scholarly journals Swine Genome Sequencing Consortium (SGSC): A Strategic Roadmap for Sequencing The Pig Genome

2005 ◽  
Vol 6 (4) ◽  
pp. 251-255 ◽  
Author(s):  
Lawrence B. Schook ◽  
Jonathan E. Beever ◽  
Jane Rogers ◽  
Sean Humphray ◽  
Alan Archibald ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Mapping Data ◽  
The Past ◽  
Physical Maps ◽  
Genome Sequencing Consortium ◽  
Pig Genome ◽  
Sequencing Strategy ◽  
Bac End Sequencing ◽  
International Participation ◽  
Minimal Tiling

The Swine Genome Sequencing Consortium (SGSC) was formed in September 2003 by academic, government and industry representatives to provide international coordination for sequencing the pig genome. The SGSC’s mission is to advance biomedical research for animal production and health by the development of DNAbased tools and products resulting from the sequencing of the swine genome. During the past 2 years, the SGSC has met bi-annually to develop a strategic roadmap for creating the required scientific resources, to integrate existing physical maps, and to create a sequencing strategy that captured international participation and a broad funding base. During the past year, SGSC members have integrated their respective physical mapping data with the goal of creating a minimal tiling path (MTP) that will be used as the sequencing template. During the recent Plant and Animal Genome meeting (January 16, 2005 San Diego, CA), presentations demonstrated that a human–pig comparative map has been completed, BAC fingerprint contigs (FPC) for each of the autosomes and X chromosome have been constructed and that BAC end-sequencing has permitted, through BLAST analysis and RH-mapping, anchoring of the contigs. Thus, significant progress has been made towards the creation of a MTP. In addition, whole-genome (WG) shotgun libraries have been constructed and are currently being sequenced in various laboratories around the globe. Thus, a hybrid sequencing approach in which 3x coverage of BACs comprising the MTP and 3x of the WG-shotgun libraries will be used to develop a draft 6x coverage of the pig genome.

scholarly journals Linking the International Wheat Genome Sequencing Consortium bread wheat reference genome sequence to wheat genetic and phenomic data

2018 ◽  
Author(s):  
Michael Alaux ◽  
Jane Rogers ◽  
Thomas Letellier ◽  
Raphaël Flores ◽  
Françoise Alfama ◽  
...  
Keyword(s):  
Bread Wheat ◽  
Genome Sequencing ◽  
Genome Sequence ◽  
Reference Genome ◽  
Wheat Genome ◽  
Reference Genome Sequence ◽  
Physical Maps ◽  
Sequence Variations ◽  
Genome Sequencing Consortium ◽  
Genome Browsers

AbstractThe Wheat@URGI portal (https://wheat-urgi.versailles.inra.fr) has been developed to provide the international community of researchers and breeders with access to the bread wheat reference genome sequence produced by the International Wheat Genome Sequencing Consortium. Genome browsers, BLAST, and InterMine tools have been established for in depth exploration of the genome sequence together with additional linked datasets including physical maps, sequence variations, gene expression, and genetic and phenomic data from other international collaborative projects already stored in the GnpIS information system. The portal provides enhanced search and browser features that will facilitate the deployment of the latest genomics resources in wheat improvement.

Wheat genome structure and function: genome sequence data and the International Wheat Genome Sequencing Consortium

2007 ◽  
Vol 58 (6) ◽  
pp. 470 ◽  
Author(s):  
P. Moolhuijzen ◽  
D. S. Dunn ◽  
M. Bellgard ◽  
M. Carter ◽  
J. Jia ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Physical Map ◽  
Genome Structure ◽  
Genetic Research ◽  
Structure And Function ◽  
Wheat Genome ◽  
D Genome ◽  
Genome Sequencing Consortium ◽  
And Function ◽  
Bac Contigs

Genome sequencing and the associated bioinformatics is now a widely accepted research tool for accelerating genetic research and the analysis of genome structure and function of wheat because it leverages similar work from other crops and plants. The International Wheat Genome Sequencing Consortium addresses the challenge of wheat genome structure and function and builds on the research efforts of Professor Bob McIntosh in the genetics of wheat. Currently, expressed sequence tags (ESTs; ~500 000 to date) are the largest sequence resource for wheat genome analyses. It is estimated that the gene coverage of the wheat EST collection is ~60%, close to that of Arabidopsis, indicating that ~40% of wheat genes are not represented in EST collections. The physical map of the D-genome donor species Aegilops tauschii is under construction (http://wheat.pw.usda.gov/PhysicalMapping). The technologies developed in this analysis of the D genome provide a good model for the approach to the entire wheat genome, namely compiling BAC contigs, assigning these BAC contigs to addresses in a high resolution genetic map, filling in gaps to obtain the entire physical length of a chromosome, and then large-scale sequencing.

