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

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

Chicken rRNA Gene Cluster Structure

<div><p>Ribosomal RNA (rRNA) genes, whose activity results in nucleolus formation, constitute an extremely important part of genome. Despite the extensive exploration into avian genomes, no complete description of avian rRNA gene primary structure has been offered so far. We publish a complete chicken rRNA gene cluster sequence here, including <i>5’ETS</i> (1836 bp), <i>18S rRNA</i> gene (1823 bp), <i>ITS1</i> (2530 bp), <i>5</i>.<i>8S rRNA</i> gene (157 bp), <i>ITS2</i> (733 bp), <i>28S rRNA</i> gene (4441 bp) and <i>3’ETS</i> (343 bp). The rRNA gene cluster sequence of 11863 bp was assembled from raw reads and deposited to GenBank under KT445934 accession number. The assembly was validated through <i>in situ</i> fluorescent hybridization analysis on chicken metaphase chromosomes using computed and synthesized specific probes, as well as through the reference assembly against <i>de novo</i> assembled rRNA gene cluster sequence using sequenced fragments of BAC-clone containing chicken NOR (nucleolus organizer region). The results have confirmed the chicken rRNA gene cluster validity.</p></div

Ribosomal DNA structure (after Singer and Berg, 1991).

<p>Ribosomal DNA structure (after Singer and Berg, 1991).</p

The list of primers for amplification of target regions of the assembled ribosomal cluster sequence.

<p>The list of primers for amplification of target regions of the assembled ribosomal cluster sequence.</p

Localization of assembled rRNA gene cluster fragments on chicken mitotic chromosomes.

<p>FISH with (A) <i>5’ETS–18S</i> rDNA fragment probe, (D) <i>ITS1–5</i>.<i>8S</i> rDNA fragment probe, (B, E) WAG137G04 BAC probe, which contains NOR, marker of GGA16, (C, F) merge. A, D–green fluorescence; B, E–red fluorescence; C, F–merge. Chromosomes are counterstained with DAPI (blue). Bar – 5 μm.</p

The chicken rRNA gene cluster structure and features.

<p>The chicken rRNA gene cluster structure and features.</p