A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae
Ensete glaucum (2n = 2x = 18) is a giant herbaceous monocotyledonous plant in the small Musaceae family along with banana (Musa). A high-quality reference genome sequence assembly of E. glaucum is a resource for functional and evolutionary studies of Ensete, Musaceae, and the Zingiberales. Using...
| Autores principales: | , , , , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Oxford University Press
2022
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| Acceso en línea: | https://hdl.handle.net/10568/119446 |
| _version_ | 1855519913275293696 |
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| author | Wang, Ziwei Rouard, Mathieu Biswas, Manosh Droc, Gaetan Cui, Dongli Roux, Nicolas Stephan M. Baurens, Franc-Christophe Ge, Xue-Jun Schwarzacher, Trude Heslop-Harrison, J.S. Liu, Qing |
| author_browse | Baurens, Franc-Christophe Biswas, Manosh Cui, Dongli Droc, Gaetan Ge, Xue-Jun Heslop-Harrison, J.S. Liu, Qing Rouard, Mathieu Roux, Nicolas Stephan M. Schwarzacher, Trude Wang, Ziwei |
| author_facet | Wang, Ziwei Rouard, Mathieu Biswas, Manosh Droc, Gaetan Cui, Dongli Roux, Nicolas Stephan M. Baurens, Franc-Christophe Ge, Xue-Jun Schwarzacher, Trude Heslop-Harrison, J.S. Liu, Qing |
| author_sort | Wang, Ziwei |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Ensete glaucum (2n = 2x = 18) is a giant herbaceous monocotyledonous plant in the small Musaceae family along with banana (Musa). A high-quality reference genome sequence assembly of E. glaucum is a resource for functional and evolutionary studies of Ensete, Musaceae, and the Zingiberales.
Using Oxford Nanopore Technologies, chromosome conformation capture (Hi-C), Illumina and RNA survey sequence, supported by molecular cytogenetics, we report a high-quality 481.5 Mb genome assembly with 9 pseudo-chromosomes and 36,836 genes. A total of 55% of the genome is composed of repetitive sequences with predominantly LTR-retroelements (37%) and DNA transposons (7%). The single 5S ribosomal DNA locus had an exceptionally long monomer length of 1,056 bp, more than twice that of the monomers at multiple loci in Musa. A tandemly repeated satellite (1.1% of the genome, with no similar sequence in Musa) was present around all centromeres, together with a few copies of a long interspersed nuclear element (LINE) retroelement. The assembly enabled us to characterize in detail the chromosomal rearrangements occurring between E. glaucum and the x = 11 species of Musa. One E. glaucum chromosome has the same gene content as Musa acuminata, while others show multiple, complex, but clearly defined evolutionary rearrangements in the change between x= 9 and 11.
The advance towards a Musaceae pangenome including E. glaucum, tolerant of extreme environments, makes a complete set of gene alleles, copy number variation, and a reference for structural variation available for crop breeding and understanding environmental responses. The chromosome-scale genome assembly shows the nature of chromosomal fusion and translocation events during speciation, and features of rapid repetitive DNA change in terms of copy number, sequence, and genomic location, critical to understanding its role in diversity and evolution. |
| format | Journal Article |
| id | CGSpace119446 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2022 |
| publishDateRange | 2022 |
| publishDateSort | 2022 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace1194462025-11-11T17:45:20Z A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae Wang, Ziwei Rouard, Mathieu Biswas, Manosh Droc, Gaetan Cui, Dongli Roux, Nicolas Stephan M. Baurens, Franc-Christophe Ge, Xue-Jun Schwarzacher, Trude Heslop-Harrison, J.S. Liu, Qing centromeres chromosome mapping gene editing dna replication translocation centrómeros cartografía cromosómica edición de genes replicación del adn Ensete glaucum (2n = 2x = 18) is a giant herbaceous monocotyledonous plant in the small Musaceae family along with banana (Musa). A high-quality reference genome sequence assembly of E. glaucum is a resource for functional and evolutionary studies of Ensete, Musaceae, and the Zingiberales. Using Oxford Nanopore Technologies, chromosome conformation capture (Hi-C), Illumina and RNA survey sequence, supported by molecular cytogenetics, we report a high-quality 481.5 Mb genome assembly with 9 pseudo-chromosomes and 36,836 genes. A total of 55% of the genome is composed of repetitive sequences with predominantly LTR-retroelements (37%) and DNA transposons (7%). The single 5S ribosomal DNA locus had an exceptionally long monomer length of 1,056 bp, more than twice that of the monomers at multiple loci in Musa. A tandemly repeated satellite (1.1% of the genome, with no similar sequence in Musa) was present around all centromeres, together with a few copies of a long interspersed nuclear element (LINE) retroelement. The assembly enabled us to characterize in detail the chromosomal rearrangements occurring between E. glaucum and the x = 11 species of Musa. One E. glaucum chromosome has the same gene content as Musa acuminata, while others show multiple, complex, but clearly defined evolutionary rearrangements in the change between x= 9 and 11. The advance towards a Musaceae pangenome including E. glaucum, tolerant of extreme environments, makes a complete set of gene alleles, copy number variation, and a reference for structural variation available for crop breeding and understanding environmental responses. The chromosome-scale genome assembly shows the nature of chromosomal fusion and translocation events during speciation, and features of rapid repetitive DNA change in terms of copy number, sequence, and genomic location, critical to understanding its role in diversity and evolution. 2022-04-30 2022-05-03T13:01:11Z 2022-05-03T13:01:11Z Journal Article https://hdl.handle.net/10568/119446 en Open Access application/pdf Oxford University Press Wang, Z.; Rouard, M.; Biswas, M.; Droc, G.; Cui, D.; Roux, N.; Baurens, F.-C.; Ge, X.-J.; Schwarzacher, T.; Heslop-Harrison, P. (J S); Liu, Q.; (2022) A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae. GigaScience 11, giac027. 21 p. ISSN: 2047-217X |
| spellingShingle | centromeres chromosome mapping gene editing dna replication translocation centrómeros cartografía cromosómica edición de genes replicación del adn Wang, Ziwei Rouard, Mathieu Biswas, Manosh Droc, Gaetan Cui, Dongli Roux, Nicolas Stephan M. Baurens, Franc-Christophe Ge, Xue-Jun Schwarzacher, Trude Heslop-Harrison, J.S. Liu, Qing A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae |
| title | A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae |
| title_full | A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae |
| title_fullStr | A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae |
| title_full_unstemmed | A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae |
| title_short | A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae |
| title_sort | chromosome level reference genome of ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the musaceae |
| topic | centromeres chromosome mapping gene editing dna replication translocation centrómeros cartografía cromosómica edición de genes replicación del adn |
| url | https://hdl.handle.net/10568/119446 |
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