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      Whole Genome Sequence of the Soybean Aphid Endosymbiont Buchnera aphidicola and Genetic Differentiation among Biotype-Specific Strains

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          Abstract

          Endosymbiosis with microorganisms is common in insects, with more than 10% of species requiring the metabolic capabilities of intracellular bacteria for their nutrient acquisition. Aphids harbor an obligate mutualism with the vertically transferred endosymbiont, Buchnera aphidicola, which produces key nutrients lacking in the aphid's phloem-based diet that are necessary for normal development and reproduction. It is thought that, in some groups of insects, bacterial symbionts may play key roles in biotype evolution against host-plant resistance. The genome of Buchnera has been sequenced in several aphid strains but little genomic data is currently available for the soybean aphid ( Aphis glycines), one of the most important pests of soybean in North America. In this study, DNA sequencing was used to assemble and annotate the genome sequence of the Buchnera A. glycines strain and to reconstruct phylogenetic relationships among different strains. In addition, we identified several fixed Buchnera SNPs between Aphis glycines biotypes that were avirulent or virulent to a soybean aphid resistance gene ( Rag1). The results of this study describe the genetic and evolutionary relationships of the Buchnera A. glycines strain, and begin to define the roles of an aphid symbiont in host-plant resistance.

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          Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

          Increased reliance on computational approaches in the life sciences has revealed grave concerns about how accessible and reproducible computation-reliant results truly are. Galaxy http://usegalaxy.org, an open web-based platform for genomic research, addresses these problems. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Pages are interactive, web-based documents that provide users with a medium to communicate a complete computational analysis.
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            Learning how to live together: genomic insights into prokaryote-animal symbioses.

            Our understanding of prokaryote-eukaryote symbioses as a source of evolutionary innovation has been rapidly increased by the advent of genomics, which has made possible the biological study of uncultivable endosymbionts. Genomics is allowing the dissection of the evolutionary process that starts with host invasion then progresses from facultative to obligate symbiosis and ends with replacement by, or coexistence with, new symbionts. Moreover, genomics has provided important clues on the mechanisms driving the genome-reduction process, the functions that are retained by the endosymbionts, the role of the host, and the factors that might determine whether the association will become parasitic or mutualistic.
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              50 million years of genomic stasis in endosymbiotic bacteria.

              Comparison of two fully sequenced genomes of Buchnera aphidicola, the obligate endosymbionts of aphids, reveals the most extreme genome stability to date: no chromosome rearrangements or gene acquisitions have occurred in the past 50 to 70 million years, despite substantial sequence evolution and the inactivation and loss of individual genes. In contrast, the genomes of their closest free-living relatives, Escherichia coli and Salmonella spp., are more than 2000-fold more labile in content and gene order. The genomic stasis of B. aphidicola, likely attributable to the loss of phages, repeated sequences, and recA, indicates that B. aphidicola is no longer a source of ecological innovation for its hosts.
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                Author and article information

                Journal
                J Genomics
                J Genomics
                jgen
                Journal of Genomics
                Ivyspring International Publisher (Sydney )
                1839-9940
                2015
                5 October 2015
                : 3
                : 85-94
                Affiliations
                1. Department of Biology, Brandon University, Brandon, MB R7A 6A9, Canada.
                2. Department of Entomology, The Ohio State University, OARDC, Wooster, OH 44691, USA.
                Author notes
                ✉ Corresponding author: Bryan J. Cassone, Brandon University, Department of Biology, Brandon, MB, R7A 6A9. cassoneb@ 123456brandonu.ca ; 204-727-7333 (Ph)

                Competing Interests: The authors have declared that no competing interest exists.

                Article
                jgenv03p0085
                10.7150/jgen.12975
                4618293
                61e7e43e-ef16-4ed6-bc95-1dd16da72ad9
                © 2015 Ivyspring International Publisher. Reproduction is permitted for personal, noncommercial use, provided that the article is in whole, unmodified, and properly cited. See http://ivyspring.com/terms for terms and conditions.
                History
                Categories
                Research Paper

                dna sequencing,host-plant resistance,de novo assembly aphis glycines

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