrapolati dal modello, sono stati messi in relazione con le esigenze di alcune specie forestali presenti nelle zone di studio e con diverso grado di tolleranza alla salinità ed al livello di umidità nel suolo. Da tali confronti è emerso che per alcune specie moderatamente tolleranti la salinità (Pinus pinea, Pinus pinaster e Juniperus communis) le condizioni critiche allo sviluppo e alla sopravvivenza sono da ricondursi, per la maggior parte dei casi, alla falda non abbastanza profonda e non tanto alla salinità che essa trasmette sull’intero profilo del suolo. Per altre specie quali Quercus robur, Populus alba, Fraxinus oxycarpa e Ulmus minor moderatamente sensibili alla salinità, ma abituate a vivere in suoli più umidi, la salinità di una falda troppo prossima alla superficie può ripercuotersi su tutto il profilo e generare condizioni critiche di sviluppo. Nei suoli di Pineta San Vitale sono stati inoltre studiati gli aspetti relativi all’inquinamento da accumulo di alcuni microtossici nei suoli quali Ag, Cd, Ni e Pb. In alcuni punti di rilievo sono stati osservati moderati fattori di arricchimento superficiale per Pb e Cd riconducibili all’attività antropica, mentre le aliquote biodisponibili risultano maggiori in superficie, ma all’interno dei valori medi dei suoli italiani. Lo studio svolto ha permesso di meglio conoscere gli impatti sul suolo, causati dalle principali pressioni esistenti, in un contesto dinamico. In particolare, si è constatato come i suoli delle zone studiate abbiano un effetto tampone piuttosto ridotto sulla mitigazione degli effetti indotti dalle pressioni esterne prese in esame (salinizzazione, sodicizzazione e innalzamento della falda freatica). Questo è dovuto principalmente alla ridotta presenza di scambiatori sulla matrice solida atti a mantenere un equilibrio dinamico con le frazioni solubili. Infine le variabili ambientali considerate sono state inserite in un modello concettuale DPSIR (Driving forces, Pressures, States, Impacts, Responces) dove sono stati prospettati, in via qualitativa, alcuni scenari in funzione di possibili risposte gestionali verosimilmente attuabili, al fine di modificare le pressioni che insistono sul sistema suolo-vegetazione delle pinete ravennati.

Influence of nitrogen and soil physical characteristics on belowground carbon flux dynamics of woody plants

At ecosystem level soil respiration (Rs) represents the largest carbon (C) flux after gross primary productivity, being mainly generated by root respiration (autotrophic respiration, Ra) and soil microbial respiration (heterotrophic respiration, Rh). In the case of terrestrial ecosystems, soils contain the largest C-pool, storing twice the amount of C contained in plant biomass. Soil organic matter (SOM), representing the main C storage in soil, is decomposed by soil microbial community. This process produces CO2 which is mainly released as Rh. It is thus relevant to understand how microbial activity is influenced by environmental factors like soil temperature, soil moisture and nutrient availability, since part of the CO2 produced by Rh, directly increases atmospheric CO2 concentration and therefore affects the phenomenon of climate change. Among terrestrial ecosystems, agricultural fields have traditionally been considered as sources of atmospheric CO2. In agricultural ecosystems, in particular apple orchards, I identified the role of root density, soil temperature, soil moisture and nitrogen (N) availability on Rs and on its two components, Ra and Rh. To do so I applied different techniques to separate Rs in its two components, the ”regression technique” and the “trenching technique”. I also studied the response of Ra to different levels of N availability, distributed either in a uniform or localized way, in the case of Populus tremuloides trees. The results showed that Rs is mainly driven by soil temperature, to which it is positively correlated, that high levels of soil moisture have inhibiting effects, and that N has a negligible influence on total Rs, as well as on Ra. Further I found a negative response of Rh to high N availability, suggesting that microbial decomposition processes in the soil are inhibited by the presence of N. The contribution of Ra to Rs was of 37% on average.

