DNA sequence organization in finger millet (Eleusine coracana)

Approximately 39 to 49% of the genome of finger millet consists of repetitive DNA sequences which intersperse with 18% of single copy DNA sequences of 1900 nucleotide pairs. Agarose gel filtration and electrophoresis experiments have yielded the sizes of interspersed repeated sequences as 4000–4200 nucleotide pairs and 150–200 nucleotide pairs. Approximately 20% of the repeated DNA sequences (4000–4200 nucleotide pairs) are involved in long range interspersion pattern, while 60% of the repeated DNA sequences (150–200 nucleotide pairs) are involved in short period interspersion pattern. Based on the data available in literature and the results described here on DNA sequence organization in plants, it is proposed that plants with haploid DNA content of more than 2.5 pg exhibit mostly the short period interspersion pattern, while those with haploid DNA content of less than 2.5 pg show diverse patterns of genome organization. NCL Communication No.: 2708     

DNA sequence organization in the soybean plant

The arrangement of repetitive and nonrepetitive DNA sequences in the soybean genome was ascertained by a comparison of the reassociation kinetics of short (250 nucleotides) and long (2700 nucleotides) DNA fragments, the size distribution of S-1 nuclease resistant repetitive duplexes, and a direct assay of the spectrum of DNA sequences present on long DNA fragments enriched in repetitive DNA. These measurements reveal the following: (1) The 1N genome size of the soybean plant is 1.97 pg. (2) Approximately 40% of the soybean genome consists of nonrepetitive or single-copy DNA sequences, while 60% is repetitive DNA. (3) The repetitive DNA is partitioned into three discrete classes termed very fast, fast, and slow, containing DNA sequences repeated an average of 290,000, 2800, and 19 times each. (4) Approximately 35–50% of the soybean genome is arranged in a short-period interspersion pattern of 250 nucleotide slow sequences and single-copy DNA averaging up to 2700 nucleotides in length. (5) From 30% to 45% of the soybean genome is organized into long stretches of repetitive DNA at least 1500 nucleotides in length. (6) Minimal interspersion of repetitive sequence classes occurs in soybean DNA.These experiments were supported by NSF Grants BMS74-21461 and PCM76-24593 and were conducted while the author was in the Department of Biology, Wayne State University, Detroit, Michigan.     

Molecular organization of great millet (Sorghum vulgare) DNA

Approximately 52% of the nuclear genome of great millet(Sorghum vulgare) consists of repetitive DNA which can be grouped into very fast, fast and slow components. The reiteration frequencies of the fast and slow reassociating components are {dy7000} and 92 respectively. Approximately 90% of the genome consists of repeated sequences interspersed amongst themselves and with single copy sequences. The interspersed repeat sequences are of three sizesviz. > 1·5 kilobase pairs, 0·5–1·0 kilobase pairs and 0·15–0·30 kilobase pairs while the size of the single copy sequences is 3·0 kilobase pairs. Hence the genome organization of great millet is essentially of a mixed type NCL communication No. 3527.     

DNA sequence organization in the genomes of five marine invertebrates

The arrangement of repetitive and non-repetitive sequence was studied in the genomic DNA of the oyster (Crassostrea virginica), the surf clam (Spisula solidissima), the horseshoe crab (Limulus polyphemus), a nemertean worm (Cerebratulus lacteus) and a jelly-fish (Aurelia aurita). Except for the jellyfish these animals belong to the protostomial branch of animal evolution, for which little information regarding DNA sequence organization has previously been available. The reassociation kinetics of short (250-300 nucleotide) and long (2,000-3,000 nucleotide) DNA fragments was studied by the hydroxyapatite method. It was shown that in each case a major fraction of the DNA consists of single copy sequences less than about 3,000 nucleotides in length, interspersed with short repetitive sequences. The lengths of the repetitive sequences were estimated by optical hyperchromicity and S1 nuclease measurements made on renaturation products. All the genomes studied include a prominent fraction of interspersed repetitive sequences about 300 nucleotides in length, as well as longer repetitive sequence regions.     

Comparison of the sequence organization of related retrovirus-like multigene families in three evolutionarily distant rodent genomes.

