Dynamic evolution of inverted repeats in Euglenophyta plastid genomes

Karnkowska, Anna; Bennett, Matthew S.; Triemer, Richard E.

doi:10.1038/s41598-018-34457-w

Cited by 20 publications

(59 citation statements)

References 65 publications

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“…1). This idea is reinforced by a similar pattern of independent multiple losses observed in other secondary endosymbiotic lineages (e.g., cryptophytes; Kim et al 2017), haptophytes (Baurain et al 2010), and euglenophytes (Karnkowska et al 2018).…”

Section: Resultsmentioning

confidence: 78%

Dictyochophyceae Plastid Genomes Reveal Unusual Variability in Their Organization

Han

Maciszewski

Graf

et al. 2019

Journal of Phycology

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Dictyochophyceae (silicoflagellates) are unicellular freshwater and marine algae (Heterokontophyta, stramenopiles). Despite their abundance in global oceans and potential ecological significance, discovered in recent years, neither nuclear nor organellar genomes of representatives of this group were sequenced until now. Here, we present the first complete plastid genome sequences of Dictyochophyceae, obtained from four species: Dictyocha speculum, Rhizochromulina marina, Florenciella parvula and Pseudopedinella elastica. Despite their comparable size and genetic content, these four plastid genomes exhibit variability in their organization: plastid genomes of F. parvula and P. elastica possess conventional quadripartite structure with a pair of inverted repeats, R. marina instead possesses two direct repeats with the same orientation and D. speculum possesses no repeats at all. We also observed a number of unusual traits in the plastid genome of D. speculum, including expansion of the intergenic regions, presence of an intron in the otherwise non‐intron‐bearing psaA gene, and an additional copy of the large subunit of RuBisCO gene (rbcL), the last of which has never been observed in any plastid genome. We conclude that despite noticeable gene content similarities between the plastid genomes of Dictyochophyceae and their relatives (pelagophytes, diatoms), the number of distinctive features observed in this lineage strongly suggests that additional taxa require further investigation.

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Section: Resultsmentioning

confidence: 78%

Dictyochophyceae Plastid Genomes Reveal Unusual Variability in Their Organization

Han

Maciszewski

Graf

et al. 2019

Journal of Phycology

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“…Rigid or slightly metabolic cells with pellicle-formed tail, 2-4 large paramylon plates and one or few large, spherical chloroplasts [381,391] ( plate F, 81); 18S rRNA gene has T in the third position of the terminal loop of the Helix 27 [381]; ribosomal operon present in the plastid genome in one copy [390]. [395]; ribosomal operon present in one copy in the plastid genome [384]. Type species: Eutreptia viridis Perty, 1852.…”

Section: Taxonomymentioning

confidence: 99%

Euglenozoa: taxonomy, diversity and ecology, symbioses and viruses

et al. 2021

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Euglenozoa is a species-rich group of protists, which have extremely diverse lifestyles and a range of features that distinguish them from other eukaryotes. They are composed of free-living and parasitic kinetoplastids, mostly free-living diplonemids, heterotrophic and photosynthetic euglenids, as well as deep-sea symbiontids. Although they form a well-supported monophyletic group, these morphologically rather distinct groups are almost never treated together in a comparative manner, as attempted here. We present an updated taxonomy, complemented by photos of representative species, with notes on diversity, distribution and biology of euglenozoans. For kinetoplastids, we propose a significantly modified taxonomy that reflects the latest findings. Finally, we summarize what is known about viruses infecting euglenozoans, as well as their relationships with ecto- and endosymbiotic bacteria.

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“…Although both plastid genomes presented in this work carry a single copy of the ribosomal RNAs, its organization differs substantially between the investigated strains. The small (rns) and large (rnl) ribosomal RNA subunit genes are clustered together in the same orientation in P. danica NY0221, which is a rather common feature in plastid genomes, as it has also been observed in another dictyochophyte, Dictyocha speculum (Han et al, 2019), as well as in certain diatoms (Cao et al, 2016), euglenids (Karnkowska et al, 2018) and chlorophytes (Turmel et al, 2017). In Pteridomonas sp.…”

Section: Recent Genome Rearrangementsmentioning

confidence: 66%

Highly Reduced Plastid Genomes of the Non-photosynthetic Dictyochophyceans Pteridomonas spp. (Ochrophyta, SAR) Are Retained for tRNA-Glu-Based Organellar Heme Biosynthesis

et al. 2020

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Organisms that have lost their photosynthetic capabilities are present in a variety of eukaryotic lineages, such as plants and disparate algal groups. Most of such non-photosynthetic eukaryotes still carry plastids, as these organelles retain essential biological functions. Most non-photosynthetic plastids possess genomes with varied protein-coding contents. Such remnant plastids are known to be present in the non-photosynthetic, bacteriovorous alga Pteridomonas danica (Dictyochophyceae, Ochrophyta), which, regardless of its obligatory heterotrophic lifestyle, has been reported to retain the typically plastid-encoded gene for ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) large subunit (rbcL). The presence of rbcL without photosynthetic activity suggests that investigating the function of plastids in Pteridomonas spp. would likely bring unique insights into understanding the reductive evolution of plastids, their genomes, and plastid functions retained after the loss of photosynthesis. In this study, we demonstrate that two newly established strains of the non-photosynthetic genus Pteridomonas possess highly reduced plastid genomes lacking rbcL gene, in contrast to the previous report. Interestingly, we discovered that all plastid-encoded proteins in Pteridomonas spp. are involved only in housekeeping processes (e.g., transcription, translation and protein degradation), indicating that all metabolite synthesis pathways in their plastids are supported fully by nuclear genome-encoded proteins. Moreover, through an in-depth survey of the available transcriptomic data of another strain of the genus, we detected no candidate sequences for nuclear-encoded, plastid-directed Fe–S cluster assembly pathway proteins, suggesting complete loss of this pathway in the organelle, despite its widespread conservation in non-photosynthetic plastids. Instead, the transcriptome contains plastid-targeted components of heme biosynthesis, glycolysis, and pentose phosphate pathways. The retention of the plastid genomes in Pteridomonas spp. is not explained by the Suf-mediated constraint against loss of plastid genomes, previously proposed for Alveolates, as they lack Suf genes. Bearing all these findings in mind, we propose the hypothesis that plastid DNA is retained in Pteridomonas spp. for the purpose of providing glutamyl-tRNA, encoded by trnE gene, as a substrate for the heme biosynthesis pathway.

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Dynamic evolution of inverted repeats in Euglenophyta plastid genomes

Cited by 20 publications

References 65 publications

Dictyochophyceae Plastid Genomes Reveal Unusual Variability in Their Organization

Dictyochophyceae Plastid Genomes Reveal Unusual Variability in Their Organization

Euglenozoa: taxonomy, diversity and ecology, symbioses and viruses

Highly Reduced Plastid Genomes of the Non-photosynthetic Dictyochophyceans Pteridomonas spp. (Ochrophyta, SAR) Are Retained for tRNA-Glu-Based Organellar Heme Biosynthesis

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