Repetitive DNA, Genome and Species Relationships in Avena and Arrhenatherum(Poaceae)

Repetitive sequences have been widely used for examining genomeand species relationships by in situ and Southern hybridization.In the present study, double-stranded DNA sequences, from denaturedDNA reannealed to Cot = 1, from Avena strigosa(2 n = 2x = 14;A genome; referred to as CotA) and Avena sativa(2n = 6 x =42; ACD genome; referred to as CotACD) were isolated with ahydroxyapatite column, and were used for in situ hybridizationon hexaploid A. sativa chromosomes. Probe CotACD labelled allchromosomes evenly throughout their length at the same intensity.Probe CotA labelled the 28 A and D genome chromosomes stronglyand the 14 C genome chromosomes weakly. Three cloned repetitivesequences, pAvKB9 (126 bp), pAvKB26 (223 bp) and pAvKB32 (721bp) were characterized in the A, B, C and D Avena genomes andthe genus Arrhenatherum using molecular and cytological methods.Clones pAvKB9 and pAvKB26 were absent from the Avena C genome,while both could identify the presence of the D genome by Southernhybridization. In situ hybridization to diploid and tetraploidAvena species revealed that the probes showed a dispersed genomicorganization and that they are present on both arms of all chromosomes.These sequences were excluded from areas where tandem repeats,such as rRNA genes and telomeres, are present. These resultsindicate the close relationship between A and D genomes andthe presence of common DNA sequences between A and C Avena genomes.All three clones hybridized to Southern blots containingArrhenatherumdigested genomic DNA, indicating Arrhenatherum’s closeaffinity to A, B and D Avena genomes. Copyright 2000 Annalsof Botany Company Cereals, DNA, hydroxyapatite, in situ hybridization, oats, reassociation kinetics, repetitive DNA     

Genomic Origin and Organization of the Hybrid Poa jemtlandica(Poaceae) Verified by Genomic In Situ Hybridization and Chloroplast DNA Sequences

Chloroplast DNA sequencing and genomic in situ hybridization(GISH) were used to investigate the genomic origin and organizationof the alpine grass Poa jemtlandica. Using genomic probes ofP. alpina and P. flexuosa, GISH clearly distinguished betweenthese two putative parental genomes and thus confirmed the hybridnature of P. jemtlandica. The chloroplast trn L intron and trnL–trn F intergenic spacer (IGS) sequence genotypes ofP. flexuosa and P. jemtlandica were 100% identical but differedfrom those of P. alpina by a total of ten or 11 nucleotide substitutionsand six indels over 866 aligned positions, identifying P. flexuosaas the maternal parent of the P. jemtlandica population studiedhere and supporting a relatively recent origin of the hybrid.GISH revealed the presence of intergenomic translocations inthe hybrid genome, indicating that the two parental genomeshave undergone some rearrangements following hybridization.It is likely that some of these chromosome changes took placesoon after hybridization in order to overcome the adverse interactionsbetween the nuclear and the cytoplasmic genomes and to facilitatethe successful establishment of the newly formed hybrid. Thepresence of intergenomic chromosome changes may play an importantrole in the evolution of natural hybrids and the establishmentof new evolutionary lineages. Copyright 2000 Annals of BotanyCompany Natural hybridization, genome origin, intergenomic translocations, GISH, chloroplast DNA sequences, Poa jemtlandica     

Quantitation of Repetitive Sequences in Human Genomic DNA and Detection of an Elevated Ribosomal Repeat Copy Number in Schizophrenia: The Results of Molecular and Cytogenetic Analyses

A modified version of quantitating repetitive sequences in genomic DNA was developed to allow comparisons for numerous individual genomes and simultaneous analysis of several sequences in each DNA specimen. The relative genomic content of ribosomal repeats (rDNA) was estimated for 75 individuals, including 33 healthy donors (HD) and 42 schizophrenic patients (SP). The rDNA copy number in HD was 427 ± 18 (mean ± SE) per diploid nucleus, ranging 250–600. In SP, the rDNA copy number was 494 ± 15 and ranged 280–670, being significantly higher than in HD. The two samples did not differ in contents of sequences hybridizing with probes directed to a subfraction of human satellite III or to the histone genes. Cytogenetic analysis (silver staining of metaphase chromosomes) showed that the content of active rRNA genes in nucleolus organizer regions is higher in SP compared with HD. The possible causes of the elevated rRNA gene dosage in SP were considered. The method employed was proposed for studying the polymorphism for genomic content of various repeats in higher organisms, including humans.     

