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1.
Yan HH Mudge J Kim DJ Larsen D Shoemaker RC Cook DR Young ND 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2003,106(7):1256-1265
A growing body of research indicates that microsynteny is common among dicot genomes. However, most studies focus on just one or a few genomic regions, so the extent of microsynteny across entire genomes remains poorly characterized. To estimate the level of microsynteny between Medicago truncatula (Mt) and Glycine max (soybean), and also among homoeologous segments of soybean, we used a hybridization strategy involving bacterial artificial chromosome (BAC) contigs. A Mt BAC library consisting of 30,720 clones was screened with a total of 187 soybean BAC subclones and restriction fragment length polymorphism (RFLP) probes. These probes came from 50 soybean contig groups, defined as one or more related BAC contigs anchored by the same low-copy probe. In addition, 92 whole soybean BAC clones were hybridized to filters of HindIII-digested Mt BAC DNA to identify additional cases of cross-hybridization after removal of those soybean BACs found to be repetitive in Mt. Microsynteny was inferred when at least two low-copy probes from a single soybean contig hybridized to the same Mt BAC or when a soybean BAC clone hybridized to three or more low-copy fragments from a single Mt BAC. Of the 50 soybean contig groups examined, 54% showed microsynteny to Mt. The degree of conservation among 37 groups of soybean contigs was also investigated. The results indicated substantial conservation among soybean contigs in the same group, with 86.5% of the groups showing at least some level of microsynteny. One contig group was examined in detail by a combination of physical mapping and comparative sequencing of homoeologous segments. A TBLASTX similarity search was performed between 1,085 soybean sequences on the 50 BAC contig groups and the entire Arabidopsis genome. Based on a criterion of sequence homologues <100 kb apart, each with an expected value of < or =1e-07, seven of the 50 soybean contig groups (14%) exhibited microsynteny with Arabidopsis. 相似文献
2.
K. E. Lee D. S. Lee G. S. Do E. Park S. G. Kang 《Russian Journal of Plant Physiology》2018,65(2):197-202
The dim1+ gene family is essential for G2/M transition during mitosis and encodes a small nuclear ribonucleoprotein that functions in the mRNA splicing machinery of eukaryotes. However, the plant homolog of DIM1 gene has not been defined yet. Here, we identified a gene named GmDim1 positioned on chromosome 9 of soybean (Glycine max (L.) Merr.) with 80% homology to other eukaryotic dim1+ family genes. A domain of soybean DIM1 protein was primarily conserved with U5 snRNP protein family and secondarily aligned with mitotic DIM1 protein family. The GmDim1 gene was expressed constitutively in all soybean organs. The transgenic Arabidopsis thaliana (L.) plants overexpressing GmDim1 showed early flowering and stem elongation, produced multiple shoots and continued flowering after the post-flowering stage. DIM1 proteins transiently expressed in onion cells were localized in the nucleus with dense deposition in the nucleolus. Therefore, we propose that the soybean GmDim1 gene is a component of plant U5 snRNP involved in mRNA splicing and normal progress of plant growth. 相似文献
3.
