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Article ; Online: Evolution: The plasticity of plastids.

Howe, Christopher J / Nisbet, R Ellen R / Barbrook, Adrian C

2023 Volume 33, Issue 20, Page(s) R1058–R1060

Abstract: Many chloroplast-bearing plants and algae lost their photosynthetic activity during evolution but retained their chloroplasts for other functions. A group of dinoflagellate algae apparently lost one half of their photosynthetic machinery but retained the ...

Abstract	Many chloroplast-bearing plants and algae lost their photosynthetic activity during evolution but retained their chloroplasts for other functions. A group of dinoflagellate algae apparently lost one half of their photosynthetic machinery but retained the other, providing a novel mechanism for light perception.
MeSH term(s)	Plastids/genetics ; Plastids/metabolism ; Chloroplasts/metabolism ; Plants ; Photosynthesis ; Dinoflagellida ; Evolution, Molecular
Language	English
Publishing date	2023-10-24
Publishing country	England
Document type	Journal Article
ZDB-ID	1071731-6
ISSN	1879-0445 ; 0960-9822
ISSN (online)	1879-0445
ISSN	0960-9822
DOI	10.1016/j.cub.2023.09.025
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Article ; Online: Integrated Genomic and Transcriptomic Analysis of the Peridinin Dinoflagellate Amphidinium carterae Plastid.

Dorrell, Richard G / Nisbet, R Ellen R / Barbrook, Adrian C / Rowden, Stephen J L / Howe, Christopher J

Protist

2019 Volume 170, Issue 4, Page(s) 358–373

Abstract: The plastid genomes of peridinin-containing dinoflagellates are highly unusual, possessing very few genes, which are located on small chromosomal elements termed "minicircles". These minicircles may contain genes, or no recognisable coding information. ... ...

Abstract	The plastid genomes of peridinin-containing dinoflagellates are highly unusual, possessing very few genes, which are located on small chromosomal elements termed "minicircles". These minicircles may contain genes, or no recognisable coding information. Transcripts produced from minicircles may undergo unusual processing events, such as the addition of a 3' poly(U) tail. To date, little is known about the genetic or transcriptional diversity of non-coding sequences in peridinin dinoflagellate plastids. These sequences include empty minicircles, and regions of non-coding DNA in coding minicircles. Here, we present an integrated plastid genome and transcriptome for the model peridinin dinoflagellate Amphidinium carterae, identifying a previously undescribed minicircle. We also profile transcripts covering non-coding regions of the psbA and petB/atpA minicircles. We present evidence that antisense transcripts are produced within the A. carterae plastid, but show that these transcripts undergo different end cleavage events from sense transcripts, and do not receive 3' poly(U) tails. The difference in processing events between sense and antisense transcripts may enable the removal of non-coding transcripts from peridinin dinoflagellate plastid transcript pools.
MeSH term(s)	Dinoflagellida/classification ; Dinoflagellida/genetics ; Gene Expression Profiling ; Genome, Protozoan/genetics ; Genomics ; Plastids/genetics ; Transcriptome/genetics
Language	English
Publishing date	2019-07-05
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2036014-9
ISSN	1618-0941 ; 1434-4610
ISSN (online)	1618-0941
ISSN	1434-4610
DOI	10.1016/j.protis.2019.06.001
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Article ; Online: The genetic intractability of Symbiodinium microadriaticum to standard algal transformation methods.

Chen, Jit Ern / Barbrook, Adrian C / Cui, Guoxin / Howe, Christopher J / Aranda, Manuel

PloS one

2019 Volume 14, Issue 2, Page(s) e0211936

Abstract: Modern transformation and genome editing techniques have shown great success across a broad variety of organisms. However, no study of successfully applied genome editing has been reported in a dinoflagellate despite the first genetic transformation of ... ...

