Analysis of expressed sequence tags generated from full-length enriched cDNA libraries of melon

Abstract Background Melon (Cucumis melo), an economically important vegetable crop, belongs to the Cucurbitaceae family which includes several other important crops such as watermelon, cucumber, and pumpkin. It has served as a model system for sex determination and vascular biology studies. However, genomic resources currently available for melon are limited. Result We constructed eleven full-length enriched and four standard cDNA libraries from fruits, flowers, leaves, roots, cotyledons, and calluses of four different melon genotypes, and generated 71,577 and 22,179 ESTs from full-length enriched and standard cDNA libraries, respectively. These ESTs, together with ~35,000 ESTs available in public domains, were assembled into 24,444 unigenes, which were extensively annotated by comparing their sequences to different protein and functional domain databases, assigning them Gene Ontology (GO) terms, and mapping them onto metabolic pathways. Comparative analysis of melon unigenes and other plant genomes revealed that 75% to 85% of melon unigenes had homologs in other dicot plants, while approximately 70% had homologs in monocot plants. The analysis also identified 6,972 gene families that were conserved across dicot and monocot plants, and 181, 1,192, and 220 gene families specific to fleshy fruit-bearing plants, the Cucurbitaceae family, and melon, respectively. Digital expression analysis identified a total of 175 tissue-specific genes, which provides a valuable gene sequence resource for future genomics and functional studies. Furthermore, we identified 4,068 simple sequence repeats (SSRs) and 3,073 single nucleotide polymorphisms (SNPs) in the melon EST collection. Finally, we obtained a total of 1,382 melon full-length transcripts through the analysis of full-length enriched cDNA clones that were sequenced from both ends. Analysis of these full-length transcripts indicated that sizes of melon 5' and 3' UTRs were similar to those of tomato, but longer than many other dicot plants. Codon usages of melon full-length transcripts were largely similar to those of Arabidopsis coding sequences. Conclusion The collection of melon ESTs generated from full-length enriched and standard cDNA libraries is expected to play significant roles in annotating the melon genome. The ESTs and associated analysis results will be useful resources for gene discovery, functional analysis, marker-assisted breeding of melon and closely related species, comparative genomic studies and for gaining insights into gene expression patterns.This work was supported by Research Grant Award No. IS-4223-09C from BARD, the United States-Israel Binational Agricultural Research and Development Fund, and by SNC Laboratoire ASL, de Ruiter Seeds B.V., Enza Zaden B.V., Gautier Semences S.A., Nunhems B.V., Rijk Zwaan B.V., Sakata Seed Inc, Semillas Fitó S.A., Seminis Vegetable Seeds Inc, Syngenta Seeds B.V., Takii and Company Ltd, Vilmorin and Cie S.A. and Zeraim Gedera Ltd (all of them as part of the support to ICuGI). CC was supported by CNRS ERL 8196.Peer Reviewe

Crack Evolution Characteristics and Cracking Mechanism of Red Beds in Central Sichuan during Seepage and Swelling

Crack is one of the important factors affecting the engineering characteristics of expansive rock and soil. In order to study the evolution characteristics and cracking mechanism of red beds in Central Sichuan during seepage and swelling, multiple groups of cracking tests are conducted under different initial states with a self-made device. In addition, combining swelling-softening mechanism of expansive rock and numerical analysis, the swelling-cracking mechanism is studied. The following research results are obtained. (1) The evolution process of swelling cracks is divided into three stages: the generation stage, the rapid development stage, and the stabilization stage. In the rapid development stage, the increase in the crack degree accounts for 90% of the whole process. (2) The final crack degree of the sample is related to the initial water content, water absorption method, and clay mineral content. The lower the initial water content, the greater the final crack degree of the sample. The final crack degree under the soaking water absorption method is greater than that under the capillary water absorption method, and the final crack degree of mudstone is greater than that of argillaceous sandstone and sandstone. (3) The development of swelling cracks is controlled by three significant values of water absorption, which are w1, w2, and w3, respectively, representing the beginning of cracking, the starting of the rapid development stage, and the starting of the stabilization stage. Among them, w2 is of great significance in engineering practice. It shows that the development of cracks has entered a stage of rapid development, and the crack degree in this stage will increase exponentially with water absorption. (4) Uneven water absorption and uneven distribution of clay minerals lead to uneven swelling of expansive rock, which in turn generates swelling stress. Under the combined action of swelling stress and water swelling-softening, the internal structure of the rock is destroyed, leading to the generation and development of the cracks. Due to the different causes of uneven expansion, the mechanical mechanism of cracking and the shape of the resulting cracks will be different

