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1.

Background

Although more than one thousand complete mitochondrial DNA (mtDNA) sequences have been determined in teleostean fishes, only a few gene rearrangements have been observed, and genome-scale rearrangements are even rarer. However, flatfishes (Pleuronectiformes) have been identified as having diverse types of mitochondrial gene rearrangements. It has been reported that tongue soles and the blue flounder mitogenomes exhibit different types of large-scale gene rearrangements.

Results

In the present study, the complete mitochondrial genome of another flatfish, Samariscus latus, was sequenced, and genome-scale rearrangements were observed. The genomic features of this flounder are different from those of any other studied vertebrates, including flatfish species too. The mitogenome of S. latus is characterized by the duplication and translocation of the control region (CR). The genes located between the two CRs are divided into two clusters in which their relative orders are maintained.

Conclusions

We propose a “Double Replications and Random Loss” model to explain the rearrangement events in S. latus mitogenome. This model consists of the following steps. First, the CR was duplicated and translocated. Subsequently, double replications of the mitogenome were successively initiated from the two CRs, leading to the duplication of the genes between the two CRs. Finally, one of each pair of duplicated genes was lost in a random event.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-352) contains supplementary material, which is available to authorized users.  相似文献   

2.
This research focused on optimizing the upstream process time for production of polyhydroxybutyrate (PHB) from sucrose by two-stage batch and fed-batch fermentation with Alcaligenes latus ATCC 29714. The study included selection of strain, two-stage batch fermentations with different time points for switching to nitrogen limited media (14, 16 or 18?h) and fed-batch fermentations with varied time points (similar to two stage) for introducing nitrogen limited media. The optimal strain to produce PHB using sucrose as carbon source was A. latus ATCC 29714 with maximum-specific growth rate of 0.38?±?0.01?h?1 and doubling time of 1.80?±?0.05?h. Inducing nitrogen limitation at 16?h and ending second stage at 26?h gave optimal performance for PHB production, resulting in a PHB content of 46.7?±?12.2?% (g PHB per g dry cell weight) at the end of fermentation. This was significantly higher (P?≤?0.05) (approximately 7?%) than the corresponding fed batch run in which nitrogen limitation was initiated at 16?h.  相似文献   

3.
A novel facultatively anaerobic moderately thermophilic bacterium, strain B-254T, was isolated from a terrestrial hot spring near the town of Goryachinsk in the Baikal lake region (Russian Federation). Motile spherical cells of the strain were present as single cocci, in pairs, or aggregates. The cells had a Gram negative cell wall and reproduced by binary fission. The isolate grew at 30–57 °C (opt. 50–54 °C) and at pH 5.1–8.4 (opt. 6.6–7.1). Strain B-254T was a chemoorganoheterotroph, growing on mono-, di- and polysaccharides (xylan, starch, galactan, galactomannan, xyloglucan, arabinan, curdlan, beta-glucan, locust bean gum, xanthan gum). Sodium chloride or yeast extract were not required for growth. Major cellular fatty acids were iso-C16:0, anteiso-C17:0, and C20:0; major polar lipid was phosphatidylethanolamine. The complete genome of strain B-254T was 5.54 Mb; its GC content was 64 %. According to the results of 16S rRNA gene sequence-based phylogenetic analysis and the conserved proteins sequences-based phylogenomic analysis strain B-254T was on a separate lineage within the order Tepidisphaerales (Phycisphaerae, Planctomycetes). Based on phylogenetic and phylogenomic analyses of Phycisphaerae, whole genome comparisons of Tepidisphaerales as well as distinctive phenotypic features of the strain, it was assigned to a novel genus and species for which the name Fontivita pretiosa gen. nov. sp. nov. is proposed. Strain B-254T = KCTC 82380T = VKM B-3507T.  相似文献   

