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Boulila M.,Institute Of Lolivier | Tiba S.B.,University of Monastir | Jilani S.,Sanguine
Journal of Genetics | Year: 2013

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.


Molecular evolution of viruses is driven by both positive selection and recombination. In an effort to determine putative recombination events in the entire genome of members of the family Closteroviridae comprising 54 accessions retrieved from the international databases, a detail study was carried out by using RDP algorithm version 3.31β. Only isolates of Citrus tristeza virus and Grapevine leafroll-associated virus 3 were potential recombinants. None of members of Crinivirus genus was possible recombinant, but in turn, they were under positive selection that might be correlated with vector and/or host interactions. In contrast, Citrus tristeza virus isolates were under purifying selection as well as one-third of isolates of Grapevine leafroll-associated virus 3. The evolutionary history of all members of the Closteroviridae showed that they split into three distinct clusters corresponding to the three genera constituting this family. Moreover, the inferred phylogeny reshuffled the existing classification actually adopted by the International Committee on Taxonomy of Viruses. In this regard, each genus should be constituted by two distinct subgroups. © 2010 Elsevier Ltd.


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.


Orlandi F.,University of Perugia | Garcia-Mozo H.,University of Cordoba, Spain | Dhiab A.B.,Institute Of Lolivier | Galan C.,University of Cordoba, Spain | And 2 more authors.
Theoretical and Applied Climatology | Year: 2014

The flowering characteristics of plant species of economic interest and the influence of climate on them are of great importance considering the implications for fruit setting and the final harvest: Olive is one of the typical species of the Mediterranean habitat. We have investigated the timing of olive full flowering during the anthesis period and flowering intensity over a period of 20 years (1990-2009), in three major cultivation areas of the Mediterranean basin: Italy, Spain and Tunisia. The importance of these characteristics from a bioclimatic point of view is considered. The biological behaviour was studied to determine its main relationships with temperature and water availability, considering also the different sub-periods and the bio-climatic variations during the study period. The flowering dates and pollen emissions show different behaviours for the Spanish monitoring area in comparison with the other two olive cultivation areas. In the Italian and Tunisian areas, the flowering period over the last decade has become earlier by about 5 and 7 days, respectively, in comparison to the previous decade. Moreover, pollen emissions have decreased in Perugia (Italy) and Zarzis (Tunisia) over the period of 2000-2009, while in Cordoba (Spain), they showed their highest values from 2005 to 2009. The climate analysis has shown an increase in temperature, which results in an increase in the growing degree days for the growth of the olive flower structures, particularly in the more northern areas monitored. Although the olive tree is a parsimonious water consumer that is well adapted to xeric conditions, the increase in the potential evapotranspiration index over the last decade in the Italian and Tunisian olive areas might create problems for olive groves without irrigation, with a negative influence on the flowering intensity. Overall, in all of these Mediterranean monitoring areas, the summer water deficit is an increasingly more important parameter in comparison to the winter parameters, which confirms that the winter period is not as limiting as the summer period for olive tree cultivation in these Mediterranean areas. © 2013 Springer-Verlag Wien.


Aguilera F.,University of Perugia | Orlandi F.,University of Perugia | Ruiz-Valenzuela L.,University of Jaén | Msallem M.,Institute Of Lolivier | Fornaciari M.,University of Perugia
Agricultural and Forest Meteorology | Year: 2015

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.


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 | Year: 2011

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.


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.


Elsayed A.I.,Zagazig University | Boulila M.,Institute Of Lolivier
Journal of Phytopathology | Year: 2014

Samples of sugarcane leaves were collected from different commercial fields and breeding stations in Egypt. Aetiology of sugarcane phytoplasma disease was investigated using nested PCR. Phytoplasma-specific primers (P1/P7 and R16F2n/R16R2) were used to amplify a fragment of the 16S rRNA gene. Sequencing and restriction fragment length polymorphism analyses revealed that the tested phytoplasmas belonged to the 16SrI (aster yellows phytoplasma) group. Phylogenetic analyses of 60 screened accessions of 16S ribosomal RNA gene sequences of Candidatus phytoplasmas comprising those collected from Egypt (this study) and those extracted from GenBank showed that they split into two distinct clusters. All the phytoplasmas form a stable phylogenetic subcluster, as judged by branch length and bootstrap values of 100% in the 16S group cluster. Results of phylogenetic analyses indicated that these phytoplasmas are closely related and share a common ancestor. Conversely, based on the analysis of the 16S-23S region, examined isolates segregated into four different clusters suggesting a notable heterogeneity between them. These results are the first record of the presence of phytoplasma in association with sugarcane yellow leaf in Egypt. © 2013 Blackwell Verlag GmbH.


A detailed study of putative recombination events and their evolution frequency in the whole genome of the currently known members of the family Tombusviridae, comprising 79 accessions retrieved from the international databases, was carried out by using the RECCO and RDP version 3.31 p algorithms. The first program allowed the detection of potential recombination sites in seven out of eight virus genera (Aureusvirus, Avenavirus, Carmovirus, Dianthovirus, Necrovirus, Panicovirus, and Tombusvirus), the second program provided the same results except for genus Dianthovirus. On the other hand, both methods failed to detect recombination breakpoints in the genome of members of genus Machlomovirus. Furthermore, based on Fisher's Exact Test of Neutrality, positive selection exerted on protein-coding genes was detected in 17 accession pairs involving 15 different lineages. Except genera Machlomovirus, and Panicovirus along with unclassified Tombusviridae, all the other taxonomical genera and the unassigned Tombusviridae encompassed representatives under positive selection. The evolutionary history of all members of the Tombusviridae family showed that they segregated into eight distinct groups corresponding to the eight genera which constitute this family. The inferred phylogeny reshuffled the classification currently adopted by the International Committee on Taxonomy of Viruses. A reclassification was proposed. © 2011, Sociedade Brasileira de Genética.


ElSayed A.I.,Zagazig University | Boulila M.,Institute Of Lolivier | Komor E.,University of Bayreuth | Zhu Y.J.,Hawaii Agriculture Research Center
Biochimie | Year: 2012

The 5898 nucleotide single-strand RNA genome of Sugarcane yellow leaf virus (SCYLV) contains one long open reading frame, which is translated into a 120.6 kDa polyprotein. The sequences of SCYLV isolates from the two SCYLV-susceptible cultivars from Hawaii had a deletion of 48-51 nt in ORF1. SCYLV from 12 sugarcane hybrid cultivars from different origins were tested by RT-PCR using a specific set of primers, to investigate the genome segment for this deletion. Only three cultivars were found not to have the deletion (H87-4319, JA-605 and CP52-43), while SCYLV from nine cultivars (H73-6110, H87-4094, H78-7750, GT54-9, G84-47, H78-4153, H65-7052, C1051-73, Ph-8013) along with aphid (Melanaphis sacchari), which fed on SCYLV-infected H73-6110, contained a deletion of about 50 nt. The deleted sequence was located in the overlap frameshift of ORF1 and ORF2. Thus, ORFs 1 and 2 of SCYLV are translated via ribosomal frameshift and yield the 120.6 kDa viral replicase. ORF1 plays most likely a role in the replication and is a source of large variability among the virus population. To identify possible recombination events located in the RdRp domain of the Hawaiian isolates, two programs were used: RDP v.4.3 and RECCO. It is noteworthy that according both methods Haw73-6110 was found as a potential recombinant. On the other hand, opposed to the RDP package, RECCO revealed that Haw87-4094 isolate was also a recombinant whereas Haw87-4319 was not. © 2012 Elsevier Masson SAS. All rights reserved.

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