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Characterization and evolutionary dynamics of complex regions in eukaryotic genomes

Science China Life Sciences volume 62, pages 467–488 (2019)Cite this article

Abstract

Complex regions in eukaryotic genomes are typically characterized by duplications of chromosomal stretches that often include one or more genes repeated in a tandem array or in relatively close proximity. Nevertheless, the repetitive nature of these regions, together with the often high sequence identity among repeats, have made complex regions particularly recalcitrant to proper molecular characterization, often being misassembled or completely absent in genome assemblies. This limitation has prevented accurate functional and evolutionary analyses of these regions. This is becoming increasingly relevant as evidence continues to support a central role for complex genomic regions in explaining human disease, developmental innovations, and ecological adaptations across phyla. With the advent of long-read sequencing technologies and suitable assemblers, the development of algorithms that can accommodate sample heterozygosity, and the adoption of a pangenomic-like view of these regions, accurate reconstructions of complex regions are now within reach. These reconstructions will finally allow for accurate functional and evolutionary studies of complex genomic regions, underlying the generation of genotype-phenotype maps of unprecedented resolution.

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Acknowledgements

This work was supported by a National Science Foundation Grant (MCB-1157876) to J.M.R.

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  1. Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA

    José Ranz & Bryan Clifton

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  1. José Ranz
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Correspondence to José Ranz.

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Ranz, J., Clifton, B. Characterization and evolutionary dynamics of complex regions in eukaryotic genomes. Sci. China Life Sci. 62, 467–488 (2019). https://doi.org/10.1007/s11427-018-9458-0

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Keywords

  • complex genomic regions
  • sequencing technologies
  • genome assembly
  • structural variation
  • tandem gene duplicates
  • evolutionary novelty