Analysis of complete chloroplast genome sequences and insight into the phylogenetic relationships of Ferula L.

BACKGROUND: Ferula L. is one of the largest and most taxonomically complicated genera as well as being an important medicinal plant resource in the family Apiaceae. To investigate the plastome features and phylogenetic relationships of Ferula and its neighboring genera Soranthus Ledeb., Schumannia Kuntze., and Talassia Korovin, we sequenced 14 complete plastomes of 12 species.  RESULTS: The size of the 14 complete chloroplast genomes ranged from 165,607 to 167,013 base pairs (bp) encoding 132 distinct genes (87 protein-coding, 37 tRNA, and 8 rRNA genes), and showed a typical quadripartite structure with a pair of inverted repeats (IR) regions. Based on comparative analysis, we found that the 14 plastomes were similar in codon usage, repeat sequence, simple sequence repeats (SSRs), and IR borders, and had significant collinearity. Based on our phylogenetic analyses, Soranthus, Schumannia, and Talassia should be considered synonymous with Ferula. Six highly divergent regions (rps16/trnQ-UUG, trnS-UGA/psbZ, psbH/petB, ycf1/ndhF, rpl32, and ycf1) were also detected, which may represent potential molecular markers, and combined with selective pressure analysis, the weak positive selection gene ccsA may be a discriminating DNA barcode for Ferula species. CONCLUSION: Plastids contain abundant informative sites for resolving phylogenetic relationships. Combined with previous studies, we suggest that there is still much room for improvement in the classification of Ferula. Overall, our study provides new insights into the plastome evolution, phylogeny, and taxonomy of this genus.

Leaf-root-soil N:P stoichiometry of ephemeral plants in a temperate desert in Central Asia.

Ephemeral plants are a crucial vegetation component in temperate deserts of Central Asia, and play an important role in biogeochemical cycle and biodiversity maintenance in desert ecosystems. However, the nitrogen (N) and phosphorus (P) status and interrelations of leaf-root-soil of ephemeral plants remain unclear. A total of 194 leaf-root-soil samples of eight ephemeral species at 37 sites in the Gurbantunggut Desert, China were collected, and then the corresponding N and P concentrations, and the N:P ratio were measured. Results showed that soil parameters presented no significant difference among the eight species. The total soil N:P was only 0.116 (geomean), indicating limited soil N, while the available soil N:P (4.896, geomean) was significantly larger than the total N:P. The leaf N (averagely 30.995 mg g-1) and P (averagely 1.523 mg g-1) concentrations were 2.64-8.46 and 0.93-3.99 times higher than the root N (averagely 8.014 mg g-1) and P (averagely 0.802 mg g-1) concentrations, respectively. Thus, leaf N:P (averagely 21.499) was 1.410-2.957 times higher than root N:P (averagely 11.803). Meanwhile, significant interspecific differences existed in plant stoichiometric traits. At the across-species level, N content scaled as the 3/4-power of P content in both leaves and roots. Leaf and root N:P ratios were mainly influenced by P; however, the leaf-to-root N or P ratio was dominated by roots. Leaf and root N, P contents and N:P were generally unrelated to soil nutrients, and the former presented lower variation than the latter, indicating a strong stoichiometric homeostasis for ephemerals. These results demonstrate that regardless of soil nutrient supply capacity in this region, the fast-growing ephemeral plants have formed a specific leaf-root-soil stoichiometric relation and nutrient use strategy adapting to the extreme desert environment.

Three-dimensional genetic networks among seed oil-related traits, metabolites and genes reveal the genetic foundations of oil synthesis in soybean.

