Genome-wide characterization of the biggest grass, bamboo, based on 10,608 putative full-length cDNA sequences

<p>Abstract</p> <p>Background</p> <p>With the availability of rice and sorghum genome sequences and ongoing efforts to sequence genomes of other cereal and energy crops, the grass family (Poaceae) has become a model system for comparative genomics and for better understanding gene and genome evolution that underlies phenotypic and ecological divergence of plants. While the genomic resources have accumulated rapidly for almost all major lineages of grasses, bamboo remains the only large subfamily of Poaceae with little genomic information available in databases, which seriously hampers our ability to take a full advantage of the wealth of grass genomic data for effective comparative studies.</p> <p>Results</p> <p>Here we report the cloning and sequencing of 10,608 putative full length cDNAs (FL-cDNAs) primarily from Moso bamboo, <it>Phyllostachys heterocycla </it>cv. <it>pubescens</it>, a large woody bamboo with the highest ecological and economic values of all bamboos. This represents the third largest FL-cDNA collection to date of all plant species, and provides the first insight into the gene and genome structures of bamboos. We developed a Moso bamboo genomic resource database that so far contained the sequences of 10,608 putative FL-cDNAs and nearly 38,000 expressed sequence tags (ESTs) generated in this study.</p> <p>Conclusion</p> <p>Analysis of FL-cDNA sequences show that bamboo diverged from its close relatives such as rice, wheat, and barley through an adaptive radiation. A comparative analysis of the lignin biosynthesis pathway between bamboo and rice suggested that genes encoding caffeoyl-CoA O-methyltransferase may serve as targets for genetic manipulation of lignin content to reduce pollutants generated from bamboo pulping.</p

Genome-wide identification and analysis of heterotic loci in three maize hybrids

Heterosis, or hybrid vigour, is a predominant phenomenon in plant genetics, serving as the basis of crop hybrid breeding, but the causative loci and genes underlying heterosis remain unclear in many crops. Here, we present a large-scale genetic analysis using 5360 offsprings from three elite maize hybrids, which identifies 628 loci underlying 19 yield-related traits with relatively high mapping resolutions. Heterotic pattern investigations of the 628 loci show that numerous loci, mostly with complete–incomplete dominance (the major one) or overdominance effects (the secondary one) for heterozygous genotypes and nearly equal proportion of advantageous alleles from both parental lines, are the major causes of strong heterosis in these hybrids. Follow-up studies for 17 heterotic loci in an independent experiment using 2225 F2 individuals suggest most heterotic effects are roughly stable between environments with a small variation. Candidate gene analysis for one major heterotic locus (ub3) in maize implies that there may exist some common genes contributing to crop heterosis. These results provide a community resource for genetics studies in maize and new implications for heterosis in plants

A noncanonical vacuolar sugar transferase required for biosynthesis of antimicrobial defense compounds in oat

Plants produce an array of natural products with important ecological functions. These compounds are often decorated with oligosaccharide groups that influence bioactivity, but the biosynthesis of such sugar chains is not well understood. Triterpene glycosides (saponins) are a large family of plant natural products that determine important agronomic traits, as exemplified by avenacins, antimicrobial defense compounds produced by oats. Avenacins have a branched trisaccharide moiety consisting of L-arabinose linked to 2 D-glucose molecules that is critical for antifungal activity. Plant natural product glycosylation is usually performed by uridine diphosphate-dependent glycosyltransferases (UGTs). We previously characterized the arabinosyltransferase that initiates the avenacin sugar chain; however, the enzymes that add the 2 remaining D-glucose molecules have remained elusive. Here we characterize the enzymes that catalyze these last 2 glucosylation steps. AsUGT91G16 is a classical cytosolic UGT that adds a 1,2-linked D-glucose molecule to L-arabinose. Unexpectedly, the enzyme that adds the final 1,4-linked D-glucose (AsTG1) is not a UGT, but rather a sugar transferase belonging to Glycosyl Hydrolase family 1 (GH1). Unlike classical UGTs, AsTG1 is vacuolar. Analysis of oat mutants reveals that AsTG1 corresponds to Sad3, a previously uncharacterized locus shown by mutation to be required for avenacin biosynthesis. AsTG1 and AsUGT91G16 form part of the avenacin biosynthetic gene cluster. Our demonstration that a vacuolar transglucosidase family member plays a critical role in triterpene biosynthesis highlights the importance of considering other classes of carbohydrate-active enzymes in addition to UGTs as candidates when elucidating pathways for the biosynthesis of glycosylated natural products in plants

