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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.

Amplicon Express | Date: 2014-05-19

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.

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.

Velasco R.,Istituto Agrario San Michele allAdige Research and Innovation Center | Zharkikh A.,Myriad Genetics | Affourtit J.,Roche Holding AG | 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.

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