-
▪ Pavloudi C.,
Vasileiadou A.,
Sarropoulou E.,
Kalantzi I.,
Papageorgiou N.,
Tsikopoulou I.,
Kasapidis P., Lagnel J.,
Kotoulas G.,
Karakassis I.,
Arvanitidis C.
[show abstract]
[hide abstract]
ABSTRACT: Lagoons are enriched habitats,with unstable environmental conditions caused by their constraint from the sea and their shallowness, hence they are considered as environments in natural disturbance, vulnerable to anthropogenic influences. The frequent changes of the abiotic parameters cause severe changes in the abundance and distribution of organisms; while this relationship has been studied for macroorganisms, only little is known about the lagoonal microbial diversity.
The aim of the present study was to explore the multivariate biodiversity patterns of microorganisms and to examine whether these patterns are associated with those of the macrofaunal polychaetes and the contextual environmental parameters.
For this purpose, sediment samples were collected from five lagoons, located in Amvrakikos Gulf (IonianSea, WesternGreece). In each lagoon, two sampling stations were chosen, with different connectivity to the sea. In addition, a number of geochemical variables (redox potential, particulate organic carbon, chlorophyll-a concentration, median grain size, sulfide concentration) were measured in every station and sediment concentrations for 45 elements were determined by an Inductively Coupled Plasma - Mass Spectrometer (ICP–MS, Thermo Fischer Scientific, Winsford, United Kingdom). Microbial DNA was extracted from the sediment upper layer (0-2cm) and was further processed through deep sequencing of the V5-V6 region of the 16S rRNA gene by next generation sequencing (454 GS FLX Titanium Series, Roche). For the assessment of macrofaunal diversity, additional sediment samples were collected, from which polychaetes were selected and identified at the species level.
More than 150000 sequenced reads were retrieved from the all the sediment samples and were further processed for removal of 454 sequencing errors, PCR single base errors and chimeras. After the processing, the 42660 clustered high quality sequences were classified according to the Ribosomal Database Project (RDP) and corresponded to 13414 OTUs, using the 3% dissimilarity level. Microbial diversity composition and abundance was estimated by a series of diversity indices and multivariate techniques and the relationship between microbial diversity and ecosystem function was studied using as proxies the changes in sediment geochemistry. The most abundant bacterial phyla represented were Bacteroidetes and Proteobacteria; from the later phylum, Gammaproteobacteria and Deltaproteobacteria were the most abundant classes. Preliminary results show that the spatial pattern of the total microbial diversity is related to the pattern resulting only from the environmental parameters characterizing the areas under study, indicating an environmental influence on the distribution of microorganisms. Moreover, our results indicate that, in most cases, microbial diversity in the stations closer to the sea is higher than the one in the stations located inside the lagoons.
14th International Symposium on Microbial Ecology, Copenhagen, Denmark; 08/2012
-
[show abstract]
[hide abstract]
ABSTRACT: European sea bass (Dicentrarchus labrax L., Moronidae, Teleostei) sustains a regional fishery and is commonly farmed in the Mediterranean basin, but has not undergone much long-term genetic improvement. An updated genetic linkage map of the European sea bass was constructed using 190 microsatellites, 176 amplified fragment length polymorphisms and two single nucleotide polymorphisms. From the 45 new microsatellite markers (including 31 type I markers) reported in this study, 28 were mapped. A total of 368 markers were assembled into 35 linkage groups. Among these markers, 28 represented type I (coding) markers, including those located within the peptide Y, SOX10, PXN1, ERA and TCRB genes (linkage groups 1, 7, 16, 17 and 27 respectively). The sex-averaged map spanned 1373.1 centimorgans (cM) of the genome. The female map measured 1380.0 cM, whereas the male map measured 1046.9 cM, leading to a female-to-male (F:M) recombination rate ratio of 1.32:1. The intermarker spacing of the second-generation linkage map of the European sea bass was 3.67 cM, which is smaller than that of the first-generation linkage map (5.03 cM). Comparative mapping of microsatellite flanking regions was performed with five model teleosts and this revealed a high percentage (33.6%) of evolutionarily conserved regions with the three-spined stickleback.
