title: The map-based genome sequence of Spirodela polyrhiza aligned with its chromosomes, a reference for karyotype evolution.
abstract: Duckweeds are aquatic monocotyledonous plants of potential economic interest with fast vegetative propagation, comprising 37 species with variable genome sizes (0.158-1.88 Gbp). The genomic sequence of Spirodela polyrhiza, the smallest and the most ancient duckweed genome, needs to be aligned to its chromosomes as a reference and prerequisite to study the genome and karyotype evolution of other duckweed species. We selected physically mapped bacterial artificial chromosomes (BACs) containing Spirodela DNA inserts with little or no repetitive elements as probes for multicolor fluorescence in situ hybridization (mcFISH), using an optimized BAC pooling strategy, to validate its physical map and correlate it with its chromosome complement. By consecutive mcFISH analyses, we assigned the originally assembled 32 pseudomolecules (supercontigs) of the genomic sequences to the 20 chromosomes of S. polyrhiza. A Spirodela cytogenetic map containing 96 BAC markers with an average distance of 0.89 Mbp was constructed. Using a cocktail of 41 BACs in three colors, all chromosome pairs could be individualized simultaneously. Seven ancestral blocks emerged from duplicated chromosome segments of 19 Spirodela chromosomes. The chromosomally integrated genome of S. polyrhiza and the established prerequisites for comparative chromosome painting enable future studies on the chromosome homoeology and karyotype evolution of duckweed species.
authors: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany.
authors: Hieu Xuan
authors: HX
authors: Cao
authors: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany.
authors: Giang Thi Ha
authors: GT
authors: Vu
authors: Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ, 08854, USA.
authors: Wenqin
authors: W
authors: Wang
authors: University of Jena, Dornburger str. 159, 07743, Jena, Germany.
authors: Klaus J
authors: KJ
authors: Appenroth
authors: Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ, 08854, USA.
authors: Joachim
authors: J
authors: Messing
authors: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany.|Faculty of Science and Central European Institute of Technology, Masaryk University, CZ-61137, Brno, Czech Republic.
authors: Ingo
authors: I
authors: Schubert
mesh_terms: D029064:Araceae / Q000235:genetics*; D022202:Chromosomes, Artificial, Bacterial; D032461:Chromosomes, Plant / Q000235:genetics*; D019143:Evolution, Molecular; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics; D017404:In Situ Hybridization, Fluorescence; D059785:Karyotype; D007621:Karyotyping; D020161:Physical Chromosome Mapping
keywords: Spirodela polyrhiza; duckweeds; fluorescence in situ hybridization (FISH); genome integration; molecular cytogenetic map