Abstract	Modern transformation and genome editing techniques have shown great success across a broad variety of organisms. However, no study of successfully applied genome editing has been reported in a dinoflagellate despite the first genetic transformation of Symbiodinium being published about 20 years ago. Using an array of different available transformation techniques, we attempted to transform Symbiodinium microadriaticum (CCMP2467), a dinoflagellate symbiont of reef-building corals, with the view to performing subsequent CRISPR-Cas9 mediated genome editing. Plasmid vectors designed for nuclear transformation containing the chloramphenicol resistance gene under the control of the CaMV p35S promoter as well as several putative endogenous promoters were used to test a variety of transformation techniques including biolistics, electroporation and agitation with silicon carbide whiskers. Chloroplast-targeted transformation was attempted using an engineered Symbiodinium chloroplast minicircle encoding a modified PsbA protein expected to confer atrazine resistance. We report that we have been unable to confer chloramphenicol or atrazine resistance on Symbiodinium microadriaticum strain CCMP2467.
MeSH term(s)	Animals ; Anthozoa/microbiology ; Atrazine/pharmacology ; Cell Nucleus/genetics ; Cell Nucleus/metabolism ; Chloramphenicol/pharmacology ; Chloroplast Proteins/genetics ; Chloroplast Proteins/metabolism ; Chloroplasts/genetics ; Chloroplasts/metabolism ; Dinoflagellida/genetics ; Dinoflagellida/metabolism ; Drug Resistance/genetics ; Transformation, Genetic
Chemical Substances	Chloroplast Proteins ; Chloramphenicol (66974FR9Q1) ; Atrazine (QJA9M5H4IM)
Language	English
Publishing date	2019-02-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0211936
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Article ; Online: The genetic intractability of Symbiodinium microadriaticum to standard algal transformation methods.

Jit Ern Chen / Adrian C Barbrook / Guoxin Cui / Christopher J Howe / Manuel Aranda

PLoS ONE, Vol 14, Iss 2, p e

2019 Volume 0211936

Abstract	Modern transformation and genome editing techniques have shown great success across a broad variety of organisms. However, no study of successfully applied genome editing has been reported in a dinoflagellate despite the first genetic transformation of Symbiodinium being published about 20 years ago. Using an array of different available transformation techniques, we attempted to transform Symbiodinium microadriaticum (CCMP2467), a dinoflagellate symbiont of reef-building corals, with the view to performing subsequent CRISPR-Cas9 mediated genome editing. Plasmid vectors designed for nuclear transformation containing the chloramphenicol resistance gene under the control of the CaMV p35S promoter as well as several putative endogenous promoters were used to test a variety of transformation techniques including biolistics, electroporation and agitation with silicon carbide whiskers. Chloroplast-targeted transformation was attempted using an engineered Symbiodinium chloroplast minicircle encoding a modified PsbA protein expected to confer atrazine resistance. We report that we have been unable to confer chloramphenicol or atrazine resistance on Symbiodinium microadriaticum strain CCMP2467.
Keywords	Medicine ; R ; Science ; Q
Subject code	572
Language	English
Publishing date	2019-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The chloroplast genome of a Symbiodinium sp. clade C3 isolate.

Barbrook, Adrian C / Voolstra, Christian R / Howe, Christopher J

Protist

2014 Volume 165, Issue 1, Page(s) 1–13

Abstract: Dinoflagellate algae of the genus Symbiodinium form important symbioses within corals and other benthic marine animals. Dinoflagellates possess an extremely reduced plastid genome relative to those examined in plants and other algae. In dinoflagellates ... ...

Abstract	Dinoflagellate algae of the genus Symbiodinium form important symbioses within corals and other benthic marine animals. Dinoflagellates possess an extremely reduced plastid genome relative to those examined in plants and other algae. In dinoflagellates the plastid genes are located on small plasmids, commonly referred to as 'minicircles'. However, the chloroplast genomes of dinoflagellates have only been extensively characterised from a handful of species. There is also evidence of considerable variation in the chloroplast genome organisation across those species that have been examined. We therefore characterised the chloroplast genome from an environmental coral isolate, in this case containing a symbiont belonging to the Symbiodinium sp. clade C3. The gene content of the genome is well conserved with respect to previously characterised genomes. However, unlike previously characterised dinoflagellate chloroplast genomes we did not identify any 'empty' minicircles. The sequences of this chloroplast genome show a high rate of evolution relative to other algal species. Particularly notable was a surprisingly high level of sequence divergence within the core polypeptides of photosystem I, the reasons for which are currently unknown. This chloroplast genome also possesses distinctive codon usage and GC content. These features suggest that chloroplast genomes in Symbiodinium are highly plastic.
MeSH term(s)	Alveolata/classification ; Alveolata/genetics ; Base Composition ; Cluster Analysis ; Codon ; DNA, Chloroplast/chemistry ; DNA, Chloroplast/genetics ; Genetic Variation ; Genome, Chloroplast ; Molecular Sequence Data ; Phylogeny ; Sequence Analysis, DNA
Chemical Substances	Codon ; DNA, Chloroplast
Language	English
Publishing date	2014-01
Publishing country	Germany
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2036014-9
ISSN	1618-0941 ; 1434-4610
ISSN (online)	1618-0941
ISSN	1434-4610
DOI	10.1016/j.protis.2013.09.006
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Article: Integrated Genomic and Transcriptomic Analysis of the Peridinin Dinoflagellate Amphidinium carterae Plastid

Dorrell, Richard G / Barbrook, Adrian C / Howe, Christopher J / Nisbet, R. Ellen R / Rowden, Stephen J.L

Protist. 2019 Aug., v. 170, no. 4

2019

Abstract: The plastid genomes of peridinin-containing dinoflagellates are highly unusual, possessing very few genes, which are located on small chromosomal elements termed “minicircles”. These minicircles may contain genes, or no recognisable coding information. ... ...

