A new gypsy-like retroelement family in Vitis vinifera

As a major part of most plant genomes, retrotransposons are distributed throughout the plant genome ubiquitously with high copy number and extensive heterogeneity. Various retrotransposon families with distinct structures differ in their distribution and roles among divergent plant species, due to unforeseen transposition activities.We had performed in silico analysis of the Vitis vinifera 'Pinot Noir' genome to search for gypsy type retroelements homologues to the one identified in Pinus radiata (IFG7) and P. pinaster (PpRT1) and in Quercus suber (Corky). We intended to see the existence and structure of gypsy-like retroelements homologues in the Vitis genome as well as the existence of integration site preference. From all data and to perform a deeper analysis we chose 36 complete sequences copies in the Vitis genome. We used three genetic distance corrections, additional to p-distance to estimate retroelements insertion time and reverse transcriptase, integrase and LTR (Long Terminal Repeat) sequences to establish a phylogeny and to see the contributions of different regions according to the evolutionary rates. We found three elements with identical LTRs and two old elements that revealed recent and very old insertions as well as insertions inside other retroelements. Additionally, we found no preference for the integration site as shown by the different target site repeat for each element.

Caracterização e medidas mitigadoras das inundações em Vilamoura, Algarve

Este artigo visa analisar as inundações da Ribeira do Vale Tesnado, zona poente de Vilamoura (Algarve), e as soluções integradas que geram a diminuição da probabilidade e da magnitude das mesmas. Para tal, esta análise foi dividida em quatro etapas: i) estudo hidrológico da bacia hidrográfica a montante, com vista à determinação de caudais de cheia; ii) estudo hidrodinâmico, no qual se efetua a modelação numérica do escoamento na zona com risco potencial significativo, considerando o efeito das diversas estruturas hidráulicas existentes; iii) identificação dos níveis atingidos pela inundação associada a períodos de retorno de 10 e 100 anos e mapeamento das áreas inundáveis; iv) análise de resultados e identificação de soluções integradas com vista à minimização da frequência e da magnitude das inundações. A aferição do modelo foi realizada através da comparação dos níveis de cheia observados a 8 de novembro de 2012 (com base em testemunhos locais, marcas de cheia, fotografias e vídeos) com os obtidos da modelação numérica.info:eu-repo/semantics/publishedVersio

Modificação das propriedades hidráulicas dos solos da Serra algarvia devido aos incêndios florestais

Os incêndios florestais produzem um solo extremamente seco coberto por cinza, resultante da combustão do coberto vegetal, que quando exposto a precipitações intensas pode dar origem a inundações extremas. As inundações após incêndio poderão estar relacionadas com a diminuição da capacidade de infiltração do solo, efeito resultante da colmatação e preenchimento por compostos voláteis dos poros e depósito da camada de cinza na superfície. Para caracterizar a condutividade hidráulica, ks, e a sorvidade, S, foram realizados ensaios laboratoriais com um infiltrómetro de duplo anel em amostras de solo não perturbadas. Para o efeito foram recolhidas 4 amostras não perturbadas de solo característico da serra algarvia, com as dimensões 50x50x25 cm. Sobre 3 amostras, foram colocadas diferentes quantidades de material combustível, conduzindo a diferentes quantidades de cinza. Posteriormente, foram realizados ensaios com um infiltrómetro de duplo anel na amostra de referência não ardida e nas 3 amostras afetadas pelo incêndio simulado em laboratório. Os resultados mostram diferentes valores de ks, S e consequentemente diferentes valores da capacidade de infiltração do solo.info:eu-repo/semantics/publishedVersio

Resultados preliminares dos testes genéticos com Cryptomeria japonica na Região Autónoma dos Açores

Congresso Florestal Nacional: a floresta e as gentes - Actas das ComunicaçõesTendo como base, a importância económica da Cryptomeria japonica na Região Autónoma dos Açores, e face ao desconhecimento sobre a origem das populações, surgiu a necessidade de avaliar a variabilidade genética da população açoriana, para tal foi instalado um ensaio de proveniências. Paralelamente, a descendência de árvores seleccionadas em povoamentos locais, está a ser avaliada em ensaios de descendências para confirmação da sua superioridade e do controlo genético das características eleitas. Simultaneamente, através da utilização de marcadores moleculares pela técnica msp-PCR pretende-se antecipar informações relativamente à variabilidade genética das populações açorianas. A taxa de sobrevivência foi muita elevada em todos os ensaios, média acima dos 85%. Os acréscimos em altura total obtidos no 2º ano após a plantação, indicam diferenciação comportamental entre as plantas das origens açorianas e as da área de distribuição natural; as açorianas demonstram, em geral, melhores comportamentos. O ensaio de descendências ainda não permite a diferenciação de agrupamentos de famílias, embora se observem diferenças significativas entre estas. A análise da matriz dos coeficientes de similaridade de Dice indicou valores médios de similaridade relativamente elevados, na ordem dos 0,64, sendo o intervalo de variação mais estreito quando as populações açorianas foram comparadas entre si

