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Sequencing Plant Genomes

  • Daniel G. PetersonEmail author
  • Mark ArickII
Chapter
Part of the Progress in Botany book series (BOTANY, volume 80)

Abstract

The first decade of the twenty-first century witnessed the development and commercialization of the so-called “second-generation” sequencing techniques. These short-read sequencing methods produced such large amounts of sequence data at such low prices that the costly and time-consuming physical map-based sequencing techniques, used to generate the human and the Arabidopsis genomes, were largely abandoned. The rise of second-generation sequencing at the cost of physical mapping resulted in a tremendous increase in the number and diversity of plant genome projects, a proliferation in the number of individuals and institutions involved in genome sequencing endeavors, and an overall decrease in the quality of resulting genome assemblies. Single-molecule (“third-generation”) sequencing techniques, which came onto the scene more recently, provide much longer (and currently lower quality) reads than second-generation techniques, and a combination of second- and third-generation technologies is resulting in higher quality, more complete genome assemblies than second-generation techniques alone. At present, excellent results are being obtained by assembling genomes with third-generation reads, polishing the resulting contigs/scaffolds with second-generation (Illumina) data, and using Hi-C chromatin conformation capture and/or optical mapping techniques to increase contig/scaffold accuracy. Because improvements in sequencing have occurred so quickly, bioinformatics tools for assembling, analyzing, and annotating genomes have not been standardized; indeed, such tools can vary widely with regard to input needs, output quality, and scalability. With hundreds of plant genomes in various states of completion, much is being learned about general trends in plant genome evolution – for example, the predominance of polyploidy and paleopolyploidy events in angiosperms and the enormous contribution of LTR retrotransposons to genome size expansions/contractions in land plants. Plant genome sequencing projects have also made apparent the difficulties associated with identifying and quantifying gene numbers. While genome sequences are powerful tools, they are simply maps; they contain information about genomic landmarks and their possible functions, but they are not equivalent to the complex organisms they represent. Nonetheless, like any maps, they represent a means by which one can explore more expeditiously. Integration of genome sequence maps with chromatin configuration, biochemical, and developmental data is critical in advancing understanding of how genes and genomes function and evolve in vivo.

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© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Institute for Genomics, Biocomputing & Biotechnology (IGBB)Mississippi State UniversityMississippi StateUSA

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