A DNA Barcoding Method to Discriminate between the Model Plant Brachypodium distachyon and Its Close Relatives B. stacei and B. hybridum (Poaceae)

Background

Brachypodium distachyon s. l. has been widely investigated across the world as a model plant for temperate cereals and biofuel grasses. However, this annual plant shows three cytotypes that have been recently recognized as three independent species, the diploids B. distachyon (2n = 10) and B. stacei (2n = 20) and their derived allotetraploid B. hybridum (2n = 30).

Methodology/Principal Findings

We propose a DNA barcoding approach that consists of a rapid, accurate and automatable species identification method using the standard DNA sequences of complementary plastid (trnLF) and nuclear (ITS, GI) loci. The highly homogenous but largely divergent B. distachyon and B. stacei diploids could be easily distinguished (100% identification success) using direct trnLF (2.4%), ITS (5.5%) or GI (3.8%) sequence divergence. By contrast, B. hybridum could only be unambiguously identified through the use of combined trnLF+ITS sequences (90% of identification success) or by cloned GI sequences (96.7%) that showed 5.4% (ITS) and 4% (GI) rate divergence between the two parental sequences found in the allopolyploid.

Conclusion/Significance

Our data provide an unbiased and effective barcode to differentiate these three closely-related species from one another. This procedure overcomes the taxonomic uncertainty generated from methods based on morphology or flow cytometry identifications that have resulted in some misclassifications of the model plant and its allies. Our study also demonstrates that the allotetraploid B. hybridum has resulted from bi-directional crosses of B. distachyon and B. stacei plants acting either as maternal or paternal parents.     

Flow Sorting and Molecular Cytogenetic Identification of Individual Chromosomes of Dasypyrum villosum L. (H. villosa) by a Single DNA Probe

Dasypyrum villosum (L.) Candargy (sin. Haynaldia villosa) is an annual wild diploid grass species (2n = 2x = 14; genome VV) belonging to the Poaceae family, which is considered to be an important source of biotic and abiotic stress resistance genes for wheat breeding. Enhanced characterization of D. villosum chromosomes can facilitate exploitation of its gene pool and its use in wheat breeding programs. Here we present the cytogenetic identification of D. villosum chromosomes on slide by fluorescent in situ hybridization (FISH), with the GAA simple sequence repeat (SSR) as a probe. We also describe the isolation and the flow cytometric analysis of D. villosum chromosomes in suspension, resulting in a distinguished flow karyotype. Chromosomes were flow sorted into three fractions, according their DNA content, one of which was composed of a single type of chromosome, namely 6 V, sorted with over 85% purity. Chromosome 6 V is known to carry genes to code for important resistance and seed storage characteristics, and its isolation represents a new source of genetic traits and specific markers useful for wheat improvement.     

The Diversity of Karyotypes and Genomes within Section Syllinum of the Genus Linum (Linaceae) Revealed by Molecular Cytogenetic Markers and RAPD Analysis

The wide variation in chromosome number found in species of the genus Linum (2n = 16, 18, 20, 26, 28, 30, 32, 36, 42, 72, 84) indicates that chromosomal mutations have played an important role in the speciation of this taxon. To contribute to a better understanding of the genetic diversity and species relationships in this genus, comparative studies of karyotypes and genomes of species within section Syllinum Griseb. (2n = 26, 28) were carried out. Elongated with 9-aminoacridine chromosomes of 10 species of section Syllinum were investigated by C- and DAPI/С-banding, CMA and Ag-NOR-staining, FISH with probes of rDNA and of telomere repeats. RAPD analysis was also performed. All the chromosome pairs in karyotypes of the studied species were identified. Chromosome DAPI/C-banding patterns of 28-chromosomal species were highly similar. Two of the species differed from the others in chromosomal location of rDNA sites. B chromosomes were revealed in all the 28-chromosomal species. Chromosomes of Linum nodiflorum L. (2n = 26) and the 28-chromosomal species were similar in DAPI/C-banding pattern and localization of several rDNA sites, but they differed in chromosomal size and number. The karyotype of L. nodiflorum was characterized by an intercalary site of telomere repeat, one additional 26S rDNA site and also by the absence of B chromosomes. Structural similarities between different chromosome pairs in karyotypes of the studied species were found indicating their tetraploid origin. RAPD analysis did not distinguish the species except L. nodiflorum. The species of section Syllinum probably originated from a common tetraploid ancestor. The 28-chromosomal species were closely related, but L. nodiflorum diverged significantly from the rest of the species probably due to chromosomal rearrangements occurring during evolution.     