Urease (EC 3.5.1.5) is a nickel-dependent metalloenzyme catalyzing the hydrolysis of urea into ammonia and carbon dioxide. It is present in many bacteria, fungi, yeasts and plants. Most species, with few exceptions, use nickel metalloenzyme urease to hydrolyze urea, which is one of the commonly used nitrogen fertilizer in plant growth thus its enzymatic hydrolysis possesses vital importance in agricultural practices. Considering the essentiality and importance of urea and urease activity in most plants, this study aimed to comparatively investigate the ureases of two important legume species such as Glycine max (soybean) and Medicago truncatula (barrel medic) from Fabaceae family. With additional plant species, primary and secondary structures of 37 plant ureases were comparatively analyzed using various bioinformatics tools. A structure based phylogeny was constructed using predicted 3D models of G. max and M. truncatula, whose crystallographic structures are not available, along with three additional solved urease structures from Canavalia ensiformis (PDB: 4GY7), Bacillus pasteurii (PDB: 4UBP) and Klebsiella aerogenes (PDB: 1FWJ). In addition, urease structures of these species were docked with urea to analyze the binding affinities, interacting amino acids and atom distances in urease-urea complexes. Furthermore, mutable amino acids which could potentially affect the protein active site, stability and flexibility as well as overall protein stability were analyzed in urease structures of G. max and M. truncatula. Plant ureases demonstrated similar physico-chemical properties with 833–878 amino acid residues and 89.39–90.91 kDa molecular weight with mainly acidic (5.15–6.10 pI) nature. Four protein domain structures such as urease gamma, urease beta, urease alpha and amidohydro 1 characterized the plant ureases. Secondary structure of plant ureases also demonstrated conserved protein architecture, with predominantly α-helix and random coil structures. In structure-based phylogeny, plant ureases from G. max, M. truncatula and C. ensiformis were clearly diverged from bacterial ureases of B. pasteurii and K. aerogenes. Glu, Thr, His and Gly were commonly found as interacting residues in most urease-urea docking complexes while Glu was available in all docked structures. Besides, Ala and Arg residues, which are reported in active-site architecture of plant and bacterial ureases were present in G. max urea-urease complex but not present in others. Moreover, Arg435 and Arg437 in M. truncatula and G. max, respectively were identified as highly mutable hotspot residues residing in amidohydro 1 domain of enzyme. In addition, a number of stabilizing residues were predicted upon mutation of these hotspot residues however Cys and Thr made strong implications since they were also found in codon-aligned sequences as substitutions of hotspot residues. Comparative analyses of primary sequence and secondary structure in 37 different plants demonstrated quite conserved natures of ureases in plant kingdom. Structure-based phylogeny indicated the presence of a possible prokaryote-eukaryote split and implicated the subjection of bacterial ureases to heavy selection in prokaryotic evolution compared to plants. Urea-urease docking complexes suggested that different species could share common interacting residues as well as may have some other uncommon residues at species-dependent way. In silico mutation analyses identified mutable amino acids, which were predicted to reside in catalytic site of enzyme therefore mutagenesis at these sites seemed to have adverse effects on enzyme efficiency or function. This study findings will become valuable preliminary resource for future studies to further understand the primary, secondary and tertiary structures of urease sequences in plants as well as it will provide insights about various binding features of urea-urease complexes. 相似文献
4.
Yanbo Cheng Qibin Ma Hailong Ren Qiuju Xia Enliang Song Zhiyuan Tan Shuxian Li Gengyun Zhang Hai Nian 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2017,130(5):1041-1051
Key message
Using a combination of phenotypic screening, genetic and statistical analyses, and high-throughput genome-wide sequencing, we have finely mapped a dominant Phytophthora resistance gene in soybean cultivar Wayao.Abstract
Phytophthora root rot (PRR) caused by Phytophthora sojae is one of the most important soil-borne diseases in many soybean-production regions in the world. Identification of resistant gene(s) and incorporating them into elite varieties are an effective way for breeding to prevent soybean from being harmed by this disease. Two soybean populations of 191 F2 individuals and 196 F7:8 recombinant inbred lines (RILs) were developed to map Rps gene by crossing a susceptible cultivar Huachun 2 with the resistant cultivar Wayao. Genetic analysis of the F2 population indicated that PRR resistance in Wayao was controlled by a single dominant gene, temporarily named RpsWY, which was mapped on chromosome 3. A high-density genetic linkage bin map was constructed using 3469 recombination bins of the RILs to explore the candidate genes by the high-throughput genome-wide sequencing. The results of genotypic analysis showed that the RpsWY gene was located in bin 401 between 4466230 and 4502773 bp on chromosome 3 through line 71 and 100 of the RILs. Four predicted genes (Glyma03g04350, Glyma03g04360, Glyma03g04370, and Glyma03g04380) were found at the narrowed region of 36.5 kb in bin 401. These results suggest that the high-throughput genome-wide resequencing is an effective method to fine map PRR candidate genes.5.
