Abstract
The chicken genome was the third vertebrate to be sequenced. To date, its sequence and feature annotations are used as the reference for avian models in genome sequencing projects developed on birds and other Sauropsida species, and in genetic studies of domesticated birds of economic and evolutionary biology interest. Therefore, an accurate description of this genome model is important to a wide number of scientists. Here, we review the location and features of a very basic element, the centromeres of chromosomes in the galGal5 genome model. Centromeres are elements that are not determined by their DNA sequence but by their epigenetic status, in particular by the accumulation of the histone-like protein CENP-A. Comparison of data from several public sources (primarily marker probes flanking centromeres using fluorescent in situ hybridization done on giant lampbrush chromosomes and CENP-A ChIP-seq datasets) with galGal5 annotations revealed that centromeres are likely inappropriately mapped in 9 of the 16 galGal5 chromosome models in which they are described. Analysis of karyology data confirmed that the location of the main CENP-A peaks in chromosomes is the best means of locating the centromeres in 25 galGal5 chromosome models, the majority of which (16) are fully sequenced and assembled. This data re-analysis reaffirms that several sources of information should be examined to produce accurate genome annotations, particularly for basic structures such as centromeres that are epigenetically determined.
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Abbreviations
- CENP-A:
-
centromere protein A
- ChIP:
-
chromatine immuno-precipitation
- DNA:
-
deoxyribonucleic acid
- G:
-
Giga
- bp:
-
base pairs
- seq:
-
sequencing
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Acknowledgements
Peter Arensburger holds a senior researcher fellowship from the STUDIUM.
Funding
This work was funded by the Project Région Centre AviGeS, the C.N.R.S., the I.N.R.A., the Groupement de Recherche CNRS 2157, and the Ministère de l’Education Nationale, de la Recherche et de la Technologie.
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YB and BP conceived the study and analyzed data. YB, PA and FG wrote the paper.
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Piégu, B., Arensburger, P., Guillou, F. et al. But where did the centromeres go in the chicken genome models?. Chromosome Res 26, 297–306 (2018). https://doi.org/10.1007/s10577-018-9585-0
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DOI: https://doi.org/10.1007/s10577-018-9585-0