Functional variations among LOV domains as revealed by FT-IR difference spectroscopy.

The two LOV domains, LOV1 and LOV2, from Chlamydomonas reinhardtii were investigated by light-induced FT-IR difference spectroscopy and compared to the LOV domain of Bacillus subtilis (YtvA-LOV). It is shown that the two S-H conformations of the reactive LOV1 cysteine C57(1) are exposed to environments of different hydrogen bonding strength. Thus, the two rotamer configurations of C57 might be related to the fact that the triplet state decays bi-exponentially into the LOV1-390 photoproduct. Exchange of the two other cysteines of LOV1 (C32S and C83S) does not alter the S-H stretching band providing evidence that this band feature arises solely from C57. The reactive cysteine of LOV2 from Chlamydomonas reinhardtii (C250) and of YtvA-LOV (C62) exhibit both a homogenous S-H stretching vibrational band which suggests a single conformer of the amino acid side chain. Finally, the FT-IR difference spectrum of YtvA from Bacillus subtilis comprising the light absorbing LOV domain and the putative signaling STAS (sulfate transporter/antisigma-factor antagonist) domain, reveals conformational changes in the latter after blue-light excitation.     

Low genetic differentiation among seasonal cohorts in Senecio vulgaris as revealed by amplified fragment length polymorphism analysis

Common groundsel, Senecio vulgaris (Asteraceae), is a highly selfing semelparous ephemeral weed that belongs to the few plant species in central Europe capable of growing, flowering and fruiting all year round. In temperate climates, flowering S. vulgaris cohorts were found to appear up to three times per year. Using amplified fragment length polymorphism (AFLP) molecular markers we examined temporal genetic differentiation among spring, summer and autumn cohorts at each of seven sites located in two regions in Switzerland. Strong genetic differentiation among cohorts may indicate the existence of seasonal races of S. vulgaris, reproductively isolated by nonoverlapping flowering phenologies. Analysis of molecular variance (amova) revealed that < 2.5% of the AFLP variation resided among cohorts within sites, whereas there was significant genetic differentiation among plants from different sites (15.6%) and among individuals within cohorts (81.9%). Significant genetic differentiation was also observed between the two regions. Isolation-by-distance was found on a regional scale, but not on a local scale. Gene flow was estimated to be approximately 15-fold higher among cohorts within sites than among sites. We further found, on average, similar levels of genetic diversity within the three seasonal cohorts. The results of this study demonstrate that season of growth represents a weak barrier for genetic exchange among S. vulgaris populations and does not affect molecular variance. Therefore, there is no evidence for the existence of seasonally specialized races of S. vulgaris. We discuss some implications of the results for the biological control of S. vulgaris using a native rust fungus.     

Spatial heterogeneity in genetic relatedness among house sparrows along an urban-rural gradient as revealed by individual-based analysis

Understanding factors that shape patterns of kinship in sedentary species is important for evolutionary ecologists as well as conservation biologists. Yet, how patterns of relatedness are hierarchically structured in space remains poorly known, even in common species. Here, we use information from 16 polymorphic microsatellite DNA markers to study how small-scale kinship structure varies among house sparrows (Passer domesticus) along an urban-rural gradient. Average levels of relatedness were higher among urban individuals than among individuals from rural areas, suggesting lower rates of dispersal in more built-up habitats. Comparison of observed levels of relatedness with simulated distributions of known kinship values showed that central urban individuals had the highest proportion of closely related conspecifics in their immediate neighbourhood. Spatial auto-correlograms supported this small-scale genetic structure and further indicated stronger effects of genetic drift and/or limited dispersal in urban populations. Results of this study underscore the importance of individual-level analyses as a complementary approach to traditional population-level analyses when studying genetic population structure over small spatial scales.     

Genetic relationships among Orobanche species as revealed by RAPD analysis

RAPD markers were used to study variation among 20 taxa in the genus OROBANCHE: O. alba, O. amethystea, O. arenaria, O. ballotae, O. cernua, O. clausonis, O. cumana, O. crenata, O. densiflora, O. foetida, O. foetida var. broteri, O. gracilis, O. haenseleri, O. hederae, O. latisquama, O. mutelii, O. nana, O. ramosa, O. rapum-genistae and O. santolinae. A total of 202 amplification products generated with five arbitrary RAPD primers was obtained and species-specific markers were identified. The estimated Jaccard's differences between the species varied between 0 and 0.864. The pattern of interspecific variation obtained is in general agreement with previous taxonomic studies based on morphology, and the partition into two different sections (Trionychon and Orobanche) is generally clear. However, the position in the dendrogram of O. clausonis did not fit this classification since it clustered with members of section TRIONYCHON: Within this section, O. arenaria was relatively isolated from the other members of the section: O. mutelii, O. nana and O. ramosa. Within section Orobanche, all O. ramosa populations showed a similar amplification pattern, whereas differences among O. crenata populations growing on different hosts were found. Orobanche foetida and O. densiflora clustered together, supporting the morphological and cytological similarities and the host preferences of these species.     