Novel techniques for the remote sensing of photosynthetic processes

Remote sensing (RS) techniques have evolved into an important instrument to investigate forest function. New methods based on the remote detection of leaf biochemistry and photosynthesis are being developed and applied in pilot studies from airborne and satellite platforms (PRI, solar-induced fluorescence; N and chlorophyll content). Non-destructive monitoring methods, a direct application of RS studies, are also proving increasingly attractive for the determination of stress conditions or nutrient deficiencies not only in research but also in agronomy, horticulture and urban forestry (proximal RS). In this work I will focus on some novel techniques recently developed for the estimation of photochemistry and photosynthetic rates based (i) on the proximal measurement of steady-state chlorophyll fluorescence yield, or (ii) the remote sensing of changes in hyperspectral leaf reflectance, associated to xanthophyll de-epoxydation and energy partitioning, which is closely coupled to leaf photochemistry and photosynthesis. I will also present and describe a mathematical model of leaf steady-state fluorescence and photosynthesis recently developed in our group. Two different species were used in the experiments: Arbutus unedo, a schlerophyllous Mediterranean species, and Populus euroamericana, a broad leaf deciduous tree widely used in plantation forestry. Results show that ambient fluorescence could provide a useful tool for testing photosynthetic processes from a distance. These results confirm also the photosynthetic reflectance index (PRI) as an efficient remote sensing reflectance index estimating short-term changes in photochemical efficiency as well as long-term changes in leaf biochemistry. The study also demonstrated that RS techniques could provide a fast and reliable method to estimate photosynthetic pigment content and total nitrogen, beside assessing the state of photochemical process in our plants’ leaves in the field. This could have important practical applications for the management of plant cultivation systems, for the estimation of the nutrient requirements of our plants for optimal growth.

Phytoremediation by poplar: polyphenols polyamines and oxidative damage in the response to heavy metals in in vitro and in hydroponic cultures.

Poplar is considered a good candidate for phytoremediation, but its tolerance to heavy metals has not been fully investigated yet. In the present work, two different culture systems (in vitro and aeroponic/hydroponic) and two different stress tolerant clones of Populus alba (AL22 and Villafranca) were investigated for their total polyphenol and flavonoid content, individual phenolic compounds, polyamine, lipid peroxidation and hydrogen peroxide levels in response to Cu. In AL22 poplar plants cultured in vitro in the presence or absence of 50 μM Cu, total leaves polyphenol and flavonoid content was higher in treated samples than in controls but unaltered in the roots. Equally the same clone, grown under aeroponic conditions and hydroponically treated for 72 h with 100 μM Cu, displayed increased amount of polyphenols and flavonoids in the leaves, in particular chlorogenic acid and quercetin, and no differences in the roots. In exudates from treated roots total polyphenols and flavonoids, in particular catechin and epicatechin, were more abundant than in controls. Polyamine levels show an increase in conjugated putrescine (Put) and spermidine (Spd) was found. In the Villafranca clone, treated with 100 μM Cu for 6, 24 and 72 h, the pattern of polyphenol and flavonoid accumulation was the same as in AL22; in Cu-treated roots these compounds decreased compared with controls while they increased in root exudates. Free polyamine levels rose at 24 and 72 h while only conjugated Put increased at 24 h. Cu-treated Villafranca plants exhibited a higher malondialdehyde production than controls indicative of membrane lipid peroxidation and, therefore, oxidative stress. An in vitro experiment was carried to investigate the antioxidant effect of the polyamine spermidine (Spd). Exogenous Spd, supplied together with 100 μM Cu, reduced the accumulation of polyphenols and flavonoids, MDA and hydrogen peroxide induced by Cu.

Genome-wide investigation reveals high evolutionary rates in annual model plants

Background: ;Rates of molecular evolution vary widely among species. While significant deviations from molecular clock have been found in many taxa, effects of life histories on molecular evolution are not fully understood. In plants, annual/perennial life history traits have long been suspected to influence the evolutionary rates at the molecular level. To date, however, the number of genes investigated on this subject is limited and the conclusions are mixed. To evaluate the possible heterogeneity in evolutionary rates between annual and perennial plants at the genomic level, we investigated 85 nuclear housekeeping genes, 10 non-housekeeping families, and 34 chloroplast;genes using the genomic data from model plants including Arabidopsis thaliana and Medicago truncatula for annuals and grape (Vitis vinifera) and popular (Populus trichocarpa) for perennials.;Results: ;According to the cross-comparisons among the four species, 74-82% of the nuclear genes and 71-97% of the chloroplast genes suggested higher rates of molecular evolution in the two annuals than those in the two perennials. The significant heterogeneity in evolutionary rate between annuals and perennials was consistently found both in nonsynonymous sites and synonymous sites. While a linear correlation of evolutionary rates in orthologous genes between species was observed in nonsynonymous sites, the correlation was weak or invisible in synonymous sites. This tendency was clearer in nuclear genes than in chloroplast genes, in which the overall;evolutionary rate was small. The slope of the regression line was consistently lower than unity, further confirming the higher evolutionary rate in annuals at the genomic level.;Conclusions: ;The higher evolutionary rate in annuals than in perennials appears to be a universal phenomenon both in nuclear and chloroplast genomes in the four dicot model plants we investigated. Therefore, such heterogeneity in evolutionary rate should result from factors that have genome-wide influence, most likely those associated with annual/perennial life history. Although we acknowledge current limitations of this kind of study, mainly due to a small sample size available and a distant taxonomic relationship of the model organisms, our results indicate that the genome-wide survey is a promising approach toward further understanding of the;mechanism determining the molecular evolutionary rate at the genomic level.