Sequences related to mouse intracisternal A-particle (IAP) genes have been isolated from rat and Syrian hamster gene libraries as recombinants in lambda phage. The sequences are moderately reiterated in both these genomes but their sequence organization in the hamster genome is different from that in the rat genome. Restriction analysis and electron microscopy indicate that the Syrian hamster IAP sequences represent a family of relatively homogeneous well-conserved units; in this, they resemble the mouse IAP genes. The rat sequences, in contrast, are heterogeneous. Both the hamster and rat IAP sequences contain regions homologous to mouse IAP genes interspersed with regions of apparent non-homology. The interspersed regions range in size from 0.5-1.0 kilobases (Kb). The regions of homology among the mouse, rat and Syrian hamster IAP sequences have been mapped to a 5-6 Kb internal region on the mouse IAP genes. Mouse IAP long terminal repeat (LTR) sequences were not detected in the rat and Syrian hamster genomes. We used the thermal stability of hybrids between cloned and genomic IAP sequences to measure family homogeneity. Mouse and Syrian hamster IAP sequences are homogeneous by this criterion, but the rat IAP sequences are heterogeneous with a Tm 6 degrees C below the self-hybrid. The contrasting organization of IAP-related elements in the genomes of these rodents indicates that amplification or homogenization of this sequence family has occurred independently and at different periods of time during their evolution.     

Mitochondrial DNA variation in pearl millet and related species

Summary Mitochondrial DNA (mtDNA) restriction endonuclease fragment patterns and patterns of mtDNA hybridized by mitochondrial gene probes were used to study phylogenetic relationships of seven Pennisetum species, including five P. americanum (pearl millet) ecotypes and a reference species from the distantly related genus, Panicum. The restriction patterns of the pearl millet ecotypes were uniform with the exception of the ecotype collected in Ethiopia. The probe hybridization method revealed more variability, with both the Rhodesian and Ethiopian ecotypes differing from the others and from each other. Considerable restriction pattern polymorphism was noted among different species of Pennisetum, and Panicum. Significant relationships were noted of Pennisetum polystachyon to P. pedicellatum and of P. purpureum to P. squamulatum using the restriction pattern method. In addition to those relationships, the hybridization method showed relationships of pearl millet to P. purpureum and to P. squamulatum. The relationships noted between species by the hybridization method agreed more closely to the cytological data than those indicated by the restriction pattern method. Therefore, the hybridization method appeared to be the preferred method for studying species relationships. The mitochondrial genome size of pearl millet was calculated to be 407 kb and the mitochondrial genome sizes of other Pennisetum species ranged from 341 to 486 kb.Florida Agricultural Experiment Station Journal Series No. 8485.     

Chloroplast DNA variation in pearl millet and related species

The evolution of specific regions of the chloroplast genome was studied in five grass species in the genus Pennisetum, including pearl millet, and one species from a related genus (Cenchrus). Three different regions of the chloroplast DNA were investigated. The first region included a 12-kilobase pair (kbp) EcoRI fragment containing the 23S, 16S and 5S ribosomal RNA genes, which is part of a larger duplicated region of reverse orientation. The second region was contained in a 21-kbp Sa/I fragment, which spans the short single-copy sequence separating the two reverse repeat structures and which overlaps the duplicated copies of the 12-kbp Eco RI fragment. The third region was a 6-kbp EcoRI fragment located in the large single-copy region of the chloroplast genome. Together these regions account for slightly less than 25% of the chloroplast genome. Each of these DNA fragments was cloned and used as hybridization probes to determine the distribution of homologous DNA fragments generated by various restriction endonuclease digests.—A survey of 12 geographically diverse collections of pearl millet showed no indication of chloroplast DNA sequence polymorphism, despite moderate levels of nuclear-encoded enzyme polymorphism. Interspecific and intergeneric differences were found for restriction endonuclease sites in both the small and the large single-copy regions of the chloroplast genome. The reverse repeat structure showed identical restriction site distributions in all materials surveyed. These results suggest that the reverse repeat region is differentially conserved during the evolution of the chloroplast genome.     

PCR-RFLP and total DNA homology revealed three related genomic species among broad-host-range Frankia strains

Abstract: Restriction fragment length polymorphism (RFLP) analysis of the PCR amplified nif D-K intergenic spacer (IGS) region was used to cluster 22 Frankia strains of the Elaeagnus host specificity group into seven genomic groups and to measure the degree of genetic similarity among them. This PCR-RFLP analysis could assign freshly isolated strains to described genomic species and revealed genomic groups not yet described among Frankia strains of the Elaeagnus specificity group. Six broad-host-range Frankia strains, infective on both Alnus and Elaeagnus , fell into three closely related PCR-RFLP clusters. DNA-DNA hybridization was then used to establish the correlations between PCR-RFLP clusters and total DNA relatedness groups. The three PCR-RFLP clusters agreed with two new and one reference genomic species, indicating that Frankia ability to nodulate with Alnus and Elaeagnus is a monophyletic trait shared by three genomic species.     

