Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor.

dc.contributor.author

Romanov, Michael N

dc.contributor.author

Farré, Marta

dc.contributor.author

Lithgow, Pamela E

dc.contributor.author

Fowler, Katie E

dc.contributor.author

Skinner, Benjamin M

dc.contributor.author

O'Connor, Rebecca

dc.contributor.author

Fonseka, Gothami

dc.contributor.author

Backström, Niclas

dc.contributor.author

Matsuda, Yoichi

dc.contributor.author

Nishida, Chizuko

dc.contributor.author

Houde, Peter

dc.contributor.author

Jarvis, Erich D

dc.contributor.author

Ellegren, Hans

dc.contributor.author

Burt, David W

dc.contributor.author

Larkin, Denis M

dc.contributor.author

Griffin, Darren K

dc.coverage.spatial

England

dc.date.accessioned

2014-12-15T17:35:40Z

dc.date.issued

2014-12-11

dc.description.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.

dc.identifier

http://www.ncbi.nlm.nih.gov/pubmed/25496766

dc.identifier

1471-2164-15-1060

dc.identifier.eissn

1471-2164

dc.identifier.uri

https://hdl.handle.net/10161/9319

dc.language

eng

dc.publisher

Springer Science and Business Media LLC

dc.relation.ispartof

BMC Genomics

dc.relation.isversionof

10.1186/1471-2164-15-1060

dc.subject

Animals

dc.subject

Chickens

dc.subject

Chromosome Painting

dc.subject

Dinosaurs

dc.subject

Evolution, Molecular

dc.subject

Gene Ontology

dc.subject

Genomics

dc.subject

In Situ Hybridization, Fluorescence

dc.subject

Karyotype

dc.subject

Passeriformes

dc.subject

Recombination, Genetic

dc.subject

Synteny

dc.title

Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor.

dc.type

Journal article

pubs.author-url

http://www.ncbi.nlm.nih.gov/pubmed/25496766

pubs.begin-page

1060

pubs.organisational-group

Basic Science Departments

pubs.organisational-group

Duke

pubs.organisational-group

Duke Institute for Brain Sciences

pubs.organisational-group

Institutes and Provost's Academic Units

pubs.organisational-group

Neurobiology

pubs.organisational-group

School of Medicine

pubs.organisational-group

University Institutes and Centers

pubs.publication-status

Published online

pubs.volume

15

Files

Original bundle

Now showing 1 - 1 of 1
Loading...
Thumbnail Image
Name:
Romanov et al 2014 genome structure provisional.pdf
Size:
1.74 MB
Format:
Adobe Portable Document Format
Description:
Accepted version