Although the biochemical and genetic basis of lipid metabolism is clear in Arabidopsis, there is limited information concerning the relevant genes in Glycine max (soybean). To address this issue, we constructed three-dimensional genetic networks using six seed oil-related traits, 52 lipid metabolism-related metabolites and 54 294 SNPs in 286 soybean accessions in total. As a result, 284 and 279 candidate genes were found to be significantly associated with seed oil-related traits and metabolites by phenotypic and metabolic genome-wide association studies and multi-omics analyses, respectively. Using minimax concave penalty (MCP) and smoothly clipped absolute deviation (SCAD) analyses, six seed oil-related traits were found to be significantly related to 31 metabolites. Among the above candidate genes, 36 genes were found to be associated with oil synthesis (27 genes), amino acid synthesis (four genes) and the tricarboxylic acid (TCA) cycle (five genes), and four genes (GmFATB1a, GmPDAT, GmPLDα1 and GmDAGAT1) are already known to be related to oil synthesis. Using this information, 133 three-dimensional genetic networks were constructed, 24 of which are known, e.g. pyruvate-GmPDAT-GmFATA2-oil content. Using these networks, GmPDAT, GmAGT and GmACP4 reveal the genetic relationships between pyruvate and the three major nutrients, and GmPDAT, GmZF351 and GmPgs1 reveal the genetic relationships between amino acids and seed oil content. In addition, GmCds1, along with average temperature in July and the rainfall from June to September, influence seed oil content across years. This study provides a new approach for the construction of three-dimensional genetic networks and reveals new information for soybean seed oil improvement and the identification of gene function.

An integrated omics analysis reveals molecular mechanisms that are associated with differences in seed oil content between Glycine max and Brassica napus.

BACKGROUND: Rapeseed (Brassica napus L.) and soybean (Glycine max L.) seeds are rich in both protein and oil, which are major sources of biofuels and nutrition. Although the difference in seed oil content between soybean (~ 20%) and rapeseed (~ 40%) exists, little is known about its underlying molecular mechanism. RESULTS: An integrated omics analysis was performed in soybean, rapeseed, Arabidopsis (Arabidopsis thaliana L. Heynh), and sesame (Sesamum indicum L.), based on Arabidopsis acyl-lipid metabolism- and carbon metabolism-related genes. As a result, candidate genes and their transcription factors and microRNAs, along with phylogenetic analysis and co-expression network analysis of the PEPC gene family, were found to be largely associated with the difference between the two species. First, three soybean genes (Glyma.13G148600, Glyma.13G207900 and Glyma.12G122900) co-expressed with GmPEPC1 are specifically enriched during seed storage protein accumulation stages, while the expression of BnPEPC1 is putatively inhibited by bna-miR169, and two genes BnSTKA and BnCKII are co-expressed with BnPEPC1 and are specifically associated with plant circadian rhythm, which are related to seed oil biosynthesis. Then, in de novo fatty acid synthesis there are rapeseed-specific genes encoding subunits ß-CT (BnaC05g37990D) and BCCP1 (BnaA03g06000D) of heterogeneous ACCase, which could interfere with synthesis rate, and ß-CT is positively regulated by four transcription factors (BnaA01g37250D, BnaA02g26190D, BnaC01g01040D and BnaC07g21470D). In triglyceride synthesis, GmLPAAT2 is putatively inhibited by three miRNAs (gma-miR171, gma-miR1516 and gma-miR5775). Finally, in rapeseed there was evidence for the expansion of gene families, CALO, OBO and STERO, related to lipid storage, and the contraction of gene families, LOX, LAH and HSI2, related to oil degradation. CONCLUSIONS: The molecular mechanisms associated with differences in seed oil content provide the basis for future breeding efforts to improve seed oil content.

Endogenously synthesized n-3 fatty acids in fat-1 transgenic mice prevent melanoma progression by increasing E-cadherin expression and inhibiting ß-catenin signaling.

