Identification and mapping of expressed genes, simple sequence repeats and transposable elements in centromeric regions of rice chromosomes.

The genomic sequences derived from rice centromeric regions were analyzed to facilitate the comprehensive understanding of the rice genome. A rice centromere-specific satellite sequence, RCS2/TrsD/CentO, was used to screen P1-derived artificial chromosome (PAC) and bacterial artificial chromosome (BAC) genomic libraries derived from Oryza sativa L. ssp. japonica cultivar Nipponbare. Physical maps of the centromeric regions were constructed by DNA fingerprinting methods and the aligned clones were analyzed by end sequencing. BLAST analysis revealed the composition of genes, centromeric satellites and other repetitive elements, such as RIRE7/CRR, RIRE8, Squiq, Anaconda, CACTA and miniature inverted-repeat transposable elements. Fiber-fluorescent in situ hybridization analysis also indicated the presence of distinct clusters of RCS2/TrsD/CentO satellite interspersed with other elements, instead of a long homogeneous region. Several expressed genes, sequences representative of ancestral organellar insertions, relatively long simple sequence repeats (SSRs), and sequences corresponding to 5S and 45S ribosomal RNA genes were also identified. Thirty-one gene sequences showed high-similarity to rice full-length cDNA sequences that had not been matched to the published rice genome sequence in silico. These results suggest the presence of expressed genes within and around the clusters of RCS2/TrsD/CentO satellites in unsequenced centromeric regions of the rice chromosomes.     

High content,size and distribution of single-stranded DNA in the mitochondria of Chenopodium album (L.)

Mitochondrial (mt) DNA of higher plants is unique in its large size and complexity. We report here a hitherto unknownfeature, the presence of large quantities of single-stranded (ss) DNA. About 2.0-8.5% of the chromosomal mtDNA from a suspension culture (depending on the growth stage) and 6.5% of the chromosomal mtDNA from whole plants of Chenopodium album were found to be in ss form by dot-blot hybridization after neutral transfer. Similar amounts of ss mtDNA were observed by binding of the single-strand binding (SSB) protein of Escherichia coli under the electron microscope. Significantly less ssDNA was found in plastids of C. album and in E. coli cells. We observed ss regions between 100 and 22 800 bases distributed in the mt genome spaced from 0.5-100 kb apart. After pulsed-field gel electrophoresis (PFGE), the well-bound fraction of mtDNA (found to consist of circular, sigma-shaped and rosette-like molecules), contained the major part of ssDNA as opposed to the migrating linear molecules. Digestion of mtDNA by ss-specific nucleases followed by PFGE mobilized all well-bound DNA and correspondingly increased the quantity of migrating linear DNA molecules. The implications of ssDNA for the structural organization on plant mt genomes are discussed.     

Metaphase I-bound arms frequency and genome analysis in wheat-Aegilops hybrids. 3. Similar relationships between the B genome of wheat and S or S l genomes of Ae. speltoides,Ae. longissima and Ae. sharonensis

The meiotic behaviour of Triticum aestivum × Aegilops speltoides, T. aestivum × Ae. sharonensis and T. aestivum × Ae. longissima tetraploid hybrids (genome constitution ABDS, ABDS ^l , and ABDS ^l , respectively) has been analysed by the C-banding technique. Of the six types of pairing normally occurring, at metaphase I three were recognized: A-D, AD-BS/AD-BS ^l and B-S/B-S ^l . The relative order observed in the low pairing hybrid, A-D> B-S ^l >AD-BS ^l , as well as that found in high-pairing Chinese Spring × Ae. speltoides hybrids, A-D>AD-BS>ß-S, revealed the existence of preferential pairing patterns among the different genomes that are in competition. In all of the hybrids analysed the mean number of bound arms per cell for the A-D type was significantly higher than the mean number of associations between the B and S/S ^l genomes. Usually the relative contribution of each type of pairing is maintained among hybrids with different Aegilops species. These results indicate that the genomes of Ae. speltoides, Ae. sharonensis and Ae. longissima show a similar affinity with the genomes of hexaploid wheat; therefore none of these species can be considered to be a distinct donor of the B genome of wheats.     