Phylogenetic relationships among Malagasy lemurs as revealed by mitochondrial DNA sequence analysis

Systematics and evolution of Malagasy lemurs has been analyzed using morphological characters, fossil evidence, ecological/ethological data, and chromosomal banding patterns. Recent developments in DNA technology have provided evolutionary biologists with additional and powerful tools for making phylogenetic inference. In the last years several studies concerning highly repeated DNA sequences (hrDNA) provided new insights about the systematic relationships among the different species of Lemuridae and Cheirogaleidae. Here, a reconstruction of molecular phylogeny of extant Malagasy lemurs based on the comparison of cytochrome-b mitochondrial DNA sequences is presented. With the Polymerase Chain Reaction (PCR) and direct sequencing of amplified DNA fragments, both the phylogenetic range and resolving power of comparative analysis can be extended. These techniques allow to gather sequence data useful to evaluate the pattern of molecular evolution offering opportunities for phylogenetic purposes. A 290-bp fragment of cytochrome-b gene has been amplified and sequenced from the following species:Tupaia glis, Galago alleni, Daubentonia madagascariensis, Indri indri, Varecia variegata, Eulemur fulvus, Eulemur coronatus, Eulemur rubriventer, Eulemur mongoz, Eulemur macaco, Lemur catta, andHapalemur griseus griseus. The phylogenetic trees obtained show the relationships among the Eulemur species and confirm the karyological and hrDNA results of a separated clade forL. catta/Hapalemur. The separation ofVarecia variegata from the other genus of the family Lemuridae is discussed.     

Diversity in the yeast Cryptococcus albidus and related species as revealed by ribosomal DNA sequence analysis

Evidence accumulated from studies based on physiological, biochemical, and molecular characteristics has pointed to the heterogeneity of the ubiquitous anamorphic basidiomycetous yeast species Cryptococcus albidus (Saito) Skinner, with its current varieties and synonyms. The taxonomic status of this species has not been reappraised because different studies, mostly involving limited numbers of strains, have not been integrated. To assess species diversity within the clade containing Cryptococcus albidus and other phylogenetically related Cryptococcus and Filobasidium species, we determined ribosomal DNA (rDNA) sequences of 69 strains from the 5' end of the 26S gene, D1/D2 region, and in some cases, the non-coding ITS2 region. Analysis of the sequence data together with available physiological, biochemical, and molecular characteristics, showed the segregation of C. albidus into at least 12 species, leading to the elevation of former varieties to the rank of species (C. aerius, C. diffluens), the reinstatement of synonyms (C. liquefaciens, C. terricola), and the proposal of new species (C. arrabidensis, C. chernovii, C. cylindricus, C. oeirensis, C. phenolicus, C. saitoi, C. uzbekistanensis, C. wieringae). The overall analyses of the results argue in favour of the use of rDNA sequence data to improve species delineation when integrated with other available physiological and molecular characteristics.     

Functional characteristics of an endophyte community colonizing rice roots as revealed by metagenomic analysis

Roots are the primary site of interaction between plants and microorganisms. To meet food demands in changing climates, improved yields and stress resistance are increasingly important, stimulating efforts to identify factors that affect plant productivity. The role of bacterial endophytes that reside inside plants remains largely unexplored, because analysis of their specific functions is impeded by difficulties in cultivating most prokaryotes. Here, we present the first metagenomic approach to analyze an endophytic bacterial community resident inside roots of rice, one of the most important staple foods. Metagenome sequences were obtained from endophyte cells extracted from roots of field-grown plants. Putative functions were deduced from protein domains or similarity analyses of protein-encoding gene fragments, and allowed insights into the capacities of endophyte cells. This allowed us to predict traits and metabolic processes important for the endophytic lifestyle, suggesting that the endorhizosphere is an exclusive microhabitat requiring numerous adaptations. Prominent features included flagella, plant-polymer-degrading enzymes, protein secretion systems, iron acquisition and storage, quorum sensing, and detoxification of reactive oxygen species. Surprisingly, endophytes might be involved in the entire nitrogen cycle, as protein domains involved in N(2)-fixation, denitrification, and nitrification were detected and selected genes expressed. Our data suggest a high potential of the endophyte community for plant-growth promotion, improvement of plant stress resistance, biocontrol against pathogens, and bioremediation, regardless of their culturability.     

