Rappemonads are haptophyte phytoplankton

Kawachi, Masanobu; Nakayama, Takuro; Kayama, Motoki; Nomura, Makoto; Miyashita, Hideaki; Bojo, Othman; Rhodes, Lesley; Sym, Stuart D.; Pienaar, Richard N.; Probert, Ian; Inouye, Isao; Kamikawa, Ryoma

doi:10.1016/j.cub.2021.03.012

Cited by 28 publications

(26 citation statements)

References 59 publications

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“…The species in Coccolithophyceae, Pavlovophyceae, and Rappephyceae all formed well supported branches, and Rappephyceae was sister to the Pavlovophyceae. The phylogenetic relationship was generally agreed with the 18S rDNA-based phylogenetic relationship in this study and previous results basing mitochondrial and plastid dataset (Kawachi et al, 2021) with minor differences, which Rappephyceae was sister to the Coccolithophyceae.…”

Section: Phylogenetic Analysis Of Haptophyte Speciessupporting

confidence: 90%

“…However, the support was only moderate (Figure 2B), suggesting that the evolutionary relationships among these three classes (Rappephyceae, Pavlovophyceae, and Prymnesiophyceae) might be more complicated. Indeed, our 18S rDNA-based phylogenetic analysis and a recent study suggested that Rappephyceae was sister to the Prymnesiophyceae, while Pavlovophyceae split from their common ancestor earlier (Kawachi et al, 2021). Their exact evolutionary relationship will be resolved with more genomes are sequenced and assembled.…”

Section: Discussionmentioning

confidence: 68%

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Large Differences in the Haptophyte Phaeocystis globosa Mitochondrial Genomes Driven by Repeat Amplifications

et al. 2021

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The haptophyte Phaeocystis globosa is a well-known species for its pivotal role in global carbon and sulfur cycles and for its capability of forming harmful algal blooms (HABs) with serious ecological consequences. Its mitochondrial genome (mtDNA) sequence has been reported in 2014 but it remains incomplete due to its long repeat sequences. In this study, we constructed the first full-length mtDNA of P. globosa, which was a circular genome with a size of 43,585 bp by applying the PacBio single molecular sequencing method. The mtDNA of this P. globosa strain (CNS00066), which was isolated from the Beibu Gulf, China, encoded 19 protein-coding genes (PCGs), 25 tRNA genes, and two rRNA genes. It contained two large repeat regions of 6.7 kb and ∼14.0 kb in length, respectively. The combined length of these two repeat regions, which were missing from the previous mtDNA assembly, accounted for almost half of the entire mtDNA and represented the longest repeat region among all sequenced haptophyte mtDNAs. In this study, we tested the hypothesis that repeat unit amplification is a driving force for different mtDNA sizes. Comparative analysis of mtDNAs of five additional P. globosa strains (four strains obtained in this study, and one strain previously published) revealed that all six mtDNAs shared identical numbers of genes but with dramatically different repeat regions. A homologous repeat unit was identified but with hugely different numbers of copies in all P. globosa strains. Thus, repeat amplification may represent an important driving force of mtDNA evolution in P. globosa.

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Section: Phylogenetic Analysis Of Haptophyte Speciessupporting

confidence: 90%

Section: Discussionmentioning

confidence: 68%

Large Differences in the Haptophyte Phaeocystis globosa Mitochondrial Genomes Driven by Repeat Amplifications

et al. 2021

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“…Remarkably, however, it is worth noting that the catalogue of these major protist groups has not been fundamentally altered since environmental sequencing, even high-throughput metabarcoding, came into play. In fact, less than a handful of highranking environmental lineages branching outside of established major groups have been discovered since the beginning of environmental sequencing (e.g., Picozoa 57 , Rappemonads 58 , or a novel group related to animals called MASHOL 59 ), some of which have now been assimilated to known groups (e.g., Rappemonads belong to haptophytes 60 ).…”

Section: Diversity and Abundance Of Protists Derived From Environmental Sequencingmentioning

confidence: 99%

Diversity and ecology of protists revealed by metabarcoding

2021

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Protists are the dominant eukaryotes in the biosphere where they play key functional roles. While protists have been studied for over a century, it is the high-throughput sequencing of molecular markers from environmental samples -the approach of metabarcoding -that has revealed just how diverse, and abundant, these small organisms are. Metabarcoding is now routine to survey environmental diversity, so data have rapidly accumulated from a multitude of environments and at different sampling scales. This mass of data has provided unprecedented opportunities to study the taxonomic and functional diversity of protists, and how this diversity is organised in space and time. Here, we use metabarcoding as a common thread to discuss the state of knowledge in protist diversity research, from technical considerations of the approach to important insights gained on diversity patterns and the processes that might have structured this diversity. In addition to these insights, we conclude that metabarcoding is on the verge of an exciting added dimension thanks to the maturation of high-throughput long-read sequencing, so that a robust eco-evolutionary framework of protist diversity is within reach. ll

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“…Despite their impact and their intriguing evolutionary history, high-quality haptophyte genome sequences remain scarce, and the available data do not reflect their diversity or new discoveries ( Burki et al 2012 ; Sibbald and Archibald 2017 ; Kawachi et al 2021 ). To bridge this knowledge gap, we assembled and annotated a high-quality genome for Diacronema lutheri ( Pavlova lutheri ), for the purpose of understanding its architecture, sequence evolution, and capacity to synthesize diverse natural products, particularly lipids.…”

Section: Introductionmentioning

confidence: 99%

The Genome of the Haptophyte Diacronema lutheri (Pavlova lutheri, Pavlovales): A Model for Lipid Biosynthesis in Eukaryotic Algae

Hulatt

Wijffels

Posewitz

2021

Genome Biology and Evolution

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Haptophytes are biogeochemically and industrially important protists with under-explored genomic diversity. We present a nuclear genome assembly for the class Pavlovales, which was assembled with PacBio long-read data into highly contiguous sequences. We sequenced strain Diacronema lutheri NIVA-4/92, formerly known as Pavlova lutheri, because it has established roles in aquaculture and has been a key organism for studying microalgal lipid biosynthesis. Our data show that Diacronema lutheri has the smallest and most streamlined haptophycean genome assembled to date, with an assembly size of 43.503 Mb and 14,446 protein coding genes. Together with its high nuclear GC content, Diacronema is an important genus for investigating selective pressures on haptophyte genome evolution, contrasting with the much larger and more repetitive genome of the coccolithophore Emiliania huxleyi. The D. lutheri genome will be a valuable resource for resolving the genetic basis of algal lipid biosynthesis and metabolic remodelling that takes place during adaptation and stress response in natural and engineered environments.

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Rappemonads are haptophyte phytoplankton

Cited by 28 publications

References 59 publications

Large Differences in the Haptophyte Phaeocystis globosa Mitochondrial Genomes Driven by Repeat Amplifications

Large Differences in the Haptophyte Phaeocystis globosa Mitochondrial Genomes Driven by Repeat Amplifications

Diversity and ecology of protists revealed by metabarcoding

The Genome of the Haptophyte Diacronema lutheri (Pavlova lutheri, Pavlovales): A Model for Lipid Biosynthesis in Eukaryotic Algae

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