Two repeated DNA sequences isolated from a partial genomic DNA library of Helianthus annuus, p HaS13 and p HaS211, were shown to represent portions of the int gene of a Ty3 /gypsy retroelement and of the RNase-Hgene of a Ty1 /copia retroelement, respectively. Southern blotting patterns obtained by hybridizing the two probes to BglII- or DraI-digested genomic DNA from different Helianthus species showed p HaS13 and p HaS211 were parts of dispersed repeats at least 8 and 7 kb in length, respectively, that were conserved in all species studied. Comparable hybridization patterns were obtained in all species with p HaS13. By contrast, the patterns obtained by hybridizing p HaS211 clearly differentiated annual species from perennials. The frequencies of p HaS13- and p HaS211-related sequences in different species were 4.3x10(4)-1.3x10(5) copies and 9.9x10(2)-8.1x10(3) copies per picogram of DNA, respectively. The frequency of p HaS13-related sequences varied widely within annual species, while no significant difference was observed among perennial species. Conversely, the frequency variation of p HaS211-related sequences was as large within annual species as within perennials. Sequences of both families were found to be dispersed along the length of all chromosomes in all species studied. However, Ty3 /gypsy-like sequences were localized preferentially at the centromeric regions, whereas Ty1/ copia-like sequences were less represented or absent around the centromeres and plentiful at the chromosome ends. These findings suggest that the two sequence families played a role in Helianthusgenome evolution and species divergence, evolved independently in the same genomic backgrounds and in annual or perennial species, and acquired different possible functions in the host genomes. 相似文献
6.
An efficient system of gene transformation is necessary for soybean [Glycine max (L.) Merrill] functional genomics and gene modification by using RNA interference (RNAi) technology. To establish such system, we improved the conditions of tissue culture and transformation for increasing the frequency of adventitious shoots and decreasing the browning and necrosis of hypocotyls. Adding N(6)-benzylaminopurine (BAP) and silver nitrate in culture medium enhanced the shoot formation on hypocotyls. BAP increased the frequency of the hypocotyls containing adventitious shoots, while silver nitrate increased the number of shoots on the hypocotyls. As a result, the number of adventitious shoots on hypocotyls cultured in medium containing both BAP and silver nitrate was 5-fold higher than the controls. Adding antioxidants in co-cultivation medium resulted in a significant decrease in occurrence of browning and necrosis of hypocotyls and increase in levels of beta-Glucuronidase (GUS) gene expression. Histochemical assays showed that the apical meristem of hypocotyls was the "target tissue" for Agrobacterium tumefaciens transformation of soybean. Gene silencing of functional gene by using RNAi technology was carried out under above conditions. A silencing construct containing an inverted-repeat fragment of the GmFAD2 gene was introduced into soybean by using the A. tumefaciens-mediated transformation. Several lines with high oleic acid were obtained, in which mean oleic acid content ranged from 71.5 to 81.9%. Our study demonstrates that this transgenic approach could be efficiently used to improve soybean quality and productivity through functional genomics. 相似文献
7.
