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      Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza

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          Abstract

          Bacterial artificial chromosome (BAC) fingerprint and end-sequenced physical maps representing the ten genome types of Oryza are presented

          Abstract

          We describe the establishment and analysis of a genus-wide comparative framework composed of 12 bacterial artificial chromosome fingerprint and end-sequenced physical maps representing the 10 genome types of Oryza aligned to the O. sativa ssp. japonica reference genome sequence. Over 932 Mb of end sequence was analyzed for repeats, simple sequence repeats, miRNA and single nucleotide variations, providing the most extensive analysis of Oryza sequence to date.

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          Evolution of genes and genomes on the Drosophila phylogeny.

          Andrew G Clark, Michael B Eisen, Douglas R Smith … (2007)
          Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.
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            A draft sequence of the rice genome (Oryza sativa L. ssp. indica).

            J. Yu (2002)
            We have produced a draft sequence of the rice genome for the most widely cultivated subspecies in China, Oryza sativa L. ssp. indica, by whole-genome shotgun sequencing. The genome was 466 megabases in size, with an estimated 46,022 to 55,615 genes. Functional coverage in the assembled sequences was 92.0%. About 42.2% of the genome was in exact 20-nucleotide oligomer repeats, and most of the transposons were in the intergenic regions between genes. Although 80.6% of predicted Arabidopsis thaliana genes had a homolog in rice, only 49.4% of predicted rice genes had a homolog in A. thaliana. The large proportion of rice genes with no recognizable homologs is due to a gradient in the GC content of rice coding sequences.
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              Human-mouse alignments with BLASTZ.

              Scott Schwartz, W. Kent, Arian Smit … (2003)
              The Mouse Genome Analysis Consortium aligned the human and mouse genome sequences for a variety of purposes, using alignment programs that suited the various needs. For investigating issues regarding genome evolution, a particularly sensitive method was needed to permit alignment of a large proportion of the neutrally evolving regions. We selected a program called BLASTZ, an independent implementation of the Gapped BLAST algorithm specifically designed for aligning two long genomic sequences. BLASTZ was subsequently modified, both to attain efficiency adequate for aligning entire mammalian genomes and to increase its sensitivity. This work describes BLASTZ, its modifications, the hardware environment on which we run it, and several empirical studies to validate its results.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Biol
                Title: Genome Biology
                Publisher: BioMed Central
                ISSN (Print): 1465-6906
                ISSN (Electronic): 1465-6914
                Publication date (Print): 2008
                Publication date (Electronic): 28 February 2008
                Volume: 9
                Issue: 2
                Page: R45
                Affiliations
                [1 ]Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
                [2 ]Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
                [3 ]Department of Agronomy, Purdue University, West Lafayette, Indiana 47907, USA
                [4 ]Department of Horticulture, Purdue University, West Lafayette, Indiana 47907, USA
                [5 ]Genome Technology Branch, NHGRI, National Institutes of Health, Bethesda, Maryland, 20892, USA
                [6 ]Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York 11794, USA
                [7 ]Arizona Genomics Computational Laboratory, University of Arizona, Tucson, Arizona 85721, USA
                [8 ]USDA-ARS NAA Plant, Soil and Nutrition Laboratory Research Unit, Ithaca, New York 14853, USA
                Article
                Publisher ID: gb-2008-9-2-r45
                DOI: 10.1186/gb-2008-9-2-r45
                PMC ID: 2374706
                PubMed ID: 18304353
                SO-VID: 2aa2a003-7480-4d41-b2d0-bf3508383aa5
                Copyright © Copyright © 2008 Kim et al.; licensee BioMed Central Ltd.
                License:

                This is an open access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 14 December 2007
                Date revision received : 12 February 2008
                Date accepted : 28 February 2008
                Categories
                Subject: Method

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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