4.
The broad mite, Polyphagotarsonemus latus (Banks), is one of the major pests causing severe economic damage in Rhododendron simsii Planch hybrid production in Belgium. In order to optimize biological control programs and to parameterize warning programs, we studied the effect of environmental temperature on the development of P. latus on R. simsii leaves. In combination with a photoperiod of 16:8 h (L:D) and a relative humidity of 80 ± 5 %, six constant temperatures (15, 17, 20, 25, 30 and 33 ± 1 °C), were studied. Total developmental times of 13.3, 10.5, 6.6, 4.2, 3.5 and 4.0 days were measured, respective to each of the aforementioned temperatures. Development of females took significantly longer than that of males at 15, 17, 20 and 30 °C. Survival rates observed between 17 and 30 °C varied between 43.5 and 96.9 %. Lower survival rates were found at 15 and 33 °C, i.e. 31.8 and 23.6 %, respectively. The lower, optimal and upper developmental threshold (t min , t opt and t max , respectively) and thermal constant (K) of the pest were estimated for each life stage by a linear and two non-linear models. Based on measurements of total development of P. latus thermal thresholds of 10.0, 30.1 and 36.0 °C were calculated for t min , t opt and t max , respectively. The number of degree-days needed to complete immature development when feeding on R. simsii was 66.7.  相似文献   

5.
The broad mite Polyphagotarsonemus latus is a key pest of physic nut (Jatropha curcas L.). The purpose of this study was to identify physic nut accessions that are less susceptible to P. latus, in support of the breeding program of J. curcas. We first evaluated population growth rate and injury symptoms of P. latus on different J. curcas accessions and then carried out physiological analyses on P. latus-infested and uninfested accessions. From the germplasm bank of the Federal University of Viçosa, 15 physic nut accessions with high seed oil content, with different genetic background, were tested. The following traits were evaluated: instantaneous population growth rate of P. latus (r i ), injury symptoms, relative leaf water content, specific leaf area, gas exchange, photosynthetic pigments, nitrogen and biomass of the aerial part. Significant differences were observed for P. latus population growth rate and injury symptoms among accessions. A positive correlation between P. latus growth rate and injury was found. The UFVJC72 accession stood out as the more resistant, considering P. latus growth rate and injury symptoms, compared with most accessions. Physiological responses did not vary among accessions, but did between infested and uninfested plants. In P. latus-infested plants, net photosynthesis was on average 50.5 % lower than in uninfested plants, whereas stomatal conductance and transpiration decreased by 46.2 and 51.6 %, respectively.  相似文献   

6.
Photosystem II light-harvesting complexes were isolated from a number of ulvophycean algae. Some of these light-harvesting complexes displayed unusual features, most notably a high apparent molecular weight (ca. 58,000) when isolated by lithium doderyl sulfate polyarrylamide gel electrophoresis. Other ulvophycean light-harvesting complexes had a low-molecular weight (ca. 30,000). The distribution of the high-molecular weight complex was limited to certain members of the Caulerpales and Blastophysa rhizopus (Siphanocladales). Within the Caulerpales, there were also spectral differences between the high-molecular weight and low-molecular weight light-harvesting complex types. The differences in light-harvesting complexes in the Ulvophyceae suggest that there are two lines of evolution in the Caulerpales and that Blastophysa may be an intermediate between the Siphon-ocladales and the Caulerpales.  相似文献   

