Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima

Gene and whole-genome duplications are widespread in plant nuclear genomes, resulting in sequence heterogeneity. Identification of duplicated genes may be particularly challenging in highly redundant genomes, especially when there are no diploid parents as a reference. Here, we developed a pipeline...

Descripción completa

Detalles Bibliográficos
Autores principales: Boutte, Julien, Aliaga, Benoît, Lima, Oscar, Ferreira de Carvalho, Julie, Ainouche, Abdelkader, Macas, Jiri, Rousseau-Gueutin, Mathieu, Coriton, Olivier, Ainouche, Malika, Salmon, Armel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Genetics Society of America 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4704722/
https://www.ncbi.nlm.nih.gov/pubmed/26530424
http://dx.doi.org/10.1534/g3.115.023242
_version_ 1782408903346094080
author Boutte, Julien
Aliaga, Benoît
Lima, Oscar
Ferreira de Carvalho, Julie
Ainouche, Abdelkader
Macas, Jiri
Rousseau-Gueutin, Mathieu
Coriton, Olivier
Ainouche, Malika
Salmon, Armel
author_facet Boutte, Julien
Aliaga, Benoît
Lima, Oscar
Ferreira de Carvalho, Julie
Ainouche, Abdelkader
Macas, Jiri
Rousseau-Gueutin, Mathieu
Coriton, Olivier
Ainouche, Malika
Salmon, Armel
author_sort Boutte, Julien
collection PubMed
description Gene and whole-genome duplications are widespread in plant nuclear genomes, resulting in sequence heterogeneity. Identification of duplicated genes may be particularly challenging in highly redundant genomes, especially when there are no diploid parents as a reference. Here, we developed a pipeline to detect the different copies in the ribosomal RNA gene family in the hexaploid grass Spartina maritima from next-generation sequencing (Roche-454) reads. The heterogeneity of the different domains of the highly repeated 45S unit was explored by identifying single nucleotide polymorphisms (SNPs) and assembling reads based on shared polymorphisms. SNPs were validated using comparisons with Illumina sequence data sets and by cloning and Sanger (re)sequencing. Using this approach, 29 validated polymorphisms and 11 validated haplotypes were reported (out of 34 and 20, respectively, that were initially predicted by our program). The rDNA domains of S. maritima have similar lengths as those found in other Poaceae, apart from the 5′-ETS, which is approximately two-times longer in S. maritima. Sequence homogeneity was encountered in coding regions and both internal transcribed spacers (ITS), whereas high intragenomic variability was detected in the intergenic spacer (IGS) and the external transcribed spacer (ETS). Molecular cytogenetic analysis by fluorescent in situ hybridization (FISH) revealed the presence of one pair of 45S rDNA signals on the chromosomes of S. maritima instead of three expected pairs for a hexaploid genome, indicating loss of duplicated homeologous loci through the diploidization process. The procedure developed here may be used at any ploidy level and using different sequencing technologies.
format Online
Article
Text
id pubmed-4704722
institution National Center for Biotechnology Information
language English
publishDate 2015
publisher Genetics Society of America
record_format MEDLINE/PubMed
spelling pubmed-47047222016-01-08 Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima Boutte, Julien Aliaga, Benoît Lima, Oscar Ferreira de Carvalho, Julie Ainouche, Abdelkader Macas, Jiri Rousseau-Gueutin, Mathieu Coriton, Olivier Ainouche, Malika Salmon, Armel G3 (Bethesda) Investigations Gene and whole-genome duplications are widespread in plant nuclear genomes, resulting in sequence heterogeneity. Identification of duplicated genes may be particularly challenging in highly redundant genomes, especially when there are no diploid parents as a reference. Here, we developed a pipeline to detect the different copies in the ribosomal RNA gene family in the hexaploid grass Spartina maritima from next-generation sequencing (Roche-454) reads. The heterogeneity of the different domains of the highly repeated 45S unit was explored by identifying single nucleotide polymorphisms (SNPs) and assembling reads based on shared polymorphisms. SNPs were validated using comparisons with Illumina sequence data sets and by cloning and Sanger (re)sequencing. Using this approach, 29 validated polymorphisms and 11 validated haplotypes were reported (out of 34 and 20, respectively, that were initially predicted by our program). The rDNA domains of S. maritima have similar lengths as those found in other Poaceae, apart from the 5′-ETS, which is approximately two-times longer in S. maritima. Sequence homogeneity was encountered in coding regions and both internal transcribed spacers (ITS), whereas high intragenomic variability was detected in the intergenic spacer (IGS) and the external transcribed spacer (ETS). Molecular cytogenetic analysis by fluorescent in situ hybridization (FISH) revealed the presence of one pair of 45S rDNA signals on the chromosomes of S. maritima instead of three expected pairs for a hexaploid genome, indicating loss of duplicated homeologous loci through the diploidization process. The procedure developed here may be used at any ploidy level and using different sequencing technologies. Genetics Society of America 2015-11-03 /pmc/articles/PMC4704722/ /pubmed/26530424 http://dx.doi.org/10.1534/g3.115.023242 Text en Copyright © 2016 Boutte et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article 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 the original work is properly cited.
spellingShingle Investigations
Boutte, Julien
Aliaga, Benoît
Lima, Oscar
Ferreira de Carvalho, Julie
Ainouche, Abdelkader
Macas, Jiri
Rousseau-Gueutin, Mathieu
Coriton, Olivier
Ainouche, Malika
Salmon, Armel
Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima
title Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima
title_full Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima
title_fullStr Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima
title_full_unstemmed Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima
title_short Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima
title_sort haplotype detection from next-generation sequencing in high-ploidy-level species: 45s rdna gene copies in the hexaploid spartina maritima
topic Investigations
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4704722/
https://www.ncbi.nlm.nih.gov/pubmed/26530424
http://dx.doi.org/10.1534/g3.115.023242
work_keys_str_mv AT bouttejulien haplotypedetectionfromnextgenerationsequencinginhighploidylevelspecies45srdnagenecopiesinthehexaploidspartinamaritima
AT aliagabenoit haplotypedetectionfromnextgenerationsequencinginhighploidylevelspecies45srdnagenecopiesinthehexaploidspartinamaritima
AT limaoscar haplotypedetectionfromnextgenerationsequencinginhighploidylevelspecies45srdnagenecopiesinthehexaploidspartinamaritima
AT ferreiradecarvalhojulie haplotypedetectionfromnextgenerationsequencinginhighploidylevelspecies45srdnagenecopiesinthehexaploidspartinamaritima
AT ainoucheabdelkader haplotypedetectionfromnextgenerationsequencinginhighploidylevelspecies45srdnagenecopiesinthehexaploidspartinamaritima
AT macasjiri haplotypedetectionfromnextgenerationsequencinginhighploidylevelspecies45srdnagenecopiesinthehexaploidspartinamaritima
AT rousseaugueutinmathieu haplotypedetectionfromnextgenerationsequencinginhighploidylevelspecies45srdnagenecopiesinthehexaploidspartinamaritima
AT coritonolivier haplotypedetectionfromnextgenerationsequencinginhighploidylevelspecies45srdnagenecopiesinthehexaploidspartinamaritima
AT ainouchemalika haplotypedetectionfromnextgenerationsequencinginhighploidylevelspecies45srdnagenecopiesinthehexaploidspartinamaritima
AT salmonarmel haplotypedetectionfromnextgenerationsequencinginhighploidylevelspecies45srdnagenecopiesinthehexaploidspartinamaritima