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Reconstruction of chromosome rearrangements between the two most ancestral duckweed species Spirodela polyrhiza and S. intermedia

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Abstract

The monophyletic duckweeds comprising five genera within the monocot order Alismatales are neotenic, free-floating, aquatic organisms with fast vegetative propagation. Some species are considered for efficient biomass production, for life stock feeding, and for (simultaneous) wastewater phytoremediation. The ancestral genus Spirodela consists of only two species, Spirodela polyrhiza and Spirodela intermedia, both with a similar small genome (~160 Mbp/1C). Reference genome drafts and a physical map of 96 BACs on the 20 chromosome pairs of S. polyrhiza strain 7498 are available and provide useful tools for further evolutionary studies within and between duckweed genera. Here we applied sequential comparative multicolor fluorescence in situ hybridization (mcFISH) to address homeologous chromosomes in S. intermedia (2n = 36), to detect chromosome rearrangements between both species and to elucidate the mechanisms which may have led to the chromosome number alteration after their evolutionary separation. Ten chromosome pairs proved to be conserved between S. polyrhiza and S. intermedia, the remaining ones experienced, depending on the assumed direction of evolution, translocations, inversion, and fissions, respectively. These results represent a first step to unravel karyotype evolution among duckweeds and are anchor points for future genome assembly of S. intermedia.

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Acknowledgements

The authors thank Jörg Fuchs, IPK Gatersleben, Klaus Appenroth, Friedrich-Schiller-Universität, and Jena for discussions and critical reading of the manuscript and JF additionally for help with artwork. This study is supported by a grant of the German Research Foundation (SCHU 951/18-1) to IS. PNTH was supported by a PhD scholarship of the Vietnam Ministry of Education and Training.

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Authors and Affiliations

  1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Corrensstrasse 3, 06466, Stadt Seeland, Germany

    Phuong T. N. Hoang & Ingo Schubert

Authors
  1. Phuong T. N. Hoang
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  2. Ingo Schubert
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Contributions

PNTH and IS designed experiments; PNTH performed experiments; PNTH and IS analyzed data; PNTH and IS wrote the manuscript. All authors read and approved the manuscript.

Corresponding author

Correspondence to Ingo Schubert.

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This article does not contain any studies with human participants or animals performed by any of the authors.

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The authors declare that they have no conflict of interest.

Electronic supplementary material

Supplemental Figure 1

Location of pseudomolecule 21b in S. polyrhiza (PDF 98kb). a) BAC 037I18 (Ψ21b) does not co-localize with 004N06 (Ψ7) and 009L02 (Ψ32); (b) BACs 006D12 and 037I18 (Ψ21b) co-localized with BACs of Ψ16 (040G15, 036F14, 003B08) and Ψ30 (006A07). According to the chromosomal position of signals, Ψ21b (red and yellow signals) appears in terminal position on ChrSp14, (c) ChrS17 includes only Ψ7 and Ψ32 (red arrow), and ChrS14 includes Ψ21b, Ψ16 and Ψ30 (yellow arrow). Probes were labelled by Cy3 (yellow), Alexa-488 (green) and Texas-Red (red), the chromosomes were counterstained with DAPI. Scale bar = 5 µm

Supplemental Figure 2

Chromosomal location of the 20 S. polyrhiza chromosome-specific probes on S. intermedia metaphases (PDF 240kb). (a) FISH signals of 20 S. polyrhiza chromosome-specific probes on two different S. intermedia metaphases confirmed 10 conserved chromosome pairs, the six new linkages (indicated by two-color arrow heads according to the false colors of signals), and parts of rearranged chromosomes that stay separately in S. intermedia, (b) Positions of 20 S. polyrhiza chromosome-specific probes are summarized: In the upper cell, labeling on the second chromosome that should be marked by ChrS07 and ChrS09 (empty red circles) are missing. These are present in the lower cell. In the lower cell the second chromosomes of pairs 10 and 20 are not labeled (empty red circles), but they appeared in the upper cell. Scale bars = 5 µm; (c) Enumeration of S. intermedia chromosomes and their labeling by S. polyrhiza chromosome-specific probes. 

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Hoang, P.T.N., Schubert, I. Reconstruction of chromosome rearrangements between the two most ancestral duckweed species Spirodela polyrhiza and S. intermedia . Chromosoma 126, 729–739 (2017). https://doi.org/10.1007/s00412-017-0636-7

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  • DOI: https://doi.org/10.1007/s00412-017-0636-7

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