A BAC-based physical map of Brachypodium distachyon and its comparative analysis with rice and wheat

<p>Abstract</p> <p>Background</p> <p><it>Brachypodium distachyon </it>(<it>Brachypodium</it>) has been recognized as a new model species for comparative and functional genomics of cereal and bioenergy crops because it possesses many biological attributes desirable in a model, such as a small genome size, short stature, self-pollinating habit, and short generation cycle. To maximize the utility of <it>Brachypodiu</it>m as a model for basic and applied research it is necessary to develop genomic resources for it. A BAC-based physical map is one of them. A physical map will facilitate analysis of genome structure, comparative genomics, and assembly of the entire genome sequence.</p> <p>Results</p> <p>A total of 67,151 <it>Brachypodium </it>BAC clones were fingerprinted with the SNaPshot HICF fingerprinting method and a genome-wide physical map of the <it>Brachypodium </it>genome was constructed. The map consisted of 671 contigs and 2,161 clones remained as singletons. The contigs and singletons spanned 414 Mb. A total of 13,970 gene-related sequences were detected in the BAC end sequences (BES). These gene tags aligned 345 contigs with 336 Mb of rice genome sequence, showing that <it>Brachypodium </it>and rice genomes are generally highly colinear. Divergent regions were mainly in the rice centromeric regions. A dot-plot of <it>Brachypodium </it>contigs against the rice genome sequences revealed remnants of the whole-genome duplication caused by paleotetraploidy, which were previously found in rice and sorghum. <it>Brachypodium </it>contigs were anchored to the wheat deletion bin maps with the BES gene-tags, opening the door to <it>Brachypodium</it>-Triticeae comparative genomics.</p> <p>Conclusion</p> <p>The construction of the <it>Brachypodium </it>physical map, and its comparison with the rice genome sequence demonstrated the utility of the SNaPshot-HICF method in the construction of BAC-based physical maps. The map represents an important genomic resource for the completion of <it>Brachypodium </it>genome sequence and grass comparative genomics. A draft of the physical map and its comparisons with rice and wheat are available at <url>http://phymap.ucdavis.edu/brachypodium/</url>.</p

Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes

<p>Abstract</p> <p>Background</p> <p>A genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their respective genomes. The same requirements complicate the development and deployment of single nucleotide polymorphism (SNP) markers in polyploid species. We report here a strategy that satisfies these requirements and deploy it in the sequencing of genes in cultivated hexaploid wheat (<it>Triticum aestivum</it>, genomes AABBDD) and wild tetraploid wheat (<it>Triticum turgidum </it>ssp. <it>dicoccoides</it>, genomes AABB) from the putative site of wheat domestication in Turkey. Data are used to assess the distribution of diversity among and within wheat genomes and to develop a panel of SNP markers for polyploid wheat.</p> <p>Results</p> <p>Nucleotide diversity was estimated in 2114 wheat genes and was similar between the A and B genomes and reduced in the D genome. Within a genome, diversity was diminished on some chromosomes. Low diversity was always accompanied by an excess of rare alleles. A total of 5,471 SNPs was discovered in 1791 wheat genes. Totals of 1,271, 1,218, and 2,203 SNPs were discovered in 488, 463, and 641 genes of wheat putative diploid ancestors, <it>T. urartu</it>, <it>Aegilops speltoides</it>, and <it>Ae. tauschii</it>, respectively. A public database containing genome-specific primers, SNPs, and other information was constructed. A total of 987 genes with nucleotide diversity estimated in one or more of the wheat genomes was placed on an <it>Ae. tauschii </it>genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed.</p> <p>Conclusions</p> <p>In a young polyploid, exemplified by <it>T. aestivum</it>, ancestral species are the primary source of genetic diversity. Low effective recombination due to self-pollination and a genetic mechanism precluding homoeologous chromosome pairing during polyploid meiosis can lead to the loss of diversity from large chromosomal regions. The net effect of these factors in <it>T. aestivum </it>is large variation in diversity among genomes and chromosomes, which impacts the development of SNP markers and their practical utility. Accumulation of new mutations in older polyploid species, such as wild emmer, results in increased diversity and its more uniform distribution across the genome.</p

Structural characteristics and deep-water hydrocarbon accumulation model of the Scotian Basin, Eastern Canada

Commercial hydrocarbon reservoirs have been discovered in shallow-water areas of the Scotian Basin, Eastern Canada. However, knowledge about the structure and hydrocarbon accumulation characteristics of the basin is still insufficient, which constrains the oil and gas exploration in deep-water areas. Based on comprehensive data of magnetic anomalies, seismic survey, and drilling, this study determines the structure characteristics of the Scotian Basin and its hydrocarbon accumulation conditions in deep waters and evaluates the deep-water hydrocarbon exploration potential. The transform faults and basement structures in the northern basin control the sedimentary framework showing thick strata in east and thin strata in west of the basin. The bowl-shaped depression formed by thermal subsidence during the transitional phase and the confined environment (micro basins) caused by salt tectonics provide favorable conditions for the development of source rocks during the depression stage (also referred to as the depression period sequence) of the basin. The progradation of large shelf-margin deltas during the drift phase and steep continental slope provide favorable conditions for the deposition of slope-floor fans on continental margins of the basin. Moreover, the source-reservoir assemblage comprising the source rocks within the depression stage and the turbidite sandstones on the continental margin in the deep waters may form large deep-water turbidite sandstone reservoirs. This study will provide a valuable reference for the deep-water hydrocarbon exploration in the Scotian Basin

