scholarly journals Genomic resources of broomcorn millet: demonstration and application of a high-throughput BAC mapping pipeline

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wei Xu ◽  
Mengjie Liang ◽  
Xue Yang ◽  
Hao Wang ◽  
Meizhong Luo
Keyword(s):  
Bac Library ◽  
Research Process ◽  
High Quality ◽  
Bac Clones ◽  
Broomcorn Millet ◽  
High Efficient ◽  
Sequencing Strategy ◽  
End Sequences ◽  
Genomic Resource ◽  
Efficient Water Use

Abstract Background With high-efficient water-use and drought tolerance, broomcorn millet has emerged as a candidate for food security. To promote its research process for molecular breeding and functional research, a comprehensive genome resource is of great importance. Results Herein, we constructed a BAC library for broomcorn millet, generated BAC end sequences based on the clone-array pooled shotgun sequencing strategy and Illumina sequencing technology, and integrated BAC clones into genome by a novel pipeline for BAC end profiling. The BAC library consisted of 76,023 clones with an average insert length of 123.48 Kb, covering about 9.9-fold of the 850 Mb genome. Of 9216 clones tested using our pipeline, 8262 clones were mapped on the broomcorn millet cultivar longmi4 genome. These mapped clones covered 308 of the 829 gaps left by the genome. To our knowledge, this is the only BAC resource for broomcorn millet. Conclusions We constructed a high-quality BAC libraray for broomcorn millet and designed a novel pipeline for BAC end profiling. BAC clones can be browsed and obtained from our website (http://eightstarsbio.com/gresource/JBrowse-1.16.5/index.html). The high-quality BAC clones mapped on genome in this study will provide a powerful genomic resource for genome gap filling, complex segment sequencing, FISH, functional research and genetic engineering of broomcorn millet.

scholarly journals Genomic Resources of Broomcorn Millet: Demonstration and Application of a High-throughput BAC Mapping Pipeline

2021 ◽  
Author(s):  
Wei Xu ◽  
Mengjie Liang ◽  
Xue Yang ◽  
Hao Wang ◽  
Meizhong Luo
Keyword(s):  
Bac Library ◽  
Research Process ◽  
High Quality ◽  
Bac Clones ◽  
Broomcorn Millet ◽  
High Efficient ◽  
Sequencing Strategy ◽  
End Sequences ◽  
Genomic Resource ◽  
Efficient Water Use

Abstract Background: With high-efficient water-use and drought tolerance, broomcorn millet has emerged as a candidate for food security. To promote its research process for molecular breeding and functional research, a comprehensive genome resource is of great importance. Results: Herein, we constructed a BAC library for broomcorn millet, generated BAC end sequences based on the clone-array pooled shotgun sequencing strategy and Illumina sequencing technology, and integrated BAC clones into genome by a novel pipeline for BAC end profiling. The BAC library is consisted of 76,023 clones with an average insert length of 123.48 Kb, covering about 9.9-fold of the 850 Mb genome. Of 9,216 clones tested using our pipeline, 8,262 clones were mapped on the broomcorn millet cultivar longmi4 genome. These mapped clones covered 308 of the 829 gaps left by the genome. To our knowledge, this is the only BAC resource for broomcorn millet.Conclusions: We constructed a high-quality BAC libraray for broomcorn millet and designed a novel pipeline for BAC end profiling. BAC clones can be browsed and obtained from our website (http://eightstarsbio.com/gresource/JBrowse-1.16.5/index.html). The high-quality BAC clones mapped on genome in this study will provide a powerful genomic resource for genome gap filling, complex segment sequencing, FISH, functional research, and genetic engineering of broomcorn millet.

scholarly journals Genomic Resources of Broomcorn Millet: Demonstration and Application of a High-throughput BAC Mapping Pipeline

2020 ◽  
Author(s):  
Wei Xu ◽  
Mengjie Liang ◽  
Hao Wang ◽  
Meizhong Luo
Keyword(s):  
Bac Library ◽  
Research Process ◽  
Bac Clones ◽  
Broomcorn Millet ◽  
High Efficient ◽  
Sequencing Strategy ◽  
End Sequences ◽  
Genomic Resource ◽  
The Cost ◽  
Efficient Water Use

