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The plastid genome in Cladophorales green algae is encoded by hairpin chromosomes

Andrea Del Cortona UGent, Frédérik Leliaert UGent, Kenny Bogaert UGent, Monique Turmel, Christian Boedeker, Jan Janouškovec, Juan M Lopez-Bautista, Heroen Verbruggen, Klaas Vandepoele UGent and Olivier De Clerck UGent (2017) CURRENT BIOLOGY. 27(24). p.3771-3782
abstract
Virtually all plastid (chloroplast) genomes are circular double-stranded DNA molecules, typically between 100 and 200 kb in size and encoding circa 80-250 genes. Exceptions to this universal plastid genome architecture are very few and include the dinoflagellates, where genes are located on DNA minicircles. Here we report on the highly deviant chloroplast genome of Cladophorales green algae, which is entirely fragmented into hairpin chromosomes. Short-and long-read high-throughput sequencing of DNA and RNA demonstrated that the chloroplast genes of Boodlea composita are encoded on 1-to 7-kb DNA contigs with an exceptionally high GC content, each containing a long inverted repeat with one or two protein-coding genes and conserved non-coding regions putatively involved in replication and/or expression. We propose that these contigs correspond to linear single-stranded DNA molecules that fold onto themselves to form hairpin chromosomes. The Boodlea chloroplast genes are highly divergent from their corresponding orthologs, and display an alternative genetic code. The origin of this highly deviant chloroplast genome most likely occurred before the emergence of the Cladophorales, and coincided with an elevated transfer of chloroplast genes to the nucleus. A chloroplast genome that is composed only of linear DNA molecules is unprecedented among eukaryotes, and highlights unexpected variation in plastid genome architecture.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
PLASMID-LIKE DNA, DINOFLAGELLATE MITOCHONDRIAL GENOMES, CHLOROPLAST GENOME, PHOTOSYNTHETIC EUKARYOTES, GENETIC-CODE, MOLECULAR-BIOLOGY, CHLOROPHYTA, SEQUENCES, ORIGIN, MINICIRCLES
journal title
CURRENT BIOLOGY
Curr. Biol.
volume
27
issue
24
pages
3771 - 3782
Web of Science type
Article
Web of Science id
000418285000021
ISSN
0960-9822
1879-0445
DOI
10.1016/j.cub.2017.11.004
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
additional info
the first two authors contributed equally
copyright statement
I have transferred the copyright for this publication to the publisher
id
8545406
handle
http://hdl.handle.net/1854/LU-8545406
date created
2018-01-18 12:56:11
date last changed
2018-02-13 07:58:00
@article{8545406,
  abstract     = {Virtually all plastid (chloroplast) genomes are circular double-stranded DNA molecules, typically between 100 and 200 kb in size and encoding circa 80-250 genes. Exceptions to this universal plastid genome architecture are very few and include the dinoflagellates, where genes are located on DNA minicircles. Here we report on the highly deviant chloroplast genome of Cladophorales green algae, which is entirely fragmented into hairpin chromosomes. Short-and long-read high-throughput sequencing of DNA and RNA demonstrated that the chloroplast genes of Boodlea composita are encoded on 1-to 7-kb DNA contigs with an exceptionally high GC content, each containing a long inverted repeat with one or two protein-coding genes and conserved non-coding regions putatively involved in replication and/or expression. We propose that these contigs correspond to linear single-stranded DNA molecules that fold onto themselves to form hairpin chromosomes. The Boodlea chloroplast genes are highly divergent from their corresponding orthologs, and display an alternative genetic code. The origin of this highly deviant chloroplast genome most likely occurred before the emergence of the Cladophorales, and coincided with an elevated transfer of chloroplast genes to the nucleus. A chloroplast genome that is composed only of linear DNA molecules is unprecedented among eukaryotes, and highlights unexpected variation in plastid genome architecture.},
  author       = {Del Cortona, Andrea and Leliaert, Fr{\'e}d{\'e}rik and Bogaert, Kenny and Turmel, Monique and Boedeker, Christian and Janou\v{s}kovec, Jan and Lopez-Bautista, Juan M and Verbruggen, Heroen and Vandepoele, Klaas and De Clerck, Olivier},
  issn         = {0960-9822},
  journal      = {CURRENT BIOLOGY},
  keyword      = {PLASMID-LIKE DNA,DINOFLAGELLATE MITOCHONDRIAL GENOMES,CHLOROPLAST GENOME,PHOTOSYNTHETIC EUKARYOTES,GENETIC-CODE,MOLECULAR-BIOLOGY,CHLOROPHYTA,SEQUENCES,ORIGIN,MINICIRCLES},
  language     = {eng},
  number       = {24},
  pages        = {3771--3782},
  title        = {The plastid genome in Cladophorales green algae is encoded by hairpin chromosomes},
  url          = {http://dx.doi.org/10.1016/j.cub.2017.11.004},
  volume       = {27},
  year         = {2017},
}

Chicago
Del Cortona, Andrea, Frédérik Leliaert, Kenny Bogaert, Monique Turmel, Christian Boedeker, Jan Janouškovec, Juan M Lopez-Bautista, Heroen Verbruggen, Klaas Vandepoele, and Olivier De Clerck. 2017. “The Plastid Genome in Cladophorales Green Algae Is Encoded by Hairpin Chromosomes.” Current Biology 27 (24): 3771–3782.
APA
Del Cortona, A., Leliaert, F., Bogaert, K., Turmel, M., Boedeker, C., Janouškovec, J., Lopez-Bautista, J. M., et al. (2017). The plastid genome in Cladophorales green algae is encoded by hairpin chromosomes. CURRENT BIOLOGY, 27(24), 3771–3782.
Vancouver
1.
Del Cortona A, Leliaert F, Bogaert K, Turmel M, Boedeker C, Janouškovec J, et al. The plastid genome in Cladophorales green algae is encoded by hairpin chromosomes. CURRENT BIOLOGY. 2017;27(24):3771–82.
MLA
Del Cortona, Andrea, Frédérik Leliaert, Kenny Bogaert, et al. “The Plastid Genome in Cladophorales Green Algae Is Encoded by Hairpin Chromosomes.” CURRENT BIOLOGY 27.24 (2017): 3771–3782. Print.