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Chromosome Research

, Volume 26, Issue 4, pp 297–306 | Cite as

But where did the centromeres go in the chicken genome models?

  • Benoît Piégu
  • Peter Arensburger
  • Florian Guillou
  • Yves BigotEmail author
Original Article

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.

Keywords

Centromere Bioinformatics Genome Repeats C-value 

Abbreviations

CENP-A

centromere protein A

ChIP

chromatine immuno-precipitation

DNA

deoxyribonucleic acid

G

Giga

bp

base pairs

seq

sequencing

Notes

Acknowledgements

Peter Arensburger holds a senior researcher fellowship from the STUDIUM.

Author contribution

YB and BP conceived the study and analyzed data. YB, PA and FG wrote the paper.

Funding information

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.

Supplementary material

10577_2018_9585_MOESM1_ESM.xlsx (38 kb)
ESM 1 (XLSX 38 kb)

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Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  • Benoît Piégu
    • 1
  • Peter Arensburger
    • 2
  • Florian Guillou
    • 1
  • Yves Bigot
    • 1
    Email author
  1. 1.PRC, UMR INRA0085, CNRS 7247, Centre INRA Val de LoireNouzillyFrance
  2. 2.Biological Sciences DepartmentCalifornia State Polytechnic UniversityPomonaUSA

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