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Advances in plant genome sequencing

已有 2412 次阅读 2012-9-9 16:52 |个人分类:自然与社会|系统分类:论文交流

  1. John P. Hamilton,
  2. C. Robin Buell*

Article first published online: 27 MAR 2012

DOI: 10.1111/j.1365-313X.2012.04894.x

  Keywords:
  • genomics;
  • sequencing;
  • computation;
  • transcriptomics;
  • next generation sequencing.
Summary
  1. Top of page
  2. Summary
  3. Biological Applications for Genome Sequencing
  4. Historical Perspective on Plant Genome Sequencing: The Early Years with the Sanger Platform
  5. Advent of Next-generation Sequencing Platforms
  6. Limitations of Next-generation Sequencing with Respect to Plant Genomes
  7. Emerging Platforms
  8. Computational Infrastructure Challenges with Next-generation Sequencing
  9. Other Components of a Genomics Project: Stuff you Really Need and Want but Don’t Always Get
  10. Going Forward: What’s Next?
  11. Acknowledgments
  12. References

The study of plant biology in the 21st century is, and will continue to be, vastly different from that in the 20th century. One driver for this has been the use of genomics methods to reveal the genetic blueprints for not one but dozens of plant species, as well as resolving genome differences in thousands of individuals at the population level. Genomics technology has advanced substantially since publication of the first plant genome sequence, that of Arabidopsis thaliana, in 2000. Plant genomics researchers have readily embraced new algorithms, technologies and approaches to generate genome, transcriptome and epigenome datasets for model and crop species that have permitted deep inferences into plant biology. Challenges in sequencing any genome include ploidy, heterozygosity and paralogy, all which are amplified in plant genomes compared to animal genomes due to the large genome sizes, high repetitive sequence content, and rampant whole- or segmental genome duplication. The ability to generate de novo transcriptome assemblies provides an alternative approach to bypass these complex genomes and access the gene space of these recalcitrant species. The field of genomics is driven by technological improvements in sequencing platforms; however, software and algorithm development has lagged behind reductions in sequencing costs, improved throughput, and quality improvements. It is anticipated that sequencing platforms will continue to improve the length and quality of output, and that the complementary algorithms and bioinformatic software needed to handle large, repetitive genomes will improve. The future is bright for an exponential improvement in our understanding of plant biology.



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