Generating a high‐confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping, and Oxford Nanopore technologies

Abstract

Duckweeds are the fastest growing angiosperms and have the potential to become a new generation of sustainable crops. Although a seed plant, Spirodela polyrhiza clones rarely flower and multiply mainly through vegetative propagation. Whole-genome sequencing using different approaches and clones yielded two reference maps. One for clone 9509, supported in its assembly by optical mapping of single DNA molecules, and one for clone 7498, supported by cytogenetic assignment of 96 fingerprinted bacterial artificial chromosomes (BACs) to its 20 chromosomes. However, these maps differ in the composition of several individual chromosome models. We validated both maps further to resolve these differences and addressed whether they could be due to chromosome rearrangements in different clones. For this purpose, we applied sequential multicolor fluorescence in situ hybridization (mcFISH) to seven S. polyrhiza clones, using 106 BACs that were mapped onto the 39 pseudomolecules for clone 7498. Furthermore we integrated high-depth Oxford Nanopore (ON) sequence data for clone 9509 to validate and revise the previously assembled chromosome models. We found no major structural rearrangements between these seven clones, identified seven chimeric pseudomolecules and Illumina assembly errors in the previous maps, respectively. A new S. polyrhiza genome map with high contiguity was produced with the ON sequence data and genome-wide synteny analysis supported the occurrence of two Whole Genome Duplication events during its evolution. This work generated a high confidence genome map for S. polyrhiza at the chromosome scale, and illustrates the complementarity of independent approaches to produce whole-genome assemblies in the absence of a genetic map.

Nanopore sequencing: Review of potential applications in functional genomics

“…In the case of plant genomes such as the fastest-growing angiosperm (greater duckweed) or tropical timber trees (teak), HMW genomic DNA extraction has been successfully performed by a CTAB method (Hoang et al, 2018;Yasodha et al, 2018), following homogenization steps to break the cell wall, where grinding with liquid nitrogen is generally used to crush the cell wall while cellular enzymes remain inactivated. Therefore, homogenization and DNA extraction methods should be optimized for each species, especially for plants or arthropods that harbor thick cell walls and cuticular exoskeletons.…”

“…Therefore, homogenization and DNA extraction methods should be optimized for each species, especially for plants or arthropods that harbor thick cell walls and cuticular exoskeletons. In the case of plant genomes such as the fastest-growing angiosperm (greater duckweed) or tropical timber trees (teak), HMW genomic DNA extraction has been successfully performed by a CTAB method (Hoang et al, 2018;Yasodha et al, 2018), following homogenization steps to break the cell wall, where grinding with liquid nitrogen is generally used to crush the cell wall while cellular enzymes remain inactivated. After sufficient homogenization, samples are then resuspended in detergent-based extraction buffers containing cetyltrimethylammonium bromide (CTAB).…”

Die Wasserlinse – eine unterschätzte Vielzweckpflanze

“…Einige diesbezügliche Untersuchungen sind in Tabelle zusammengestellt. Die kürzlich erfolgte Sequenzierung und Kartierung des Genoms von Spirodela polyrhiza , gefolgt von mehreren wesentlichen Verbesserungen hat nun auch das Interesse an dem molekularbiologischen Potential von Wasserlinsen entfacht . Auch ein Entwurf für das Genom von Lemna minor ist bereits bekannt, und in mehreren Fachtagungen ist die baldige Veröffentlichung der Genome von weiteren Wasserlinsenarten wie Spirodela intermedia , Lemna gibba und Wolffia australiana angekündigt worden.…”

Chromosome-Scale Genome Assembly Provides Insights into Speciation of Allotetraploid and Massive Biomass Accumulation of Elephant Grass (Pennisetum purpureumSchum.)

“…These techniques have been adopted to construct high-quality assemblies of large genomes, such as human 22 , Arabidopsis thaliana 23 , Solanum pennellii 24 and sorghum 25 . In addition, long-range scaffolding technologies, such as Bionano Genomics optical maps and high-throughput chromatin conformation capture (Hi-C) proximity ligation 26 , in combination with long-read ONT sequences can generate chromosome-scale scaffolds, which have been applied to sequence the genomes of sorghum 25 , Brassica rapa 27 , and Spirodela polyrhiza 28 .…”