7.
Dibothriocephalus latus and Dibothriocephalus dendriticus are found throughout the temperate and sub-arctic zones of the northern hemisphere, but they are also found in the southern core countries of South America, Chile and Argentina. Genetic characteristics of D. latus and D. dendriticus from South America have yet to be fully defined. The present study aimed to understand the genetic characteristics of D. latus and D. dendriticus from Chile by haplotype network analysis of mitochondrial cytochrome c oxidase subunit I gene (cox1) and cytochrome b gene (cob), as well as their origins. Dibothriocephalus latus and D. dendriticus plerocercoid larvae were obtained from feral and/or wild salmonids captured in Lake Llanquihue in Región de Los Lagos, and Lake Panguipulli in Región de Los Ríos, located south of central Chile. Haplotype analysis of D. latus revealed that H1 in cox1 and H2 in cob are the key haplotypes common to D. latus across the world, including Chile, and both genes exhibited limited genetic diversity in D. latus. It was assumed that D. latus was brought into South America by European and Russian immigrants in the 19th century as previously reported. In contrast, both the cox1 and cob of D. dendriticus display considerable genetic diversity, with no common haplotypes between D. dendriticus populations from Chile and the northern hemisphere. More intriguingly, two cob haplotypes (H24, H25) detected in Chilean D. dendriticus were closely linked to haplotypes (H30, H31) detected in North American D. dendriticus, strongly implying that D. dendriticus in Chile was brought by piscivorous migrating birds from North America. It has also been estimated that the D. dendriticus from Chile genetically diverged from the D. dendriticus from the northern hemisphere approximately 1.11 million years ago, long before humans migrated to the southern parts of South America.  相似文献   

8.
The teichoic acids (TAs) of type strains, viz. Bacillus licheniformis VKM B-511T and Bacillus pumilus VKM B-508T, as well as phylogenetically close bacteria VKM B-424, VKM B-1554, and VKM B-711 previously assigned to Bacillus pumilus on the basis of morphological, physiological, and biochemical properties, were investigated. Three polymers were found in the cell wall of each of the 5 strains under study. Strains VKM B-508T, VKM B-424, and VKM B-1554 contained polymers of the same core: unsubstituted 1,3-poly(glycerol phosphate) (TA I) and 1,3-poly(glycerol phosphate) with O-D-Ala and N-acetyl-??-D-glucosamine substituents (TA II and TA III??, respectively). The cell walls of two remaining strains contained TA I, TA II, and a poly(glycosylpolyol phosphate) with the following structure of repeating units: -6)-??-D-GlcpNAc(1??1)-snGro-(3-P-(TA III?) in ??Bacillus pumilus?? VKM B-711 (100% 16S rRNA gene similarity with the type strain of Bacillus safensis) and -6)-??-D-Galp-(1??2)-snGro-(3-P-(TA III?) in Bacillus licheniformis VKM B-511T. The simultaneous presence of three different TAs in the cell walls was confirmed by the NMR spectroscopic DOSY methods. The structure of the polymers and localization of O-D-Ala residues were investigated by the chemical and NMR spectroscopic methods.  相似文献   

9.
Polyhydroxyalkanoates (PHAs) make a large class of biodegradable biopolymers that are naturally synthesized by numerous microorganisms. These biopolymers could be an alternative to commonly used plastics based on petroleum. Production of PHAs in bioreactors using microorganisms is not widely applied due to its unprofitability. Using transgenic plants for this purpose may be cheaper and more environmental friendly because the biosynthesis of PHAs in plants is based only on water, mineral salts, CO2 and light. Additionally, plants are not capable of degrading PHAs as bacteria do, and extraction of PHAs from plant tissues is not always necessary. The main objective of this work is a review of possibilities of PHA biosynthesis in transgenic plants and presentation of general information on properties and potential application possibilities of these biopolymers. The possibility of syntheses and accumulation of PHA in several transgenic plants has been studied for some years. Many experiments were performed on model plant Arabidopsis thaliana, however, the research has also revealed a great potential of transgenic crop plants such as camelina (Camelina sativa), tobacco (Nicotiana tabacum) or sugarcane (Saccharum officinarum) as a good sources of PHAs. The highest level of PHAs accumulation in plants was achieved in transgenic A. thaliana (up to 40% of the dry weight of the leaf), and among crop plants in C. sativa (up to 20% of the dry weight of the seed). Increasing knowledge on PHAs permits expansion of the possibilities of these biopolymers use even at a low level of their accumulation in plant tissues.  相似文献   

