Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution

Griffin, Darren K.; Robertson, Lindsay; Tempest, Helen G.; Vignal, Alain; Fillon, Valérie; Crooijmans, R.P.M.A.; Groenen, Martien A. M.; Deryusheva, Svetlana; Gaginskaya, Elena; Carré, Wilfrid; Waddington, David; Talbot, Richard; Volker, Martin A.; Masabanda, Julio S.; Burt, David W.

doi:10.1186/1471-2164-9-168

Cited by 126 publications

(161 citation statements)

References 40 publications

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“…Nearly 85 % of the probes hybridized to quail LBCs in our experiments. This efficiency of heterologous hybridization corresponds to that previously observed for FISH with large-size chicken probes on metaphase chromosomes from different galliform species (Shibusawa et al 2001(Shibusawa et al , 2002Kasai et al 2003;Schmid et al 2005;Kayang et al 2006;Griffin et al 2008). The high-resolution comparative FISH mapping combined with fine detection of centromere positions on lampbrush chromosomes allows us to determine gene order relative to centromeres most precisely.…”

Section: Resultssupporting

confidence: 81%

Centromere positions in chicken and Japanese quail chromosomes: de novo centromere formation versus pericentric inversions

et al. 2012

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Chicken (Gallus gallus domesticus, GGA) and Japanese quail (Coturnix coturnix japonica, CCO) karyotypes are very similar. They have identical chromosome number (2n078) and show a high degree of synteny. Centromere positions on the majority of orthologous chromosomes are different in these two species. To explore the nature of this divergence, we used highresolution comparative fluorescent in situ hybridization mapping on giant lampbrush chromosomes (LBCs) from growing oocytes. We applied 41 BAC clones specific for GGA1, 2, 3, 11, 12, 13, 14, and 15 to chicken and quail LBCs. This approach allowed us to rule out a pericentric inversion earlier proposed to explain the difference between GGA1 and CCO1. In addition to a well-established large-scale pericentric inversion that discriminates GGA2 and CCO2, we identified another, smaller one in the large inverted region. For the first time, we described in detail inversions that distinguish GGA3 from CCO3 and GGA11 from CCO11. Despite the newly identified and confirmed inversions, our data suggest that, in chicken and Japanese quail, the difference in centromere positions is not mainly caused by pericentric inversions but is instead due to centromere repositioning events and the formation of new centromeres. We also consider the formation of short arms of quail microchromosomes by heterochromatin accumulation as a third scenario that could explain the discrepancy in centromeric indexes.

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Section: Resultssupporting

confidence: 81%

Centromere positions in chicken and Japanese quail chromosomes: de novo centromere formation versus pericentric inversions

et al. 2012

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“…Similarly, overall karyotype structure is highly conserved in birds, with the vast majority of extant species displaying a karyotype with about 2n = 80 chromosomes, comprising few macro-and many small microchromosomes, and a ZZ/ZW sex chromosome pair (Christidis 1990;Rodionov 1997;Griffin et al 2007). In line with the above data, recent studies of CNVs in turkey and duck (relative to chicken) have suggested that bird genomes also contain a low number of CNVs compared to mammalian genomes (Griffin et al 2008;Skinner et al 2009). Recombination rates in chicken and zebra finch, the only two bird species for which there is information on absolute rates of recombination (The International Chicken Genome Sequencing Consortium 2004; Groenen et al 2009;Backström et al 2010), are higher overall than in mammals.…”

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confidence: 68%

Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution

Volker

Backström²,

Skinner³

et al. 2010

Genome Res.

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Chromosomal rearrangements and copy number variants (CNVs) play key roles in genome evolution and genetic disease; however, the molecular mechanisms underlying these types of structural genomic variation are not fully understood. The availability of complete genome sequences for two bird species, the chicken and the zebra finch, provides, for the first time, an ideal opportunity to analyze the relationship between structural genomic variation (chromosomal and CNV) and recombination on a genome-wide level. The aims of this study were therefore threefold: (1) to combine bioinformatics, physical mapping to produce comprehensive comparative maps of the genomes of chicken and zebra finch. In so doing, this allowed the identification of evolutionary chromosomal rearrangements distinguishing them. The previously reported interchromosomal conservation of synteny was confirmed, but a larger than expected number of intrachromosomal rearrangements were reported; (2) to hybridize zebra finch genomic DNA to a chicken tiling path microarray and identify CNVs in the zebra finch genome relative to chicken; 32 interspecific CNVs were identified; and (3) to test the hypothesis that there is an association between CNV, chromosomal rearrangements, and recombination by correlating data from (1) and (2) with recombination rate data from a high-resolution genetic linkage map of the zebra finch. We found a highly significant association of both chromosomal rearrangements and CNVs with elevated recombination rates. The results thus provide support for the notion of recombination-based processes playing a major role in avian genome evolution.

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“…A special case is represented by chromosome 4 where the highest recombination rate, GC content, and cohesion density is observed within the p-arm of this chromosome. Interestingly, a comparison between the karyotypes of chicken, turkey, and other birds indicates that chicken chromosome 4 is the result of a fusion between a macrochromosome and a microchromosome in the lineage leading to chicken (Griffin et al 2008). The density plots for chromosome 4 shown in Figure 4 provide further support for the microchromosomal origin of the p-arm of this chromosome.…”

Section: Discussionmentioning

confidence: 85%

A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate

Groenen¹,

Wahlberg²,

Foglio³

et al. 2008

Genome Res.

278

350

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The resolution of the chicken consensus linkage map has been dramatically improved in this study by genotyping 12,945 single nucleotide polymorphisms (SNPs) on three existing mapping populations in chicken: the Wageningen (WU), East Lansing (EL), and Uppsala (UPP) mapping populations. As many as 8599 SNPs could be included, bringing the total number of markers in the current consensus linkage map to 9268. The total length of the sex average map is 3228 cM, considerably smaller than previous estimates using the WU and EL populations, reflecting the higher quality of the new map. The current map consists of 34 linkage groups and covers at least 29 of the 38 autosomes. Sex-specific analysis and comparisons of the maps based on the three individual populations showed prominent heterogeneity in recombination rates between populations, but no significant heterogeneity between sexes. The recombination rates in the F 1 Red Jungle fowl/White Leghorn males and females were significantly lower compared with those in the WU broiler population, consistent with a higher recombination rate in purebred domestic animals under strong artificial selection. The recombination rate varied considerably among chromosomes as well as along individual chromosomes. An analysis of the sequence composition at recombination hot and cold spots revealed a strong positive correlation between GC-rich sequences and high recombination rates. The GC-rich cohesin binding sites in particular stood out from other GC-rich sequences with a 3.4-fold higher density at recombination hot spots versus cold spots, suggesting a functional relationship between recombination frequency and cohesin binding.

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Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution

Cited by 126 publications

References 40 publications

Centromere positions in chicken and Japanese quail chromosomes: de novo centromere formation versus pericentric inversions

Centromere positions in chicken and Japanese quail chromosomes: de novo centromere formation versus pericentric inversions

Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution

A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate

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