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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 MN, Farré M, Lithgow PE, Fowler KE, Skinner BM, O'Connor R, Fonseka G, Backström N, Matsuda Y, Nishida C, Houde P, Jarvis ED, Ellegren H, Burt DW, Larkin DM, Griffin DK - BMC Genomics (2014)

Bottom Line: Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace.All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count.Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor.

View Article: PubMed Central - PubMed

Affiliation: School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK. dlarkin@rvc.ac.uk.

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.

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Rates of recombination and their association with EBRs for chicken (red) and zebra finch (blue). In chicken, recombination rates are near identical in windows with and without EBRs (2.90 and 2.80, respectively). In zebra finch recombination rates are slightly higher in windows with EBRs (1.60 and 1.29, respectively) but the difference does not reach statistical significance (P = 0.1 for both tests used).
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Fig5: Rates of recombination and their association with EBRs for chicken (red) and zebra finch (blue). In chicken, recombination rates are near identical in windows with and without EBRs (2.90 and 2.80, respectively). In zebra finch recombination rates are slightly higher in windows with EBRs (1.60 and 1.29, respectively) but the difference does not reach statistical significance (P = 0.1 for both tests used).

Mentions: In chicken the analysis revealed no association between presence of EBR and the regional recombination rate. The 1 Mb non-overlapping windows containing EBRs (n = 35) had an average recombination rate of 2.80 (±3.00, SD) cM/Mb while windows without EBRs (n = 963) had an average recombination rate of 2.90 (±3.00) cM/Mb (Wilcoxon’s test, W = 13492, P = 0.42; randomization test, empirical difference in mean between classes = -0.11, P = 0.28; Figure 5).Figure 5


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

Romanov MN, Farré M, Lithgow PE, Fowler KE, Skinner BM, O'Connor R, Fonseka G, Backström N, Matsuda Y, Nishida C, Houde P, Jarvis ED, Ellegren H, Burt DW, Larkin DM, Griffin DK - BMC Genomics (2014)

Rates of recombination and their association with EBRs for chicken (red) and zebra finch (blue). In chicken, recombination rates are near identical in windows with and without EBRs (2.90 and 2.80, respectively). In zebra finch recombination rates are slightly higher in windows with EBRs (1.60 and 1.29, respectively) but the difference does not reach statistical significance (P = 0.1 for both tests used).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4362836&req=5

Fig5: Rates of recombination and their association with EBRs for chicken (red) and zebra finch (blue). In chicken, recombination rates are near identical in windows with and without EBRs (2.90 and 2.80, respectively). In zebra finch recombination rates are slightly higher in windows with EBRs (1.60 and 1.29, respectively) but the difference does not reach statistical significance (P = 0.1 for both tests used).
Mentions: In chicken the analysis revealed no association between presence of EBR and the regional recombination rate. The 1 Mb non-overlapping windows containing EBRs (n = 35) had an average recombination rate of 2.80 (±3.00, SD) cM/Mb while windows without EBRs (n = 963) had an average recombination rate of 2.90 (±3.00) cM/Mb (Wilcoxon’s test, W = 13492, P = 0.42; randomization test, empirical difference in mean between classes = -0.11, P = 0.28; Figure 5).Figure 5

Bottom Line: Intra- and interchromosomal changes were explained most parsimoniously by a series of inversions and translocations respectively, with breakpoint reuse being commonplace.All but one species showed the expected number of microchromosomal rearrangements predicted by the haploid chromosome count.Of the species analyzed, the chicken lineage appeared to have undergone the fewest changes compared to the dinosaur ancestor.

View Article: PubMed Central - PubMed

Affiliation: School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK. dlarkin@rvc.ac.uk.

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.

Show MeSH
Related in: MedlinePlus