To investigate the biocontrol effectiveness of the antibiotic producing bacterium, Pseudomonas aureofaciens 63–28 against the phytopathogen Rhizoctonia solani AG-4 on Petri plates and in soybean roots, growth response and induction of PR-proteins were estimated after inoculation
with P. aureofaciens 63–28 (P), with R. solani AG-4 (R), or with P. aureofaciens 63–28 + R. solani AG-4 (P + R). P. aureofaciens 63–28 showed strong antifungal activity against R. solani AG-4 pathogens in Petri plates. Treatment with P. aureofaciens 63–28 alone increased the emergence rate, shoot fresh weight, shoot dry weight and root fresh weight at 7 days after inoculation,
when compared to R. solani AG-4; P + R treatment showed similar effects. Peroxidase (POD) and β-1,3-glucanase activity of P. aureofaciens 63–28 treated roots increased by 41.1 and 49.9%, respectively, compared to control roots. POD was 26% greater in P + R treated
roots than R. solani treated roots. Two POD isozymes (59 and 27 kDa) were strongly induced in P + R treated roots. The apparent molecular weight
of chitinase from treated roots, as determined through SDS-PAGE separation and comparison with standards, was about 29 kDa.
Five β-1,3-glucanase isozymes (80, 70, 50, 46 and 19 kDa) were observed in all treatments. These results suggest that inoculation
of soybean plants with P. aureofaciens 63–28 elevates plant growth inhibition by R. solani AG-4 and activates PR-proteins, potentially through induction of systemic resistance mechanisms. 相似文献
8.
Trigonelline (TRG) is known as a compatible solute in response to stress as well as a cell cycle regulator, and is more concentrated
in legumes than other non-legume dicots. Four Glycine max L. genotypes (Essex, ExF 67, Forrest and Stressland) were used to examine TRG concentration in seeds and seedlings exposed
to 30 or 100 mM NaCl, and to determine the association of TRG concentrations in seedlings with seedling growth. Seed germination
across genotypes was inhibited by elevated salinity (71–91 %) in ExF 67 and Forrest and by accelerated aging (77–92 %) in
Forrest. Length of seedlings in most genotypes stressed with NaCl apparently decreased. The TRG content in mature seeds of
four genotypes was 44.4–74.6 μg g−1(d.m.). TRG content significantly increased during early young seedling development, but remained or significantly reduced
in some genotypes stressed with NaCl. 相似文献
9.
Hai Ping Hong Hongyi Zhang Paula Olhoft Steve Hill Hunt Wiley Effie Toren Helke Hillebrand Todd Jones Ming Cheng 《In vitro cellular & developmental biology. Plant》2007,43(6):558-568
A regeneration and transformation system has been developed using organogenic calluses derived from soybean axillary nodes
as the starting explants. Leaf-node or cotyledonary-node explants were prepared from 7 to 8-d-old seedlings. Callus was induced
on medium containing either Murashige and Skoog (MS) salts or modified Finer and Nagasawa (FNL) salts and B5 vitamins with
various concentrations of benzylamino purine (BA) and thidiazuron (TDZ). The combination of BA and TDZ had a synergistic effect
on callus induction. Shoot differentiation from the callus occurred once the callus was transferred to medium containing a
low concentration of BA. Subsequently, shoots were elongated on medium containing indole-3-acetic acid (IAA), zeatin riboside,
and gibberellic acid (GA). Plant regeneration from callus occurred 90 ∼ 120 d after the callus was cultured on shoot induction
medium. Both the primary callus and the proliferated callus were used as explants for Agrobacterium-mediated transformation. The calluses were inoculated with A. tumefaciens harboring a binary vector with the bar gene as the selectable marker gene and the gusINT gene for GUS expression. Usually 60–100% of the callus showed transient GUS expression 5 d after inoculation. Infected
calluses were then selected on media amended with various concentrations of glufosinate. Transgenic soybean plants have been
regenerated and established in the greenhouse. GUS expression was exhibited in various tissues and plant organs, including
leaf, stem, and roots. Southern and T1 plant segregation analysis of transgenic events showed that transgenes were integrated into the soybean genome with a copy
number ranging from 1–5 copies. 相似文献
10.