Animal Genetics 10/2008; 39(6):623-34. · 2.40 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Nine polymorphic microsatellites were isolated from sprat (Sprattus sprattus) using a microsatellite enrichment protocol and selective hybridization with a biotinylated (AC)(12) probe. The loci showed different variation patterns in a Baltic Sea population (44 individuals) with mean number of alleles at 12.7 and mean observed heterozygosity at 0.78. These microsatellite loci are expected to be used for taxonomic considerations in sprat, stock differentiation and population genetic analysis.
Molecular Ecology Resources 07/2008; 8(4):861-863. · 3.06 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: We studied the biotype identity and the genetic
relationships of Bemisia tabaci from different localities
in Greece (mainland Greece and the island of Crete)
between 2002 and 2006. Two different approaches
were used, sequencing of the mitochondrial
cytochrome oxidase I (mtCOI) gene and genotyping
using microsatellite markers. Analyses of mtCOI
sequences revealed a high homogeneity between
samples; only five polymorphic sites were detected in
sequences of an 879 bp mtCOI fragment from 16
Greek insects. Comparison of the mtCOI sequences
from Greek B. tabaci with sequences from reference
biotypes identified only the Q biotype within Greece.
Greek whiteflies clustered with other Q biotype B.
tabaci from Spain, Portugal, and Morocco, and were
loosely separated from a group that included Q biotype
sequences from more eastern Mediterranean countries
(Turkey, Cyprus and Israel). Based on sequence
differences, two molecular diagnostic tests for
discriminating between Q and B and non Q / B
biotypes were developed involving amplification of
biotype specific mtCOI fragments or digestion of
mtCOI PCR fragment with AluI. These tools showed
the absence of the B biotype and presence of the Q
biotype in all 40 Greek samples examined. In contrast,
a high genetic differentiation was detected between Q
biotype samples from Crete using six microsatellite
markers. Gene flow appeared low even between
populations separated by just a few kilometres (FST
estimates ranging from 0.437 to 0.025; P < 0.01). This
differentiation was supported by Bayesian analyses
showing that individuals clustered into at least two
groups based on microsatellite data.
Fourth International Bemisia Workshop International Whitefly Genomics Workshop, December 3–8, 2006, Duck Key, Florida, USA; 01/2008
-
[show abstract]
[hide abstract]
ABSTRACT: The genetic polymorphism and the biotype identity of the tobacco whitefly Bemisia tabaci (Gennadius) have been studied in population samples taken from different localities within Greece from cultivated plants growing in greenhouses or in open environments and from non-cultivated plants. Two different approaches were used: sequencing of the mitochondrial cytochrome oxidase I (mtCOI) gene and genotyping using microsatellite markers. Analyses of the mtCOI sequences revealed a high homogeneity between the Greek samples which clustered together with Q biotype samples that had been collected from other countries. When genetic polymorphism was examined using six microsatellite markers, the Greek samples, which were all characterized as Q biotype were significantly differentiated from each other and clustered into at least two distinct genetic populations. Moreover, based on the fixed differences revealed by the mtCOI comparison of known B. tabaci biotype sequences, two diagnostic tests for discriminating between Q and B and non-Q/non-B biotypes were developed. Implementation of these diagnostic tools allowed an absence of the B biotype and presence of the Q biotype in the Greek samples to be determined.
Bulletin of Entomological Research 03/2007; 97(1):29-40. · 1.88 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: The extrachromosomal DNA of Sodalis glossinidius from two tsetse fly species was sequenced and contained four circular elements: three plasmids, pSG1 (82 kb), pSG2 (27 kb), and pSG4 (11 kb), and a bacteriophage-like pSG3 (19 kb) element. The information suggests S. glossinidius is evolving towards an obligate association with tsetse flies.
Journal of Bacteriology 08/2005; 187(14):5003-7. · 3.83 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: The genetic structure of a greenhouse population of the mite Tetranychus urticae was studied by the analysis of five microsatellite loci. Genetic variation was compared during a crop season between periods of population foundation and rapid population increase and was investigated in two consecutive years. The population displayed significant heterozygote deficiency at all the sampling periods. However, inbreeding tended to decrease with increasing density (FIS coefficient between 0.13 and 0.25). No significant genetic differentiation between samples was found either at a spatial scale within the greenhouse or at a temporal scale between two growing seasons (FST between 0.008 and 0.09). Estimations of the genetic relatedness between pairs of individuals indicated that the distances between pairs of sisters and unrelated mites in the greenhouse were not significantly different, suggesting that mites do not tend to form patches that reside close to the point of birth.