Relationships among the bdellovibrios revealed by partial sequences of 16S ribosomal RNA

Members of the genusBdellovibrio possess the unifying phenotypic trait of attacking and preying upon other Gram-negative bacteria. It has been suggested that this common lifestyle arose by convergent evolution. Physiological and G + C studies have led to the notion that bdellovibrios are a heterogeneous group of loosely related bacteria. We have inferred the phylogenetic relatedness of 12 strains ofBdellovibrio through the analysis of partial 16S ribosomal RNA sequences. Similarity and degree of homology were assessed, and a phylogenetic tree was constructed by the distance matrix method. One branch of the two-branched tree consisted ofB. bacteriovorus and related strains (W, 6-5-S, 109, 109D, 109J, 114, HI Ox9-2, and HI Ox9-3). The other branch was itself branched, withB. starrii, B. stolpii, and marine strain BM4 in separate sub-branches. AllBdellovibrio strains in turn clustered with representatives of the delta division of theProteobacteria. The results indicate that there are at least two subdivisions of the genusBdellovibrio and that present-day bdellovibrios arose from a common ancestor. The placement of the genusBdellovibrio within the delta division of theProteobacteria was confirmed.     

Microsatellite analysis revealed genetic diversity and population structure among Chinese cashmere goats

Most cashmere goats are found in northern China and Mongolia. They are regarded as precious resources for their production of high quality natural fibre for the textile industry. It was the first time that the genetic diversity and population structure of nine Chinese cashmere populations has been assessed using 14 ISAG/FAO microsatellite markers. In addition, two Iranian populations and one West African goat population were genotyped for comparison. Results indicated that the genetic diversity of Chinese cashmere goats was rich, but less than those of the Iranian goat populations. All pairwise F_ST values between the Chinese cashmere goat populations reached a highly significant level (P < 0.001), suggesting that they should all be considered as separate breeds. Finally, clustering analysis divided Chinese cashmere goats into at least two clusters, with the Tibetan Hegu goats alone in one cluster. An extensive admixture was detected among the Chinese goat breeds (except the Hegu), which have important implications for breeding management.     

Phylogenetic relationships among the subfamily Coregoninae as revealed by mitochondrial DNA restriction analysis

Mitochondria1 DNA (mtDNA) restriction analysis was used to assess phylogenetic patterns among 21 taxa of the subfamily Coregoninae. The genus Prosopium formed a very distinct group differing by 10% (sequence divergence estimate) from other species. Coregonus and Stenodus species were closely related, diverging by sequence divergence estimates of less than 5.6%. These species split into two major sister groups. One comprised all 'true whitefish' (subgenus Coregonus ) and four cisco species (subgenus Leucichrhys ). The most distant species within this assemblage was the Acadian whitefish ( C. huntsmani ). The other group included all other cisco species and also the Inconnu ( Stenodus leucichthys ). These results supported a polyphyletic origin of the ciscoes, and did not support Stenodus as a sister taxon of the genus Coregonus . The levels of sequence divergence observed suggested that most extant coregonines radiated during the Pleistocene.     

Kinship and genetic divergence among populations of tuatara Sphenodon punctatus as revealed by minisatellite DNA profiling

Tuatara represent the last surviving member of the order Rhynchocephalia, a group of reptiles the members of which first appeared in the fossil record 200 million years ago. We report the existence of extensive minisatellite DNA variation in island populations of tuatara, as revealed by the use of heterologous DNA probes and compare this variation to that found in other vertebrates. Patterns of minisatellite variation within and among populations of tuatara on the Taranga and Marotere Islands off the coast of New Zealand are detailed. Individuals from West Bay and South Cove on Motumuka Island show higher levels of bandsharing than that recorded between randomly sampled individuals from the same island. We suggest that these populations comprise a proportion of closely related individuals and that populations within islands are genetically structured. Moreover, we identified individuals which have high levels of bandsharing with substantial proportions of the sampled population, suggesting close kinship. A pairwise, inter-island comparison of individuals from Motumuka, Whatupuke and Mauimua Islands, reveals significant differences in distribution of restriction fragments in minisatellite DNA profiles.     