Phylogenetic Analysis of AA-genome Oryza Species (Poaceae) Based on Chloroplast, Mitochondrial, and Nuclear DNA Sequences

Species in the genus Oryza (Poaceae) contain 10 genomic types and are distributed in pan-tropics of the world. To explore phylogenetic relationships of Oryza species having the AA-genome, DNA sequences of the chloroplast trnL intron and trnL-trnF spacer, mitochondrial nad1 intron 2, and nuclear internal transcribed spacer were analyzed, based on materials from 6 cultivated (O. sativa and O. glaberrima) and 13 wild accessions, in addition to a CC-genome species (O. officinalis) that was used as an outgroup. Analyses of the combined sequence data set from different sources provide a much better resolution of the AA-genome species than the individual data set, indicating the limitation of a single gene in phylogenetic reconstruction. The phylogeny based on the combined data set demonstrated an apparent grouping of the AA-genome Oryza species that was well associated with their geographic origin, although the Australian O. meridionalis showed its affinity with the African species. The geographic pattern of the phylogenetic relationship was probably attributed to the frequent genetic exchange and introgression among the AA-genome species from the same continents. In addition, Asian cultivated rice O. sativa showed its close relation to O. rufipogon and O. nivara, whereas African cultivated rice O. glaberrima was closely linked to O. barthii and O. longistaminata, indicating the independent domestication of the two cultivated species in different geographic locations.     

A simulation model of Avena fatua L. (wild-oat) growth and development

An eco-physiological simulation model of the growth and development of Avena fatua was parameterised and tested. The model simulates growth ofA. fatua, in kg dry matter ha^-1 day^-1 from sowing to maturity as a function of irradiance, temperature and various species characteristics. Parameter values were derived from the literature and from field experiments, including both autumn and spring sowings of A. fatua over three years at two sites in southern England. With two exceptions, a single set of parameter values was sufficient to accurately simulate the emergence, growth and development of both autumn and spring cohorts over all years and sites. The two exceptions were the result of differences between autumn and spring cohorts of A. fatua in the rate of early leaf area growth and in the relationship between specific leaf area and developmental stage.     

从D环和细胞色素b基因序列探讨懒猴属的分子系统发育关系(英文)

本研究测定了懒猴属(Nycticebus)D环的部分序列和细胞色素b基因的全序列(1140bp),分析了该属物种之间的系统发育进化关系。在DNA水平上,序列分析结果一致地提供了新的分类学证据：支持Rataiszczak和Groves的观点,即N．intermedus只是N．pygmaeus的成体(Ratajszczak,1998;Groves,1971)。对两种序列的数据做了联合及个别分析,获得相似的系统树,支持懒猴属由两个单系群组成：第一群由N．pygmaeus聚成,第二群由N．coucang聚成。该结果也提供了新的分子遗传证据,支持懒猴属由N．coucang和N．pygmaeus两物种组成。     

Speciation and Species Separation in Hordeum L. (Poaceae) Resolved by Discontinuous Molecular Markers1

Abstract: Amplified fragment length polymorphisms (AFLPs) were used to evaluate the capacity of discontinuous markers to reveal genetic structure within Hordeum , a challenging higher plant genus from the standpoint of natural systematics. Phylogenies of 63 accessions encompassing nine species from four Hordeum sections were inferred from polymorphisms scored at 600 loci. Phylogenies based on sequences from the nuclear internal transcribed spacer (ITS) region were constructed for comparison, but revealed severe sampling errors inherent to single genes. Although superior by virtue of providing genome-wide estimates of genetic similarity, the adoption of AFLPs in infrageneric studies requires caution. Comigrating AFLP bands studied here could be divided on the basis of band intensity variation into two types that are □ 100 % identical and < 40 % identical in DNA sequence, respectively, in infrageneric comparisons. Thus, the careful selection of AFLP bands to be analyzed bears heavily upon their phylogenetic utility. Within the H. murinum complex, which encompasses three morphologically distinct subspecies, AFLP data from 37 accessions reveal unexpected genetic differentiation between H. murinum, glaucum populations to the east and west of Alexandria (Egypt), suggesting the presence of allopatric speciation in the wake of human settlement.     

