Selenastraceae (Sphaeropleales, Chlorophyceae): rbcL, 18S rDNA and ITS-2 secondary structure enlightens traditional taxonomy, with description of two new genera, Messastrum gen. nov. and Curvastrum gen. nov.

Silva, Thaís Garcia da; Böck, Christina; Sant’Anna, Célia Leite; Bagatini, Inessa Lacativa; Wodniok, Sabina; Vieira, Armando Augusto Henriques

doi:10.5507/fot.2016.010

Cited by 33 publications

(10 citation statements)

References 72 publications

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“…The ITS is often used to base taxonomic measures on the occurrence of complementary base changes within the secondary structure of either ITS1 or ITS2 or both (luo et al 2006;Bock et al 2011a,b;da silva et al 2016). darienko et al (2015 even recommended the use of the V9 and ITS region as barcode for the green algae Coccomyxa.…”

Section: Discussionmentioning

confidence: 99%

Genetic diversity in chrysophytes: Comparison of different gene markers

Böck¹,

Chatzinotas²,

Boenigk³

2017

Fottea

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Abstract:Chrysophytes are a diverse group of protists belonging to the Stramenopiles. They encompass a broad range of nutrition strategies (phototrophy, mixotrophy and heterotrophy) and morphological forms (unicellular, colonial, branched, non-scaled to silica-scaled). However, taxonomy, identification and delineation of genera and species are hampered by the polyphyletic origin of several morphotypes and the low resolution of morphological features; moreover, description of these features requires in many cases special equipment like TEM or SEM. To test the congruent phylogeny, genetic resolution and to reveal the genetic diversity of chrysophytes, we evaluated in this study different gene markers, in particular SSU and LSU rRNA genes, ITS, and COI in terms of phylogenetic clustering, separation of phylogenetic lineages and genetic distances within and between clades. Our results showed that the general topology of the SSU rRNA gene phylogeny is similar to that of the LSU rRNA gene phylogeny, with a higher genetic divergence for the latter. The topology of the COI phylogeny differed from the ribosomal data, and showed the highest genetic divergence within groups and between groups for all compared markers. The 5.8S rRNA gene offered only a limited phylogenetic resolution with low genetic divergence. ITS showed a high genetic divergence, but phylogenetic analyses were hampered by high variance in sequence lengths between clades.

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Section: Discussionmentioning

confidence: 99%

Genetic diversity in chrysophytes: Comparison of different gene markers

Böck¹,

Chatzinotas²,

Boenigk³

2017

Fottea

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“…The typical secondary structure of ITS2 of the most representatives of the family Selenastraceae has four helixes and forked helix I (Hoshina 2014, Garcia da Silva et al. 2017). The ITS2 secondary structure of MZ–Ch62 and the one available sequence for Nephrochlamys subsolitaria , the strain GM4d (Hoshina 2014) were analyzed (Fig.…”

Section: Resultsmentioning

confidence: 99%

A New Species of Freshwater Algae Nephrochlamys yushanlensis sp. nov. (Selenastraceae, Sphaeropleales) and Its Lipid Accumulation during Nitrogen and Phosphorus Starvation

Maltsev

Maltseva

et al. 2021

Journal of Phycology

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The new species Nephrochlamys yushanlensis sp. nov. is described from a freshwater plankton sample. A comparison of morphology, 18S rDNA gene and ITS2 sequences, and fatty acid profiles showed that the novel strain represents a new lineage within the genus Nephrochlamys. For the first time with a member of the Selenastraceae, experiments with phosphate and nitrate deprivation were conducted to evaluate changes in biomass, lipid and triacylglycerol (TAGs) accumulation, and composition of fatty acids. Biomass dry weight under simultaneous nitrogen and phosphorus depletion was 1.73 g · L−1, which is significantly lower than the 2.41 g · L−1 observed in the control. All conditions of nutrient restriction significantly increased the lipid content in comparison with the control. The largest increase in the total lipid content, reaching 58.64% DW per cell at the end of cultivation, occurred with nitrogen deficiency. Significant increases in TAGs content (to 23.69% and 21.74%, respectively) occurred in phosphorus‐ and nitrogen‐depleted conditions in comparison to the control (16.90%). Oleic (49.8–64.1%), palmitic (21.1–22.7%), and linoleic (8.6–10.3%) acids were the dominant fatty acids when cultured on standard BBM medium, as well as with the shortage of nutrients. Phosphorus deprivation as well as absence of both nitrogen and phosphorus led to the appearance of FAMEs α‐linolenic (1.5–4.1%) and stearidonic (1.0–1.8%) acids. In general, FAME profiles revealed that the relative percentage of saturated and monounsaturated fatty acids increased (88.9% of total fatty acids) in nitrogen‐depletion conditions, suggesting this strain may be suitable for biodiesel production.

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“…However, it is the best available representation of genetic diversity across the genus and indicates that A. falcatus is a reasonable representative of Ankistrodesmus for genomic purposes. In fact, considering that the generic relationships among the Selenastraceae are poorly resolved and most genera appear to be polyphyletic, [48] A. falcatus may be a reasonable representative of the whole family.…”

Section: Plos Onementioning

confidence: 99%

“…falcatus to be reliable. Studies which have investigated the phylogenetic relationships for other members of the Selanastraceae family and the Ankistrodesmus genus suggest that species within the Ankistrodesmus genus exhibit typical variation for the Selenastraceae [ 13 , 47 , 48 ]. Garcia da Silva et al .…”

Section: Introductionmentioning

confidence: 99%

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De novo transcriptome assembly of the green alga Ankistrodesmus falcatus

Schomaker

Dudycha

2021

PLoS ONE

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Ankistrodesmus falcatus is a globally distributed freshwater chlorophyte that is a candidate for biofuel production, is used to study the effects of toxins on aquatic communities, and is used as food in zooplankton research. Each of these research fields is transitioning to genomic tools. We created a reference transcriptome for of A. falcatus using NextGen sequencing and de novo assembly methods including Trinity, Velvet-Oases, and EvidentialGene. The assembled transcriptome has a total of 17,997 contigs, an N50 value of 2,462, and a GC content of 64.8%. BUSCO analysis recovered 83.3% of total chlorophyte BUSCOs and 82.5% of the eukaryotic BUSCOs. A portion (7.9%) of these supposedly single-copy genes were found to have transcriptionally active, distinct duplicates. We annotated the assembly using the dammit annotation pipeline, resulting in putative functional annotation for 68.89% of the assembly. Using available rbcL sequences from 16 strains (10 species) of Ankistrodesmus, we constructed a neighbor-joining phylogeny to illustrate genetic distances of our A. falcatus strain to other members of the genus. This assembly will be valuable for researchers seeking to identify Ankistrodesmus sequences in metatranscriptomic and metagenomic field studies and in experiments where separating expression responses of zooplankton and their algal food sources through bioinformatics is important.

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Selenastraceae (Sphaeropleales, Chlorophyceae): rbcL, 18S rDNA and ITS-2 secondary structure enlightens traditional taxonomy, with description of two new genera, Messastrum gen. nov. and Curvastrum gen. nov.

Cited by 33 publications

References 72 publications

Genetic diversity in chrysophytes: Comparison of different gene markers

Genetic diversity in chrysophytes: Comparison of different gene markers

A New Species of Freshwater Algae Nephrochlamys yushanlensis sp. nov. (Selenastraceae, Sphaeropleales) and Its Lipid Accumulation during Nitrogen and Phosphorus Starvation

De novo transcriptome assembly of the green alga Ankistrodesmus falcatus

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