Effects of water-deficit stress and paclobutrazol on growth,relative water content,electrolyte leakage,proline content and some antioxidant changes in Curcuma alismatifolia Gagnep. cv. Chiang Mai Pink

Effects of water-deficit stress and paclobutrazol (PBZ) on the physiological and biochemical changes in Curcuma alismatifolia Gagnep. cv. Chiang Mai Pink (Zingiberaceae) were investigated. One hundred rhizomes were grown for 30–35 days and then divided into the following 4 treatments: (1) well-watered, (2) not watered, (3) well-watered and treated with 1500 ppm PBZ being applied once to the soil, and (4) not watered but treated with 1500 ppm PBZ. After 50 days of growth, watering was withheld for 30 days. After water stress was initiated, plant height, plant fresh weight, soil water content, relative water content (RWC), electrolyte leakage (EL), proline content, vitamin C and E content, as well as the activities of catalase (CAT) and superoxide dismutase (SOD) in the leaves were determined every 10 days. The results showed that water-deficit stress decreased plant height and plant fresh weight, whereas this stress and PBZ did not result in a decrease in these parameters. Water stress reduced RWC, but induced EL and proline content in the leaves. However, the leaves showed opposite results when PBZ was added to the treatments. Some antioxidants such as vitamin C, vitamin E, and the activities of CAT and SOD were induced in the leaves by PBZ. Moreover, the content of vitamin C, vitamin E and CAT activity were higher in relation to water-deficit stress and PBZ treatments. This indicates that PBZ induced a number of some physiological and biochemical adaptations (maintaining growth and RWC, decreasing EL and proline content, increasing the vitamin C and vitamin E levels, and CAT and SOD activities) that enable the Curcuma plant to tolerate drought.     

Establishing genomic tools and resources for Guizotia abyssinica (L.f.) Cass.-the development of a library of expressed sequence tags, microsatellite loci, and the sequencing of its chloroplast genome

We present an EST library, chloroplast genome sequence, and nuclear microsatellite markers that were developed for the semi-domesticated oilseed crop noug (Guizotia abyssinica) from Ethiopia. The EST library consists of 25 711 Sanger reads, assembled into 17 538 contigs and singletons, of which 4781 were functionally annotated using the Arabidopsis Information Resource (TAIR). The age distribution of duplicated genes in the EST library shows evidence of two paleopolyploidizations—a pattern that noug shares with several other species in the Heliantheae tribe (Compositae family). From the EST library, we selected 43 microsatellites and then designed and tested primers for their amplification. The number of microsatellite alleles varied between 2 and 10 (average 4.67), and the average observed and expected heterozygosities were 0.49 and 0.54, respectively. The chloroplast genome was sequenced de novo using Illumina’s sequencing technology and completed with traditional Sanger sequencing. No large re-arrangements were found between the noug and sunflower chloroplast genomes, but 1.4% of sites have indels and 1.8% show sequence divergence between the two species. We identified 34 tRNAs, 4 rRNA sequences, and 80 coding sequences, including one region (trnH-psbA) with 15% sequence divergence between noug and sunflower that may be particularly useful for phylogeographic studies in noug and its wild relatives.     

DNA sequence of the control region of phage D108: the N-terminal amino acid sequences of repressor and transposase are similar both in phage D108 and in its relative, phage Mu.

We have determined the DNA sequence of the control region of phage D108 up to position 1419 at the left end of the phage genome. Open reading frames for the repressor gene, ner gene, and the 5' part of the A gene (which codes for transposase) are found in the sequence. The genetic organization of this region of phage D108 is quite similar to that of phage Mu in spite of considerable divergence, both in the nucleotide sequence and in the amino acid sequences of the regulatory proteins of the two phages. The N-terminal amino acid sequences of the transposases of the two phages also share only limited homology. On the other hand, a significant amino acid sequence homology was found within each phage between the N-terminal parts of the repressor and transposase. We propose that the N-terminal domains of the repressor and transposase of each phage interact functionally in the process of making the decision between the lytic and the lysogenic mode of growth.     

The linkage disequilibrium between chloroplast DNA and mitochondrial DNA haplotypes in Beta vulgaris ssp. maritima (L.): the usefulness of both genomes for population genetic studies

The structure and evolution of the plant mitochondrial genome may allow recurrent appearance of the same mitochondrial variants in different populations. Whether the same mitochondrial variant is distributed by migration or appears recurrently by mutation (creating homoplasy) in different populations is an important question with regard to the use of these markers for population genetic analyses. The genetic association observed between chloroplasts and mitochondria (i.e. two maternally inherited cytoplasmic genomes) may indicate whether or not homoplasy occurs in the mitochondrial genome. Four-hundred and fourteen individuals sampled in wild populations of beets from France and Spain were screened for their mitochondrial and chloroplast polymorphisms. Mitochondrial DNA (mtDNA) polymorphism was investigated with restriction fragment length polymorphism (RFLP) and chloroplast DNA (cpDNA) polymorphism was investigated with polymerase chain reaction PCR-RFLP, using universal primers for the amplification. Twenty and 13 variants for mtDNA and cpDNA were observed, respectively. Most exhibited a widespread geographical distribution. As a very strong linkage disequilibrium was estimated between mtDNA and cpDNA haplotypes, a high rate of recurrent mutation was excluded for the mitochondrial genome of beets. Identical mitochondrial variants found in populations of different regions probably occurred as a result of migration. We concluded from this study that mtDNA is a tool as valuable as cpDNA when a maternal marker is needed for population genetics analyses in beet on a large regional scale.     

