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Hammam Sousse, Tunisia

Boulila M.,Institute Of Lolivier | Tiba S.B.,University of Monastir | Jilani S.,Sanguine
Journal of Genetics

The sequence alignments of five Tunisian isolates of Prunus necrotic ringspot virus (PNRSV) were searched for evidence of recombination and diversifying selection. Since failing to account for recombination can elevate the false positive error rate in positive selection inference, a genetic algorithm (GARD) was used first and led to the detection of potential recombination events in the coat protein-encoding gene of that virus. The Recco algorithm confirmed these results by identifying, additionally, the potential recombinants. For neutrality testing and evaluation of nucleotide polymorphism in PNRSV CP gene, Tajima's D, and Fu and Li's D and F statistical tests were used. About selection inference, eight algorithms (SLAC, FEL, IFEL, REL, FUBAR, MEME, PARRIS, and GA branch) incorporated in HyPhy package were utilized to assess the selection pressure exerted on the expression of PNRSV capsid. Inferred phylogenies pointed out, in addition to the three classical groups (PE-5, PV-32, and PV-96), the delineation of a fourth cluster having the new proposed designation SW6, and a fifth clade comprising four Tunisian PNRSV isolates which underwent recombination and selective pressure and to which the name Tunisian outgroup was allocated. © 2013 Indian Academy of Sciences. Source

To enhance the knowledge of recombination as an evolutionary process, 267 accessions retrieved from GenBank were investigated, all belonging to five economically important viruses infecting fruit crops (Plum pox, Apple chlorotic leaf spot, Apple mosaic, Prune dwarf, and Prunus necrotic ringspot viruses). Putative recombinational events were detected in the coat protein (CP)-encoding gene using RECCO and RDP version 3.31β algorithms. Based on RECCO results, all five viruses were shown to contain potential recombination signals in the CP gene. Reconstructed trees with modified topologies were proposed. Furthermore, RECCO performed better than the RDP package in detecting recombination events and exhibiting their evolution rate along the sequences of the five viruses. RDP, however, provided the possible major and minor parents of the recombinants. Thus, the two methods should be considered complementary. © Springer Science+Business Media, LLC 2009. Source

Aguilera F.,University of Perugia | Orlandi F.,University of Perugia | Ruiz-Valenzuela L.,University of Jaen | Msallem M.,Institute Of Lolivier | Fornaciari M.,University of Perugia
Agricultural and Forest Meteorology

The aim of the present study was to analyse long temporal trends in cumulative temperatures and olive (. Olea europaea L.) reproductive features, including full flowering dates and daily pollen concentrations, in three Mediterranean areas. The study used a 19-year database (1993-2011) of pollen and temperature records from the sites of Perugia (Italy), Jaen (Spain) and Zarzis (Tunisia). The analysis of long-term trends in both temperatures and olive reproductive cycles was performed using two approaches. The first is a seasonal trend decomposition procedure based on locally weighted regression (Loess) smoothing (STL), which is a filtering procedure for decomposing seasonal time series into three components: trend, seasonal, and remainder. The second approach analyses the trend components using Mann-Kendall tests. Loess smoothing provides a good approach to study long-term meteorological and phenological trends. Removing both the seasonal and the remainder components, the real rising trends over time can be interpreted. In general, a significant and clear increasing trend in the spring cumulative temperature was revealed, with decreasing trends in the full flowering dates of the olive trees located in Perugia and Zarzis. Moreover, olive pollen emissions are decreasing, which is more evident for the highest and lowest latitudinal study sites. These data indicate that increasing temperatures result in both anticipation of olive tree flowering and lower airborne pollen emission. As a consequence, the lower atmospheric pollen levels will reduce human exposure to olive pollen in the Mediterranean area. These patterns are evident for the highest and lowest latitudes, but not clear in the intermediate latitudes of Jaen, where further analysis is needed. © 2014 Elsevier B.V. Source

Charfi Masmoudi C.,Institute Of Lolivier | Masmoudi M.,Institute National Agronomique Of Tunisie | Abid-Karray J.,Institute National Agronomique Of Tunisie | Mechlia N.B.,Institute National Agronomique Of Tunisie
Scientia Horticulturae

Measurements of sap flux were carried out from May 2003 to March 2004 on 6. year-old irrigated olive trees of cultivar Chétoui cultivated at 6. m × 6. m spacing in Mornag (36.5°N, 10.2°E), Northern Tunisia. The aim of the research is to evaluate the sap flux technique for its applicability with young olive trees and to estimate their water consumption under field conditions. Three thermal sensors were implanted in the trunk of three olive trees following to North (N), South-East (SE) and South-West (SW) directions. Data were analyzed following to the procedure of Do and Rocheteau (2002b) that derives from Granier (1985). In this paper, data on probe calibration, wood conductive section estimation and sap flux spatial-variability are presented and discussed. Relationships between sap flux measurements, climate and soil water status have been investigated. Results show that sap flux values vary with sensor position, soil water content and climate demand. Good agreements between sap fluxes and global radiation and reference evapotranspiration measurements were observed. Some variations were recorded under water shortage conditions. Maximum and minimum daily fluxes of 4.5. l and 41.0. l per tree were found in February 2003 and in August 2003, respectively. Maximum transpiration represented only 53% of the crop evapotranspiration as determined by the F.A.O. method. © 2011 Elsevier B.V. Source

In an effort to enhance the knowledge on molecular evolution of currently the known members of the families Luteoviridae and Tymoviridae, in-depth molecular investigations in the entire genome of 147 accessions retrieved from the international databases, were carried out. Two algorithms (RECCO and RDP version 3.31β) adapted to the mosaic structure of viruses were utilized. The recombination frequency along the sequences was dissected and demonstrated that the three virus genera of the family Luteoviridae comprise numerous members subjected to recombination. It has pointed out that the major viruses swapped a few but long genomic segments. In addition, in Barley yellow dwarf virus, heredity material might be exchanged between two different serotypes. Even more, putative recombination events occurred between two different genera. Based on Fisher's Exact Test of Neutrality, positive selection acting on protein expression was detected only in the poleroviruses Cereal yellow dwarf virus, Potato leafroll virus and Wheat yellow dwarf virus. In contrast, several components of the family Tymoviridae were highly recombinant. Genomic portion exchange arose in many positions consisting of short fragments. Furthermore, no positive selection was detected. The evolutionary history showed, in the Luteoviridae, that all screened isolates split into three clusters corresponding to the three virus genera forming this family. Moreover, in the serotype PAV of Barley yellow dwarf virus, two major clades corresponding to PAV-USA and PAV-China, were delineated. Similarly, in the Tymoviridae, all analyzed isolates fell into four groups corresponding to the three virus genera composing this family along with the unclassified Tymoviridae. Inferred phylogenies reshuffled the existing classification and showed that Wheat yellow dwarf virus-RPV was genetically closely related to Cereal yellow dwarf virus and the unclassified Tymoviridae Grapevine syrah virus-1 constituted an integral part of the genus Marafivirus. © 2010 Elsevier Masson SAS. All rights reserved. Source

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