AbstractBackgroundWith high-efficient water-use and drought tolerance, broomcorn millet has emerged as candidate for food security. To promote its research process for molecular breeding and functional research, a comprehensive genome resources is of great important.ResultsHerein, we constructed the first BAC library for broomcorn millet, generated BAC end sequences and integrated BAC clones into genome by a novel pipeline for BAC end profiling depending on clone-array pooled shotgun sequencing strategy and Illumina sequencing technology. The BAC library is consisted of 76,023 clones with average insert length of 123.48 Kb, about 9.9x coverage of 850 Mb genome. Then, 8262 of 9216 clones were mapped on broomcorn millet cultivar longmi4 genome using our pipeline. Furthermore, we also extracted and assembled unmapped reads against longmi4 genome. A total of 135 deletion sequences, 64 specific sequences and some sample contamination sequences were identified.ConclusionsBAC clones in this library can be browsed and obtained from our website (http://flyinguineapig.com/gresource/JBrowse-1.16.5/index.html). This pipeline designed for BAC end profiling can greatly reduce the cost of acquiring BAC end sequences and shorten the period of the experiment compared with the Sanger sequencing method. These high-quality BAC clones related with genome in this study provide a useful and convinient genomic resource for genome gap filling, complex segment sequencing, FISH, functional research, and genetic engineering.

Construction and characterization of bacterial artificial chromosome library of black-handed spider monkey (Ateles geoffroyi)

Genome ◽  
2004 ◽  
Vol 47 (2) ◽  
pp. 239-245 ◽  
Author(s):  
Yaping Qian ◽  
Li Jin ◽  
Bing Su
Keyword(s):  
Bacterial Artificial Chromosome ◽  
Large Scale ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Spider Monkey ◽  
Ateles Geoffroyi ◽  
Comparative Genomic ◽  
Average Insert Size ◽  
Bac Clones ◽  
Genomic Study

The large-insert genomic DNA library is a critical resource for genome-wide genetic dissection of target species. We constructed a high-redundancy bacterial artificial chromosome (BAC) library of a New World monkey species, the black-handed spider monkey (Ateles geoffroyi). A total of 193 152 BAC clones were generated in this library. The average insert size of the BAC clones was estimated to be 184.6 kb with the small inserts (50-100 kb) accounting for less than 3% and the non-recombinant clones only 1.2%. Assuming a similar genome size with humans, the spider monkey BAC library has about 11× genome coverage. In addition, by end sequencing of randomly selected BAC clones, we generated 367 sequence tags for the library. When blasted against human genome, they showed a good correlation between the number of hit clones and the size of the chromosomes, an indication of unbiased chromosomal distribution of the library. This black-handed spider monkey BAC library would serve as a valuable resource in comparative genomic study and large-scale genome sequencing of nonhuman primates.Key words: black-handed spider monkeys, Ateles geoffroyi, BAC library.

Welding of Thicker Steel Joints of Container Ships

2007 ◽  
Vol 23 (01) ◽  
pp. 46-52
Author(s):  
Osamu Baba ◽  
Yasuhisa Okumoto ◽  
Akinori Abe
Keyword(s):  
Plate Thickness ◽  
High Heat ◽  
Steel Plates ◽  
High Quality ◽  
Butt Welding ◽  
High Efficient ◽  
Steel Maker ◽  
Co2 Welding ◽  
High Heat Input ◽  
Steel Joints

Recently, many container ships have been built worldwide, and the size of them is skyrocketing to 10, 000 TEU (Twenty Equivalent Unit) capacity. As a result, the plate thickness in the area of upper deck torsion box becomes thicker and thicker with higher-strength steel, up to 60 mm, to keep longitudinal strength, and then the welding work becomes more difficult and severe. For such joints of super thick plates IHI Marine United Inc. Kure shipyard has established high-quality and high-efficient welding methods:Development of new steel plates. In order to weld the thicker plates by high heat input such as 450 KJ/cm, new steel plates were applied in cooperation with a steel maker in Japan.Automation of butt welding. Electro-gas arc welding was applied for skin plates, and CO2 welding robot system was also introduced for longitudinals around the torsion box.Establishment of high quality welding practice. Welding without defects became possible by establishing adequate groove shape and welding procedure, as a result of many welding tests and inspections. This paper describes the improved methods and the test results in detail.

scholarly journals Additive Modulated Perovskite Microstructures for High Performance Photodetectors

Micromachines ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1090
Author(s):  
Zhan Gao ◽  
Yifan Zheng ◽  
Guancheng Huang ◽  
Genjie Yang ◽  
Xinge Yu ◽  
...  
Keyword(s):  
Molecular Interactions ◽  
Dark Current ◽  
High Performance ◽  
Visible Region ◽  
Carbonyl Groups ◽  
High Quality ◽  
Inorganic Hybrid ◽  
Simple Route ◽  
High Efficient ◽  
Crystallographic Defects