Abstract	The plastid genomes of peridinin-containing dinoflagellates are highly unusual, possessing very few genes, which are located on small chromosomal elements termed “minicircles”. These minicircles may contain genes, or no recognisable coding information. Transcripts produced from minicircles may undergo unusual processing events, such as the addition of a 3' poly(U) tail. To date, little is known about the genetic or transcriptional diversity of non-coding sequences in peridinin dinoflagellate plastids. These sequences include empty minicircles, and regions of non-coding DNA in coding minicircles. Here, we present an integrated plastid genome and transcriptome for the model peridinin dinoflagellate Amphidinium carterae, identifying a previously undescribed minicircle. We also profile transcripts covering non-coding regions of the psbA and petB/atpA minicircles. We present evidence that antisense transcripts are produced within the A. carterae plastid, but show that these transcripts undergo different end cleavage events from sense transcripts, and do not receive 3' poly(U) tails. The difference in processing events between sense and antisense transcripts may enable the removal of non-coding transcripts from peridinin dinoflagellate plastid transcript pools.
Keywords	Amphidinium ; genes ; genomics ; intergenic DNA ; models ; non-coding RNA ; plastid genome ; plastids ; tail ; transcription (genetics) ; transcriptome ; transcriptomics
Language	English
Dates of publication	2019-08
Size	p. 358-373.
Publishing place	Elsevier GmbH
Document type	Article
ZDB-ID	2036014-9
ISSN	1618-0941 ; 1434-4610
ISSN (online)	1618-0941
ISSN	1434-4610
DOI	10.1016/j.protis.2019.06.001
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Genetic transformation of the dinoflagellate chloroplast.

Nimmo, Isabel C / Barbrook, Adrian C / Lassadi, Imen / Chen, Jit Ern / Geisler, Katrin / Smith, Alison G / Aranda, Manuel / Purton, Saul / Waller, Ross F / Nisbet, R Ellen R / Howe, Christopher J

eLife

2019 Volume 8

Abstract: Coral reefs are some of the most important and ecologically diverse marine environments. At the base of the reef ecosystem are dinoflagellate algae, which live symbiotically within coral cells. Efforts to understand the relationship between alga and ... ...

Abstract	Coral reefs are some of the most important and ecologically diverse marine environments. At the base of the reef ecosystem are dinoflagellate algae, which live symbiotically within coral cells. Efforts to understand the relationship between alga and coral have been greatly hampered by the lack of an appropriate dinoflagellate genetic transformation technology. By making use of the plasmid-like fragmented chloroplast genome, we have introduced novel genetic material into the dinoflagellate chloroplast genome. We have shown that the introduced genes are expressed and confer the expected phenotypes. Genetically modified cultures have been grown for 1 year with subculturing, maintaining the introduced genes and phenotypes. This indicates that cells continue to divide after transformation and that the transformation is stable. This is the first report of stable chloroplast transformation in dinoflagellate algae.
MeSH term(s)	Chloroplasts/genetics ; Dinoflagellida/genetics ; Dinoflagellida/growth & development ; Gene Expression ; Genetics, Microbial/methods ; Genomic Instability ; Phenotype ; Transformation, Genetic
Language	English
Publishing date	2019-07-18
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.45292
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Article: The Chloroplast Genome of a Symbiodinium sp. Clade C3 Isolate

