Establishing a chromosome map for Spirodela polyrhiza, chromosome homeology and karyotype evolution within the aquatic, largely asexual Lemnoideae, a basic monocot group of potential economic importance
Final Report Abstract
The aim of the project was to study cytological features and the composition, diversity and evolution of genomes, karyotypes of selected species of the five aquatic monocot genera of duckweeds, which are of growing economic and scientific interest, but little studied under these aspects. The main achievements of the project are: Epigenetic characterization of eu- and heterochromatic features and determination of chromosome number, genome size, rDNA loci number and nuclear and cell volumes (of guard cells) for species of all five genera. The heterochromatin distribution of these neotenic organisms remembered this of very young Arabidopsis seedlings, independent of genome size. Nuclear and cell volumes correlate positively with genome size, but negatively with phylogenetic age and frond size, while chromosome and rDNA loci number do not correlate with genome size. No deviating chromosome numbers were found for clones of the same species; chromosome numbers and genome size gave no unambiguous hint on recent natural whole genome duplications. Genome assemblies from various sequencing technologies were validated, corrected and integrated by serial mcFISH with single copy BACs into the 20 chromosomes of Spirodela polyrhiza. Combining several independent approaches yielded a robust chromosome scale genome map and revealed no gross karyotypic alterations between 7 asexual S. polyrhiza clones of different geographic origin. Homeology and evolutionary chromosome rearrangements between the only two species of the basic duckweed genus Spirodela have been elucidated and a cytogenomic map for two clones of the second species, S. intermedia, has been established. The limits of resolution of cross-FISH with BAC and unique oligo probe samples for elucidation of chromosome homeology and the routes of karyotype evolution across the duckweed genera were determined. Contributions were made to support the generation of a genome map for Landoltia punctata, the only species of the 2nd duckweed genus, and for taxonomic studies resulting in a reduction of Lemna species from 13 to 12 by our collaboration partners.
Publications
- (2020) A taxonomic revision of Lemna sect. Uninerves (Lemnaceae). TAXON 69 (1) 56–66
Bog, Manuela; Sree, K. Sowjanya; Fuchs, Joerg; Hoang, Phuong T.N.; Schubert, Ingo; Kuever, Jan; Rabenstein, Andreas; Paolacci, Simona; Jansen, Marcel A.K.; Appenroth, Klaus‐J.
(See online at https://doi.org/10.1002/tax.12188) - (2015) Chromatin organization in duckweed interphase nuclei in relation to the nuclear DNA content. Plant Biol. 17: 120-124
Cao Hx, Vu Gth, Wang W, Messing J, Schubert I
(See online at https://doi.org/10.1111/plb.12194) - The first draft genome of the aquatic model plant Lemna minor opens the route for future stress physiology research and biotechnological applications. Biotechnology for Biofuels, 2015. 8: 1-13
Van Hoeck A, Horemans N, Monsieur P, Cao Hx, H. Vandenhove H, Blust R
(See online at https://doi.org/10.1186/s13068-015-0381-1) - (2016) The map-based genome sequence of Spirodela polyrhiza aligned with its chromosomes, a reference for karyotype evolution. New Phytologist, 209: 354-363
Cao Hx, Vu Gth, Wang W, Appenroth Kj, Messing J, Schubert I
(See online at https://doi.org/10.1111/nph.13592) - (2017) Reconstruction of chromosome rearrangements between the two most ancestral duckweed species Spirodela polyrhiza and S. intermedia, Chromosoma, 126: 729-739
Hoang Pnt, Schubert I
(See online at https://doi.org/10.1007/s00412-017-0636-7) - (2018) Generating a high-confidence reference genome map of the Greater duckweed by integration of cytogenomic, optical mapping and Oxford Nanopore technologies. Plant J 96: 670-684
Hoang Pnt, Michael Tp, Gilbert S, Chu P, Motley M, Appenroth K, Schubert I, Lam E
(See online at https://doi.org/10.1111/tpj.14049) - (2019) Combination of Various Sequencing, Assembly and Mapping Approaches, Creating a Reliable Genome Assembly for Emerging Aquatic Crops. G.I.T. Laboratory J 1/2019
Hoang Ntp, Schubert I
- (2019) Comparative cytology and cytogenomics for representative species of the five duckweed genera. Dissertation, Martin-Luther-Universität Halle-Wittenberg
Hoang Ntp
- (2019) Variation in genome size, cell volume, nucleus volume, chromosome number and rDNA loci between duckweed genera. Scientific Rep.
Hoang Pnt, Schubert V, Meister A, Fuchs J, Schubert I
(See online at https://doi.org/10.1038/s41598-019-39332-w)