Analysis of genetic stability at SSR loci during somatic embryogenesis in maritime pine (Pinus pinaster)

Somatic embryogenesis (SE) is a propagation tool of particular interest for accelerating the deployment of new high-performance planting stock in multivarietal forestry. However, genetic conformity in in vitro propagated plants should be assessed as early as possible, especially in long-living trees such as conifers. The main objective of this work was to study such conformity based on genetic stability at simple sequence repeat (SSR) loci during somatic embryogenesis in maritime pine (Pinus pinaster Ait.). Embryogenic cell lines (ECLs) subjected to tissue proliferation during 6, 14 or 22 months, as well as emblings regenerated from several ECLs, were analyzed. Genetic variation at seven SSR loci was detected in ECLs under proliferation conditions for all time points, and in 5 out of 52 emblings recovered from somatic embryos. Three of these five emblings showed an abnormal phenotype consisting mainly of plagiotropism and loss of apical dominance. Despite the variation found in somatic embryogenesis-derived plant material, no correlation was established between genetic stability at the analyzed loci and abnormal embling phenotype, present in 64% of the emblings. The use of microsatellites in this work was efficient for monitoring mutation events during the somatic embryogenesis in P. pinaster. These molecular markers should be useful in the implementation of new breeding and deployment strategies for improved trees using SE

Polyploidization as a Retraction Force in Plant Genome Evolution: Sequence Rearrangements in Triticale

BACKGROUND: Polyploidization is a major evolutionary process in plants where hybridization and chromosome doubling induce enormous genomic stress and can generate genetic and epigenetic modifications. However, proper evaluation of DNA sequence restructuring events and the precise characterization of sequences involved are still sparse. METHODOLOGY/PRINCIPAL FINDINGS: Inter Retrotransposons Amplified Polymorphism (IRAP), Retrotransposons Microsatellite Amplified Polymorphism (REMAP) and Inter Simple Sequence Repeat (ISSR) largely confirmed the absence of any intraspecific variation in wheat, rye and triticale. The comparative analysis of banding profiles between wheat and rye inbred lines revealed 34% of monomorphic (common to both parental species) bands for the ten different primer combinations used. The analysis of triticale plants uncovered nearly 51% of rearranged bands in the polyploid, being the majority of these modifications, due to the loss of rye bands (83%). Sequence analysis of rye fragments absent in triticale revealed for instance homology with hydroxyproline-rich glycoproteins (HRGP), a protein that belongs to a major family of inducible defence response proteins. Conversely, a wheat-specific band absent in triticale comprises a nested structure of copia-like retrotransposons elements, namely Claudia and Barbara. Sequencing of a polyploid-specific band (absent in both parents) revealed a microsatellite related sequence. Cytological studies using Fluorescent In Situ Hybridization (FISH) with REMAP products revealed a widespread distribution of retrotransposon and/or microsatellite flanking sequences on rye chromosomes, with a preferential accumulation in heterochromatic sub-telomeric domains. CONCLUSIONS/SIGNIFICANCE: Here, we used PCR-based molecular marker techniques involving retrotransposons and microsatellites to uncover polyploidization induced genetic restructuring in triticale. Sequence analysis of rearranged genomic fragments either from rye or wheat origin showed these to be retrotransposon-related as well as coding sequences. Further FISH analysis revealed possible chromosome hotspots for sequence rearrangements. The role of chromatin condensation on the origin of genomic rearrangements mediated by polyploidization in triticale is also discussed