Allozyme Diversity and Interspecific Differentiation o the Two Diploid Bromegrass Species, Bromus tectorum L. and B. sterilis L (Poaceae)

Abstract: Genetic diversity among 50 accessions of Bromus tectorum and 43 of B. sterilis from different sites of their Eurasian ranges has been studied by electrophoretic analysis of ten enzymes encoded by 18 loci. The two species proved clearly differentiated by alternate allozymes at seven isozymes. Populations of both taxa showed differentiation into eleven (B. tectorum ) and six (B. sterilis ) multilocus allozyme lineages (MLALs). The extent of interspecific allozyme divergence estimated by Manhattan distance exceeded more than three times intraspecific differentiation between the multilocus lineages. Only two MLALs in each species have wide geographical distribution from the Near East to Europe. Other MLAL5 were found each for only one or two populations and were region-specific. Most geographically marginal European populations had widespread MLALs.     

Relationship Between Phenolic Content Determined by LC/MS/MS and Antioxidant Capacity and Enzyme Inhibition of Cyclotrichium niveum L.

Cyclotrichium niveum (Boiss.) Manden & Scheng belonging to the Lamiaceae family, which is an endemic species in the eastern Anatolian region of Turkey, has an important place in terms of ethno-botany. The phytochemical composition of the plant, inhibition of acetylcholinesterase (AChE) (which hydrolyzes the neurotransmitter acetylcholine), inhibition of paraoxonase for antiatherosclerotic activity (hPON 1) (which detoxifies organophosphates), and antioxidant capacity were all investigated in this study. Phytochemical content was determined by LC/MS/MS, and enzyme inhibition and antioxidant capacity studies were determined by spectrophotometer. Antioxidant capacity of C. niveum extracts (methanol, hexane, and water) was determined by applying ABTS⋅⁺, DPPH⋅, FRAP, and CUPRAC methods. Both the water and the methanol extracts of the C. niveum exhibited significant inhibition on the AChE (IC₅₀ value for methanol and water extract 0.114±0.14 mg/mL (R2:0.997) and 0.178±0.12 mg/mL (R²: 0.994), respectively). In contrast, the methanol and water extracts of the C. niveum did not exhibit the inhibition effect on hPON 1. The highest activity for ABTS⋅⁺ was 66.53 % in the water extract, and DPPH⋅ was 55.03 % in the methanol extract. In the metal-reducing power assay, the absorbance was 0.168±0.04 for FRAP water extract and 0.621±0.01 for CUPRAC methanol extract. According to LC/MS/MS analyses, hydroxybenzoic acid, salicylic acid, syringic acid, acetohydroxamic acid and luteolin determined in the plant extract. As a consequence, C. niveum which has antioxidant, anti-atherogenic and anti-neurodegenerative properties has the potential to be used as a natural medication instead of synthetic drugs used in Alzheimer's patients.     

Comparative Analysis of Triticum aestivum L. (Poaceae,Poales) and Pisum sativum L. (Fabaceae,Fabales) Resistance to Heavy Metals

Biology Bulletin - Abstract—Heavy metals are widespread soil pollutants frequently identified in agricultural lands. In many cases, their pollution levels significantly exceed the maximum...     

A Preliminary Molecular Phylogeny of Planthoppers (Hemiptera: Fulgoroidea) Based on Nuclear and Mitochondrial DNA Sequences

The planthopper superfamily Fulgoroidea (Insecta: Hemiptera) is one of the most dominant groups of phytophagous insects. It comprises about 20 families, containing a total of 9000 species worldwide. Despite several recent studies, the phylogeny of Fulgoroidea is not yet satisfactorily resolved and the phylogenetic positions of several key families, especially Cixiidae, Delphacidae, Tettigometridae, Nogodinidae, Acanaloniidae and Issidae, are contentious. Here, we expand upon recent phylogenetic work using additional nuclear (18S and 28S) and novel mitochondrial (16S and cytb) markers. Maximum likelihood and Bayesian analyses yielded robust phylogenetic trees. In these topologies, a group containing Cixiidae and Delphacidae is recovered as the sister group to the remaining taxa. Tettigometridae is placed in a more nested position and is grouped with Caliscelidae. Sister relationships are found between Flatidae and Ricaniidae, and between Dictyopharidae and Fulgoridae. Nogodinidae and Issidae are confirmed to be non-monophyletic families. For major nodes of interest, divergence date estimates are generally older than those from the fossil record.     