Somatic embryogenesis and DNA organization of genomes from selected Daucus species

Under identical culture conditions, only 8 out of 12 species and subspecies of the genus Daucus proved capable of somatic embryogenesis. Random amplified polymorphic DNA analysis indicated a polymorphism between the genomes of individual species that were capable of embryogenesis and those that were not. Two specific bands (1.1 kbp, 0.68 kbp) were detected only in the genomes of individuals with the capacity for embryogenesis. These were cloned and sequenced, and the homology of the nucleotide sequences of the various species was detected: this ranged from 74% to 92% for the larger sequence and from 92% to 97% for the smaller one. These DNA sequences would appear to be useful as a marker of the capacity for somatic embryogenesis in the genus Daucus.     

Evolutionary sequence divergence within repeated DNA families of higher plant genomes

The higher proportion of repeated DNA sequences in the garden pea (Pisum sativum) than in the mung bean (Vigna radiata), as well as other differences between these legume genomes, are consistent with a higher rate of sequence amplification in the former. This hypothesis leads to a prediction that repeated sequence families inPisum are mostly heterogeneous, as defined by Bendich and Anderson (1977), whileVigna families are homogeneous. An assay developed by these authors to distinguish between the two types of families, by comparison of reassociation rates at different temperatures, was utilized. The results forVigna defied the predictions of the assay for either homogeneous or hetereogeneous model. Evaluation of the kinetic data in light of the great diversity of repeated family copy numbers in both genomes enabled an interpretation of the results as consistent with hetereogenous families inPisum and homogeneous families inVigna. These tentative conclusions were supported by the results of a thermal denaturation (melting) assay described in the accompanying paper.Abbreviations used C_ot the product of molar concentration of DNA nucleotides and time of incubation (mol s/L) - EC_ot equivalent - C_ot the value after correction to standard reassociation conditions (120 mM sodium phosphate buffer, 60°C) - (Et)₄NCl tetraethylammonium chloride - T_m the temperature at which half of the nucleotides in solution are unpaired This paper is Carnegie Institution of Washington Department of Plant Biology Publication No. 708 and is based on a portion of a dissertation submitted by R.S.P. in partial fulfillment of the Ph.D. requirements at Stanford University     

Discrimination between closely related Triticeae species using genomic DNA as a probe

Summary Labelled total genomic DNA was used as a probe in combination with blocking DNA to discriminate between taxonomically closely related species in the genera Hordeum and Secale. Discrimination was possible both by Southern hybridization to size-fractionated restriction enzyme digests of genomic DNA and by in situ hybridization to chromosome preparations. To distinguish between two species (e.g. H. vulgare and H. bulbosum), genomic DNA from one species was used as the labelled probe, while unlabelled DNA from the other species was applied at a much higher concentration as a block. The blocking DNA presumably hybridized to sequences in common between the block and the labelled probe, and between the block and DNA sequences on the membrane or chromosomes in situ. If so, mainly species-specific sequences would remain as sites for probe hybridization. These species-specific sequences are dispersed and represent a substantial proportion of the genome (unlike many cloned, species-specific sequences). Consequently, rapid nonradioactive methods detected probe hybridization sites satisfactorily. The method was able to confirm the parentage of hybrid plants. It has potentially wide application in plant breeding for the detection of alien DNA transfer, and it can be easily adapted to many species.     

Deleterious mutation in related species of the plant genus Amsinckia with contrasting mating systems

Theory for the evolution of modifiers of the rate of mutation suggests that a lower rate of mutation may evolve after the breakdown of mechanisms that enforce outcrossing. Mutation accumulation (MA) experiments were conducted to compare deleterious mutation parameters in two closely related species of the plant genus Amsinckia, a group that exhibits wide variation in the mating system. One of the two species studied (A. douglasiana) is predominantly outcrossed in natural populations, where as the other species (A. gloriosa) is predominantly self-pollinated. Progeny assays of flower number per plant from generation 1 lines (control) and generation 11 lines (MA treatment) were conducted in both species. Dry weight measurements of progeny from the control and MA treatment in A. douglasiana also were made. Estimation of mutation parameters was conducted using maximum likelihood under the assumption of a gamma distribution of mutational effects. The two species exhibited similar rates and effects of deleterious mutation affecting flower number. Estimates of mutation rate for dry weight in A. douglasiana are close to those for flower number. Overall, the estimates of mutation parameters observed in these species are intermediate within the range reported for fitness components in other eukaryotes. The results are discussed within the context of evolutionary change in deleterious mutation accompanying mating system evolution and with respect to previous estimates of mutation parameters based on assays of inbreeding depression and the assumption of mutation-selection equilibrium.     

