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Plant genomics

A genome conserved and a genome expanded

Nature Reviews Genetics volume 15, page 66 (2014)Cite this article

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Chamala et al. describe a new sequencing and assembly pipeline strategy for non-model species that have large and complex genomes. They first produced a whole-genome assembly using a combination of 454, Illumina and Sanger sequencing of bacterial artificial chromosome ends. They then evaluated the accuracy of the assembly by fluorescence in situ hybridization — a technique that has not been exploited in this way before. Finally, to further improve the contiguity of the assembly, they carried out whole-genome mapping (formally known as optical mapping), which allows the ordering of restriction enzyme-digested fragments of the genome, that closed up the remaining gaps in the assembly.

The Amborella Genome Project team annotated the A. trichopoda nuclear sequence and used it to analyse the evolution of angiosperms. Structural analysis confirmed a whole-genome duplication event in the common ancestor of angiosperms but revealed no further such events in the lineage that led to A. trichopoda. This nuclear genome therefore serves as an excellent reference for elucidating genome evolution in other flowering plants. For example, the authors were able to reconstruct the ancestral, pre-hexaploid gene arrangement of core eudicots, which constitute some 75% of angiosperms.

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References

  1. Chamala, S. et al. Assembly and validation of the genome of the nonmodel basal angiosperm Amborella. Science 342, 1516–1517 (2013)

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  2. Amborella Genome Project. The Amborella genome and the evolution of flowering plants. Science 342, 1241089 (2013)

  3. Rice, D. W. et al. Horizontal transfer of entire genomes via mitochondrial fusion in the angiosperm Amborella. Science 342, 1468–1473 (2013)

    Article  CAS  Google Scholar 

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Authors
  1. Hannah Stower
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Stower, H. A genome conserved and a genome expanded. Nat Rev Genet 15, 66 (2014). https://doi.org/10.1038/nrg3657

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