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Structure of the intergenic spacers in chicken ribosomal DNA

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 sing...

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Autores principales: Dyomin, Alexander, Galkina, Svetlana, Fillon, Valerie, Cauet, Stephane, Lopez-Roques, Celine, Rodde, Nathalie, Klopp, Christophe, Vignal, Alain, Sokolovskaya, Anastasia, Saifitdinova, Alsu, Gaginskaya, Elena
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6815422/
https://www.ncbi.nlm.nih.gov/pubmed/31655542
http://dx.doi.org/10.1186/s12711-019-0501-7
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author Dyomin, Alexander
Galkina, Svetlana
Fillon, Valerie
Cauet, Stephane
Lopez-Roques, Celine
Rodde, Nathalie
Klopp, Christophe
Vignal, Alain
Sokolovskaya, Anastasia
Saifitdinova, Alsu
Gaginskaya, Elena
author_facet Dyomin, Alexander
Galkina, Svetlana
Fillon, Valerie
Cauet, Stephane
Lopez-Roques, Celine
Rodde, Nathalie
Klopp, Christophe
Vignal, Alain
Sokolovskaya, Anastasia
Saifitdinova, Alsu
Gaginskaya, Elena
author_sort Dyomin, Alexander
collection PubMed
description 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.
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spelling pubmed-68154222019-10-31 Structure of the intergenic spacers in chicken ribosomal DNA Dyomin, Alexander Galkina, Svetlana Fillon, Valerie Cauet, Stephane Lopez-Roques, Celine Rodde, Nathalie Klopp, Christophe Vignal, Alain Sokolovskaya, Anastasia Saifitdinova, Alsu Gaginskaya, Elena Genet Sel Evol Research Article 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. BioMed Central 2019-10-26 /pmc/articles/PMC6815422/ /pubmed/31655542 http://dx.doi.org/10.1186/s12711-019-0501-7 Text en © The Author(s) 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Dyomin, Alexander
Galkina, Svetlana
Fillon, Valerie
Cauet, Stephane
Lopez-Roques, Celine
Rodde, Nathalie
Klopp, Christophe
Vignal, Alain
Sokolovskaya, Anastasia
Saifitdinova, Alsu
Gaginskaya, Elena
Structure of the intergenic spacers in chicken ribosomal DNA
title Structure of the intergenic spacers in chicken ribosomal DNA
title_full Structure of the intergenic spacers in chicken ribosomal DNA
title_fullStr Structure of the intergenic spacers in chicken ribosomal DNA
title_full_unstemmed Structure of the intergenic spacers in chicken ribosomal DNA
title_short Structure of the intergenic spacers in chicken ribosomal DNA
title_sort structure of the intergenic spacers in chicken ribosomal dna
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6815422/
https://www.ncbi.nlm.nih.gov/pubmed/31655542
http://dx.doi.org/10.1186/s12711-019-0501-7
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