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

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 ( BAC s) 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 (mc FISH ) to seven S. polyrhiza clones, using 106 BAC s 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 withmore » 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.« less

Authors:

Hoang, Phuong N. T. ^[1]; Michael, Todd P. ^[2]; Gilbert, Sarah ^[3]; Chu, Philomena ^[3]; Motley, S. Timothy ^[2]; Appenroth, Klaus J. ^[4]; Schubert, Ingo  ^[5];

• Search DOE PAGES for author "Schubert, Ingo"
• Search DOE PAGES for ORCID "0000-0002-6300-2068"

Lam, Eric  ^[3]

• Search DOE PAGES for author "Lam, Eric"
• Search DOE PAGES for ORCID "0000-0002-2461-4133"

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+ Show Author Affiliations

1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) (Germany); Dalat University (Vietnam)
2. J. Craig Venter Institute, Carlsbad, CA (United States)
3. Rutgers Univ., New Brunswick, NJ (United States)
4. Friedrich Schiller Univ., Jena (Germany)
5. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) (Germany)

Publication Date:

Fri Sep 28 00:00:00 EDT 2018

Research Org.:

Cold Spring Harbor Laboratory Cold Spring Harbor, NY (United States)

Sponsoring Org.:

USDOE Office of Science (SC)

OSTI Identifier:

1612897

Alternate Identifier(s):

OSTI ID: 1474786

Grant/Contract Number:  

SC0018244; DE‐SC0018244

Resource Type:

Accepted Manuscript

Journal Name:

The Plant Journal

Additional Journal Information:

Journal Volume: 96; Journal Issue: 3; Journal ID: ISSN 0960-7412

Publisher:

Society for Experimental Biology

Country of Publication:

United States

Language:

English

Subject:

59 BASIC BIOLOGICAL SCIENCES; Plant Sciences; Spirodela polyrhiza, duckweeds; multicolor-FISH; optical map; cytogenetic map; Oxford Nanopore sequencing; syntenous regions