DNA content, interphase AgNOR-area, number of 3 HrDNA hybridization signals and the methylation level in coding rDNA sequence in different organs of Lupinus luteus L.

Nuclear DNA and AgNOR-area quantity have been measured cytophotometrically, the number of silver grains afterin situ³H rDNA/DNA hybridization has been counted, and the level of rDNA methylation has been estimated in root meristems, differentiated root zones, hypocotyls, cotyledons, and leaves of 7-day-old seedlings ofLupinus luteus. DNA content increases by endoreplication, reaching the average DNA C-value of 4.2 in the meristem, 6.6C in hypocotyl, 15.9C in cotyledon, and 3.3C in leaf. The quantity of AgNOR-area, the highest in root meristem, does not follow DNA C-value. Number of grains afterin situ³H rDNA/DNA hybridization corresponds to DNA amount, but their distribution differs, showing in many cases perinucleolar localization in organs displaying low AgNOR-area quantity. Southern hybridization has not demonstrated detectable changes in level rDNA methylation. We suggest that the low level of rDNA expression in non-meristematic tissues could be related to rDNA inactivation caused by its translocation into nucleolus-associated heterochromatin.     

Unexpected DNA content in the endosperm of Cupressus dupreziana A. Camus seeds and its implications in the reproductive process

 Nuclear DNA content of embryo and endosperm from mature and immature Cupressus dupreziana A. Camus seeds was estimated using laser flow cytometry. Relative DNA content of endosperm nuclei corresponded to four ploidy levels: 2C, 4C, 6C and 8C. The embryo nuclei invariably exhibited a diploid pattern. In all endosperm tissue analyzed no haploid nucleus was found. This is problematic since, in gymnosperms, endosperm and female gametes originate from one functional haploid megaspore produced by meiosis. The possible origin and derivation of C. dupreziana endosperm are discussed in light of previous results concerning the two other Mediterranean cypresses, C. sempervirens and C. atlantica. Received: 15 January 1998 / Revision accepted: 27 March 1998     

Evaluation of ergosterol and its esters in the pileus,gill, and stipe tissues of agaric fungi and their relative changes in the comminuted fungal tissues

A gradient reversed-phase high-performance liquid chromatography (HPLC) method was developed for the rapid determination of free ergosterol, ergosteryl esters, and ergocalciferol. The HPLC method was used to evaluate the distribution of ergosterol and ergosteryl esters in the different parts (stipe, pileus, and gills) of the agaric fungi, Agrocybe aegerita, Termitomyces albuminosus, and Lentinus edodes, and the relative changes of free and esterified ergosterols during the degradation of ergosterol in the comminuted fungal tissues. The results showed that total ergosterol levels and the relative abundances of free to esterified ergosterols were different among the various species and in the different parts of these agaric fungi. The results also indicated that ergosteryl esters were more stable than free ergosterol. While the content of free ergosterol markedly decreased, substantial amounts of ergosteryl esters remained for a long period, and even an increase in the contents of ergosteryl esters was also found in some comminuted fungal tissues. Therefore, it is possible that free ergosterol in the cell membrane of the dead fungal hyphae undergoes degradation or esterification, by which excess free ergosterol may be removed, and stored in cytosolic lipid particles. It is suggested that free ergosterol (not total ergosterol) should be used as a biomarker for fungal biomass.     

Mitogen-stimulated events in nuclei of Swiss 3T3 cells. Evidence for a direct link between changes of inositol lipids, protein kinase C requirement and the onset of DNA synthesis.