Organic-inorganic hybrid perovskites have been widely used as light sensitive components for high-efficient photodetectors due to their superior optoelectronic properties. However, the unwanted crystallographic defects of perovskites typically result in high dark current, and thus limit the performance of the device. Herein, we introduce a simple route of microstructures control in MAPbI3 perovskites that associates with introducing an additive of 3,3,4,4-benzophenonetetracarboxylic dianhydridean (BPTCD) for crystallization adjustment of the perovskite film. The BPTCD additive can facilitate the formation of high-quality perovskite film with a compact and nearly pinhole-free morphology. Through characterizing the molecular interactions, it was found that the carbonyl groups in BPTCD is the key reason that promoted the nucleation and crystallization of MAPbI3. As a result, we obtained high-efficient and stable perovskite photodetectors with low dark current of 9.98 × 10−8 A at −0.5 V, an on/off ratio value of 103, and a high detectivity exceeding 1012 Jones over the visible region.

Numerical Study on the CZ Silicon Melt Convection for High Efficient Solar Cell

Solar Energy ◽  
2003 ◽  
Author(s):  
Tetsuo Munakata ◽  
Satoshi Someya
Keyword(s):  
Magnetic Field ◽  
Solar Cell ◽  
High Frequency ◽  
High Quality ◽  
High Efficient ◽  
Silicon Melt ◽  
Frequency Magnetic Field ◽  
High Frequency Magnetic Field ◽  
Melt Convection

Conversion efficiency of solar cell is strongly affected by quality of substrate and the quality of substrate is influenced by melt convection if the substrate crystal is grown by melt growth technique. Therefore, melt convection control techniques are important to produce a high quality single crystal. In this paper, we have proposed a high frequency magnetic field applied CZ method and investigated the effect of high frequency magnetic field on silicon melt convection. The result reveals that the high frequency magnetic fields affect the tendency of the melt convection: until certain intensity of the high frequency magnetic field, the melt convection is suppressed and above such intensity of the high frequency magnetic field, the melt convection intensity is enhanced. This result indicates that the melt convection can be controlled by the high frequency magnetic field and the high quality silicon single crystals will be grown by this method.

scholarly journals Use of a Mycobacterium tuberculosisH37Rv Bacterial Artificial Chromosome Library for Genome Mapping, Sequencing, and Comparative Genomics

1998 ◽  
Vol 66 (5) ◽  
pp. 2221-2229 ◽  
Author(s):  
Roland Brosch ◽  
Stephen V. Gordon ◽  
Alain Billault ◽  
Thierry Garnier ◽  
Karin Eiglmeier ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Bacterial Artificial Chromosome ◽  
Genome Mapping ◽  
Sequence Data ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Excellent Correlation ◽  
Sequencing Project ◽  
Polysaccharide Biosynthesis ◽  
Bac Clones

ABSTRACT The bacterial artificial chromosome (BAC) cloning system is capable of stably propagating large, complex DNA inserts in Escherichia coli. As part of the Mycobacterium tuberculosis H37Rv genome sequencing project, a BAC library was constructed in the pBeloBAC11 vector and used for genome mapping, confirmation of sequence assembly, and sequencing. The library contains about 5,000 BAC clones, with inserts ranging in size from 25 to 104 kb, representing theoretically a 70-fold coverage of the M. tuberculosisgenome (4.4 Mb). A total of 840 sequences from the T7 and SP6 termini of 420 BACs were determined and compared to those of a partial genomic database. These sequences showed excellent correlation between the estimated sizes and positions of the BAC clones and the sizes and positions of previously sequenced cosmids and the resulting contigs. Many BAC clones represent linking clones between sequenced cosmids, allowing full coverage of the H37Rv chromosome, and they are now being shotgun sequenced in the framework of the H37Rv sequencing project. Also, no chimeric, deleted, or rearranged BAC clones were detected, which was of major importance for the correct mapping and assembly of the H37Rv sequence. The minimal overlapping set contains 68 unique BAC clones and spans the whole H37Rv chromosome with the exception of a single gap of ∼150 kb. As a postgenomic application, the canonical BAC set was used in a comparative study to reveal chromosomal polymorphisms between M. tuberculosis, M. bovis, and M. bovis BCG Pasteur, and a novel 12.7-kb segment present in M. tuberculosis but absent from M. bovis and M. bovis BCG was characterized. This region contains a set of genes whose products show low similarity to proteins involved in polysaccharide biosynthesis. The H37Rv BAC library therefore provides us with a powerful tool both for the generation and confirmation of sequence data as well as for comparative genomics and other postgenomic applications. It represents a major resource for present and future M. tuberculosis research projects.

