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      Structural variations in plant genomes

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          Abstract

          Differences between plant genomes range from single nucleotide polymorphisms to large-scale duplications, deletions and rearrangements. The large polymorphisms are termed structural variants (SVs). SVs have received significant attention in human genetics and were found to be responsible for various chronic diseases. However, little effort has been directed towards understanding the role of SVs in plants. Many recent advances in plant genetics have resulted from improvements in high-resolution technologies for measuring SVs, including microarray-based techniques, and more recently, high-throughput DNA sequencing. In this review we describe recent reports of SV in plants and describe the genomic technologies currently used to measure these SVs.

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          Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome".

          H Tettelin, V Masignani, M. J. Cieslewicz … (2005)
          The development of efficient and inexpensive genome sequencing methods has revolutionized the study of human bacterial pathogens and improved vaccine design. Unfortunately, the sequence of a single genome does not reflect how genetic variability drives pathogenesis within a bacterial species and also limits genome-wide screens for vaccine candidates or for antimicrobial targets. We have generated the genomic sequence of six strains representing the five major disease-causing serotypes of Streptococcus agalactiae, the main cause of neonatal infection in humans. Analysis of these genomes and those available in databases showed that the S. agalactiae species can be described by a pan-genome consisting of a core genome shared by all isolates, accounting for approximately 80% of any single genome, plus a dispensable genome consisting of partially shared and strain-specific genes. Mathematical extrapolation of the data suggests that the gene reservoir available for inclusion in the S. agalactiae pan-genome is vast and that unique genes will continue to be identified even after sequencing hundreds of genomes.
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            Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection.

            Hon-Ming Lam, Xun Xu, Xin Liu … (2010)
            We report a large-scale analysis of the patterns of genome-wide genetic variation in soybeans. We re-sequenced a total of 17 wild and 14 cultivated soybean genomes to an average of approximately ×5 depth and >90% coverage using the Illumina Genome Analyzer II platform. We compared the patterns of genetic variation between wild and cultivated soybeans and identified higher allelic diversity in wild soybeans. We identified a high level of linkage disequilibrium in the soybean genome, suggesting that marker-assisted breeding of soybean will be less challenging than map-based cloning. We report linkage disequilibrium block location and distribution, and we identified a set of 205,614 tag SNPs that may be useful for QTL mapping and association studies. The data here provide a valuable resource for the analysis of wild soybeans and to facilitate future breeding and quantitative trait analysis.
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              Whole-genome sequencing of multiple Arabidopsis thaliana populations.

              Jun Cao, Korbinian Schneeberger, Stephan Ossowski … (2011)
              The plant Arabidopsis thaliana occurs naturally in many different habitats throughout Eurasia. As a foundation for identifying genetic variation contributing to adaptation to diverse environments, a 1001 Genomes Project to sequence geographically diverse A. thaliana strains has been initiated. Here we present the first phase of this project, based on population-scale sequencing of 80 strains drawn from eight regions throughout the species' native range. We describe the majority of common small-scale polymorphisms as well as many larger insertions and deletions in the A. thaliana pan-genome, their effects on gene function, and the patterns of local and global linkage among these variants. The action of processes other than spontaneous mutation is identified by comparing the spectrum of mutations that have accumulated since A. thaliana diverged from its closest relative 10 million years ago with the spectrum observed in the laboratory. Recent species-wide selective sweeps are rare, and potentially deleterious mutations are more common in marginal populations.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Brief Funct Genomics
                Journal ID (iso-abbrev): Brief Funct Genomics
                Journal ID (publisher-id): bfgp
                Journal ID (hwp): bfgp
                Title: Briefings in Functional Genomics
                Publisher: Oxford University Press
                ISSN (Print): 2041-2649
                ISSN (Electronic): 2041-2657
                Publication date (Print): July 2014
                Publication date (Electronic): 06 June 2014
                Publication date PMC-release: 06 June 2014
                Volume: 13
                Issue: 4 , Special Issue: Plant genomic variation
                Pages: 296-307
                Author notes
                Corresponding author. R.K. Varshney, Research Program Director—Grain Legumes, and Director of the Centre of Excellence in Genomics, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Andhra Pradesh, India. Tel.: 914030713305; Fax: 914030713071; E-mail: r.k.varshney@ 123456cgiar.org
                Article
                Publisher ID: elu016
                DOI: 10.1093/bfgp/elu016
                PMC ID: 4110416
                PubMed ID: 24907366
                SO-VID: 985ebd4f-095b-4d5d-b551-e10036ef2a7c
                Copyright © © The Author 2014. Published by Oxford University Press.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

                History
                Page count
                Pages: 12
                Categories
                Subject: Papers

                ScienceOpen disciplines: Genetics
                Keywords: structural variations (svs),next-generation sequencing (ngs),copy number variations (cnvs),presence and absence variations (pavs),inversions,translocations
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: structural variations (svs), next-generation sequencing (ngs), copy number variations (cnvs), presence and absence variations (pavs), inversions, translocations

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