Fast Single-Parameter Energy Function Thresholding for Image Segmentation Based on Region Information

To solve the problems of image threshold segmentation based on weak continuous constraint theory, the running time is long, and the two parameters need to be selected manually, and therefore a fast single-parameter energy function thresholding for image segmentation based on region information (FSEFTISRI) is proposed in this paper. The proposed FSEFTISRI algorithm uses simple linear iterative clustering (SLIC) technology to pre-block the image, extract the image super-pixels, and then map the image super-pixels to the interval type-2 fuzzy set (IT2FS), so as to construct the single-parameter energy function to search the optimal threshold, and adaptively select the penalty parameters in the energy function through the class uncertainty theory. On a non-destructive testing (NDT) database and Berkeley segmentation datasets and benchmarks (BSDS), the proposed FSEFTISRI is compared with five related algorithms. The average misclassification error (ME) of the proposed FSEFTISRI algorithm on NDT and BSDS are 0.0466 and 0.0039, respectively. The results show that the proposed FSEFTISRI has acquired more satisfactory results in visual effect and evaluation index, and the running time of the proposed FSEFTISRI algorithm is shorter, which shows the effectiveness of the proposed FSEFTISRI

Airy transform of an electron Landau state in a longitudinal constant magnetic field

In this article, a relationship between the electron beams in a longitudinal constant magnetic field and light beams in a parabolic refractive index distribution medium is revealed and demonstrated analytically. We propose a new method to work out the properties of the singularity in that analytical expression and have a discussion on some universal features of electron beams in a longitudinal constant magnetic field. Based on the theories above, we introduce a new type of structured electron beams, which is the Airy transform of electron Landau states (ATLSs). We not only study the dynamic of ATLSs and the magnetic field analytically and numerically but also carry out the movement of centroid and the dual auto-focusing property of ATLSs. Moreover, we have a discussion on the influence on ATLSs of Airy control parameters and the parameters of electron Landau states

Distribution and gas-bearing properties of Permian igneous rocks in Sichuan Basin, SW China