Two different clones of Swiss 3T3 cells belonging to the same original cell line have been obtained, one of which was unresponsive to mitogenic stimulation (e.g. insulin-like growth factor-I, bombesin, insulin-like growth factor-I + bombesin), while the other clone showed a very high rate of DNA synthesis under identical conditions as demonstrated by 5-bromodeoxyuridine incorporation. Both types of cells expressed the IGF-I receptor and showed high contact inhibition. When highly purified nuclei from responsive cells, treated for a short time with bombesin and insulin-like growth factor-I or insulin-like growth factor-I alone, were incubated with [gamma-32P]adenosine triphosphate, the labelling of phosphatidylinositol-mono- and diphosphate decreased when compared to controls, while this transient effect did not appear in the nuclei from unresponsive cells. Similarly nuclear protein kinase C is activated only in responsive cells. Therefore, it seems that a direct link exists between polyphosphoinositide metabolism, protein kinase C activation and the early events leading to cell division, since the rapid changes in the labelling of both phosphatidylinositol mono- and di-phosphate occur only in nuclei from Swiss 3T3 cells, which respond to the mitogenic stimulus determined by insulin-like growth factor-I on its own, or in combination with bombesin.     

The complete DNA sequence of the mitochondrial genome of the self-fertilizing fish Rivulus marmoratus (Cyprinodontiformes, Rivulidae) and the first description of duplication of a control region in fish

We isolated Rivulus marmoratus mitochondrial DNA by long-polymerase chain reaction with conserved primers, and sequenced it with 36 sets of internal conserved primers, which were designed from the extensive sequence similarities of mitochondrial DNA from several fish species. The R. marmoratus mitochondrial DNA has 17,329 bp with a conserved structural organization compared to those of other fish. Rivulus marmoratus mitochondrial DNA also has two nearly identical control regions. The basic characteristics of the R. marmoratus mitochondrial genome are discussed.     

Purification, cloning and sequence analysis of RsrI DNA methyltransferase: lack of homology between two enzymes, RsrI and EcoRI, that methylate the same nucleotide in identical recognition sequences.

RsrI DNA methyltransferase (M-RsrI) from Rhodobacter sphaeroides has been purified to homogeneity, and its gene cloned and sequenced. This enzyme catalyzes methylation of the same central adenine residue in the duplex recognition sequence d(GAATTC) as does M-EcoRI. The reduced and denatured molecular weight of the RsrI methyltransferase (MTase) is 33,600 Da. A fragment of R. sphaeroides chromosomal DNA exhibited M.RsrI activity in E. coli and was used to sequence the rsrIM gene. The deduced amino acid sequence of M.RsrI shows partial homology to those of the type II adenine MTases HinfI and DpnA and N4-cytosine MTases BamHI and PvuII, and to the type III adenine MTases EcoP1 and EcoP15. In contrast to their corresponding isoschizomeric endonucleases, the deduced amino acid sequences of the RsrI and EcoRI MTases show very little homology. Either the EcoRI and RsrI restriction-modification systems assembled independently from closely related endonuclease and more distantly related MTase genes, or the MTase genes diverged more than their partner endonuclease genes. The rsrIM gene sequence has also been determined by Stephenson and Greene (Nucl. Acids Res. (1989) 17, this issue).     

Construction and analysis of a BAC library in the grass<Emphasis Type="Italic"> Brachypodium sylvaticum</Emphasis>: its use as a tool to bridge the gap between rice and wheat in elucidating gene content

A BAC library of 30,228 clones with an average insert size of 102 kb was constructed in the grass Brachypodium sylvaticum. Brachypodium has a simple genome, similar in size and repetitive DNA content to that of rice, and is more closely related than rice both to the major temperate cereals wheat and barley, and to the forage grasses. The library represents 6.6 genome equivalents, implying a 99.9% probability of recovering any specific sequence. The library was arrayed onto two high-density colony filters, which were screened with heterologous DNA probes from rice chromosome nine and from syntenous regions of wheat, barley, maize and oat. The construction of Brachypodium BAC contigs revealed that synteny between rice, wheat and Brachypodium was largely maintained over several regions of rice chromosome nine. This suggests that Brachypodium will be a useful tool in the elucidation of gene content in agronomically important cereal crops, complementing rice as a grass genome model.     

Study of the stimulating action of sturin, its fractions, and the internal protein of T2 phage in transfection of E. coli spheroplasts by Lambda phage DNA

The stimulating action of sturin and its fractions in the transfection of E. coli spheroplasts with DNA of phage lambda has been shown, and the optimum conditions for the infection of sturin-treated spheroplasts with phage DNa have been established. The biological effect was most pronounced in arginine-enriched low-molecular sturin fraction B. The treatment of spheroplasts with the internal protein of phage T2 did not stimulate transfection. These findings suggest that the specificity of the stimulating action of protamine depends on the peculiarities of its amino acid composition, viz. a high content of arginine which is present in protein molecules in the form of blocks made up of 2-6 amino acid residues.