Study on Creep Characteristics of Expansive Soil in High-Fill Channel of South-to-North Water Transfer Project

In the Nanyang section of the midroute of the South-to-North Water Transfer Project, the expansive soil is often used as a filler for high-fill channels. After the channel is stabilized, the expansive soil undergoes creep deformation over time. Studying the creep characteristics of expansive soils in different environments is particularly important for evaluating the safe operation of high-fill channels. In the current study, the creep test of expansive soil under different moisture content and dry density was carried out. It is proposed that the slope of the fitted straight line in the compression curve of the expansive soil can be used to represent the secondary consolidation coefficient of unsaturated expansive soil, and the variation law of the secondary consolidation coefficient under different environmental factors is obtained. The modified Bjerrum calculation method considering the influence of additional load and lateral deformation yields the postexpansion soil settlement curve model to determine the control index range of the project site. Moreover, it is also observed that the secondary consolidation coefficient of unsaturated expansive soil increases with the increase of moisture content and decreases with the increase of dry density. The coefficient of secondary compression of unsaturated expansive soil is linearly related to dry density and moisture content. After the preconsolidation treatment of the expansive soil, when the load level is less than the preload, the secondary consolidation coefficient is smaller, otherwise the secondary consolidation coefficient is larger

Strength Characteristics and Slope Stability Analysis of Expansive Soil with Filled Fissures

Fissured expansive soils were widely distributed in the South-to-North Water Transfer Project. Most of the fissures were filled with clay, which controlled the stability of the slope. With the method of layered filling—bevel cutting—refilling and a modular design idea, the sample with a filled fissure preparation device for triaxial test was designed. After setting the filled fissures of gray-green clay in the expansive soil, triaxial tests were carried out for the samples with no filled fissures and with filled fissures with inclination angles of 15°, 30°, and 45°. Then, considering the spatial distribution and the strength of the filled fissures in the slope, the stability analysis method for the expansive soil slope with filled fissures was proposed. The stability of a typical slope in Nanyang was analyzed. The results show that the c of expansive soil with filled fissures was about 12 to 15 kPa and the φ was 3° to 6°. Filled fissures had an attenuation effect on the strength of the expansive soil. The larger the inclination of filled fissures, the more significant the effect of soil strength attenuation. The fissured slope stability was controlled by the filled fissures. The sliding surface was affected by the vertical fissures on the top of the slope and the slow-inclined long-large fissures in the slope, and the shape of the sliding surface was a broken line, which was basically consistent with the actual landslide

A Hypoelastic Dynamic Constitutive Model to Account for the Hysteretic Behaviour of Soil Subjected to Cyclic Loads

To reduce the difficulties associated with dynamic constitutive models, a model was established for soil in this study based on hypoelasticity. The stress-strain relationship in soil under a cyclic load was divided into three stages: initial loading, unloading, and reloading. The stress-strain relationship in each stage was ascertained using a hyperbolic equation. On this basis, the physical significance of the parameters in the model and their method of determination were described. The effects of the parameters on the stress-strain relationship were investigated and the integration algorithm of the model was established. Finally, the rationality of the proposed model was verified by conducting triaxial tests under conventional and cyclic loads. The results show that the model is able to adequately demonstrate all the stress-strain relations in the soil under both static and dynamic loads

Stability Control of Staged Filling Construction on Soft Subsoil Using Hyperbolic Settlement Prediction Method: A Case Study of a Tidal Flat in China

An improved method, which combines in situ measured settlement data, hyperbolic method, and deep lateral displacement rate, is presented in this study to predict the consolidation and stability of the ground, which can be used in conducting staged filling construction on soft subsoil. A case history of a highway embankment construction in a tidal flat with thick mucky clay is studied in Xia Pu, China. Preloading with the prefabricated vertical drain method is adopted to accelerate the consolidation of a subgrade. The field behavior of soft ground under filling load is observed through in situ monitoring sensors in four typical sections. The final ground settlement in each stage is determined using the field monitoring data based on the hyperbolic settlement prediction method. For each stage of graded filling load, the ground settlement with a strain consolidation degree of 95% is defined as the standard settlement, and the corresponding settlement time is set as the standard settlement time. The preloading period is estimated according to the standard settlement time. The deep lateral displacement rate of the ground is monitored to control the stability of the foundation and recommended to guide the embankment construction. Results indicate that the presented method can predict the preloading time of graded filling, reduce the frequency of observation, and ensure the consolidation and stability of the ground