Malignant melanoma is the most lethal form of skin cancer. Although preclinical studies have shown that n-3 polyunsaturated fatty acids (PUFAs) are beneficial for prevention of melanoma, the molecular mechanisms underlying the protective effects of n­3 PUFAs on melanoma remain largely unknown. In the present study, endogenously increased levels of n-3 PUFAs in the tumor tissues of omega­3 fatty acid desaturase (fat­1) transgenic mice was associated with a reduction in the growth rate of melanoma xenografts. This reduction in tumor growth in fat­1 mice compared with wild­type controls may have been associated, in part, to the: i) Increased expression of E­cadherin and the reduced expression of its transcriptional repressors, the zinc finger E­box binding homeobox 1 and snail family transcriptional repressor 1; ii) significant repression of the epidermal growth factor receptor/Akt/ß­catenin signaling pathway; and iii) formation of significant levels of n­3 PUFA­derived lipid mediators, particularly resolvin D2 and E1, maresin 1 and 15­hydroxyeicosapentaenoic acid. In addition, vitamin E administration counteracted n­3 PUFA­induced lipid peroxidation and enhanced the antitumor effect of n­3 PUFAs, which suggests that the protective role of n­3 PUFAs against melanoma is not mediated by n­3 PUFAs­induced lipid peroxidation. These results highlight a potential role of n­3 PUFAs supplementation for the chemoprevention of melanoma in high­risk individuals, and as a putative adjuvant agent in the treatment of malignant melanoma.

An Integrated Bioinformatics Analysis Reveals Divergent Evolutionary Pattern of Oil Biosynthesis in High- and Low-Oil Plants.

Seed oils provide a renewable source of food, biofuel and industrial raw materials that is important for humans. Although many genes and pathways for acyl-lipid metabolism have been identified, little is known about whether there is a specific mechanism for high-oil content in high-oil plants. Based on the distinct differences in seed oil content between four high-oil dicots (20~50%) and three low-oil grasses (<3%), comparative genome, transcriptome and differential expression analyses were used to investigate this mechanism. Among 4,051 dicot-specific soybean genes identified from 252,443 genes in the seven species, 54 genes were shown to directly participate in acyl-lipid metabolism, and 93 genes were found to be associated with acyl-lipid metabolism. Among the 93 dicot-specific genes, 42 and 27 genes, including CBM20-like SBDs and GPT2, participate in carbohydrate degradation and transport, respectively. 40 genes highly up-regulated during seed oil rapid accumulation period are mainly involved in initial fatty acid synthesis, triacylglyceride assembly and oil-body formation, for example, ACCase, PP, DGAT1, PDAT1, OLEs and STEROs, which were also found to be differentially expressed between high- and low-oil soybean accessions. Phylogenetic analysis revealed distinct differences of oleosin in patterns of gene duplication and loss between high-oil dicots and low-oil grasses. In addition, seed-specific GmGRF5, ABI5 and GmTZF4 were predicted to be candidate regulators in seed oil accumulation. This study facilitates future research on lipid biosynthesis and potential genetic improvement of seed oil content.

[Ecological stoichiometry of surface soil nutrient and its influencing factors in the wild fruit forest in Yili region, Xinjiang, China.] / ä¼ŠçŠé‡Žæžœæž—æµ å±‚åœŸå£¤å »åˆ†ç”Ÿæ€åŒ–å­¦è®¡é‡ç‰¹å¾åŠå ¶å½±å“å› ç´ .

Soil samples and environmental factors in 60 plots of 20 communities in the wild fruit forest in Yili valley were investigated, and then the stoichiometric characteristics of soil organic carbon (C), total nitrogen (N), total phosphorus (P) and total potassium (K) in 0-10 cm and 10-20 cm layers and their influencing factors were studied. The results showed that soil C, N, P and K contents in 0-10 cm layer were 73.15, 7.00, 1.14 and 14.74 g·kg-1, respectively. Soil C:N, C:P, C:K, N:P, N:K and P:K were 10.37, 62.73, 5.05, 6.05, 0.48 and 0.08, respectively. Except for K and C:N, the stoichiometric values in 0-10 cm layer were significantly higher than that in 10-20 cm layer. Soil P, K, C:N and P:K presented high stability (CV=8%-24%), while others showed moderate variability (CV=28%-46%). Soil nutrient contents and their stoichiometric ratios differed markedly in different sampling sites, communities and slope aspects. Except the power relationship between C and N, all the soil nutrient contents and their stoichiometric ratios represented quadratic relationships, indicating nonlinear coupling among soil stoichiometric traits. Slope aspect, precipitation and temperature were the main factors influencing soil stoichiometry in the wild fruit forest in Yili region.

