Chromosome‑scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries
Duckweeds are small, free-floating, morphologically highly reduced organisms belonging to the 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...
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2022
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Thư viện Trường Đại học Đà Lạt |
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English |
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Duckweeds are small, free-floating, morphologically highly reduced organisms belonging to the
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 |
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Hoàng, Thị Như Phương |
| spellingShingle |
Hoàng, Thị Như Phương Chromosome‑scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries |
| author_facet |
Hoàng, Thị Như Phương |
| 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 |
| publishDate |
2022 |
| url |
http://scholar.dlu.edu.vn/handle/123456789/1028 |
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1768305921004404736 |
| spelling |
oai:scholar.dlu.edu.vn:123456789-10282022-09-15T11:39:00Z Chromosome‑scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries Hoàng, Thị Như Phương Duckweeds are small, free-floating, morphologically highly reduced organisms belonging to the 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 19230 2022-09-15T11:38:57Z 2022-09-15T11:38:57Z 2020 Journal article Bài báo đăng trên tạp chí thuộc ISI, bao gồm book chapter http://scholar.dlu.edu.vn/handle/123456789/1028 10.1038/s41598-020-75728-9 en Scientific Reports Goswami, C., Majumder, A., Misra, A. K. & Bandyopadhyay, K. Arsenic uptake by Lemna minor in hydroponic system. Int. J. 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. 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