Functional analysis of rice bidirectional promoters

Bidirectional promoters regulate adjacent genes organized in a divergent fashion (head to head orientation). Several Reports pertaining to bidirectional promoters on a genomic scale exists in mammals. This work provides the essential background on theoretical and experimental work to carry out a genomic scale analysis of bidirectional promoters in plants. A computational study was performed to identify putative bidirectional promoters and the over-represented cis-regulatory motifs from three sequenced plant genomes: rice (Oryza sativa), Arabidopsis thaliana, and Populus trichocarpa using the Plant Cis-acting Regulatory DNA Elements (PLACE) and PLANT CARE databases. Over-represented motifs along with their possible function were described with the help of a few conserved representative putative bidirectional promoters from the three model plants. By doing so a foundation was laid for the experimental evaluation of bidirectional promoters in plants. A novel Agrobacterium tumefaciens mediated transient expression assay (AmTEA) was developed for young plants of different cereal species and the model dicot Arabidopsis thaliana. AmTEA was evaluated using five promoters (six constructs) and two reporter genes, gus and egfp. Efficacy and stability of AmTEA was compared with stable transgenics using the Arabidopsis DEAD-box RNA helicase family gene promoter. AmTEA was primarily developed to overcome the many problems associated with the development of transgenics and expression studies in plants. Finally a possible mechanism for the bidirectional activity of bidirectional promoters was highlighted. Deletion analysis using promoter-reporter gene constructs identified three rice promoters to be bidirectional. Regulatory elements located in the 5’- untranslated regions (UTR) of one of the genes of the divergent gene pair were found to be responsible for their bidirectional ctivity

Retention of canopy trees as biological legacies for balancing woody biomass production and biodiversity in managed aspen forests of the Great Lakes Region

Green-tree retention under the conceptual framework of ecological forestry has the potential to provide both biomass feedstock for industry and maintain quality wildlife habitat. I examined the effects of retained canopy trees as biological legacies (“legacy trees”) in aspen (Populus spp.) forests on above-ground live woody biomass, understory plant floristic quality, and bird diversity. Additionally, I evaluated habitat quality for a high conservation priority species, the Golden-winged Warbler (Vermivora chrysoptera). I selected 27 aspen-dominated forest stands in northern Wisconsin with nine stands in each of three legacy tree retention treatments (conifer retention, hardwood retention, and clearcuts or no retention) across a chronosequence (4-36 years post-harvest). Conifer retention stands had greater legacy tree and all tree species biomass but lower regenerating tree biomass than clearcuts. Coniferous but not hardwood legacy trees appeared to suppress regenerating tree biomass. I evaluated the floristic quality of the understory plant assemblage by estimating the mean coefficient of conservatism (C). Mean C was lower in young stands than in middle-age or old stands; there was a marginally significant (p=0.058) interaction effect between legacy tree retention treatment and stand age. Late-seral plant species were positively associated with stand age and legacy tree diameter or age revealing an important relationship between legacy tree retention and stand development. Bird species richness was greatest in stands with hardwood retention particularly early in stand development. Six conservation priority bird species were indicators of legacy tree retention or clearcuts. Retention of legacy trees in aspen stands provided higher quality nest habitat for the Golden-winged Warbler than clearcuts based on high pairing success and nesting activity. Retention of hardwoods, particularly northern red oak (Quercus rubra), yielded the most consistent positive effects in this study with the highest bird species richness and the highest quality habitat for the Golden-winged Warbler. This treatment maintained stand biomass comparable to clearcuts and did not suppress regenerating tree biomass. In conclusion, legacy tree retention can enhance even-aged management techniques to produce a win-win scenario for the conservation of declining bird species and late-seral understory plants and for production of woody biomass feedstock from naturally regenerating aspen forests.

