title: Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor.
abstract: BACKGROUND
  The availability of multiple avian genome sequence assemblies greatly improves our ability to define overall genome organization and reconstruct evolutionary changes. In birds, this has previously been impeded by a near intractable karyotype and relied almost exclusively on comparative molecular cytogenetics of only the largest chromosomes. Here, novel whole genome sequence information from 21 avian genome sequences (most newly assembled) made available on an interactive browser (Evolution Highway) was analyzed.
  
  
  RESULTS
  Focusing on the six best-assembled genomes allowed us to assemble a putative karyotype of the dinosaur ancestor for each chromosome. Reconstructing evolutionary events that led to each species' genome organization, we determined that the fastest rate of change occurred in the zebra finch and budgerigar, consistent with rapid speciation events in the Passeriformes and Psittaciformes. Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace. Analyzing chicken and zebra finch, we found little evidence to support the hypothesis of an association of evolutionary breakpoint regions with recombination hotspots but some evidence to support the hypothesis that microchromosomes largely represent conserved blocks of synteny in the majority of the 21 species analyzed. All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count. Ostrich, however, appeared to retain an overall karyotype structure of 2n=80 despite undergoing a large number (26) of hitherto un-described interchromosomal changes.
  
  
  CONCLUSIONS
  Results suggest that mechanisms exist to preserve a static overall avian karyotype/genomic structure, including the microchromosomes, with widespread interchromosomal change occurring rarely (e.g., in ostrich and budgerigar lineages). Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor.
authors.forename: Michael N
authors.initials: MN
authors.lastname: Romanov
authors.forename: Marta
authors.initials: M
authors.lastname: Farré
authors.forename: Pamela E
authors.initials: PE
authors.lastname: Lithgow
authors.forename: Katie E
authors.initials: KE
authors.lastname: Fowler
authors.forename: Benjamin M
authors.initials: BM
authors.lastname: Skinner
authors.forename: Rebecca
authors.initials: R
authors.lastname: O'Connor
authors.forename: Gothami
authors.initials: G
authors.lastname: Fonseka
authors.forename: Niclas
authors.initials: N
authors.lastname: Backström
authors.forename: Yoichi
authors.initials: Y
authors.lastname: Matsuda
authors.forename: Chizuko
authors.initials: C
authors.lastname: Nishida
authors.forename: Peter
authors.initials: P
authors.lastname: Houde
authors.forename: Erich D
authors.initials: ED
authors.lastname: Jarvis
authors.forename: Hans
authors.initials: H
authors.lastname: Ellegren
authors.forename: David W
authors.initials: DW
authors.lastname: Burt
authors.affiliation: School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK. dlarkin@rvc.ac.uk.
authors.forename: Denis M
authors.initials: DM
authors.lastname: Larkin
authors.forename: Darren K
authors.initials: DK
authors.lastname: Griffin
mesh_terms: D000818:Animals; D002645:Chickens / Q000235:genetics*; D020223:Chromosome Painting; D025061:Dinosaurs / Q000235:genetics*; D019143:Evolution, Molecular; D063990:Gene Ontology; D023281:Genomics; D017404:In Situ Hybridization, Fluorescence; D059785:Karyotype; D046109:Passeriformes / Q000235:genetics; D011995:Recombination, Genetic; D026801:Synteny