scholarly journals PCR identification of durum wheat BAC clones containing genes coding for carotenoid biosynthesis enzymes and their chromosome localization

Genome ◽  
2004 ◽  
Vol 47 (5) ◽  
pp. 911-917 ◽  
Author(s):  
A Cenci ◽  
S Somma ◽  
N Chantret ◽  
J Dubcovsky ◽  
A Blanco
Keyword(s):  
Tetraploid Wheat ◽  
Bac Library ◽  
Pcr Amplification ◽  
Carotenoid Biosynthesis ◽  
Quality Trait ◽  
Substitution Lines ◽  
D Genome ◽  
Pcr Screening ◽  
Bac Clones ◽  
Essential Components

Carotenoids are essential components in all plants. Their accumulation in wheat seed determines the endosperm colour, which is an important quality trait in wheat. In this study, we report the isolation of BAC clones containing genes coding for three different enzymes of the carotenoid biosynthesis pathway: phytoene synthase (PSY), phytoene desaturase (PDS), and ζ-carotene desaturase (ZDS). Primers were designed on the basis of wheat ESTs similar to the sequences of these three genes in other species, and used to screen a BAC library from Triticum turgidum var. durum (2n = 28, genomes AABB). Eight, six, and nine 384-well plates containing at least one positive clone were found for PSY, PDS, and ZDS, respectively. BACs selected for each of these genes were then divided in two groups corresponding to the A and B genomes of tetraploid wheat, based on differences in the length of the PCR amplification products, conformation-sensitive gel electrophoresis (CSGE), or cleavage amplification polymorphisms. Positive clones were then assigned to chromosomes using a set of D genome substitution lines in T. turgidum var. durum 'Langdon'. PSY clones were localized on chromosomes 5A and 5B, PDS on chromosomes 4A and 4B, and ZDS on chromosomes 2A and 2B. The strategies used for the PCR screening of large BAC libraries and for the differentiation of BAC clones from different genomes in a polyploid species are discussed.Key words: wheat, carotenoid biosynthesis, BAC.

Construction of a hexaploid wheat (Triticum aestivumL.) bacterial artificial chromosome library for cloning genes for stripe rust resistance

Genome ◽  
2005 ◽  
Vol 48 (6) ◽  
pp. 1028-1036 ◽  
Author(s):  
P Ling ◽  
X M Chen
Keyword(s):  
Triticum Aestivum ◽  
Stripe Rust ◽  
Hexaploid Wheat ◽  
Rust Resistance ◽  
Puccinia Striiformis ◽  
Bac Library ◽  
Artificial Chromosome ◽  
Stripe Rust Resistance ◽  
Insert Size ◽  
Bac Clones

A hexaploid wheat (Triticum aestivum L.) bacterial artificial chromosome (BAC) library was constructed for cloning Yr5 and other genes conferring resistance to stripe rust (Puccinia striiformis f. sp. tritici). Intact nuclei from a Yr5 near-isogenic line were used to isolate high molecular weight DNA, which was partially cleaved with HindIII and cloned into pECBAC1 and pIndigoBAC-5 vectors. The wheat BAC library consisted of 422 400 clones arrayed in 1100 micro-titer plates (each plate with 384 wells). Random sampling of 300 BAC clones indicated an average insert size of 140 kb, with a size range from 25 to 365 kb. Ninety percent of the clones in the library had an insert size greater than 100 kb and fewer than 5% of the clones did not contain inserts. Based on an estimated genome size of 15 966 Mb for hexaploid wheat, the BAC library was estimated to have a total coverage of 3.58× wheat genome equivalents, giving approximately 96% probability of identifying a clone representing any given wheat DNA sequence. Twelve BAC clones containing an Yr5 locus-specific marker (Yr5STS7/8) were successfully selected by PCR screening of 3-dimensional BAC pools. The results demonstrated that the T. aestivum BAC library is a valuable genomic resource for positional cloning of Yr5. The library also should be useful in cloning other genes for stripe rust resistance and other traits of interest in hexaploid wheat.Key words: BAC library, BAC pools, hexaploid wheat, Puccinia striiformis f. sp. tritici, resistance gene, stripe rust, Triticum aestivum.

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