Molecular genetic diversity of Punica granatum L. (pomegranate) as revealed by microsatellite DNA markers (SSR)

Pomegranate (Punica granatum L.) is one of the oldest known edible fruits and more and more it arouse interest of scientific community given its numerous biological activities. However, information about its genetic resources and characterization using reliable molecular markers are still scarce. In the present study, we report the development of 4 new polymorphic SSR markers. They have been used in addition to 11 SSRs previously published to investigate molecular diversity of 33 P. granatum ecotypes. Based on the multi-locus profiles, twenty-two distinctive genotypes were identified. Globally, quite low genetic diversity has been revealed, as measured by allele richness (2.83 per locus) and heterozygosity (He = 0.245; Ho = 0.243), reflecting the narrow genetic background of the plant material. Four synonymous groups could be detected involving 15 accessions. Results of ordination and cluster analysis suggested that almost all the Tunisian cultivars share similar genetic background, and are likely derived from a small number of introductions in ancient times. Results issued from this study provide essential information to project a pomegranate core-collection without plant material duplication and for sustainable management of pomegranate landraces at national and international level. Furthermore, these SSR markers are powerful tool for marker assisted selection (MAS) program and for QTL studies.     

Embryogenic cells in Dactylis glomerata L. (Poaceae) explants identified by cell tracking and by SERK expression

 Single mesophyll cells in leaf explants of Dactylis glomerata L. (Dactylis) that were competent to form somatic embryos directly or through callus were identified by semi-automatic cell tracking. These competent cells were a subpopulation of small, isodiametric, cytoplasm-rich cells located close to the vascular bundles. Using whole mount in situ hybridization, we showed that a similar subpopulation of cells expressed the Somatic Embryogenesis Receptor-like Kinase (SERK) gene during the induction of embryogenic cell formation. In both leaf explants and suspension cultures, a transient pattern of SERK gene expression was found during early embryo development, up to the globular stage. In later embryo stages, SERK mRNA was present in the shoot apical meristem, scutellum, coleoptile and coleorhiza. Received: 14 May 1999 / Revision received: 27 August 1999 / Accepted: 8 September 1999     

Environmental Pollution and Relationship Between Total Antioxidant Capacity and Heavy Metals (Pb,Cd, Zn,Mn, and Fe) in Solanum tuberosum L. and Allium cepa L.

In the natural environment, plants are exposed to different stress factors that are responsible for overproduction of reactive oxygen species. Exposure to heavy metals is one of these factors. The present article highlights the correlation between the effects of bioaccumulation of heavy metals in a highly polluted region as the industrial zone of the Thermo Power Plants “Kosova” in Kosovo on the antioxidant capacity of two selected target species: Solanum tuberosum L. and Allium cepa L. The results show that environmental pollution in the industrial zone of the Thermo Power Plants “Kosova” generates a significant bioaccumulation of heavy metals such as Pb, Cd, Zn, Mn, and Fe. The high concentration of heavy metals leads to an increased production of reactive radical species. The extracts of target plants cultivated in this region display a lower antioxidant capacity than the same plants grown in a control rural area. The Fe bioaccumulation markedly influences the antioxidant capacity of plant samples analyzed.     

Genomic variation and relationships in aerial yam (Dioscorea bulbifera L.) detected by random amplified polymorphic DNA.

Random amplified polymorphic DNA (RAPD) markers were used to assess intraspecific variability and relationships in aerial yam (Dioscorea bulbifera L.). A total of 23 accessions from different geographic locations in Africa, Asia, and Polynesia were analyzed by 10 arbitrarily chosen GC-rich decamer primers. Using cesium chloride purified genomic template DNA, highly reproducible polymorphic fingerprints were generated by all 10 primers, resulting in a total of 375 informative characters. Only eight bands were monomorphic among all investigated accessions. A binary character matrix was generated by scoring for presence/absence of a band at a particular position, transformed into a matrix of pairwise distances using either the Jaccard or a simple matching coefficient, and analyzed by neighbour joining, UPGMA (unweighted pair group method with arithmetic averaging) cluster analysis, or split decomposition. All methods of data evaluation resulted in similar groupings that reflected the geographical origin of the samples. The African accessions formed a distinct isolated group, whereas Asian and Polynesian accessions proved to be more heterogeneous. With two exceptions (var. suavior and var. sativa), the RAPD data supported previous varietal classification based on morphological characters. Stepwise reduction of the number of evaluated characters did not affect branching patterns of the trees above a minimum threshold of 150. Key words : Dioscorea bulbifera, random amplified polymorphic DNA (RAPD), genetic variation, genetic relatedness.     

重离子辐照玉米种子引起的基因组DNA变异分析

利用HI-13串列加速器产生的10 Gy、20 Gy、30 Gy和50 Gy ~7Li和~(12)C重离子束对玉米自交系478的干种子进行辐照,并用RAPD分析技术分析其变异情况.结果表明重离子~7Li和~(12)C辐照玉米种子可引起当代基因组DNA水平上的变异,一定范围内变异频率与注入剂量有关,在相同剂量下~7Li离子辐照的诱变率高于~(12)C离子辐照.