10.
Leuconostoc mesenteroides strain NRRL B-1355 produces two soluble extracellular α-D-glucans from sucrose: alternan and dextran. An unusual mutant strain derived from NRRL B-1355 has recently been isolated which produces practically no soluble polysaccharide, but significant amounts of an insoluble D-glucan. Methylation analysis shows it contains linear (1→3) and (1→6) linkages as well as (1→2) and (1→3) branch linkages. The insoluble glucan was partially digestible by endodextranase, giving rise to a series of oligosaccharides, a high-molecular weight soluble fraction and an insoluble residue. Treatment of the soluble dextranase-limit fraction with an α(1→2) debranching enzyme led to further dextranase susceptibility. Methylation, FTIR and NMR analyses of the dextranase-treated fractions indicate a non-uniform structure with domains bearing similarities to L. mesenteroides strain NRRL B-1299 dextran and to insoluble streptococcal D-glucans. Received 05 November 1998/ Accepted in revised form 31 March 1999  相似文献   

11.
Three halophilic archaea, strains B-1T, B-3 and B-4, were isolated from evaporitic salt crystals from Namhae, Korea. Cells of the strains were Gram-stain-negative, motile and pleomorphic, and colonies were red-pigmented. The three isolates had identical 16S rRNA gene sequences and formed a tight phylogenetic clade with Halogranum rubrum RO2-11T in the genus Halogranum, showing 99.5% sequence similarity. The next most closely related species were Halogranum amylolyticum and Halogranum gelatinilyticum (97.4 and 96.3% similarity to the respective type strains). The phylogeny based on the full-length RNA polymerase subunit B′ gene (rpoB′) was in agreement with the 16S rRNA gene sequence analysis, but allowed better discrimination. DNA-DNA hybridization between a representative strain (B-1T) and the type strains of Hgn. rubrum, Hgn. amylolyticum and Hgn. gelatinilyticum revealed less than 40% relatedness. Polar lipid analysis showed that the three isolates contained phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester and three glycolipids. Combined genotypic and phenotypic data supported the conclusion that strains B-1T, B-3 and B-4 represent a novel species of the genus Halogranum, for which the name Halogranum salarium sp. nov. is proposed. The type strain is B-1T (=KCTC 4066T = DSM 23171T).  相似文献   

12.
13.
A novel facultatively anaerobic moderately thermophilic bacterium, strain B-154 T, was isolated from a terrestrial hot spring in the Baikal lake region (Russian Federation). Gram-negative, motile, spherical cells were present singly, in pairs, or aggregates, and reproduced by binary fission. The strain grew at 30–57 °C and within a pH range of 5.1–8.4 with the optimum at 50 °C and pH 6.8–7.1. Strain B-154 T was a chemoorganoheterotroph, growing on mono-, di- and polysaccharides (xylan, starch, galactan, galactomannan, glucomannan, xyloglucan, pullulan, arabinan, lichenan, beta-glucan, pachyman, locust bean gum, xanthan gum). It did not require sodium chloride or yeast extract for growth. Major cellular fatty acids were anteiso-C15:0, iso-C16:0 and iso-C14:0. The respiratory quinone was MK-7. The complete genome of strain B-154 T was 4.73 Mbp in size; its G + C content was 61%. According to the phylogenomic analysis strain B-154 T forms a separate family-level phylogenetic lineage. Moreover, together with Limisphaera ngatamarikiensis and “Pedosphaera parvula” this strain forms a separate order-level phylogenetic lineage within Verrucomicrobiae class. Hence, we propose a novel order, Limisphaerales ord. nov., with two families Limisphaeraceae fam. nov. and Fontisphaeraceae fam. nov., and a novel genus and species Fontisphaera persica gen. nov., sp. nov. with type strain B-154 T. Ecogenomic analysis showed that representatives of the Limisphaerales are widespread in various environments. Although some of them were detected in hot springs the majority of Limisphaerales (54% of the studied metagenome-assembled genomes) were found in marine habitats. This study allowed a better understanding of physiology and ecology of Verrucomicrobiota – a rather understudied bacterial phylum.  相似文献   

