Pullman, WA, United States
Pullman, WA, United States

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Patent
Amplicon Express | Date: 2017-03-29

This disclosure describes modified methods and compositions of matter pertaining to mate pair sequencing. In an implementation of the invention, mate pair sequence data is generated without cloning in a host system. In an implementation of the invention, a nucleic acid fragment is ligated into a vector. The vector containing the inserted nucleic acid fragment is digested with a restriction endonuclease that cuts at two or more places on the insert but does not cut the vector. Following the restriction endonuclease digest, the vector with portions of the nucleic acid fragment remaining after the restriction endonuclease digestion is again ligated. This ligation connects the cut ends of the insert to each other. The re-ligated product may be sequenced to obtain sequence data for both a right and left side of the originally inserted nucleic acid fragment.


PubMed | Paris-Sorbonne University, University of Algarve, Leibniz Institute of Marine Science, University of Groningen and 12 more.
Type: Journal Article | Journal: Nature | Year: 2016

Seagrasses colonized the sea on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet. Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes, genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae and that is important for ion homoeostasis, nutrient uptake and O2/CO2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming, to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants.


News Article | November 14, 2016
Site: www.prnewswire.com

SEOUL, South Korea, Nov. 14, 2016 /PRNewswire/ -- DNA Link, Inc. and Amplicon Express announced that they established an agreement today for a strategic partnership for the delivery of the best quality genomics solutions. This strategic partnership will further strengthen the cooperative...


News Article | November 14, 2016
Site: www.prnewswire.com

SEOUL, South Korea, Nov. 14, 2016 /PRNewswire/ -- DNA Link, Inc. and Amplicon Express announced that they established an agreement today for a strategic partnership for the delivery of the best quality genomics solutions. This strategic partnership will further strengthen the cooperative...


Velasco R.,Instituto Agrario San Michele allAdige Research and Innovation Center | Zharkikh A.,Myriad Genetics | Affourtit J.,Hoffmann-La Roche | Dhingra A.,Washington State University | And 83 more authors.
Nature Genetics | Year: 2010

We report a high-quality draft genome sequence of the domesticated apple (Malus × domestica). We show that a relatively recent (>50 million years ago) genome-wide duplication (GWD) has resulted in the transition from nine ancestral chromosomes to 17 chromosomes in the Pyreae. Traces of older GWDs partly support the monophyly of the ancestral paleohexaploidy of eudicots. Phylogenetic reconstruction of Pyreae and the genus Malus, relative to major Rosaceae taxa, identified the progenitor of the cultivated apple as M. sieversii. Expansion of gene families reported to be involved in fruit development may explain formation of the pome, a Pyreae-specific false fruit that develops by proliferation of the basal part of the sepals, the receptacle. In apple, a subclade of MADS-box genes, normally involved in flower and fruit development, is expanded to include 15 members, as are other gene families involved in Rosaceae-specific metabolism, such as transport and assimilation of sorbitol. © 2010 Nature America, Inc. All rights reserved.


News Article | November 14, 2016
Site: en.prnasia.com

SEOUL, South Korea, Nov 14, 2016 /PRNewswire/ -- DNA Link, Inc. and Amplicon Express announced that they established an agreement today for a strategic partnership for the delivery of the best quality genomics solutions. This strategic partnership will further strengthen the cooperative relationship between two companies, which have developed over the past several years. DNA Link and Amplicon Express have agreed to cooperate in areas including nucleic acid extraction, library preparation, and PacBio sequencing. Under the terms Amplicon Express will extract HMW DNA samples of NGS-quality from crude materials such as bacteria, plants, animals and humans. These samples will be then forwarded to DNA Link to be made into a long-inserted library ideal for PacBio sequencing for genome or transcriptome analysis by the fleet of PacBio sequencers including Sequel and RSII units at DNA Link. Jongeun Lee, CEO and the founder of DNA Link said, "Amplicon Express is an expert in nucleic acid extraction and library preparation with a long proven track of success, and DNA Link is one of the best sequencing facility that has the most experience with PacBio sequencers. This partnership will bring a tremendous synergy, and the researchers will enjoy the best quality of sequence data using the third-generation sequencers." Robert Bogden, President and founder of Amplicon Express remarked, "DNA Link is one of the few PacBio service providers that can fully realize the added value of having very long starting DNA fragments. PacBio data from DNA Link maximizes the long reads from our HMW DNA preps in 20Kb or 30Kb libraries." DNA Link, Inc. is a genomics company who is a certified service provider for Pacific Bioscience, Illumina, Ion Torrent and Affymetrix. As one of the first companies that adopted Pacific Bioscience RS II system, DNA Link has become one of the world's leading expert in NGS and Bioinformatics, capable of providing an integrated genome analysis service using various platforms. Incorporated in 2000, DNA Link has accumulated profound experiences in various types of projects for sequencing and analysis of diverse organisms such as bacteria, fungi, plants, animals, and human. Headquartered in Seoul, Republic of Korea, it has a branch office and lab in San Diego, US. Amplicon Express Inc since 1996 has made 2,500+ custom BAC libraries, picked 55+ million BAC clones, and made thousands of quality HMW gDNA preps from practically every organism imaginable. The Amplicon Express distribution network includes: Japan, Singapore, Malaysia, Taiwan, Mainland China, India, and offices in the EU. Amplicon is privately held, based in Washington State. To view the original version on PR Newswire, visit:http://www.prnewswire.com/news-releases/dna-link-and-amplicon-express-announce-joint-partnership-for-genomics-services-300361245.html


Castoe T.A.,Aurora University | de Koning A.J.,Aurora University | Hall K.T.,Aurora University | Yokoyama K.D.,Aurora University | And 12 more authors.
Genome Biology | Year: 2011

The Consortium for Snake Genomics is in the process of sequencing the genome and creating transcriptomic resources for the Burmese python. Here, we describe how this will be done, what analyses this work will include, and provide a timeline. © 2011 BioMed Central Ltd.


Castoe T.A.,Aurora University | Braun E.L.,University of Florida | Bronikowski A.M.,Iowa State University | Cox C.L.,University of Texas at Arlington | And 16 more authors.
Standards in Genomic Sciences | Year: 2012

This report summarizes the proceedings of the 1st Snake Genomics and Integrative Biology Meeting held in Vail, CO USA, 5-8 October 2011. The meeting had over twenty registered participants, and was conducted as a single session of presentations. Goals of the meeting in-cluded coordination of genomic data collection and fostering collaborative interactions among researchers using snakes as model systems.


Koid A.,University of Southern California | Nelson W.C.,University of Southern California | Mraz A.,Amplicon Express | Heidelberg K.B.,University of Southern California
Applied and Environmental Microbiology | Year: 2012

Eukaryotic marine microbes play pivotal roles in biogeochemical nutrient cycling and ecosystem function, but studies that focus on the protistan biogeography and genetic diversity lag-behind studies of other microbes. 18S rRNA PCR amplification and clone library sequencing are commonly used to assess diversity that is culture independent. However, molecular methods are not without potential biases and artifacts. In this study, we compare the community composition of clone libraries generated from the same water sample collected at the San Pedro Ocean Time Series (SPOTs) station in the northwest Pacific Ocean. Community composition was assessed using different cell lysis methods (chemical and mechanical) and the extraction of different nucleic acids (DNA and RNA reverse transcribed to cDNA) to build Sanger ABI clone libraries. We describe specific biases for ecologically important phylogenetic groups resulting from differences in nucleic acid extraction methods that will inform future designs of eukaryotic diversity studies, regardless of the target sequencing platform planned. © 2012, American Society for Microbiology.

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