Functional domains of the Escherichia coli dnaK heat shock protein as revealed by mutational analysis

The employment of a set of truncated dnaK peptides produced by deletion and insertion mutations in the Escherichia coli dnaK gene allowed us to define regions of the dnaK protein which are involved in particular enzymatic functions. The results obtained suggest that the dnaK polypeptide is organized into at least two distinct functional domains. The highly conserved amino-terminal portion is required for the ATPase activity. The carboxyl-terminal portion, characterized by relatively low similarity among species, is responsible for the autophosphorylating activity. The mutant dnaK protein C[74], which lacks amino acid sequences at the extreme carboxyl-terminal portion of the protein, retains both the ATPase and the autophosphorylating activities. The results obtained with the full-length (70-kDa) dnaK756 protein suggest that the thermolabile defect of the dnaK756 mutation affects directly or indirectly the ATPase active site of the enzyme. The autophosphorylating activity of the dnaK+, dnaK756, and C[74] polypeptides was activated at least 10-fold by the addition of CaCl2.     

Interspecific genetic variability of the oyster mushroom Pleurotus ostreatus as revealed by allozyme gene analysis

Allozyme variation in natural populations of basidiomycetes fungus Pleurotus ostreatus (88 individuals) from three regions of central Russia was studied. The species was shown to have 92.86% of polymorphic allozyme loci and expected heterozygosity He = 0.49. The mean number of alleles per locus was 3.5. The genetic differences among populations were supported by F-statistics (FST = 0.750). The low level of inbreeding (FIS = 0.018) suggests that the P. ostreatus populations are panmictic, and the main reproduction mode involves basidiospores dispersing at long distances. Using cluster analysis, geographically isolated populations and intersterile groups were differentiated within the complex P. ostreatus species.     

准噶尔无叶豆5个自然居群ISSR遗传变异的空间自相关分析

采用空间自相关分析方法对准噶尔无叶豆(Eremosparton songoricum)5个居群遗传变异的空间结构进行了研究。根据8对ISSR引物扩增的多态性位点,选择了基因频率在30–70%的ISSR位点,运用GenAlEx6和SAAP4.3软件以及地理距离间隔方法分别计算了5个居群的空间自相关系数。结果表明:准噶尔无叶豆居群具有明显的空间遗传结构,绝大多数ISSR位点变异呈非随机分布。位于沙漠腹地的B、D居群和位于沙漠东缘的F居群的遗传变异呈现渐变模式,分别在7m,7m及9m范围内个体呈现显著正相关,推测与克隆繁殖占绝对优势、有性更新罕见发生有关,而克隆大小的差别则主要由微生境差异所引起。位于沙漠北缘的G居群的遗传变异呈现双向渐变模式,在3m内个体呈现显著正相关,这与该居群实生幼苗增补密切相关,但花粉和种子的有限散布所导致的距离隔离对该居群空间遗传结构产生了重要影响。而沙漠腹地的A居群呈现衰退模式,是因为小居群增加了近交的几率,并引起了遗传漂变。     

Genetic relationships among wheat genotypes, as revealed by microsatellite markers and pedigree analysis

Genetic relationships among 20 elite wheat genotypes were studied using microsatellite markers and pedigree analysis. A total of 93 polymorphic bands were obtained with 25 microsatellite primer pairs. Coefficient of parentage (COP) values were calculated using parentage information at the expansion level of 5. The pedigree-based similarity (mean 0.115, range 0.00-0.53) was lower than the similarity assessed using microsatellite markers (mean 0.70, range 0.47-0.91). Similarity estimates were used to construct dendrograms by using the unweighted pair-group method with arithmetic averages (UPGMA). Clustering of genotypes in respect of marker-based similarity revealed two groups. Genotype PBW442 diverged and appeared as distinct from all other genotypes in both marker-based and pedigree-based analysis. The correlation of COP values with genetic similarity values based on microsatellite markers is low (r = 0.285, p < 0.05). The results indicate a need to develop wheat varieties with a diverse genetic background and to incorporate new variability into the existing wheat gene pool.     

Genetic diversity among summer and winter Beauveria bassiana populations as revealed by AFLP analysis

The genetic diversity of Beauveria bassiana was investigated by comparing 40 isolates collected from summer and overwintering populations of Sunn pest from different areas in Syria and Turkey, using amplified fragment length polymorphism (AFLP) markers. Considerable genetic variability among B. bassiana isolates was revealed. The examined isolates were divided into three distinct clusters (A, B, and C). Within these clusters, the summer isolates from Syria and Turkey were grouped together in three sub-clusters (A3, A4, and B2). Also, principal coordinate analyses (PCA) showed clear separation (62.5%) between summer and winter isolates. These differences in the genetic structure may be explained by the variety of eco-geography over the sampled areas of B. bassiana isolates. This information on genetic variation among summer and winter B. bassiana isolates is helpful in designing an effective integrated pest management program for Sunn pest.