Study on the dynamic development law of fissure in expansive soil under different soil thickness

Fissures are an important factor to induce slope instability of expansive soil channel, which destroys the integrity of soil mass and deteriorates soil mass. Currently, the research is limited to the fissures in the plane direction, and it is very important to reveal the development mechanism of fissures in expansive soils along the depth direction by studying the development law of fissures in expansive soils with different thicknesses. In this study, taking expansive soil on channel slope of the Middle Route Project of South-to-North Water Transfer as an example, crack expansion tests with thickness of 10 mm, 20 mm, 30 mm and 40 mm are carried out based on self-designed crack expansion test device. An innovative test method for volumetric fracturing rate is proposed and the following conclusions are drawn: (1) the later the cracking time of soil body is, the lower the water content of cracking and the higher the water content after stabilization when the soil body is thicker; (2) When the fissures develop in soils of different thicknesses, their plane fissure rate changes with time in accordance with the logistic law; (3) Volumetric fracturing increases significantly with thickness; (4) The development of fissures is the form of stress release of soil mass, and the release along depth direction is the main form for soil mass with large thickness. (5) It is of great significance to study the law of fracture development in depth direction for further exploring the mechanism of fracture propagation

Laboratory Model Tests on Flow Erosion Failure Mechanism of a Slope Consisting of Anqing Group Clay Gravel Layer

The Anqing group clay gravel layer is a special geological body composed of gravel and clay. In excavation projects, involving this soil, such a gravel layer, is prone to slope collapse and instability under the influence of rainfall. To clearly understand the failure mechanism and influencing factors of clay gravel slopes, an indoor artificial rainfall erosion model testing was carried out to analyse the effect of various slope ratios, gravel contents, and rainfall intensities. The slope erosion damage form, runoff rate, infiltration rate, scoured material, and slope stability of the clay gravel slope were studied. The test results show that sloping surfaces of the gentle slope were mainly damaged by erosion, and the degree of damage gradually increased from the top to the bottom of the sloping surface; however, the stability of the surface was good. In the case of the sloping surface layer of the steep slope, large-scale landslides occurred, and the stability of the surface was poor. When the gravel content was small, the surface failure was manifested as a gully failure. When the gravel content was large, it was manifested as a “layer-by-layer sliding” failure. The degree of influence of different conditions on the stable runoff rate was as follows: rainfall intensity>slope ratio>gravel content. The degree of influence of the parameters on the stable infiltration rate was as follows: slope ratio>rainfall intensity>gravel content. On gentle slopes, the total mass of the scoured material was inversely proportional to the gravel content and directly proportional to the rainfall intensity; on a steep slope, the total mass of the scoured material increased with an increase in the rainfall intensity and gravel content. Moreover, the slope ratio was the key influencing factor to decide whether there was gravel in the scoured material

Swelling behaviors of heterogeneous red-bed mudstone subjected to different vertical stresses

In this study, the axial swelling strain of red-bed mudstone under different vertical stresses are measured by swell-under-load method, and the microstructure of mudstone after hygroscopic swelling is studied by mercury intrusion porosimetry (MIP). The weakening coefficient and Weibull distribution function are introduced into the coupling model of mudstone moisture diffusion–swelling deformation–fracture based on finite–discrete element method (FDEM). The weakening effect of moisture on mudstone's mechanical parameters, as well as the heterogeneity of swelling deformation and stress distribution, is considered. The microcrack behavior and energy evolution of mudstone during hygroscopic swelling deformation under different vertical stresses are studied. The results show that the axial swelling strain of mudstone decreases with increase of the vertical stress. At low vertical stresses, moisture absorption in mudstone leads to formation of cracks caused by hydration-induced expansion. Under high vertical stresses, a muddy sealing zone forms on the mudstone surface, preventing further water infiltration. The simulation results of mudstone swelling deformation also demonstrate that it involves both swelling of the mudstone matrix and swelling caused by crack expansion. Notably, crack expansion plays a dominant role in mudstone swelling. With increasing vertical stress, the cracks in mudstone change from tensile cracks to shear cracks, resulting in a significant reduction in the total number of cracks. While the evolution of mudstone kinetic energy shows similarities under different vertical stresses, the evolution of strain energy varies significantly due to the presence of different types of cracks in the mudstone. The findings provide a theoretical basis for understanding the hygroscopic swelling deformation mechanism of red-bed mudstone at various depths