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DNA Res. 2019 May 16. pii: dsz009. doi: 10.1093/dnares/dsz009. [Epub ahead of print]

Analysis of an improved Cyanophora paradoxa genome assembly.

Author information

1
Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, USA.
2
Department of Biology, Washington University, St. Louis, MO 63130, USA.
3
Washington University Center for Cellular Imaging, Washington University School of Medicine, St. Louis, MO 63110, USA.
4
Department of Botany, University of British Columbia, Vancouver, BC V6T-1Z4, Canada.
5
Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam, Germany.
6
School of Biological Sciences, Nanyang Technological University, Singapore 639798.
7
Institute for Plant Biochemistry, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine-University, D-40225 Düsseldorf, Germany.
8
Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS-USTL, Université des Sciences et Technologies de Lille, 59655 Villeneuve d'Ascq Cedex, France.
9
Institute for Molecular Bioscience and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
10
Department of Biochemistry and Microbiology, Rutgers, Rutgers University, New Brunswick, NJ 08901, USA.
11
Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea.

Abstract

Glaucophyta are members of the Archaeplastida, the founding group of photosynthetic eukaryotes that also includes red algae (Rhodophyta), green algae, and plants (Viridiplantae). Here we present a high-quality assembly, built using long-read sequences, of the ca. 100 Mb nuclear genome of the model glaucophyte Cyanophora paradoxa. We also conducted a quick-freeze deep-etch electron microscopy (QFDEEM) analysis of C. paradoxa cells to investigate glaucophyte morphology in comparison to other organisms. Using the genome data, we generated a resolved 115-taxon eukaryotic tree of life that includes a well-supported, monophyletic Archaeplastida. Analysis of muroplast peptidoglycan (PG) ultrastructure using QFDEEM shows that PG is most dense at the cleavage-furrow. Analysis of the chlamydial contribution to glaucophytes and other Archaeplastida shows that these foreign sequences likely played a key role in anaerobic glycolysis in primordial algae to alleviate ATP starvation under night-time hypoxia. The robust genome assembly of C. paradoxa significantly advances knowledge about this model species and provides a reference for exploring the panoply of traits associated with the anciently diverged glaucophyte lineage.

KEYWORDS:

Cyanophora paradoxa ; Archaeplastida; phylogenomics; tree of eukaryotes; ultrastructure

PMID:
31098614
DOI:
10.1093/dnares/dsz009

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