Based on the analysis of outcrop, seismic, logging and drilling data, combined with exploration practice, the characteristics, distribution, reservoir performance and gas-bearing properties of Permian igneous rocks in Sichuan Basin are studied. The study shows that central volcanic eruptive facies are developed in Sichuan Basin, and their lithological assemblages and distribution characteristics show obvious differences. The igneous rocks are mainly distributed in three regions: the southwestern part of the basin has dominantly large- scale overflow facies basalts; the central and western part of the basin, Jianyang-Santai area, develop intrusive rocks, volcanic lavas (basalts) and pyroclastic rocks; and the eastern part of Sichuan, Dazhou-Liangping area, only develop diabase and basalts. Five aspects of understandings are achieved: (1) The Upper Permian igneous rocks can be divided into intrusive rocks and extrusive rocks, with the extrusive rocks as the main body. The chemical compositions of the extrusive rocks are characterized by both alkaline basalt and tholeiitic basalt, and belong to the subalkaline type of transitional basalt magma eruption. (2) There are obvious rhythmic structures vertically among overflow facies basalt, and the single rhythmic layer consists of, from bottom up, pyroclastic rocks (undeveloped), gray and dark gray porphyritic basalts (unstable), dark gray and purple microcrystalline-cryptocrystalline basalts, dark greyish green porous and amygdaloid basalts; the central volcanic eruption shows the rhythm and the vertical sequence of volcanic clastic rocks (agglomerates and breccias), volcanic lava, tuffaceous lava from bottom to top. (3) The pore types of basalt and pyroclastic rocks are diverse, mainly dissolution pore and de-vitrification micropore, but their physical properties are different. Basalt is characterized by ultra-low pore permeability, small reservoir thickness, and reservoirs are distributed in the upper and middle parts of the cycle, with poor lateral comparability. Volcanic clastic rocks are medium to high porous reservoirs (Well YT1: porosity: 8.66%−16.48%, average 13.76%) with large thickness and good reservoir quality. (4) Natural gas in basalts in southwestern basin mainly comes from Middle Permian, and natural gas in volcanic clastic rocks in central and western basin comes from Cambrian Qiongzhusi Formation. (5) Analysis of igneous reservoir-forming conditions in different areas shows that there are relatively insufficient gas sources and great differences in preservation conditions in southwestern basin. Reservoirs are poorly developed and gas-bearing is complex. The Jianyang-Santai area in the central and western part of Sichuan Basin has abundant hydrocarbon sources, developed reservoir, favorable preservation conditions and favorable gas geological conditions, and it is a favorable area for gas exploration. Key Words: Sichuan Basin, Upper Permian, Maokou Formation, igneous rock, volcanic lava, pyroclastic rock, reservoir property, gas bearing, natural gas reservoi

Analysis of Artificial Corner Reflector\u27s Radar Cross Section: a Physical Optics Perspective

Among many of the differential interferometric synthetic-aperture radar technologies, artificial corner reflectors (ACR) are widely used in monitoring earthquake deformation and urban subsidence due to their relative stability on synthetic-aperture radar (SAR) acquisition. Apparently, the detection and extraction of ACRs on remotely sensed images would be of utmost importance. Many different geometric types of ACRs are designed to achieve maximum detection. Among them, dihedral, rectangle trihedral, and pyramidal ACRs are the most commonly employed. The cost and difficulty of deploying ACRs in the field, however, render comparison among the three types rather impractical, if not impossible. The current study attempts to tackle the issue from a physical optics perspective. Adopting radar cross section (RCS) as the measure of ACRs\u27 detectability, we examined the relationships between the ACRs\u27 RCS under vertical polarity with various parameters including the radar incident angles, width and heights of the ACRs and the azimuthal angles. The analyses indicate that under vertical polarity, among the three types of ACRs, the rectangle trihedral ACR is the most tolerant to its deploying surroundings. To verify the physical optics analysis results, we collected ENVISAT data from a variety of deployed ACRs in the Yan-Huai Basin, China, and derived their reflectance characteristics. The field data agree with the theoretical analyses. From this practice, it seems that the physical optics method might prove to be a rather economical and effective approach to design and select appropriate ACRs in field deployment

Genome-wide identification and analysis of heterotic loci in three maize hybrids

Heterosis, or hybrid vigour, is a predominant phenomenon in plant genetics, serving as the basis of crop hybrid breeding, but the causative loci and genes underlying heterosis remain unclear in many crops. Here, we present a large-scale genetic analysis using 5360 offsprings from three elite maize hybrids, which identifies 628 loci underlying 19 yield-related traits with relatively high mapping resolutions. Heterotic pattern investigations of the 628 loci show that numerous loci, mostly with complete–incomplete dominance (the major one) or overdominance effects (the secondary one) for heterozygous genotypes and nearly equal proportion of advantageous alleles from both parental lines, are the major causes of strong heterosis in these hybrids. Follow-up studies for 17 heterotic loci in an independent experiment using 2225 F2 individuals suggest most heterotic effects are roughly stable between environments with a small variation. Candidate gene analysis for one major heterotic locus (ub3) in maize implies that there may exist some common genes contributing to crop heterosis. These results provide a community resource for genetics studies in maize and new implications for heterosis in plants