Chromosome-scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries
monocot order Alismatales. They display the most rapid growth among flowering plants, vary ~ 14-fold in genome size and comprise five genera. Spirodela is the phylogenetically oldest genus with only two mainly asexually propagating species: S. polyrhiza (2n = 40; 160 Mbp/1C) and S. intermedia (2n...
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Nature Publishing Group UK
2023
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| Truy cập trực tuyến: | https://scholar.dlu.edu.vn/handle/123456789/3092 https://doi.org/10.1038/s41598-020-75728-9 |
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oai:scholar.dlu.edu.vn:123456789-3092 |
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Thư viện Trường Đại học Đà Lạt |
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English |
| description |
monocot order Alismatales. They display the most rapid growth among flowering plants, vary ~ 14-fold
in genome size and comprise five genera. Spirodela is the phylogenetically oldest genus with only two
mainly asexually propagating species: S. polyrhiza (2n = 40; 160 Mbp/1C) and S. intermedia (2n = 36;
160 Mbp/1C). This study combined comparative cytogenetics and de novo genome assembly based
on PacBio, Illumina and Oxford Nanopore (ON) reads to obtain the first genome reference for S.
intermedia and to compare its genomic features with those of the sister species S. polyrhiza. Both
species’ genomes revealed little more than 20,000 putative protein-coding genes, very low rDNA copy
numbers and a low amount of repetitive sequences, mainly Ty3/gypsy retroelements. The detection of
a few new small chromosome rearrangements between both Spirodela species refined the karyotype
and the chromosomal sequence assignment for S. intermedia. |
| format |
Journal article |
| author |
Hoàng, Thị Như Phương Anne Fiebig Petr Novák Jiří Macas Hieu X Cao Anton Stepanenko Guimin Chen Nikolai Borisjuk Uwe Scholz Ingo Schubert |
| spellingShingle |
Hoàng, Thị Như Phương Anne Fiebig Petr Novák Jiří Macas Hieu X Cao Anton Stepanenko Guimin Chen Nikolai Borisjuk Uwe Scholz Ingo Schubert Chromosome-scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries |
| author_facet |
Hoàng, Thị Như Phương Anne Fiebig Petr Novák Jiří Macas Hieu X Cao Anton Stepanenko Guimin Chen Nikolai Borisjuk Uwe Scholz Ingo Schubert |
| author_sort |
Hoàng, Thị Như Phương |
| title |
Chromosome-scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries |
| title_short |
Chromosome-scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries |
| title_full |
Chromosome-scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries |
| title_fullStr |
Chromosome-scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries |
| title_full_unstemmed |
Chromosome-scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries |
| title_sort |
chromosome-scale genome assembly for the duckweed spirodela intermedia, integrating cytogenetic maps, pacbio and oxford nanopore libraries |
| publisher |
Nature Publishing Group UK |
| publishDate |
2023 |
| url |
https://scholar.dlu.edu.vn/handle/123456789/3092 https://doi.org/10.1038/s41598-020-75728-9 |
| _version_ |
1783866427086733312 |
| spelling |
oai:scholar.dlu.edu.vn:123456789-30922023-11-15T04:52:33Z Chromosome-scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries Hoàng, Thị Như Phương Anne Fiebig Petr Novák Jiří Macas Hieu X Cao Anton Stepanenko Guimin Chen Nikolai Borisjuk Uwe Scholz Ingo Schubert monocot order Alismatales. They display the most rapid growth among flowering plants, vary ~ 14-fold in genome size and comprise five genera. Spirodela is the phylogenetically oldest genus with only two mainly asexually propagating species: S. polyrhiza (2n = 40; 160 Mbp/1C) and S. intermedia (2n = 36; 160 Mbp/1C). This study combined comparative cytogenetics and de novo genome assembly based on PacBio, Illumina and Oxford Nanopore (ON) reads to obtain the first genome reference for S. intermedia and to compare its genomic features with those of the sister species S. polyrhiza. Both species’ genomes revealed little more than 20,000 putative protein-coding genes, very low rDNA copy numbers and a low amount of repetitive sequences, mainly Ty3/gypsy retroelements. The detection of a few new small chromosome rearrangements between both Spirodela species refined the karyotype and the chromosomal sequence assignment for S. intermedia. 10 1 19230 2023-10-24T04:12:38Z 2023-10-24T04:12:38Z 2020-05-11 Journal article Bài báo đăng trên tạp chí thuộc ISI, bao gồm book chapter https://scholar.dlu.edu.vn/handle/123456789/3092 https://doi.org/10.1038/s41598-020-75728-9 en Scientific reports Phytoremediation 16, 1221–1227. https ://doi.org/10.1080/15226 514.2013.82145 2 (2014). 2. Tatar, ŞY. & Öbek, E. Potential of Lemna gibba L. and Lemna minor L. for accumulation of Boron from secondary effluents. Ecol. Eng. 70, 332–336. https ://doi.org/10.1016/j.ecole ng.2014.06.033 (2014). 3. Teixeira, S., Vieira, M. N., Espinha Marques, J. & Pereira, R. 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Genetic characterization and barcoding of taxa in the genera Landoltia and Spirodela (Lemnaceae) by three plastidic markers and amplified fragment length polymorphism (AFLP). Hydrobiologia 749, 169–182. https ://doi.org/10.1007/s1075 0-014- 2163-3 (2015). 18. Hoang, P. T. N., Schubert, V., Meister, A., Fuchs, J. & Schubert, I. Variation in genome size, cell and nucleus volume, chromosome number and rDNA loci among duckweeds. Sci. Rep. 9, 3234. https ://doi.org/10.1038/s4159 8-019-39332 -w (2019). 19. Landolt, E. The family of Lemnaceae: a monographic study (Vol 1) (Veröffentlichungen des Geobotanischen Institutes der Eidg. Techn. Hochschule, Zürich, 1986). 20. Wang, W., Kerstetter, R. A. & Michael, T. P. Evolution of genome size in duckweeds (Lemnaceae). J. Bot. 1–9, 2011. https ://doi. org/10.1155/2011/57031 9 (2011). 21. Wang, W. et al. The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle. Nat. 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