Biology Faculty Articles

Title

New high copy tandem repeat in the content of the chicken W chromosome

Document Type

Article

Publication Date

3-1-2018

Publication Title

Chromosoma

Keywords

Gallus gallus Domesticus, Kmer analysis, Lampbrush chromosomes, Raw reads analysis, Satellite DNA, Tandem repeats

ISSN

14320886

Volume

127

Issue/No.

1

First Page

73

Last Page

83

Abstract

The content of repetitive DNA in avian genomes is considerably less than in other investigated vertebrates. The first descriptions of tandem repeats were based on the results of routine biochemical and molecular biological experiments. Both satellite DNA and interspersed repetitive elements were annotated using library-based approach and de novo repeat identification in assembled genome. The development of deep-sequencing methods provides datasets of high quality without preassembly allowing one to annotate repetitive elements from unassembled part of genomes. In this work, we search the chicken assembly and annotate high copy number tandem repeats from unassembled short raw reads. Tandem repeat (GGAAA) n has been identified and found to be the second after telomeric repeat (TTAGGG)n most abundant in the chicken genome. Furthermore, (GGAAA) n repeat forms expanded arrays on the both arms of the chicken W chromosome. Our results highlight the complexity of repetitive sequences and update data about organization of sex W chromosome in chicken.

DOI

10.1007/s00412-017-0646-5

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