Insect Molecular Biology 05/2002; 11(2):157-65. · 2.53 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Three species of scorpions have been reported from Tunisia: Androctonus amoreuxi Audoin, A. aeneas Koch, and A. australis L. The latest has been divided in two subspecies: A. australis garzonii Goyffon & Lamy and A. australis hector Koch. Despite the public health importance of these animals, which cause several cases of poisoning each year, nothing is know about the genetic diversity of the group. To gain a better understanding of the group, we studied the variation of rDNA sequences of the ITS1, 5.8S, and ITS2 region of 14 representatives of the four taxa in Tunisia. The main result is the high polymorphism of the ITS regions. In some instances in both intra- and interspecific comparisons, it was difficult to unambiguously align the sequences. However, some representatives of different species were relatively similar, so that it appeared difficult to recognize the species on the basis of these sequences. A phylogenetic analysis was conducted that inquires the validity of the subspecies status of A. australis garzonii and A. australis hector. Moreover, the taxonomic status of A. aeneas is also questioned. Our studies highlighted the need of a revision of the taxonomy of the scorpions in Tunisia; however, the use of other genetic markers will be necessary to solve this question.
Journal of Medical Entomology 11/2000; 37(6):787-90. · 1.76 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: The complexity of some sexual reproductive systems in arthropods still leaves both their genetic and epigenetic determinism and their evolutionary significance poorly understood. Pseudoarrhenotoky is characterized by obligate fertilization and differential inactivation and/or elimination of paternal chromosomes in embryos that develop into males. Here, we investigate how the paternal genome is transmitted in a pseudoarrhenotokous mite, Neoseiulus californicus, using codominant genetic markers detected by DALP (direct amplification of length polymorphism). Transmission patterns of parental alleles through one and two generations are reported at four or five loci corresponding to four linkage groups. Our data provide strong evidence for selective elimination of the paternal genome among male tissues. Sperm contained maternal genes exclusively, whereas some male somatic tissues retained most if not all paternal chromosomes. No recombination between parental genomes prior to paternal genome elimination from the embryonic germ line was observed. These data allow a reinterpretation of previous phenotypic and cytogenetic observations in these mites, from which we suggest some relevant mechanistic and evolutionary implications. In addition, this is the first published study using polymorphic codominant loci detected by the recently developed DALP method.
Heredity 07/2000; 84 ( Pt 6):702-9. · 4.60 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: We report the first application of a new method designed to isolate polymorphic loci in any organism, the direct amplification of length polymorphism. Five polymorphic loci were readily isolated in the predatory mite Neoseiulus californicus (Acari: Phytoseiidae). Two to five alleles were identified among 46 isofemale lines based on fragment size variation due to micro-deletions/insertions. Genotyping F1 and F2 progenies from controlled heterogametic crosses and backcrosses allowed to establish the Mendelian inheritance of these alleles, their codominance, and pairwise recombination rates. Nucleotidic sequence divergence due to single base substitution was also found in the flanking regions of the polymorphism. We discuss the usefulness of these markers in studies of reproductive systems as well as population genetics, in particular, in mite species where the amount of DNA or richness in microsatellites could be limiting factors in the isolation of polymorphic loci.
Enperimental and Applied Acarology 02/2000; 24(10-11):795-803. · 1.73 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Based on allozyme electrophoresis at the Pgm locus and nuclear ribosomal DNA (ITS2) sequences, we studied the genetic variation of the two-spotted spider mite Tetranychus urticae Koch collected on rose bay, Nerium oleander L. (Apocynaceae), from several localities around the Mediterranean basin. In addition, we compared these results with those of Navajas et al. (1998) and Tsagkarakou (1997) who collected from several other host plants from the Mediterranean. In the western part of this area (Spain, France, Tunisia), we found the individuals collected from rose bay to be clearly genetically differentiated from other samples. No evidence of such host-associated differentiation was detected in the eastern Mediterranean (Italy and Greece). The genetic differentiation of mites collected on rose bay was investigated further by studying the reproductive incompatibilities between populations in Greece and in France and a laboratory strain reared on bean, Phaseolus vulgaris, in France. Reciprocal crosses performed between these strains revealed variable levels of incompatibility, spanning from partial to complete reproductive isolation. In all cases incompatibility was asymmetric. We designed a test based on double-mating to establish the fertilization status of females in fully incompatible crosses. These crosses showed that the females had been inseminated, which suggests that the barrier to reproduction is not of a prezygotic behavioral nature. The data raises the question of the relative role of ecological factors (host plant) and geographical distance, in the ongoing differentiation process potentially leading to speciation.
