Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions (original) (raw)

  1. Laurie Gordon1,2,5,
  2. Shan Yang1,5,
  3. Mary Tran-Gyamfi1,2,
  4. Dan Baggott1,
  5. Mari Christensen1,2,
  6. Aaron Hamilton1,
  7. Richard Crooijmans3,
  8. Martien Groenen3,
  9. Susan Lucas2,
  10. Ivan Ovcharenko2,4, and
  11. Lisa Stubbs1,6
  12. 1 Genome Biology Group, Lawrence Livermore National Laboratory, Livermore, California 94550, USA;
  13. 2 Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA;
  14. 3 Wageningen University, Wageningen 6709 PG, The Netherlands;
  15. 4 Computations Group, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
  16. ↵5 These authors contributed equally to this work.

Abstract

The chicken genome draft sequence has provided a valuable resource for studies of an important agricultural and experimental model species and an important data set for comparative analysis. However, some of the most gene-rich segments are missing from chicken genome draft assemblies, limiting the analysis of a substantial number of genes and preventing a closer look at regions that are especially prone to syntenic rearrangements. To facilitate the functional and evolutionary analysis of one especially gene-rich, rearrangement-prone genomic region, we analyzed sequence from BAC clones spanning chicken microchromosome GGA28; as a complement we also analyzed a gene-sparse, stable region from GGA11. In these two regions we documented the conservation and lineage-specific gain and loss of protein-coding genes and precisely mapped the locations of 31 major human-chicken syntenic breakpoints. Altogether, we identified 72 lineage-specific genes, many of which are found at or near syntenic breaks, implicating evolutionary breakpoint regions as major sites of genetic innovation and change. Twenty-two of the 31 breakpoint regions have been reused repeatedly as rearrangement breakpoints in vertebrate evolution. Compared with stable GC-matched regions, GGA28 is highly enriched in CpG islands, as are break-prone intervals identified elsewhere in the chicken genome; evolutionary breakpoints are further enriched in GC content and CpG islands, highlighting a potential role for these features in genome instability. These data support the hypothesis that chromosome rearrangements have not occurred randomly over the course of vertebrate evolution but are focused preferentially within “fragile” regions with unusual DNA sequence characteristics.

Footnotes