Generating a high‐confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping, and Oxford Nanopore technologies. (28th September 2018)

• Record Type: Journal Article
• Authors: Hoang, Phuong N.T.; Michael, Todd P.; Gilbert, Sarah; Chu, Philomena; Motley, S. Timothy; Appenroth, Klaus J.; Schubert, Ingo; Lam, Eric
• Is Part Of: Plant journal. Volume 96:Number 3(2018)
• Page Start: 670
• Page End: 684
• Publication Date: 2018-09-28
• Subjects: Spirodela polyrhiza -- duckweeds -- multicolor FISH -- optical map -- cytogenetic map -- Oxford Nanopore sequencing -- syntenous regions; Plant molecular biology -- Periodicals; Plant cells and tissues -- Periodicals; Botany -- Periodicals; 580
• DOI: 10.1111/tpj.14049
• Languages: English
• ISSNs: 0960-7412

Abstract

Summary: 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. Significance statement: Cytogenomic studies with 106 fingerprinted BACs, along with integration of Oxford Nanopore‐derived sequence data, enable full resolution of previous discrepancies between two genome maps for S. polyrhiza and provide a validated chromosome map for comparative genome mapping of other duckweed species, therefore demonstrating the utility of combinatorial approaches to generate high‐quality genome maps from organisms without available genetic maps.