Enperimental and Applied Acarology 02/2000; 24(5-6):365-76. · 1.73 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Preliminary work is needed to assess the usefulness of different markers at different taxonomic scales when a new group is analyzed, such as the commercially important Phytoseiidae mites. We investigate here the level of sequence variation of the nuclear ribosomal spacers ITS 1 and 2 and the 5.8S gene in six species of Phytoseiidae: Neoseiulus culifornicus, N. fallacis, Euseius concordis, Metaseiulus occidentalis, Typhlodromus pyri and Phytoseiulus persimilis. As expected, the 5.8S gene (148 base pairs) is markedly conserved and displays little variation in between genera comparisons. ITS1 and ITS2 show contrasting patterns: while the ITS2 is short (80-89 bp) and shows little variation, the ITS1 is longer (303-404 bp) and is very variable in sequence. This fact compromises reliable nucleotide homologies when comparing the genera. The comparison of ITS1 sequence similarity at the species level might be useful for species identification, however, the value of ITS in taxonomic studies does not extend to the level of the family. The intraspecific variations of ITS were investigated in three species: N. californicus, N. fallacis and E. concordis. The first species has identical ITS1 sequences and the last two display low polymorphism (2 nucleotide substitutions). The ITS2 and 5.8S sequences were identical in all three subspecies comparisons.
Enperimental and Applied Acarology 12/1999; 23(11):851-9. · 1.73 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Nasonovia ribisnigri, a main pest of salad crops, has developed resistance to various insecticides in southern France, including the carbamate pirimicarb and the cyclodiene endosulfan, two insecticides widely used to control this aphid. Here we have investigated the mechanisms of resistance to these two insecticides by studying cross-resistance, synergism, activity of detoxifying enzymes, and possible modifications of the target proteins. Resistance to pirimicarb was shown to be mainly due to a decreased sensitivity of the target acetylcholinesterase; this modification conferred also, resistance to propoxur but not to methomyl and the two tested organophosphates (acephate and paraoxon). Endosulfan resistance was associated with a moderate level of resistance to dieldrin, and resistance to both insecticides was due, in part, to increased detoxification by glutathione S-transferases (GST). The endosulfan resistant strain displayed the same amino acid at position 302 of the Rdl gene (GABA receptor) as susceptible aphids (e.g. Ala), indicating that the Ala to Ser (or to Gly) mutation observed among dieldrin resistant strains of other insect species was not present.
Insect Biochemistry and Molecular Biology 05/1999; 29(4):385-91. · 3.25 Impact Factor
-
Entomologia Experimentalis et Applicata 01/1999; 90(2):113-122. · 1.53 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Microsatellites are known to be a common feature of eukaryote genomes. Here we investigate the presence of microsatellite sequences in the genome of two mite species, Tetranychus urticae and Amblyseius fallacis, based on screening of both mite genomic libraries and Southern blots of these mites that we compare to two vertebrates. No signal with GT15 or a faint smear with CT10 were obtained in Southern analysis for the two mites, whereas both probes strongly bound with vertebrate DNA. Genomic libraries constructed in plasmid and lambda vectors were probed and only two CT microsatellites were isolated for T. urticae. Among eight trinucleotides probes tested, the strongest hybridization signal was detected for T. urticae with CAT and TGA probes. These two classes of repeats were also the most represented in genomic library screenings. However, only sequences with short numbers of units could be detected (<CAT4 or TGA9). Congruency of Southern analysis and screening of partial genomic libraries indicates an under-representation of microsatellite sequences in the two mite genomes. The potential of the scarce repetitive DNA isolated from mites to serve as population genetics markers is discussed on the basis of preliminary assessment of their polymorphism.