The sulfur pathway and diagnosis of sulfate depletion in grapevine

Sulfur is an essential nutrient to all plant species. Plants assimilate sulfur in a well-described pathway, which has been taken up by roots. Regulatory mech- anism has been the subject of many research papers. However, recent studies highlighted differences between crop plants and the model plant Arabidopsis thaliana. Our work focuses on the identification of genes involved in the sulfur metabolism in the Vitis vinifera genome, and their response to sulfur deficiency and other abiotic stress endured by grapevine in the field, namely water stress. Here, we describe the identification and brief characterization of the first assimilation enzymes involved in the sulfur pathway, the enzyme responsible for sulfur activa- tion, ATP sulfurylase (ATPS), and the two enzymes that reduce sulfate to sulfide, Adenosine 50-phosphosulate reductase (APR) and Sulfite reductase (SiR). A reduc- tion was observed in the number of ATPS and APR isoforms identified in V. vinifera genome when compared to A. thaliana or Glycine max genomes. Two ATPS isoforms were present in the Vitis genome, of which only ATPS1 transcript was detected in the tested tissues, and one APR isoform, suggesting an absence of redundancy in the role of both enzymes. ATPS1, APR and SiR transcript level was up-regulated in response to 2 days exposure to sulfur deficiency in V. vinifera cell cultures, which was completely reversed by the addition of GSH to the culture medium. Apparently, oxidative stress triggered GSH has a pivotal role in the regulation of ATPS1, APR and SiR transcription level, since their up-regulation was observed in mRNA from field grapevine berries under water stress, which is known to induce oxidative stress.info:eu-repo/semantics/publishedVersio

A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing

Background: Cork oak (Quercus suber) is one of the rare trees with the ability to produce cork, a material widely used to make wine bottle stoppers, flooring and insulation materials, among many other uses. The molecular mechanisms of cork formation are still poorly understood, in great part due to the difficulty in studying a species with a long life-cycle and for which there is scarce molecular/genomic information. Cork oak forests are of great ecological importance and represent a major economic and social resource in Southern Europe and Northern Africa. However, global warming is threatening the cork oak forests by imposing thermal, hydric and many types of novel biotic stresses. Despite the economic and social value of the Q. suber species, few genomic resources have been developed, useful for biotechnological applications and improved forest management. Results: We generated in excess of 7 million sequence reads, by pyrosequencing 21 normalized cDNA libraries derived from multiple Q. suber tissues and organs, developmental stages and physiological conditions. We deployed a stringent sequence processing and assembly pipeline that resulted in the identification of ~159,000 unigenes. These were annotated according to their similarity to known plant genes, to known Interpro domains, GO classes and E.C. numbers. The phylogenetic extent of this ESTs set was investigated, and we found that cork oak revealed a significant new gene space that is not covered by other model species or EST sequencing projects. The raw data, as well as the full annotated assembly, are now available to the community in a dedicated web portal at http://www.corkoakdb.org. Conclusions: This genomic resource represents the first trancriptome study in a cork producing species. It can be explored to develop new tools and approaches to understand stress responses and developmental processes in forest trees, as well as the molecular cascades underlying cork differentiation and disease response.Peer Reviewe

Characterization of the serine acetyltransferase gene family of Vitis vinifera uncovers defferences in regulation of OAS synthesis in woody plants

In higher plants cysteine biosynthesis is catalyzed by O-acetylserine(thiol)lyase (OASTL) and represents the last step of the assimilatory sulfate reduction pathway. It is mainly regulated by provision of O-acetylserine (OAS), the nitrogen/carbon containing backbone for fixation of reduced sulfur. OAS is synthesized by Serine acetyltransferase (SERAT), which reversibly interacts with OASTL in the cysteine synthase complex (CSC).In this study we identify and characterize the SERAT gene family of the crop plant Vitis vinifera. The identified four members of the VvSERAT protein family are assigned to three distinct groups upon their sequence similarities to Arabidopsis SERATs. Expression of fluorescently labeled VvSERAT proteins uncover that the sub-cellular localization of VvSERAT1;1 and VvSERAT3;1 is the cytosol and that VvSERAT2;1 and VvSERAT2;2 localize in addition in plastids and mitochondria, respectively. The purified VvSERATs of group 1 and 2 have higher enzymatic activity than VvSERAT3;1, which display a characteristic C-terminal extension also present in AtSERAT3;1. VvSERAT1;1 and VvSERAT2;2 are evidenced to form the CSC. CSC formation activates VvSERAT2;2, by releasing CSC-associated VvSERAT2;2 from cysteine inhibition. Thus, subcellular distribution of SERAT isoforms and CSC formation in cytosol and mitochondria is conserved between Arabidopsis and grapevine. Surprisingly, VvSERAT2;1 lack the canonical C-terminal tail of plant SERATs, does not form the CSC and is almost insensitive to cysteine inhibition (IC50 =1.9mM cysteine). Upon sulfate depletion VvSERAT2;1 is strongly induced at the transcriptional level, while transcription of other VvSERATs is almost unaffected in sulfate deprived grapevine cell suspension cultures. Application of abiotic stresses to soil grown grapevine plants revealed isoform-specific induction of VvSERAT2;1 in leaves upon drought, whereas high light- or temperature- stress hardly trigger VvSERAT2;1 transcriptio