Complete sequence and analysis of plastid genomes of
            <i>Pseudo-nitzschia multiseries</i>
            (Bacillariophyta)

Cao, Min; Yuan, Xiaolong; Bi, Guoan

doi:10.3109/19401736.2015.1060428

Cited by 14 publications

(9 citation statements)

References 9 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Furthermore, only one operon was found in Dictyocha speculum. This IR-less genome structure of D. speculum, although not common in most plastid-bearing groups, was also observed in the Pelagophyceae (Ong et al 2010) as well as in the diatom Pseudo-nitzschia multiseries (Cao et al 2016). Because the sister groups of Dictyochophyceae and Pelagophyceae (i.e., Bacillariophyceae, Bolidophyceae) possess IRs in their plastid genomes (Tajima et al 2016), it is likely that IRs losses occurred multiple times independently ( Fig.…”

Section: Resultsmentioning

confidence: 68%

See 1 more Smart Citation

Dictyochophyceae Plastid Genomes Reveal Unusual Variability in Their Organization

Han

Maciszewski

Graf

et al. 2019

Journal of Phycology

View full text Add to dashboard Cite

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.

show abstract

Section: Resultsmentioning

confidence: 68%

“…) as well as in the diatom Pseudo‐nitzschia multiseries (Cao et al. ). Because the sister groups of Dictyochophyceae and Pelagophyceae (i.e., Bacillariophyceae, Bolidophyceae) possess IRs in their plastid genomes (Tajima et al.…”

Section: Resultsmentioning

confidence: 99%

Dictyochophyceae Plastid Genomes Reveal Unusual Variability in Their Organization

Han

Maciszewski

Graf

et al. 2019

Journal of Phycology

View full text Add to dashboard Cite

show abstract

“…], and Pseudo‐nitzschia multiseries [6,111 bp; Cao et al. ]. Similarly, the number and length of introns in cox1 varies among different species.…”

Section: Discussionmentioning

confidence: 99%

“…The complete sequence length of cox1 in diatoms varies from~1,000 to 6,500 bp (e.g., Berkeleya fennica [1,434 bp; An et al 2016], Thalassiosira pseudonana [3,838 bp; Armbrust et al 2004], Phaeodactylum tricornutum [6,295 bp; Outdot-Le Secq and Green 2011], Synedra acus [6,468 bp; Ravin et al 2010], and Pseudo-nitzschia multiseries [6,111 bp;Cao et al 2016]. Similarly, the number and length of introns in cox1 varies among different species.…”

Section: Discussionmentioning

confidence: 99%

Phylogeny and species delineation in the marine diatomPseudo‐nitzschia(Bacillariophyta) usingcox1,LSU, andITS2rRNAgenes: A perspective in character evolution

Lim

Tan

Teng

et al. 2018

Journal of Phycology

View full text Add to dashboard Cite

Analyses of the mitochondrial cox1, the nuclear-encoded large subunit (LSU), and the internal transcribed spacer 2 (ITS2) RNA coding region of Pseudo-nitzschia revealed that the P. pseudodelicatissima complex can be phylogenetically grouped into three distinct clades (Groups I-III), while the P. delicatissima complex forms another distinct clade (Group IV) in both the LSU and ITS2 phylogenetic trees. It was elucidated that comprehensive taxon sampling (sampling of sequences), selection of appropriate target genes and outgroup, and alignment strategies influenced the phylogenetic accuracy. Based on the genetic divergence, ITS2 resulted in the most resolved trees, followed by cox1 and LSU. The morphological characters available for Pseudo-nitzschia, although limited in number, were overall in agreement with the phylogenies when mapped onto the ITS2 tree. Information on the presence/absence of a central nodule, number of rows of poroids in each stria, and of sectors dividing the poroids mapped onto the ITS2 tree revealed the evolution of the recently diverged species. The morphologically based species complexes showed evolutionary relevance in agreement with molecular phylogeny inferred from ITS2 sequence-structure data. The data set of the hypervariable region of ITS2 improved the phylogenetic inference compared to the cox1 and LSU data sets. The taxonomic status of P. cuspidata and P. pseudodelicatissima requires further elucidation.

show abstract

“…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

View full text Add to dashboard Cite

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.

show abstract

Complete sequence and analysis of plastid genomes of Pseudo-nitzschia multiseries (Bacillariophyta)

Cited by 14 publications

References 9 publications

Dictyochophyceae Plastid Genomes Reveal Unusual Variability in Their Organization

Dictyochophyceae Plastid Genomes Reveal Unusual Variability in Their Organization

Phylogeny and species delineation in the marine diatomPseudo‐nitzschia(Bacillariophyta) usingcox1,LSU, andITS2rRNAgenes: A perspective in character evolution

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

Contact Info

Product

Resources

About