Chromosome-scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries

0538723 - BC 2021 RIV GB eng J - Článek v odborném periodiku
Hoang, P.T. N. - Fiebig, A. - Novák, Petr - Macas, Jiří - Cao, H.X. - Stepanenko, A. - Chen, G. - Borisjuk, N. - Scholz, U. - Schubert, I.
Chromosome-scale genome assembly for the duckweed Spirodela intermedia, integrating cytogenetic maps, PacBio and Oxford Nanopore libraries.
Scientific Reports. Roč. 10, č. 1 (2020), č. článku 19230. ISSN 2045-2322. E-ISSN 2045-2322
Grant CEP: GA MŠMT(CZ) LM2015047
Institucionální podpora: RVO:60077344
Klíčová slova: lemna-minor * annotation * polyrhiza * sequence * evolution * l.
Obor OECD: Genetics and heredity (medical genetics to be 3)
Impakt faktor: 4.380, rok: 2020
Způsob publikování: Open access
https://www.nature.com/articles/s41598-020-75728-9

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 similar to 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.
Trvalý link: http://hdl.handle.net/11104/0316459