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Structure of the intergenic spacers in chicken ribosomal DNA

Authors :
Svetlana Galkina
Anastasia Sokolovskaya
Elena Gaginskaya
Nathalie Rodde
Stéphane Cauet
Céline Lopez-Roques
Alsu Saifitdinova
Christophe Klopp
Alexander Dyomin
Valerie Fillon
Alain Vignal
Génétique Physiologie et Systèmes d'Elevage (GenPhySE )
École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT)
Institut National Polytechnique (Toulouse) (Toulouse INP)
Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP)
Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées
Centre National de Ressources Génomiques Végétales (CNRGV)
Institut National de la Recherche Agronomique (INRA)
Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe)
Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET)
Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL)
Université Toulouse III - Paul Sabatier (UT3)
Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT)
Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3)
Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL)
Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Système d'Information des GENomes des Animaux d'Elevage (SIGENAE)
Russian Foundation for Basic Research (RFBR) 18-04-01276A / Saint Petersburg State University's Programme 4 1.40.1625.2017
Institut National des Sciences Appliquées - Toulouse (INSA Toulouse)
Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3)
Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse)
INRA (GeT-PlaGE)
Source :
Genetics Selection Evolution, Genetics Selection Evolution, BioMed Central, 2019, 51 (1), pp.59. ⟨10.1186/s12711-019-0501-7⟩, Genetics Selection Evolution, Vol 51, Iss 1, Pp 1-13 (2019), Genetics Selection Evolution 1 (51), Non paginé. (2019), Genetics, Selection, Evolution : GSE
Publication Year :
2019
Publisher :
Springer Science and Business Media LLC, 2019.

Abstract

Background Ribosomal DNA (rDNA) repeats are situated in the nucleolus organizer regions (NOR) of chromosomes and transcribed into rRNA for ribosome biogenesis. Thus, they are an essential component of eukaryotic genomes. rDNA repeat units consist of rRNA gene clusters that are transcribed into single pre-rRNA molecules, each separated by intergenic spacers (IGS) that contain regulatory elements for rRNA gene cluster transcription. Because of their high repeat content, rDNA sequences are usually absent from genome assemblies. In this work, we used the long-read sequencing technology to describe the chicken IGS and fill the knowledge gap on rDNA sequences of one of the key domesticated animals. Methods We used the long-read PacBio RSII technique to sequence the BAC clone WAG137G04 (Wageningen BAC library) known to contain chicken NOR elements and the HGAP workflow software suit to assemble the PacBio RSII reads. Whole-genome sequence contigs homologous to the chicken rDNA repetitive unit were identified based on the Gallus_gallus-5.0 assembly with BLAST. We used the Geneious 9.0.5 and Mega software, maximum likelihood method and Chickspress project for sequence evolution analysis, phylogenetic tree construction and analysis of the raw transcriptome data. Results Three complete IGS sequences in the White Leghorn chicken genome and one IGS sequence in the red junglefowl contig AADN04001305.1 (Gallus_gallus-5.0) were detected. They had various lengths and contained three groups of tandem repeats (some of them being very GC rich) that form highly organized arrays. Initiation and termination sites of rDNA transcription were located within small and large unique regions (SUR and LUR), respectively. No functionally significant sites were detected within the tandem repeat sequences. Conclusions Due to the highly organized GC-rich repeats, the structure of the chicken IGS differs from that of IGS in human, apes, Xenopus or fish rDNA. However, the chicken IGS shares some molecular organization features with that of the turtles, which are other representatives of the Sauropsida clade that includes birds and reptiles. Our current results on the structure of chicken IGS together with the previously reported ribosomal gene cluster sequence provide sufficient data to consider that the complete chicken rDNA sequence is assembled with confidence in terms of molecular DNA organization.

Details

ISSN :
12979686 and 0999193X
Volume :
51
Database :
OpenAIRE
Journal :
Genetics Selection Evolution
Accession number :
edsair.doi.dedup.....5fbc8b912119527e702ca6ad28c2bc97