Nucleotide sequence of diatom plasmids: identification of open reading frames with similarity to site-specific recombinases

Hildebrand, Mark; Hasegawa, Paul M.; Rw, Ord; Vs, Thorpe; Ca, Glass; Be, Volcani

doi:10.1007/bf00027072

Cited by 22 publications

(18 citation statements)

References 34 publications

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“…Some of these foreign sequences were acquired from plasmids (Imanian et al 2010; Brembu et al 2013; Wang et al 2013), whose cellular localization in diatoms includes both the nucleus and plastid (Hildebrand et al 1992). Most notably, plasmids have introduced intact and putatively functional site-specific recombinase genes into the plastid genomes of several diatoms (fig.…”

Section: Resultsmentioning

confidence: 99%

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Serial Gene Losses and Foreign DNA Underlie Size and Sequence Variation in the Plastid Genomes of Diatoms

Ruck

Nakov

Jansen

et al. 2014

Genome Biology and Evolution

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Photosynthesis by diatoms accounts for roughly one-fifth of global primary production, but despite this, relatively little is known about their plastid genomes. We report the completely sequenced plastid genomes for eight phylogenetically diverse diatoms and show them to be variable in size, gene and foreign sequence content, and gene order. The genomes contain a core set of 122 protein-coding genes, with 15 additional genes exhibiting complex patterns of 1) gene losses at varying phylogenetic scales, 2) functional transfers to the nucleus, 3) gene duplication, divergence, and differential retention of paralogs, and 4) acquisitions of putatively functional recombinase genes from resident plasmids. The newly sequenced genomes also contain several previously unreported genes, highlighting how poorly characterized diatom plastid genomes are overall. Genome size variation reflects major expansions of the inverted repeat region in some cases but, more commonly, large-scale expansions of intergenic regions, many of which contain unique open reading frames of likely foreign origin. Although many gene clusters are conserved across species, rearrangements appear to be frequent in most lineages.

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Section: Resultsmentioning

confidence: 99%

“…S1, Supplementary Material online). Asterionellopsis , Eunotia , and Cylindrotheca also contain sequences matching noncoding sequences and ORFs from known diatom plasmids (Hildebrand et al 1991, 1992). …”

Section: Resultsmentioning

confidence: 99%

Serial Gene Losses and Foreign DNA Underlie Size and Sequence Variation in the Plastid Genomes of Diatoms

Ruck

Nakov

Jansen

et al. 2014

Genome Biology and Evolution

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“…Each of these two plasmids includes several ORFs, two pairs of which share considerable similarity (ORF217 of pCf2 and ORF218 of pCf1 with almost 80% aa identity and ORF484 of pCf2 and ORF482 of pCf1 with 54%) [49]. K. foliaceum ORF141 (region VI) shares 57% and 47% aa identity with ORF484 (aa 186 to aa 324) from pCf2 and ORF482 from pCf1 plasmid, respectively.…”

Section: Resultsmentioning

confidence: 99%

The Complete Plastid Genomes of the Two ‘Dinotoms’ Durinskia baltica and Kryptoperidinium foliaceum

2010

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BackgroundIn one small group of dinoflagellates, photosynthesis is carried out by a tertiary endosymbiont derived from a diatom, giving rise to a complex cell that we collectively refer to as a ‘dinotom’. The endosymbiont is separated from its host by a single membrane and retains plastids, mitochondria, a large nucleus, and many other eukaryotic organelles and structures, a level of complexity suggesting an early stage of integration. Although the evolution of these endosymbionts has attracted considerable interest, the plastid genome has not been examined in detail, and indeed no tertiary plastid genome has yet been sequenced.Methodology/Principal FindingsHere we describe the complete plastid genomes of two closely related dinotoms, Durinskia baltica and Kryptoperidinium foliaceum. The D. baltica (116470 bp) and K. foliaceum (140426 bp) plastid genomes map as circular molecules featuring two large inverted repeats that separate distinct single copy regions. The organization and gene content of the D. baltica plastid closely resemble those of the pennate diatom Phaeodactylum tricornutum. The K. foliaceum plastid genome is much larger, has undergone more reorganization, and encodes a putative tyrosine recombinase (tyrC) also found in the plastid genome of the heterokont Heterosigma akashiwo, and two putative serine recombinases (serC1 and serC2) homologous to recombinases encoded by plasmids pCf1 and pCf2 in another pennate diatom, Cylindrotheca fusiformis. The K. foliaceum plastid genome also contains an additional copy of serC1, two degenerate copies of another plasmid-encoded ORF, and two non-coding regions whose sequences closely resemble portions of the pCf1 and pCf2 plasmids.Conclusions/SignificanceThese results suggest that while the plastid genomes of two dinotoms share very similar gene content and genome organization with that of the free-living pennate diatom P. tricornutum, the K. folicaeum plastid genome has absorbed two exogenous plasmids. Whether this took place before or after the tertiary endosymbiosis is not clear.

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“…2 Gene order surrounding the serC2 gene. Chloroplast genomes of four diatoms and one diatom endosymbiont of K. foliaceum (a), and two plasmids of diatom C. fusiformis (b) shares similarity to the pCf1 and pCf2 plasmids of the diatom C. fusiformis (Hildebrand et al 1992), and includes a putative serine recombinase gene, serC2. The serC2 gene of Fistulifera sp.…”

Section: Comparison Of Sequence Identitymentioning

confidence: 99%

High-throughput pyrosequencing of the chloroplast genome of a highly neutral-lipid-producing marine pennate diatom, Fistulifera sp. strain JPCC DA0580

et al. 2011

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The chloroplast genome of the highly neutral-lipid-producing marine pennate diatom Fistulifera sp. strain JPCC DA0580 was fully sequenced using high-throughput pyrosequencing. The general features and gene content were compared with three other complete diatom chloroplast genomes. The chloroplast genome is 134,918 bp with an inverted repeat of 13,330 bp and is slightly larger than the other diatom chloroplast genomes due to several low gene-density regions lacking similarity to the other diatom chloroplast genomes. Protein-coding genes were nearly identical to those from Phaeodactylum tricornutum. On the other hand, we found unique sequence variations in genes of photosystem II which differ from the consensus in other diatom chloroplasts. Furthermore, five functional unknown ORFs and a putative serine recombinase gene, serC2, are located in the low gene-density regions. SerC2 was also identified in the plasmids of another pennate diatom, Cylindrotheca fusiformis, and in the plastid genome of the diatom endosymbiont of Kryptoperidinium foliaceum. Exogenous plasmids might have been incorporated into the chloroplast genome of Fistulifera sp. by lateral gene transfer. Chloroplast genome sequencing analysis of this novel diatom provides many important insights into diatom evolution.

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Nucleotide sequence of diatom plasmids: identification of open reading frames with similarity to site-specific recombinases

Cited by 22 publications

References 34 publications

Serial Gene Losses and Foreign DNA Underlie Size and Sequence Variation in the Plastid Genomes of Diatoms

Serial Gene Losses and Foreign DNA Underlie Size and Sequence Variation in the Plastid Genomes of Diatoms

The Complete Plastid Genomes of the Two ‘Dinotoms’ Durinskia baltica and Kryptoperidinium foliaceum

High-throughput pyrosequencing of the chloroplast genome of a highly neutral-lipid-producing marine pennate diatom, Fistulifera sp. strain JPCC DA0580

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