Genetic and brain imaging contributions to neuropsychological functioning in preclinical dementia

2002 ◽  
Vol 8 (7) ◽  
pp. 915-917 ◽  
Author(s):  
MARK W. BONDI
Keyword(s):  
Human Genome ◽  
Cholinesterase Inhibitors ◽  
Neuropsychological Functioning ◽  
Clinical Manifestations ◽  
The Past ◽  
Preclinical Phase ◽  
Genome Sequencing Consortium ◽  
Human Genome Sequencing ◽  
Brain Changes ◽  
International Human

A veritable explosion of research in neuropsychology has occurred over the past decade in the search for cognitive and brain changes during a so-called “preclinical” phase of dementia that precedes its overt clinical manifestations. Fueling this explosion, in part, has been the revolution in the genetic bases of disease formulated from the international work of decoding the human genome (International Human Genome Sequencing Consortium, 2001; see also Patenaude et al., 2002, for discussion). The discovery of preclinical cognitive, brain, and genetic markers of dementia is helping to push back the point at which diseases can be reliably identified. Very early detection of dementia is extremely important now that a variety of investigational treatments that might prevent or delay disease progression (e.g., amyloid vaccine, anti-oxidants, nonsteroidal anti-inflammatory agents, cholinesterase inhibitors, estrogens, and others in the case of Alzheimer's disease) are on the horizon.

scholarly journals Genome sequencing in the clinic: the past, present, and future of genomic medicine

2018 ◽  
Vol 50 (8) ◽  
pp. 563-579 ◽  
Author(s):  
Jeremy W. Prokop ◽  
Thomas May ◽  
Kim Strong ◽  
Stephanie M. Bilinovich ◽  
Caleb Bupp ◽  
...  
Keyword(s):  
Precision Medicine ◽  
Genome Sequencing ◽  
Clinical Setting ◽  
Structural Changes ◽  
New Technologies ◽  
Cancer Genomics ◽  
Genomic Medicine ◽  
Driver Gene ◽  
The Past ◽  
The Future

Genomic sequencing has undergone massive expansion in the past 10 yr, from a rarely used research tool into an approach that has broad applications in a clinical setting. From rare disease to cancer, genomics is transforming our knowledge of biology. The transition from targeted gene sequencing, to whole exome sequencing, to whole genome sequencing has only been made possible due to rapid advancements in technologies and informatics that have plummeted the cost per base of DNA sequencing and analysis. The tools of genomics have resolved the etiology of disease for previously undiagnosable conditions, identified cancer driver gene variants, and have impacted the understanding of pathophysiology for many diseases. However, this expansion of use has also highlighted research’s current voids in knowledge. The lack of precise animal models for gene-to-function association, lack of tools for analysis of genomic structural changes, skew in populations used for genetic studies, publication biases, and the “Unknown Proteome” all contribute to voids needing filled for genomics to work in a fast-paced clinical setting. The future will hold the tools to fill in these voids, with new data sets and the continual development of new technologies allowing for expansion of genomic medicine, ushering in the days to come for precision medicine. In this review we highlight these and other points in hopes of advancing and guiding precision medicine into the future for optimal success.

scholarly journals De NovoSequencing and Characterization of the Transcriptome of Dwarf Polish Wheat (Triticum polonicumL.)

2016 ◽  
Vol 2016 ◽  
pp. 1-6 ◽  
Author(s):  
Yi Wang ◽  
Chao Wang ◽  
Xiaolu Wang ◽  
Fan Peng ◽  
Ruijiao Wang ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Wheat Genome ◽  
The Other ◽  
Crucial Step ◽  
Functional Types ◽  
Other Hand ◽  
Genome Sequencing Consortium ◽  
Stems And Leaves ◽  
Wheat Transcriptome

Construction as well as characterization of a polish wheat transcriptome is a crucial step to study useful traits of polish wheat. In this study, a transcriptome, including 76,014 unigenes, was assembled from dwarf polish wheat (DPW) roots, stems, and leaves using the software of Trinity. Among these unigenes, 61,748 (81.23%) unigenes were functionally annotated in public databases and classified into differentially functional types. Aligning this transcriptome against draft wheat genome released by the International Wheat Genome Sequencing Consortium (IWGSC), 57,331 (75.42%) unigenes, including 26,122 AB-specific and 2,622 D-specific unigenes, were mapped on A, B, and/or D genomes. Compared with the transcriptome ofT. turgidum, 56,343 unigenes were matched with 103,327 unigenes ofT. turgidum. Compared with the genomes of rice and barley, 14,404 and 7,007 unigenes were matched with 14,608 genes of barley and 7,708 genes of rice, respectively. On the other hand, 2,148, 1,611, and 2,707 unigenes were expressed specifically in roots, stems, and leaves, respectively. Finally, 5,531 SSR sequences were observed from 4,531 unigenes, and 518 primer pairs were designed.

FastqCLS: a FASTQ Compressor for Long-read Sequencing via read reordering using a novel scoring model

2021 ◽  
Author(s):  
Dohyoen Lee ◽  
Giltae Song
Keyword(s):  
Genome Sequencing ◽  
Supplementary Information ◽  
Sequencing Analysis ◽  
Sequencing Data ◽  
File Size ◽  
Scoring Model ◽  
The Past ◽  
Long Read ◽  
Benchmark Datasets ◽  
Processing Steps

Abstract Motivation Over the past decades, vast amounts of genome sequencing data have been produced, requiring an enormous level of storage capacity. The time and resources needed to store and transfer such data cause bottlenecks in genome sequencing analysis. To resolve this issue, various compression techniques have been proposed to reduce the size of original FASTQ raw sequencing data, but these remain suboptimal. Long-read sequencing has become dominant in genomics, whereas most existing compression methods focus on short-read sequencing only. Results We designed a compression algorithm based on read reordering using a novel scoring model for reducing FASTQ file size with no information loss. We integrated all data processing steps into a software package called FastqCLS and provided it as a Docker image for ease of installation and execution to help users easily install and run. We compared our method with existing major FASTQ compression tools using benchmark datasets. We also included new long-read sequencing data in this validation. As a result, FastqCLS outperformed in terms of compression ratios for storing long-read sequencing data. Availability and implementation FastqCLS can be downloaded from https://github.com/krlucete/FastqCLS Supplementary information Supplementary data are available at Bioinformatics online.

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