Track planning of coal gangue sorting robot for dynamic target stable grasping

When the robot is used to sort coal gangue, in order to solve the problems such as inaccurate positioning of gangue, failure of grasping by end of the manipulator and load impact caused by slippage and left-right swing of belt conveyor, a track planning method of coal gangue sorting robot for dynamic target stable grasping based on machine vision is proposed. Firstly, the target gangue is identified and the pose of the target gangue is obtained by using the HU moment invariants image matching algorithm. Secondly, the kinematic equations of the robot and the camera-robot are established respectively, and the forward and inverse solutions are carried out to realize the accurate positioning of the target gangue based on vision. Finally, the position-velocity-acceleration three-loop PID control algorithm is used to dynamically track the target gangue. The input of the position loop controller is the obtained precise position of the target gangue, the output of the position loop controller is used as the input of the velocity loop controller, the output of the velocity loop controller is used as the input of the acceleration loop controller, and the output of the acceleration loop controller is superimposed on the servo motor. Therefore, the end of the manipulator and the target gangue can achieve the effect of synchronous movement of position and velocity, so as to achieve stable and fast grasping. Matlab is used to compare the three-loop PID control algorithm, the three-dimensional proportional navigation algorithm and the three-dimensional biased proportional navigation algorithm. The results show that in the following, synchronous and intercepting cases of the tracking and grasping of dynamic targets, the response time and tracking and grasping time of the three-loop PID control algorithm are better than those of the proportional navigation algorithm and the biased proportional navigation algorithm. And the three-loop PID control algorithm is continuous and smooth in the speed and acceleration of each axis in the whole process without sudden change, which can realize synchronous tracking of dynamic targets and precise grasping. The three-loop PID control algorithm, proportional navigation algorithm and biased proportional navigation algorithm are applied to the coal gangue sorting system platform to carry out adaptability experiments. The results show that the three algorithms do not exceed the limit of each joint during robot operation. The average time of the three-loop PID control algorithm to complete the grasping is shorter than those of the proportional navigation algorithm and the biased proportional navigation algorithm. The average speed error of the three-loop PID control algorithm at the grasping point is about 1 mm/s, and the tracking speed error is small, which can meet the requirements of synchronous tracking and precise grasping of high-speed targets

BatchPrimer3: A high throughput web application for PCR and sequencing primer design

Abstract Background Microsatellite (simple sequence repeat – SSR) and single nucleotide polymorphism (SNP) markers are two types of important genetic markers useful in genetic mapping and genotyping. Often, large-scale genomic research projects require high-throughput computer-assisted primer design. Numerous such web-based or standard-alone programs for PCR primer design are available but vary in quality and functionality. In particular, most programs lack batch primer design capability. Such a high-throughput software tool for designing SSR flanking primers and SNP genotyping primers is increasingly demanded. Results A new web primer design program, BatchPrimer3, is developed based on Primer3. BatchPrimer3 adopted the Primer3 core program as a major primer design engine to choose the best primer pairs. A new score-based primer picking module is incorporated into BatchPrimer3 and used to pick position-restricted primers. BatchPrimer3 v1.0 implements several types of primer designs including generic primers, SSR primers together with SSR detection, and SNP genotyping primers (including single-base extension primers, allele-specific primers, and tetra-primers for tetra-primer ARMS PCR), as well as DNA sequencing primers. DNA sequences in FASTA format can be batch read into the program. The basic information of input sequences, as a reference of parameter setting of primer design, can be obtained by pre-analysis of sequences. The input sequences can be pre-processed and masked to exclude and/or include specific regions, or set targets for different primer design purposes as in Primer3Web and primer3Plus. A tab-delimited or Excel-formatted primer output also greatly facilitates the subsequent primer-ordering process. Thousands of primers, including wheat conserved intron-flanking primers, wheat genome-specific SNP genotyping primers, and Brachypodium SSR flanking primers in several genome projects have been designed using the program and validated in several laboratories. Conclusion BatchPrimer3 is a comprehensive web primer design program to develop different types of primers in a high-throughput manner. Additional methods of primer design can be easily integrated into future versions of BatchPrimer3. The program with source code and thousands of PCR and sequencing primers designed for wheat and Brachypodium are accessible at http://wheat.pw.usda.gov/demos/BatchPrimer3/.</p

Various types of primer design can be selected from the primer type pull-up combo-box, and corresponding parameter setting panels are placed below the sequence input box

Pre-analysis of input sequences can be performed before batch primer design.<p><b>Copyright information:</b></p><p>Taken from "BatchPrimer3: A high throughput web application for PCR and sequencing primer design"</p><p>http://www.biomedcentral.com/1471-2105/9/253</p><p>BMC Bioinformatics 2008;9():253-253.</p><p>Published online 29 May 2008</p><p>PMCID:PMC2438325.</p><p></p

Any unwanted regions for primer design in sequences can be masked using a pair of "" to keep the sequence unchanged

Alternatively, the unwanted regions can be replaced with "Ns" (). The included region can be specified by one pair "{}" and only one included region can be masked.<p><b>Copyright information:</b></p><p>Taken from "BatchPrimer3: A high throughput web application for PCR and sequencing primer design"</p><p>http://www.biomedcentral.com/1471-2105/9/253</p><p>BMC Bioinformatics 2008;9():253-253.</p><p>Published online 29 May 2008</p><p>PMCID:PMC2438325.</p><p></p

The picture shows the primer design results of sequence ID (rs16791736) for tetra-primer ARMS PCR

<p><b>Copyright information:</b></p><p>Taken from "BatchPrimer3: A high throughput web application for PCR and sequencing primer design"</p><p>http://www.biomedcentral.com/1471-2105/9/253</p><p>BMC Bioinformatics 2008;9():253-253.</p><p>Published online 29 May 2008</p><p>PMCID:PMC2438325.</p><p></p