Plant extracts abated pathogenic Fusarium species of millet seedlings

Millet is an important crop threatened by soil-borne pathogenic fungi worldwide, but the position of these soil-borne fungi most especially Fusarium has not been evaluated in south-western Nigeria alongside their biocontrol using plant extracts. This study investigates the effects (in vitro and in vivo) of Moringa oleifera, Manihot esculenta (peels) and Senna alata at 5, 10 and 15% g/ml concentrations on Fusarium anthophilum, Fusarium verticillioides, Fusarium oxysporum and Fusarium scirpi. The in vivo experimental layout was arranged in a completely randomised design and all obtained data, both in vitro and in vivo, were statistically analysed using Minitab version 15. The extract of Moringa oleifera, Manihot esculenta (peels) and S. alata at 5, 10 and 15% g/ml concentrations showed significant (p?<?0.05) antagonistic effect in vitro and in vivo on F. anthophilum, F. verticillioides and F. oxysporum. Moringa oleifera and S. alata at 5 and 10% g/ml significantly (p?<?0.05) reduced the disease incidence and disease severity of F. scirpi on millet seedlings. Thus, Moringa oleifera appears to be the most effective extract followed by Manihot esculenta, while S. alata was the least effective plant extract. Hence, the effectiveness of plant extracts on pathogenic Fusarium of millet justified their management strategy geared towards sustainable millet growth in Nigeria.     

气候暖干化对甘肃省谷子产量的影响及对策

基于甘肃省甘州（河西温和干旱绿洲灌溉区）、安定（陇中温和半干旱旱作区）、西峰（陇东温和半湿润旱作区）气温、降水和谷子产量资料,计算出各区域谷子生育期内≥0 ℃、≥5 ℃、≥10 ℃、≥15 ℃、≥20 ℃活动积温以及生育关键期平均气温和降水量,用正交多项式拟合分离出谷子气候产量,并采用线性倾向、累积距平、Mann-Kendall法分析研究区气候和谷子气候产量的变化特征,以及气候变化对谷子产量的影响.结果表明：气候暖干化是甘肃各区域现代气候变化的主要特征,各地气温从20世纪90年代初开始呈显著上升趋势,降水从20世纪80年代后期开始显著减少;该区谷子产量与温度、降水量呈显著相关关系,旱作区谷子产量随生育关键期内气温增高、降水量增多而提高,河西走廊绿洲灌区谷子产量随气温增高而提高;气候暖干化严重影响谷子产量,西峰、安定、甘州谷子产量的气象波动指数分别占实际产量变异系数的73%、72%和54%,变暖后（1993-2008年）较变暖前（1985-1992年）所占百分率明显增大;气候变暖有利于谷子产量增加,与气候变暖前相比,气候变暖后西峰、安定、甘州谷子年均气候产量的增加量分别为30.6、43.1和121.1 kg·hm^-2.针对甘肃省未来气候继续暖干化的趋势,应进一步扩大谷子种植面积、调整谷子种植结构,同时,要根据不同气候类型区域、不同气候年型选种不同特性的品种,采取不同的种植措施.     

DNA fingerprinting detects genetic variability in the pearl millet downy mildew pathogen (Sclerospora graminicola)

Genetic variability in six host genotype-specific pathotypes of pearl millet downy mildew pathogen S. graminicola was studied at the molecular level using mini- and micro-satellites. Our results indicated that microsatellites (GAA)₆, (GACA)₄, and especially (GATA)₄ were quite informative and showed high levels of polymorphism among the pathotypes. The six pathotypes could be classified into five groups based on the cluster analysis of their genetic similarities, thereby confirming the existence of distinct host genotype-specific virulence in S. graminicola pathotypes. We demonstrate, for the first time, the use of DNA fingerprinting to detect genetic variation in downy mildew fungus of pearl millet.     