A genetic transformation system has been developed for callus cells of Crataegus
aronia using Agrobacterium
tumefaciens. Callus culture was established from internodal stem segments incubated on Murashige and Skoog (MS) medium supplemented with
5 mg l−1 Indole-3-butyric acid (IBA) and 0.5 mg l−1 6-benzyladenine (BA). In order to optimize the callus culture system with respect to callus growth and coloration, different
types and concentrations of plant growth regulators were tested. Results indicated that the best average fresh weight of red
colored callus was obtained on MS medium supplemented with 2 mg l−1 2,4-dichlorophenoxyacetic acid (2,4-D) and 1.5 mg l−1 kinetin (Kin) (callus maintenance medium). Callus cells were co-cultivated with Agrobacterium harboring the binary plasmid pCAMBIA1302 carrying the mgfp5 and hygromycin phosphotransferase (hptII) genes conferring green fluorescent protein (GFP) activity and hygromycin resistance, respectively. Putative transgenic calli
were obtained 4 weeks after incubation of the co-cultivated explants onto maintenance medium supplemented with 50 mg l−1 hygromycin. Molecular analysis confirmed the integration of the transgenes in transformed callus. To our knowledge, this
is the first time to report an Agrobacterium-mediated transformation system in Crataegus
aronia. 相似文献
11.
The soybean aphid, Aphis glycines Matsumura is a new invasive pest of soybean in North America. We studied the ability of the existing predator community in soybean to reduce A. glycines establishment in field studies using either predator exclusion, open, or leaky cages that allowed aphid emigration but limited predation. Cages were infested with uniform initial densities of A. glycines adults and subsequent populations of aphids and predators were monitored over 24 h. The most abundant predators in these trials included the carabid beetles Elaphropus anceps (Le Conte), Clavina impressefrons Le Conte, Bembidion quadrimaculatum Say and spiders (Salticidae and Lycosidae). Foliar predators were less abundant and included; Harmonia axyridis Pallas, Coccinella septempunctata (L.), and Orius insidious (Say). Over the 2-year study, we found statistically significant predation on adult A. glycines in one out of six trials at 15 h and two out of six trials at 24 h. There was never significant evidence for predation of nymphs in any trial, however overall survival (adults + nymphs) was significantly reduced in one out of six trials at 15 h and three out of six trials at 24 h. Based on these results we suggest that generalist predators can be a significant but variable factor influencing the establishment of A. glycines populations in soybean. The impact of existing predator communities should be further investigated as a means of managing A.␣glycines populations in North American soybean production systems. 相似文献
12.
Noel H. Holmgren 《Brittonia》2018,70(1):115-139
A revision of Penstemon sect. Saccanthera subsect. Serrulati includes a new species (P. salmonensis), a new variety (P. triphyllus var. infernalis), and the elevation of a subspecies to species (P. curtiflorus), bringing the total number of species to eight, which are keyed and described, complete with nomenclature and type citations. 相似文献
13.
14.
Jin Hee Shin Kyujung Van Dong Hyun Kim Kyung Do Kim Young Eun Jang Beom-Soon Choi Moon Young Kim Suk-Ha Lee 《BMC plant biology》2008,8(1):133
Background
Soybean lipoxygenases (Lxs) play important roles in plant resistance and in conferring the distinct bean flavor. Lxs comprise a multi-gene family that includes GmLx1, GmLx2 and GmLx3, and many of these genes have been characterized. We were interested in investigating the relationship between the soybean lipoxygenase isozymes from an evolutionary perspective, since soybean has undergone two rounds of polyploidy. Here we report the tetrad genome structure of soybean Lx regions produced by ancient and recent polyploidy. Also, comparative genomics with Medicago truncatula was performed to estimate Lxs in the common ancestor of soybean and Medicago. 相似文献15.
Studying Pneumocystis has proven to be a challenge from the perspective of propagating a significant amount of the pathogen in a facile manner.
The study of several fungal pathogens has been aided by the use of invertebrate model hosts. Our efforts to infect the invertebrate
larvae Galleria
mellonella with Pneumocystis proved futile since P. murina neither caused disease nor was able to proliferate within G. mellonella. It did, however, show that the pathogen could be rapidly cleared from the host. 相似文献
16.