[Leaf and soil stoichiometry of four herbs in the Gurbantunggut Desert, China].

The leaf and soil stoichiometric characteristics and their relationships of two ephemeral plants (Hypecoum erectum and Euphorbia turczaninowii) and two ephemeroid plants (Ferula meyeri and Astragalus flexus) were analyzed in extreme desert environment. There was no significant difference among each soil factor in different sampling plots of each species. Soil nitrogen (N) content (0.18-0.22 mg . g-1) was far lower than soil phosphorus (P) content (1.58-1.62 mg . g-1), and the N/P only ranged 0.12-0.15, indicating a serious lack of soil N. N, P and N/P all represented significant difference among the four species, in which A. flexus had the highest values with 57.36 mg . g-1, 2.46 mg . g-1 and 23.43, followed by H. erectum with 34.05 mg . g-1, 1.98 mg . g-1 and 17.56, the values for E. turczaninowii were 27.07 mg . g-1, 1.87 mg . g-1 and 14.51, and the values for F. meyeri were 28.63 mg . g-1, 2.20 mg . g-1 and 13.10, respectively. N and P contents showed significant correlation of each species, while most soil factors did not show significant correlation with leaf stoichiometric values.

Feasibility of EPS-producing bacterial inoculation to speed up the sand aggregation in the Gurbantunggut Desert, Northwestern China.

Exopolymers are known to be useful in improving sand aggregation and the development of biological soil crusts (BSCs). A facultative bacterium KLBB0001 was isolated from BSCs in the Gurbantunggut Desert in northwestern China. With the strong effective production of extracellular polymeric substances (EPS), this strain exhibits a multifunctional role for sand stabilization and maintenance of water under laboratory conditions. Practical testing of the feasibility of its inoculation to speed up BSC recovery in the field was also conducted in this experiment. This strain stimulated the heterotrophic community assembly in the topsoil layer (0-2 cm) before the commencement of autotrophic cyanobacteria, while also significantly increasing the number of bacteria, actinomycetes, and content of total phosphorus, available nitrogen, and available phosphorus. However, the low nitrogenase activity (NA) (0.57 µmol/h) that was observed caused us to doubt the previous identification as Azotobacter Beijerinck that was based on physiological and biochemical properties. A phylogenetic analysis based on 16S rRNA gene sequences revealed that this strain was a member of the genus Paenibacillus. It exhibited the closest phylogenetic affinity and highest sequence similarity to the strain Paenibacillus mucilaginosus VKPM B-7519 (sequence similarity 99.698%), which is well known as a typical silicate-weathering bacteria that releases lots of nutritional ions from minerals and the soil. Because P. mucilaginosus can excrete carbonic anhydrase (CA) to capture atmospheric CO2 through hydration of CO2 , it is possible that KLBB0001 might use a similar strategy for heterotrophs in the BSCs to sequester CO2 from the air. Because of its potential role in the reestablishment of the BSC ecosystem due to its ability to improve water relations, sand stabilization, and chemical erosion, EPS-producing bacterial inoculation was concluded to be a suitable and effective treatment for BSC recovery, especially in environments with limited water and nutrients.

[Establishment and analysis of chronic periodontitis and atherosclerosis model in Wistar rat].

