Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa
Traditionally, reference genomes in crop species rely on the assembly of one accession, thus occulting most of intraspecific diversity. However, rearrangements, gene duplications, and transposable element content may have a large impact on the genomic structure, which could generate new phenotypic t...
| Main Authors: | , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2020-11-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2020.577536/full |
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| author | Julien Boutte Loeiz Maillet Thomas Chaussepied Sébastien Letort Jean-Marc Aury Caroline Belser Franz Boideau Anael Brunet Olivier Coriton Gwenaëlle Deniot Cyril Falentin Virginie Huteau Maryse Lodé-Taburel Jérôme Morice Gwenn Trotoux Anne-Marie Chèvre Mathieu Rousseau-Gueutin Julie Ferreira de Carvalho |
| author_facet | Julien Boutte Loeiz Maillet Thomas Chaussepied Sébastien Letort Jean-Marc Aury Caroline Belser Franz Boideau Anael Brunet Olivier Coriton Gwenaëlle Deniot Cyril Falentin Virginie Huteau Maryse Lodé-Taburel Jérôme Morice Gwenn Trotoux Anne-Marie Chèvre Mathieu Rousseau-Gueutin Julie Ferreira de Carvalho |
| author_sort | Julien Boutte |
| collection | DOAJ |
| description | Traditionally, reference genomes in crop species rely on the assembly of one accession, thus occulting most of intraspecific diversity. However, rearrangements, gene duplications, and transposable element content may have a large impact on the genomic structure, which could generate new phenotypic traits. Comparing two Brassica rapa genomes recently sequenced and assembled using long-read technology and optical mapping, we investigated structural variants and repetitive content between the two accessions and genome size variation among a core collection. We explored the structural consequences of the presence of large repeated sequences in B. rapa ‘Z1’ genome vs. the B. rapa ‘Chiifu’ genome, using comparative genomics and cytogenetic approaches. First, we showed that large genomic variants on chromosomes A05, A06, A09, and A10 are due to large insertions and inversions when comparing B. rapa ‘Z1’ and B. rapa ‘Chiifu’ at the origin of important length differences in some chromosomes. For instance, lengths of ‘Z1’ and ‘Chiifu’ A06 chromosomes were estimated in silico to be 55 and 29 Mb, respectively. To validate these observations, we compared using fluorescent in situ hybridization (FISH) the two A06 chromosomes present in an F1 hybrid produced by crossing these two varieties. We confirmed a length difference of 17.6% between the A06 chromosomes of ‘Z1’ compared to ‘Chiifu.’ Alternatively, using a copy number variation approach, we were able to quantify the presence of a higher number of rDNA and gypsy elements in ‘Z1’ genome compared to ‘Chiifu’ on different chromosomes including A06. Using flow cytometry, the total genome size of 12 Brassica accessions corresponding to a B. rapa available core collection was estimated and revealed a genome size variation of up to 16% between these accessions as well as some shared inversions. This study revealed the contribution of long-read sequencing of new accessions belonging to different cultigroups of B. rapa and highlighted the potential impact of differential insertion of repeat elements and inversions of large genomic regions in genome size intraspecific variability. |
| first_indexed | 2024-12-11T16:20:32Z |
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| id | doaj.art-66b622a6ded94448a2da0db8bbc2f766 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-11T16:20:32Z |
| publishDate | 2020-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-66b622a6ded94448a2da0db8bbc2f7662022-12-22T00:58:51ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2020-11-011110.3389/fpls.2020.577536577536Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapaJulien Boutte0Loeiz Maillet1Thomas Chaussepied2Sébastien Letort3Jean-Marc Aury4Caroline Belser5Franz Boideau6Anael Brunet7Olivier Coriton8Gwenaëlle Deniot9Cyril Falentin10Virginie Huteau11Maryse Lodé-Taburel12Jérôme Morice13Gwenn Trotoux14Anne-Marie Chèvre15Mathieu Rousseau-Gueutin16Julie Ferreira de Carvalho17IGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, FranceIGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, FranceIGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, FranceIRISA/INRIA, Campus de Beaulieu, Rennes, FranceGénomique Métabolique, Genoscope, Institut de biologie François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, FranceGénomique Métabolique, Genoscope, Institut de biologie François-Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, FranceIGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, FranceIGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, FranceIGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, FranceIGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, FranceIGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, FranceIGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, FranceIGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, FranceIGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, FranceIGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, FranceIGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, FranceIGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, FranceIGEPP, INRAE, Institut Agro, Univ Rennes, Le Rheu, FranceTraditionally, reference genomes in crop species rely on the assembly of one accession, thus occulting most of intraspecific diversity. However, rearrangements, gene duplications, and transposable element content may have a large impact on the genomic structure, which could generate new phenotypic traits. Comparing two Brassica rapa genomes recently sequenced and assembled using long-read technology and optical mapping, we investigated structural variants and repetitive content between the two accessions and genome size variation among a core collection. We explored the structural consequences of the presence of large repeated sequences in B. rapa ‘Z1’ genome vs. the B. rapa ‘Chiifu’ genome, using comparative genomics and cytogenetic approaches. First, we showed that large genomic variants on chromosomes A05, A06, A09, and A10 are due to large insertions and inversions when comparing B. rapa ‘Z1’ and B. rapa ‘Chiifu’ at the origin of important length differences in some chromosomes. For instance, lengths of ‘Z1’ and ‘Chiifu’ A06 chromosomes were estimated in silico to be 55 and 29 Mb, respectively. To validate these observations, we compared using fluorescent in situ hybridization (FISH) the two A06 chromosomes present in an F1 hybrid produced by crossing these two varieties. We confirmed a length difference of 17.6% between the A06 chromosomes of ‘Z1’ compared to ‘Chiifu.’ Alternatively, using a copy number variation approach, we were able to quantify the presence of a higher number of rDNA and gypsy elements in ‘Z1’ genome compared to ‘Chiifu’ on different chromosomes including A06. Using flow cytometry, the total genome size of 12 Brassica accessions corresponding to a B. rapa available core collection was estimated and revealed a genome size variation of up to 16% between these accessions as well as some shared inversions. This study revealed the contribution of long-read sequencing of new accessions belonging to different cultigroups of B. rapa and highlighted the potential impact of differential insertion of repeat elements and inversions of large genomic regions in genome size intraspecific variability.https://www.frontiersin.org/articles/10.3389/fpls.2020.577536/fullBrassicagenome evolutiontransposable elementsLTR Gypsyintraspecific diversityribosomal DNA |
| spellingShingle | Julien Boutte Loeiz Maillet Thomas Chaussepied Sébastien Letort Jean-Marc Aury Caroline Belser Franz Boideau Anael Brunet Olivier Coriton Gwenaëlle Deniot Cyril Falentin Virginie Huteau Maryse Lodé-Taburel Jérôme Morice Gwenn Trotoux Anne-Marie Chèvre Mathieu Rousseau-Gueutin Julie Ferreira de Carvalho Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa Frontiers in Plant Science Brassica genome evolution transposable elements LTR Gypsy intraspecific diversity ribosomal DNA |
| title | Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa |
| title_full | Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa |
| title_fullStr | Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa |
| title_full_unstemmed | Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa |
| title_short | Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa |
| title_sort | genome size variation and comparative genomics reveal intraspecific diversity in brassica rapa |
| topic | Brassica genome evolution transposable elements LTR Gypsy intraspecific diversity ribosomal DNA |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2020.577536/full |
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