Effects of conifer sawdust, hardwood sawdust, and peat on soil properties and a barefoot conifer seedling development

Organic amendments are commonly used to improve tree nursery soil conditions for increased seedling growth. However, few studies compare organic amendments effects on soil conditions, and fewer compare subsequent effects on seedling growth. The effects of three organic amendments on soil properties and seedling growth were investigated at the USDA Forest Service J.W. Toumey Nursery in Watersmeet, MI. Pine sawdust (red pine, Pinus resinosa), hardwood sawdust (maple, Acer spp. and aspen, Populus spp.), and peat were individually incorporated into a loamy sand nursery soil in August, 2006, and soil properties were sampled periodically for the next 14 months. Jack (Pinus banksiana), red, and white pine (Pinus strobus) were sown into test plots in June, 2007 and sampled for growth responses at the end of the growing season. It is hypothesized; pine sawdust and peat can be used as a satisfactory soil amendment to improve soil conditions and produce high quality seedlings, when compared to hardwood sawdust in bareroot nursery soils. This study has the potential to reduce nursery costs while broadening soil amendment options. The addition of peat and pine sawdust increased soil organic matter above control soil conditions after 14 months. However, hardwood sawdust-amended soils did not differ from control soils after same time period. High N concentrations in peat increased total soil N over the other treatments. Similarly, the addition of peat increased soil matric potential and available water over all other treatments. Seedlings grew tallest with the largest stem diameter, and had the largest biomass in both control soil and soil amended with peat, compared to either sawdust treatment. Seedlings grown in peat-amended soils had higher N concentrations than those grown in soils treated with pine sawdust, though neither was different from seedlings grown in control or hardwood sawdust-amended soils. Overall, peat is a well suited organic soil amendment for the enhancement of soil properties, but no amendments were able to increase one-year seedling growth over control soils.

Regulation of woody plant development by gibberellin catabolic and signaling genes

Gibberellin (GA) is a growth promoting hormone implicated in regulating a diversity of plant processes. This dissertation examines the role of GA metabolic and signaling genes in woody plant growth and development. Transgenic modifications, expression analysis, physiological/biochemical assays, biometric measurements and histological analysis were used to understand the regulatory roles these genes play in the model woody plant, Populus. Our results highlight the importance of GA regulatory genes in woody perennial growth, including: phenology, wood formation, phenotypic plasticity, and growth/survival under field conditions. We characterize two putative Populus orthologs of the SHORT INTERNODES (SHI) gene from Arabidopsis, a negative regulator of GA signaling. RNAi-mediated suppression of Populus SHI-like genes increased several growth-related traits, including extent of xylem proliferation, in a dose-dependent manner. Three Populus genes, sharing sequence homology to the positive regulator of GA signaling gene PHOTOPERIOD-RESPONSIVE 1 (PHOR1) from Solanum, are up-regulated in GA-deficient and insensitive plants suggesting a conserved role in GA signaling. We demonstrate that Populus PHOR1-like genes have overlapping and divergent function(s). Two PHOR1-like genes are highly expressed in roots, predominantly affect root growth (e.g., morphology, starch quantity and gravitropism), and induced by short-days (SD). The other PHOR1-like gene is ubiquitously expressed with a generalized function in root and shoot development. The effects of GA catabolic and signaling genes on important traits (e.g., adaptive and productivity traits) were studied in a multi-year field trial. Transgenics overexpressing GA 2-oxidase (GA2ox) and DELLA genes showed tremendous variation in growth, form, foliage, and phenology (i.e., vegetative and reproductive). Observed gradients in trait modifications were correlated to transgene expression levels, in a manner suggesting a dose-dependent relationship. We explore GA2ox and DELLA genes involvement in mediating growth responses to immediate short-term drought stress, and SD photoperiods, signaling prolonged periods of stress (e.g., winter bud dormancy). GA2ox and DELLA genes show substantial up-regulation in response to drought and SDs. Transgenics overexpressing homologs of these genes subjected to drought and SD photoperiods show hypersensitive growth restraint and increased stress resistances. These results suggest growth cessation (i.e., dormancy) in response to adverse conditions is mediated by GA regulatory genes.