Using Phylogenomic Patterns and Gene Ontology to Identify Proteins of Importance in Plant Evolution

We use measures of congruence on a combined expressed sequenced tag genome phylogeny to identify proteins that have potential significance in the evolution of seed plants. Relevant proteins are identified based on the direction of partitioned branch and hidden support on the hypothesis obtained on a 16-species tree, constructed from 2,557 concatenated orthologous genes. We provide a general method for detecting genes or groups of genes that may be under selection in directions that are in agreement with the phylogenetic pattern. Gene partitioning methods and estimates of the degree and direction of support of individual gene partitions to the overall data set are used. Using this approach, we correlate positive branch support of specific genes for key branches in the seed plant phylogeny. In addition to basic metabolic functions, such as photosynthesis or hormones, genes involved in posttranscriptional regulation by small RNAs were significantly overrepresented in key nodes of the phylogeny of seed plants. Two genes in our matrix are of critical importance as they are involved in RNA-dependent regulation, essential during embryo and leaf development. These are Argonaute and the RNA-dependent RNA polymerase 6 found to be overrepresented in the angiosperm clade. We use these genes as examples of our phylogenomics approach and show that identifying partitions or genes in this way provides a platform to explain some of the more interesting organismal differences among species, and in particular, in the evolution of plants

Predicting tree pollen season start dates using thermal conditions

Thermal conditions at the beginning of the year determine the timing of pollen seasons of early flowering trees. The aims of this study were to quantify the relationship between the tree pollen season start dates and the thermal conditions just before the beginning of the season and to construct models predicting the start of the pollen season in a given year. The study was performed in Krakow (Southern Poland); the pollen data of Alnus, Corylus and Betula were obtained in 1991–2012 using a volumetric method. The relationship between the tree pollen season start, calculated by the cumulated pollen grain sum method, and a 5-day running means of maximum (for Alnus and Corylus) and mean (for Betula) daily temperature was found and used in the logistic regression models. The estimation of model parameters indicated their statistically significance for all studied taxa; the odds ratio was higher in models for Betula, comparing to Alnus and Corylus. The proposed model makes the accuracy of prediction in 83.58 % of cases for Alnus, in 84.29 % of cases for Corylus and in 90.41 % of cases for Betula. In years of model verification (2011 and 2012), the season start of Alnus and Corylus was predicted more precisely in 2011, while in case of Betula, the model predictions achieved 100 % of accuracy in both years. The correctness of prediction indicated that the data used for the model arrangement fitted the models well and stressed the high efficacy of model prediction estimated using the pollen data in 1991–2010

Transition from two to one integument in Prunus species: expression pattern of INNER NO OUTER (INO), ABERRANT TESTA SHAPE (ATS) and ETTIN (ETT)

12 Pags.- 8 Figs.While gymnosperm ovules have one integument, in most angiosperms two integuments surround the ovules. Unitegmic ovules have arisen independently several times during the evolution of angiosperms, but the ultimate genetic cause of the presence of a single integument remains elusive. We compared species of the genus Prunus that have different numbers of integuments: bitegmic species, such as Prunus armeniaca (apricot) and Prunus persica (peach), and unitegmic species, such as Prunus incisa, analyzing the expression pattern of genes that are involved in integument development in Arabidopsis thaliana: INNER NO OUTER (INO), ABERRANT TESTA SHAPE (ATS) and ETTIN (ETT). Bitegmic and unitegmic species showed similar INO expression patterns, indicative of the conservation of an outer integument. However, expression of ETT, which occurs in the boundary of the outer and inner integuments, was altered in unitegmic ovules, which showed lack of ETT expression. These results strongly suggest that the presence of a single integument could be attributable to the amalgamation of two integuments and support the role of ETT in the fusion of the outer and inner integuments in unitegmic ovules, a situation that could be widespread in other unitegmic species of angiosperms.This work was supported by Ministerio de Economía y Competitividad–European Regional Development Fund, European Union (AGL2012-40239, and AGL2013-43732-R), and Gob. Aragón A-43. J.L. was supported by a Juan de la Cierva postdoctoral grant of the Spanish Ministry of Science and Innovation, a James R. Jewett prize of the Arnold Arboretum of Harvard University and an EMBO short-term fellowship at the University of Freiburg, Germany.Peer reviewe

Characteristics and Trends of Selected Pollen Seasons Recorded in Parma (Northern Italy) from 1994 to 2011

This study examines variations in the start date, end date, duration, date of peak, peak value and Seasonal Pollen Index (SPI) of airborne pollen seasons recorded in Parma, Northern Italy, in relation to meteorological data (1994–2011). Pollen data were collected in the city of Parma by volumetric spore trap. The following taxa were analysed: Alnus, Ambrosia, Artemisia, Betula, Amaranthaceae, Corylus, Cupressaceae, Plantago, Platanus, Poaceae and Urticaceae. Spearman’s rank correlation tests were used to establish whether significant relationships existed between the different characteristics of the pollen seasons. Simple linear regression analysis was also carried out in order to investigate trends over time. Only 12 % of the 66 characteristics examined showed significant changes over the study period. Temperatures increased significantly during the spring, but this did not appear to have a corresponding impact on seasonal characteristics related to the timing of pollen seasons (i.e. start date, peak date and end date). All of the observed changes were associated with characteristics that can be related to exposure (i.e. duration, peak value and SPI). For arboreal taxa, the SPI of Betula decreased significantly, and Platanus pollen seasons became significantly shorter. For herbaceous species, the SPI and peak values of Artemisia became significantly lower, whereas the SPI and peak values of Ambrosia became significantly higher. The SPI of Poaceae and Urticaceae also decreased significantly. The results of correlation analysis showed that various characteristics of pollen seasons are significantly related. This study provides an essential baseline for determining exposure of the allergic population to allergenic pollen and aids understanding of the incidence of pollinosis in Parma. Gaps still exist in current knowledge; not least, the need to quantify the degree of influence exerted by some of the principal factors driving environmental change, climate and land use