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Genome Biol Evol. 2016 Aug 25;8(8):2442-51. doi: 10.1093/gbe/evw166.

Novel Insights into Chromosome Evolution in Birds, Archosaurs, and Reptiles.

Author information

1
Department of Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, University of London, NW1 0TU, UK.
2
Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, SY23 3DA, UK.
3
Illinois Informatics Institute, University of Illinois, Urbana, IL 61801, USA.
4
China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, 1350, Denmark.
5
Department of Neurobiology, Duke University Medical Center, Durham, NC, 27710, USA Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
6
Department of Genomics and Genetics, the Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK.
7
School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK.
8
Department of Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, University of London, NW1 0TU, UK dlarkin@rvc.ac.uk.

Abstract

Homologous synteny blocks (HSBs) and evolutionary breakpoint regions (EBRs) in mammalian chromosomes are enriched for distinct DNA features, contributing to distinct phenotypes. To reveal HSB and EBR roles in avian evolution, we performed a sequence-based comparison of 21 avian and 5 outgroup species using recently sequenced genomes across the avian family tree and a newly-developed algorithm. We identified EBRs and HSBs in ancestral bird, archosaurian (bird, crocodile, and dinosaur), and reptile chromosomes. Genes involved in the regulation of gene expression and biosynthetic processes were preferably located in HSBs, including for example, avian-specific HSBs enriched for genes involved in limb development. Within birds, some lineage-specific EBRs rearranged genes were related to distinct phenotypes, such as forebrain development in parrots. Our findings provide novel evolutionary insights into genome evolution in birds, particularly on how chromosome rearrangements likely contributed to the formation of novel phenotypes.

KEYWORDS:

birds; chromosome rearrangements; comparative genomics; genome evolution; reptiles

PMID:
27401172
PMCID:
PMC5010900
DOI:
10.1093/gbe/evw166
[Indexed for MEDLINE]
Free PMC Article

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