AR Torres G Kaschuk GP Saridakis M Hungria 《World journal of microbiology & biotechnology》2012,28(4):1831-1835
Brazil has succeeded in sustaining production of soybean [Glycine max (L.) Merrill] by relying mainly on symbiotic N2 fixation, thanks to the selection and use in inoculants of very effective strains of Bradyrhizobium japonicum and Bradyrhizobium elkanii. It is desirable that rhizobial strains used in inoculants have stable genetic and physiological traits, but experience confirms
that rhizobial strains nodulating soybean often lose competitiveness in the field. In this study, soybean cultivar BR 16 was
single-inoculated with four B. japonicum strains (CIAT 88, CIAT 89, CIAT 104 and CIAT 105) under aseptic conditions. Forty colonies were isolated from nodules produced
by each strain. The progenitor strains, the isolates and four other commercially recommended strains were applied separately
to the same cultivar under controlled greenhouse conditions. We observed significant variability in nodulation, shoot dry
weight, shoot total N, nodule efficiency (total N mass over nodule mass) and BOX-PCR fingerprinting profiles between variant
and progenitor strains. Some variant strains resulted in significantly larger responses in terms of shoot total N, dry weight
and nodule efficiency, when compared to their progenitor strain. These results highlight the need for intermittent evaluation
of stock bacterial cultures to guarantee effective symbiosis after inoculation. Most importantly, it indicates that it is
possible to improve symbiotic effectiveness by screening rhizobial strains for higher N2 fixation capacity within the natural variability that can be found within each progenitor strain. 相似文献
17.
18.
The maT clade of transposons is a group of transposable elements intermediate in sequence and predicted protein structure to mariner and Tc transposons, with a distribution thus far limited to a few invertebrate species. We present evidence, based on searches of publicly available databases, that the nematode Caenorhabditis briggsae has several maT-like transposons, which we have designated as CbmaT elements, dispersed throughout its genome. We also describe two additional transposon sequences that probably share their evolutionary history with the CbmaT transposons. One resembles a fold back variant of a CbmaT element, with long (380-bp) inverted terminal repeats (ITRs) that show a high degree (71%) of identity to CbmaT1. The other, which shares only the 26-bp ITR sequences with one of the CbmaT variants, is present in eight nearly identical copies, but does not have a transposase gene and may therefore be cross mobilised by a CbmaT transposase. Using PCR-based mobility assays, we show that CbmaT1 transposons are capable of excising from the C. briggsae genome. CbmaT1 excised approximately 500 times less frequently than Tcb1 in the reference strain AF16, but both CbmaT1 and Tcb1 excised at extremely high frequencies in the HK105 strain. The HK105 strain also exhibited a high frequency of spontaneous induction of unc-22 mutants, suggesting that it may be a mutator strain of C. briggsae. 相似文献
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20.
Nongporn Hutadilok-Towatana Wantana Reanmongkol Pharkphoom Panichayupakaranant 《Journal of applied phycology》2010,22(5):599-605
In this study, the methanol extract of Arthrospira (Spirulina) platensis was examined for acute and subchronic toxicities. The extract did not produce any sign of toxicity within 7 days after feeding
it at a single high dose of 6 g kg−1 body weight to female and male Swiss mice. For the subchronic toxicity test, the extract at doses of 6, 12, and 24 mg kg−1 body weight was orally administered to six male and six female Wistar rats daily for 12 weeks. Throughout the study period,
we did not observe any abnormalities on behavior, food and water intakes, and health status among the treated animals. The
hematology and clinical chemistry parameters of treated groups did not significantly differ from those of the controls in
both sexes. Postmortem examination of the test groups also showed no abnormalities in both gross and histological findings.
These results thus suggest that the methanol extract of A. platensis did not cause acute or subchronic toxicity in our experimental animals. 相似文献