Barbrook, Adrian C / Christian R. Voolstra / Christopher J. Howe

Protist. 2014 Jan., v. 165

2014

Abstract	Dinoflagellate algae of the genus Symbiodinium form important symbioses within corals and other benthic marine animals. Dinoflagellates possess an extremely reduced plastid genome relative to those examined in plants and other algae. In dinoflagellates the plastid genes are located on small plasmids, commonly referred to as âminicirclesâ. However, the chloroplast genomes of dinoflagellates have only been extensively characterised from a handful of species. There is also evidence of considerable variation in the chloroplast genome organisation across those species that have been examined. We therefore characterised the chloroplast genome from an environmental coral isolate, in this case containing a symbiont belonging to the Symbiodinium sp. clade C3. The gene content of the genome is well conserved with respect to previously characterised genomes. However, unlike previously characterised dinoflagellate chloroplast genomes we did not identify any âemptyâ minicircles. The sequences of this chloroplast genome show a high rate of evolution relative to other algal species. Particularly notable was a surprisingly high level of sequence divergence within the core polypeptides of photosystem I, the reasons for which are currently unknown. This chloroplast genome also possesses distinctive codon usage and GC content. These features suggest that chloroplast genomes in Symbiodinium are highly plastic.
Keywords	algae ; chloroplast genome ; corals ; evolution ; genes ; photosystem I ; plasmids ; polypeptides ; Symbiodinium ; symbionts
Language	English
Dates of publication	2014-01
Size	p. 1-13.
Publishing place	Elsevier GmbH
Document type	Article
ZDB-ID	2036014-9
ISSN	1618-0941 ; 1434-4610
ISSN (online)	1618-0941
ISSN	1434-4610
DOI	10.1016/j.protis.2013.09.006
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Genetic transformation of the dinoflagellate chloroplast

Isabel C Nimmo / Adrian C Barbrook / Imen Lassadi / Jit Ern Chen / Katrin Geisler / Alison G Smith / Manuel Aranda / Saul Purton / Ross F Waller / R Ellen R Nisbet / Christopher J Howe

eLife, Vol

2019 Volume 8

Abstract	Coral reefs are some of the most important and ecologically diverse marine environments. At the base of the reef ecosystem are dinoflagellate algae, which live symbiotically within coral cells. Efforts to understand the relationship between alga and coral have been greatly hampered by the lack of an appropriate dinoflagellate genetic transformation technology. By making use of the plasmid-like fragmented chloroplast genome, we have introduced novel genetic material into the dinoflagellate chloroplast genome. We have shown that the introduced genes are expressed and confer the expected phenotypes. Genetically modified cultures have been grown for 1 year with subculturing, maintaining the introduced genes and phenotypes. This indicates that cells continue to divide after transformation and that the transformation is stable. This is the first report of stable chloroplast transformation in dinoflagellate algae.
Keywords	dinoflagellate ; Amphidinium ; chloroplast ; transformation ; zooxanthella ; coral reef ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2019-07-01T00:00:00Z
Publisher	eLife Sciences Publications Ltd
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The remarkable chloroplast genome of dinoflagellates.

Howe, Christopher J / Nisbet, R Ellen R / Barbrook, Adrian C

Journal of experimental botany

2008 Volume 59, Issue 5, Page(s) 1035–1045

Abstract: Dinoflagellates are an economically and ecologically important eukaryotic algal group. The organization of their chloroplast genome appears to be radically different from that in plants and other algae. The gene content has been dramatically reduced in ... ...

Abstract	Dinoflagellates are an economically and ecologically important eukaryotic algal group. The organization of their chloroplast genome appears to be radically different from that in plants and other algae. The gene content has been dramatically reduced in dinoflagellates, with the large-scale transfer of genes to the nucleus. Most of the remaining genes encode subunits of Photosystems I and II, the cytochrome b(6)f complex, and ATP synthase, as well as rRNAs and a few tRNAs. Whereas conventional chloroplast genomes have all their genes physically linked on one molecule, dinoflagellate chloroplast genes are located on small plasmids, termed 'minicircles'. Each minicircle has at most a few genes, and a distinguishable 'core' region. Genes are always in the same orientation with respect to the core region. There are also non-coding minicircles, including aberrant forms of minicircles apparently derived from other minicircles by rearrangement. The evidence that the minicircles are located in the chloroplast and that there is no conventional chloroplast genome in addition to the minicircles is discussed. Transcription of minicircles is probably initiated close to the core, generating transcripts corresponding to an almost entire minicircle. The transcripts are then cleaved to molecules corresponding to individual genes. Post-transcriptional modifications include editing and addition of a polyU tail. It is discussed why these particular genes have been retained in the dinoflagellate chloroplast, together with the possibility that the chloroplast supplies fMet-tRNA to the mitochondrion.
MeSH term(s)	Animals ; DNA, Chloroplast/genetics ; DNA, Protozoan/genetics ; Dinoflagellida/genetics ; Evolution, Molecular ; Genome, Chloroplast ; Genome, Protozoan ; Molecular Sequence Data ; Plasmids ; Transcription, Genetic
Chemical Substances	DNA, Chloroplast ; DNA, Protozoan
Language	English
Publishing date	2008
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2976-2
ISSN	1460-2431 ; 0022-0957
ISSN (online)	1460-2431
ISSN	0022-0957
DOI	10.1093/jxb/erm292
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