RFLP analysis of mitochondrial DNA from cytoplasmic male-sterile lines of pearl millet

Mitochondrial DNA (mtDNA) from 13 cytoplasmic male-sterile (cms) lines from diverse sources were characterized by Southern blot hybridization to pearl millet and maize mtDNA probes. Hybridization patterns of mtDNA digested with PstI, BamHI, SmaI or XhoI and probed with 13.6-, 10.9-, 9.7- or 4.7-kb pearl millet mtDNA clones revealed similarities among the cms lines 5141 A and ICMA 1 (classified as the S-A1 type of cytoplasm based on fertility restoration patterns), PMC 30A and ICMA 2. The remaining cms lines formed a distinct group, within which three subgroups were evident. Among the maize mitochondiral gene clones used, the coxI probe revealed two distinct groups of cytoplasms similar to the pearl millet mtDNA clones. The atp9 probe differentiated the cms line 81 A4, derived from P. glaucum subsp. monodii, while the coxII gene probe did not detect any polymorphism among the cms lines studied. MtDNA digested with BamHI, PstI or XhoI and hybridized to the atp6 probe revealed distinct differences among the cms lines. The maize atp6 gene clone identified four distinct cytoplasmic groups and four subgroups within a main group. The mtDNA fragments hybridized to the atp6 gene probe with differing intensities, suggesting the presence of more than one copy of the gene in different stoichiometries. Rearrangements involving the coxI and/or rrn18-rrn5 genes (mapped within the pearl millet clones) probably resulted in the S-A1 type of sterility. Rearrangements involving the atp6 gene (probably resulting in chimeric form) may be responsible for male sterility in other cms lines of pearl millet.     

海南岛维管植物物种多样性的现状

热带岛屿的植物多样性一直是全球生物多样性保护的重点和热点。海南岛地处热带北缘, 是中国的第二大岛屿, 具有丰富的植物多样性。经过近几十年的考察研究, 关于海南岛的植物物种数量出现了多个版本。本文通过文献梳理和野外考证的方法进行了全面的植物多样性调查, 以确定其维管植物种数。结果表明: 截止到2015年12月, 海南岛记录并能考证实物或标本的维管植物共有6,036种, 包括野生种4,579种(含特有植物483种和珍稀濒危植物512种)、外来逸生及归化植物163种(含外来入侵种57种)、外来引种的纯栽培植物1,294种。自1964-1977年《海南植物志》出版至今, 新增野生及引种的栽培植物所占的比例均较大, 分别占海南岛野生和栽培植物总种数的35.9%和75.9%。本文还对其中1,220种的拉丁学名进行了异名处理等的订正。     

Properties of satellite DNA of three plant species of the subtribe Citrinae

The properties of stDNA of three species of the subtribe Citrinae have been investigated. The buoyant density of the main component is 1.693 g/cm3, that of satellite component is 1.712 g/cm3 and 1.715 g/cm3. The differential melting curves of satellite components reveal two melting zones. Some of stDNAs are melted within a broad temperature range, while others--at higher temperatures as a narrow peak. The reassociation kinetics suggest that 50-54% of stDNA are a fast reassociating fraction with the length of repeating sequences of 0.8-1.1 x 10(2) base pairs. Based on the values of Tm and buoyant density the 5-methylcytosine content in stDNA was calculated and was found equal to 20-35%. Using equilibrium ultracentrifugation in the actinomycin D--CsCl density gradient the stDNAs of the subtribe Citrinae were separated into constituent components.     

Co-evolution of plant LTR-retrotransposons and their host genomes

zTransposable elements (TEs), particularly, long terminal repeat retrotransposons (LTR-RTs), are the most abundant DNA components in all plant species that have been investigated, and are largely responsible for plant genome size variation. Although plant genomes have experienced periodic proliferation and/or recent burst of LTRretrotransposons, the majority of LTR-RTs are inactivated by DNA methylation and small RNA-mediated silencing mechanisms, and/or were deleted/truncated by unequal homologous recombination and illegitimate recombination, as suppression mechanisms that counteract genome expansion caused by LTR-RT amplification. LTR-RT DNA is generally enriched in pericentromeric regions of the host genomes, which appears to be the outcomes of preferential insertions of LTR-RTs in these regions and low effectiveness of selection that purges LTR-RT DNA from these regions relative to chromosomal arms. Potential functions of various TEs in their host genomes remain blurry; nevertheless, LTR-RTs have been recognized to play important roles in maintaining chromatin structures and centromere functions and regulation of gene expressions in their host genomes.