OBJECTIVE: To investigate the possible correlation between atherosclerosis and chronic periodontitis by establishing an animal model of chronic periodontitis and atherosclerosis in Wistar rat. METHODS: Sixty male Wistar rats were divided into four groups: A (control group), B (chronic periodontitis group), C (atherosclerosis group), D (chronic periodontitis accompany with atherosclerosis group). Every group was accepted the corresponding treatment. Animals were sacrificed after 12 weeks. The periodontal index, levels of serum total cholesterol (TC) and low-density lipoprotein (LDL), the concentration of TNF-alpha and matrix metalloproteinase (MMP-3) were examined. The severity of chronic periodontitis and atherosclerosis was quantified by histopathology. The date were statistically analyzed. RESULTS: Through detection of periodontal tissue of experimental teeth, serum and histopathology, animal models were successful. Histopathologic observation revealed:obvious inflammation of periodontal tissue was observed in group B and D. Attachment loss level in group B [(137.86 +/- 28.39) microm] and D [(162.36 +/- 22.69) microm] was higher than that in group A [(4.26 +/- 1.07) microm] and C [(68.07 +/- 18.25) microm] (P < 0.05), and that in group C was higher than group A (P < 0.05). Atherosclerotic lesions of abdominal aorta were formed in group C and D. The level of TC, LDL in group C and D was higher than that in group A and B (P < 0.05), and that in group D was higher than group C (P < 0.05). Animals in group B and D showed higher level of TNF-alpha, MMP-3 in serum than that in group A and C (P < 0.05). There was no correlation between the level of MMP-3 and TC (P = 0.971) or LDL (P = 0.604). CONCLUSIONS: Chronic periodontitis may be a risk factor and contribute to the pathogenesis of atherosclerosis. MMP-3 may be an independent risk factor of atherosclerosis exclude TC and LDL.

Mapping quantitative trait loci using naturally occurring genetic variance among commercial inbred lines of maize (Zea mays L.).

Many commercial inbred lines are available in crops. A large amount of genetic variation is preserved among these lines. The genealogical history of the inbred lines is usually well documented. However, quantitative trait loci (QTL) responsible for the genetic variances among the lines are largely unexplored due to lack of statistical methods. In this study, we show that the pedigree information of the lines along with the trait values and marker information can be used to map QTL without the need of further crossing experiments. We develop a Monte Carlo method to estimate locus-specific identity-by-descent (IBD) matrices. These IBD matrices are further incorporated into a mixed-model equation for variance component analysis. QTL variance is estimated and tested at every putative position of the genome. The actual QTL are detected by scanning the entire genome. Applying this new method to a well-documented pedigree of maize (Zea mays L.) that consists of 404 inbred lines, we mapped eight QTL for the maize male flowering trait, growing degree day heat units to pollen shedding (GDUSHD). These detected QTL contributed >80% of the variance observed among the inbred lines. The QTL were then used to evaluate all the inbred lines using the best linear unbiased prediction (BLUP) technique. Superior lines were selected according to the estimated QTL allelic values, a technique called marker-assisted selection (MAS). The MAS procedure implemented via BLUP may be routinely used by breeders to select superior lines and line combinations for development of new cultivars.

Genetic analysis of the low critical sterility temperature point in photoperiod-thermo sensitive genic male sterile rice.

It has been a long haul but photoperiod- and thermo-sensitive genic male sterile (PTGMS) rice has not been freely used in hybrid rice production because there are two perplexing problems corresponding to the critical sterility temperature point (CSTP): the uncertainty of the CSTP segregating pattern and the instability of CSTP for every originally useful line. N5088S, the most widely commercialized japonica-type PTGMS line in China, also saw that its CSTP variants have been isolated but with all other agronomic characteristics unchanged. In this report we analyzed the genetic basis of CSTP, by employing the iterated expectation and conditional maximization (IECM) algorithm on four tiller-splitting-formed sets of seven generations from N5088S and its CSTP-variant H5088S, each set treated with one temperature regime. The main results indicated that there are two dominant major genes and polygene, as well as their respective epistasis conditioning the CSTP in the 23.5 degrees C regime. Based on the results obtained, the strategy for breeding of PTGMS lines with stable low CSTP was outlined.