14.
Due to the established health benefits of omega-3 long-chain polyunsaturated fatty acids (LC-PUFA), there is a globally increasing demand for alternative natural resources with appropriate fatty acid profiles. To assess the suitability of macroalgae as a source, 16 species (nine Phaeophyceae, five Rhodophyta and two Chlorophyta) were collected at two seasons (June and November) from the Irish west Coast, and total fatty acid contents and specific profiles were determined. Total fatty acid contents, expressed per percentage of dry weight, ranged from 6.4 %?±?0.3 (Pelvetia canaliculata, Phaeophyceae) to 0.8 %?±?0.2 (Porphyra dioica, Rhodophyta). Most common fatty acids were palmitic (16:0), oleic (OLE, 18:1 n-9), α-linolenic (ALA, 18:3 n-3), arachidonic (ARA, 20:4 n-6) and eicosapentaenoic (EPA, 20:5 n-3) acids. Fatty acid profiles were highly variable between and within algal groups; red and brown seaweeds were generally richer in LC-PUFA (e.g. 20:4 n-6 and 20:5 n-3), while high levels of saturated fatty acids such as palmitic acid (16:0) were observed in green species. Most omega-3 PUFA-rich species investigated had a omega-6/omega-3 fatty acid ratio close to 1, which is favourable for human health. The two seasonal sampling times revealed significant differences in total fatty acid and 20:5 n-3 (EPA) contents, with changes depending on species, thus implying varying suitability as potential target species for EPA production. At both times of the year, Palmaria palmata was identified as most promising species as a source of 20:5 n-3 (EPA) amongst all species investigated, with levels ranging from 0.44 to 0.58 % of dry weight in June and November, respectively.  相似文献   

15.
In laboratory studies, individuals ofEuseius stipulatus Athias-Henriot,Typhlodromus rickeri Chant,T. porresi McMurtry andT. annectens DeLeon offered broad mite,Polyphagotarsonemus latus (Banks), as prey had developmental and ovipositional rates comparable to those offered a known favorable food (tetranychid mites or pollen).Euseius hibisci (Chant) had a longer developmental period and a markedly lower oviposition rate onP. latus than on the control food. Immature survival and ovipositional rates ofEuseius concordis Chant,Typhlodromus occidentalis Nesbitt,Amblyseius limonicus Garman and McGregor andIphiseius degenerans (Berlese) were very low onP. latus compared to control foods.  相似文献   

16.
A variant of B-16 F1 mouse melanoma was selected for its ability to survive and replicate in the presence of melanocyte-stimulating hormone (MSH). Although the variant (MR-4) was completely resistant to growth inhibition by MSH, cyclic AMP was still able to block cell replication. Tyrosinase activity in MR-4 cells was considerably lower than in B-16 F1 cells. MSH induced a twofold to three-fold increase in tyrosinase activity in both cell types, but the absolute activity in MR-4 remained significantly less than in the parental cells. MR-4 cells were also found to have a markedly depressed cyclic AMP-dependent protein kinase activity relative to B-16 F1 cells. The protein kinase from both cell types was stimulated by cyclic AMP, but the level of MR-4 kinase activity at maximal cyclic AMP concentrations remained considerably lower than B-16 F1 kinase activity under the same conditions. In both cell types adenylate cyclase activity was markedly stimulated by MSH. When equal numbers of viable F1 and MR-4 cells were injected subcutaneously into C57/B1 mice, the MR-4 cells formed tumors earlier and killed the host sooner than the parental F1 cells. We conclude that the biochemical alteration which allows MR-4 cells to replicate in the presence of MSH is a low level of tyrosinase activity, which in turn may be the result of low cyclic AMP-dependent protein kinase activity.  相似文献   

