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

Romanov, Michael N, Farré, Marta, Lithgow, Pamela E, Fowler, Katie E., Skinner, Benjamin M., O'Connor, Rebecca E., Fonseka, Gothami, Backström, Niclas, Matsuda, Yoichi, Nishida, Chizuko, and others. (2014) Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor. BMC Genomics, 15 . Article Number 1060. ISSN 1471-2164. E-ISSN 1471-2164. (doi:10.1186/1471-2164-15-1060) (KAR id:46269)

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https://doi.org/10.1186/1471-2164-15-1060

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.

Item Type: Article
DOI/Identification number: 10.1186/1471-2164-15-1060
Subjects: Q Science > QH Natural history > QH426 Genetics
Q Science > QL Zoology
Divisions: Divisions > Division of Natural Sciences > School of Biosciences
Signature Themes: Food Systems, Natural Resources and Environment
Depositing User: Mike Romanov
Date Deposited: 20 Dec 2014 11:44 UTC
Last Modified: 20 Jul 2021 07:39 UTC
Resource URI: https://kar.kent.ac.uk/id/eprint/46269 (The current URI for this page, for reference purposes)
Romanov, Michael N: https://orcid.org/0000-0003-3584-4644
Farré, Marta: https://orcid.org/0000-0001-9170-5767
Fowler, Katie E.: https://orcid.org/0000-0003-0359-2390
Skinner, Benjamin M.: https://orcid.org/0000-0002-7152-1167
O'Connor, Rebecca E.: https://orcid.org/0000-0002-4270-970X
Larkin, Denis M.: https://orcid.org/0000-0001-7859-6201
Griffin, Darren K.: https://orcid.org/0000-0001-7595-3226
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