Insect Molecular Biology 08/1998; 7(3):249-56. · 2.53 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: We compared patterns of intraspecific polymorphism of two markers with contrasted modes of evolution, nuclear ribosomal DNA (rDNA) and mitochondrial DNA (mtDNA), in the phytophagous mite Tetranychus urticae Koch. The second internal transcribed spacer (ITS2) of rDNA and a fragment in the mtDNA gene coding for Cytochrome Oxidase I (COI), were PCR-amplified and sequenced in samples of various geographical origins distributed worldwide. The 15 COI haplotypes found fell into two major phylogenetic lineages differing by an average of 5% nucleotide divergence. Samples from the Mediterranean basin were represented in both lineages, and showed no phylogeographical structure. The other samples, from temperate regions of the northern hemisphere, were clustered in one of the lineages and displayed little variation, indicating a recent colonization of this region. In contrast, no variation at all was found at the ITS2 in this species. We sequenced both COI and ITS2 in four other species of the genus Tetranychus and found that, despite the absence of intraspecific polymorphism, ITS appears to evolve 2.5 times faster than COI. We argue that rDNA homogeneity over the species range of T. urticae results from the high colonization potential of this species, preventing long-term differentiation. Preliminary data on two other mite species (Amphitetranychus viennensis Zacher and Mononychellus progresivus Doreste) with stricter ecological requirements and more restricted colonization potential revealed substantial and concordant geographical differentiation for both ITS2 and COI.
Heredity 07/1998; 80 ( Pt 6):742-52. · 4.60 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Direct amplification of length polymorphisms (DALP) uses an arbitrarily primed PCR (AP-PCR) to produce genomic fingerprints and to enable sequencing of DNA polymorphisms in virtually any species. Oligonucleotide pairs were designed to each produce a specific multi-banded pattern and all the fragments thus generated can be directly sequenced with the same two universal M13 sequencing primers. This strategy combines the advantages of a high resolution fingerprint technique and the possibility of characterizing the polymorphisms. The use of family members as templates in the multi-locus detection step allows a direct test of allele transmission, as well as early mapping of the markers or selection of loci associated with some traits or diseases. We used this method to detect micro-deletions/insertions and microsatellite DNA loci useful in population genetics studies, but it could be applied in many other fields of biology, such as genome mapping for definition of polymorphic sequence tagged sites, directly localized on a genetic map.
Nucleic Acids Research 04/1998; 26(6):1458-65. · 8.03 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: The polymorphism of four isozymes was studied on single females of Tetranychus urticae from Crete (Greece), using an isoelectric focusing technique. Genetic differentiation was found to be correlated with distance but not with the species of colonized host-plants. Thus no differentiation was observed between samples collected on citrus trees, tomato, pumpkin, okra or weed plants located within a 50 m(2) area, showing that at this geographical scale T. urticae populations are panmictic. In contrast, samples from plants at 150 m or more from one another displayed a significant genetic differentiation. These results are discussed in relation to the known pattern of migration in the species.
Heredity 02/1997; 78(Pt 1):84-92. · 4.60 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Studies of mitochondrial DNA sequences in a variety of animals have shown important differences between phyla, including differences in the genetic codes used, and varying constraints on base composition. In that respect, little is known of mites, an important and diversified group. We sequenced a portion (340 nt) of the cytochrome oxidase subunit I (COI) encoding gene in twenty species of phytophagous mites belonging to nine genera of the two families Tetranychidae and Tenuipalpidae. The mitochondrial genetic code used in mites appeared to be the same as in insects. As is generally also the case in insects, the mite sequences were very rich in A + T (75% on average), especially at the third codon position (94%). However, important variations of base composition were observed among mite species, one of them showing as little as 69% A + T. Variations of base composition occur mostly through synonymous transitions, and do not have detectable effects on polypeptide evolution in this group.
Insect Molecular Biology 12/1996; 5(4):281-5. · 2.53 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Studies of mitochondrial DNA sequences in a variety of animals have shown important differences between phyla, including differences in the genetic codes used, and varying constraints on base composition. In that respect, little is known of mites, an important and diversified group. We sequenced a portion (340 nt) of the cytochrome oxidase subunit I (COI) encoding gene in twenty species of phytophagous mites belonging to nine genera of the two families Tetranychidae and Tenuipalpidae. The mitochondrial genetic code used in mites appeared to be the same as in insects. As is generally also the case in insects, the mite sequences were very rich in A + T (75% on average), especially at the third codon position (94%). However, important variations of base composition were observed among mite species, one of them showing as little as 69% A + T. Variations of base composition occur mostly through synonymous transitions, and do not have detectable effects on polypeptide evolution in this group.
Insect Molecular Biology 10/1996; 5(4):281 - 285. · 2.53 Impact Factor