17.
18.
Three pigmented strains of halophilic archaea (RS75, RS77, RS79) were isolated from the monoliths of mottled sylvinite from the Verkhnekamsk salt deposit (Solikamsk, Russia). The cells were nonmotile, gram-negative, pleomorphic, disk-shaped or ovoid, 0.8–1.0 × 1.5–2.5 μm. The organism was a chemoorganotrophic obligate aerobe producing catalase and oxidase. A number of carbohydrates and carboxylic acids were used as growth substrates. Growth occurred in the presence of 7–27 % NaCl (with the optimum at 15–18 %), 0.02–20 % KCl (0.2–1 %), 0.2–16 % MgCl2 (2–3 %), in the temperature range from 23 to 51 °C (40–45 °C), and pH 5.5–8.0 (6.8–7.0). The membranes contained carotenoids of the bacterioruberin series. Phosphatidylglyceromethylphosphate (PGP-Me), phosphatidylglycerol (PG), sulfated diglycosyl diether (S-DGD-1) predominated among the polar lipids. The DNA G + C content was 64.0–65.0 mol %. Phylogenetic analysis of the 16S rRNA gene sequences showed high similarity of the new strains to Haloferax species: H. denitrificans (99.2 %) and H. volcanii (99.1 %), H. larsenii (96.9 %) and H. elongans (96.6 %). DNA–DNA hybridization revealed 93–95 % similarity between strain RS75 and strains RS77 and RS79; the similarity levels between strain RS75 and the type strains of Haloferax denitrificans VKM B-1754T and Halobacterium salinarum VKM B-1769T were 50 and 10 %, respectively. According to its phenotypic and genotypic characteristics, the organism was classified as a member of the genus Haloferax, forming a new species with the proposed name Haloferax chudinovii sp. nov. type strain is RS75T (=VKPM B-11279T).  相似文献   

19.
The starting point for generating a pest control decision-making system is a conventional sampling plan. Because the mites Polyphagotarsonemus latus and Tetranychus bastosi are among the most important pests of the physic nut (Jatropha curcas), in the present study, we aimed to establish sampling plans for these mite species on physic nut. Mite densities were monitored in 12 physic nut crops. Based on the obtained results, sampling of P. latus and T. bastosi should be performed by assessing the number of mites per cm2 in 160 samples using a handheld 20× magnifying glass. The optimal sampling region for T. bastosi is the abaxial surface of the 4th most apical leaf on the branch of the middle third of the canopy. On the abaxial surface, T. bastosi should then be observed on the side parts of the middle portion of the leaf, near its edge. As for P. latus, the optimal sampling region is the abaxial surface of the 4th most apical leaf on the branch of the apical third of the canopy on the abaxial surface. Polyphagotarsonemus latus should then be assessed on the side parts of the leaf’s petiole insertion. Each sampling procedure requires 4 h and costs US$ 7.31.  相似文献   

20.
Several isolates of three Fusarium species associated with the Gibberella fujikuroi species complex were characterized for their ability to synthesize gibberellins (GAs): Fusarium sacchari (mating population B), Fusarium konzum (mating population I) and Fusarium subglutinans (mating population E). Of these, F. sacchari is phylogenetically related to Fusarium fujikuroi and is grouped in the Asian clade of the complex, while F. konzum and F. subglutinans are only distantly related to Fusarium fujikuroi and belong to the American clade. Variability was found between the different F. sacchari strains tested. Five isolates (B-12756; B-1732, B-7610, B-1721 and B-1797) were active in GA biosynthesis and accumulated GA3 in the culture fluid (2.76–28.4 μg/mL), while two others (B-3828 and B-1725) were inactive. GA3 levels in strain B-12756 increased by 2.9 times upon complementation with ggs2 and cps-ks genes from F. fujikuroi. Of six F. konzum isolates tested, three (I-10653; I-11616; I-11893) synthesized GAs, mainly GA1, at a low level (less than 0.1 μg/mL). Non-producing F. konzum strains contained no GA oxidase activities as found for the two F. subglutinans strains tested. These results indicate that the ability to produce GAs is present in other species of the G. fujikuroi complex beside F. fujikuroi, but might differ significantly in different isolates of the same species.  相似文献   

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