Revisiting the taxonomic significance of aplanozygote morphologies of two cosmopolitan snow species of the genus<i>Chloromonas</i>(Volvocales, Chlorophyceae)

Matsuzaki, Ryo; Kawai-Toyooka, Hiroko; Hara, Yoshiaki; Nozaki, Hisayoshi

doi:10.2216/15-33.1

Cited by 40 publications

(89 citation statements)

References 48 publications

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“…However, environmental sequences can be tricky and must be of high quality when used as references for HTS data (Rimet et al 2018). A polyphasic approach (i.e., collectively using genetic, chemotaxonomic and phenotypic methods) is required to determine accurately the taxonomic identity of species found in field samples (Matsuzaki et al 2015). Alternatively, single cells with identifiable morphologies, can be picked out of mixed samples for single-cell sequencing to link morphology to genotype (Bock et al 2014).…”

Section: Discussionmentioning

confidence: 99%

“…Christen (Remias et al 2016), Chloromonas nivalis (Chodat) Hoham et Mullet (Procházková et al 2018a;Remias et al 2010) or Chloromonas brevispina (F.E. Fritsch) Hoham, Roemer et Mullet (Matsuzaki et al 2015). Nonetheless, we are only scratching the surface of snow algal diversity characterization and the abovementioned species likely constitute a small proportion of the true diversity.…”

Section: Introductionmentioning

confidence: 86%

“…In Gonium pectorale less than 5% of the nucleotide positions differ in pairwise comparisons and less than 7% vary between all clones (Coleman et al 1993). Similarly, only few nucleotide differences have been reported among strains of Chloromonas reticulata (3.4-4.1%), and of Chlamydomonas reinhardtii NIES-2463 and SAG 11-32a (3.3%), with the latter one being able to cross and produce zygotes (Matsuzaki et al 2015). A similar low identity threshold for OTU picking (95%) as in our case was also successfully applied during Illumina barcoding of soil fungal communities (Schmidt et al 2013).…”

Section: Clustering Sequences Into Otus and Creation Of Otu Tablementioning

confidence: 95%

“…Wolf et al (2013) reported a probability of ~0.99 that no intragenomic CBC took place, based on the comparison of ITS2 of 178 species of land plants. However, some Chloromonas species in snow possess intragenomic CBCs (Matsuzaki et al 2015). As a consequence, evaluation of CBCs detection should be carried out carefully; i.e., not only the pure presence or absence of CBCs, but also the exact position in the ITS2 molecule (i.e., whether it is in or outside the most conserved part) and the overall level of genetic difference of ITS2 between OTUs should be taken into account.…”

Section: Advantages Of the Its2 Markermentioning

confidence: 99%

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Evaluating amplicon high-throughput sequencing data of microalgae living in melting snow: improvements and limitations

Lutz¹,

Procházková²,

Benning³

et al. 2019

Fottea

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Melting snowfields are dominated by closely related green algae. Although microscopy-based classification are evaluable distinction tools, they can be challenging and may not reveal the diversity. High-throughput sequencing (HTS) allows for a comprehensive community evaluation but has been rarely used in such ecosystems. We found that assigning taxonomy to DNA sequences strongly depends on the quality of the reference databases. Furthermore, for an accurate identification, a combination of manual inspection of automated assignments, and oligotyping of the abundant 18S OTUs and ITS2 secondary structure analyses were needed. The use of one marker can be misleading because of low variability (18S) or the scarcity of references (ITS2). Our evaluation reveals that HTS outputs need to be thoroughly checked when the organisms are poorly represented in databases. We recommend an optimized workflow including consistent sampling, a two-molecular marker approach, light microscopy-based guidance, generation of appropriate reference sequences and a final manual verification of taxonomic assignments as a best approach for accurate diversity analyses.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 86%

Section: Clustering Sequences Into Otus and Creation Of Otu Tablementioning

confidence: 95%

Section: Advantages Of the Its2 Markermentioning

confidence: 99%

See 2 more Smart Citations

Evaluating amplicon high-throughput sequencing data of microalgae living in melting snow: improvements and limitations

Lutz¹,

Procházková²,

Benning³

et al. 2019

Fottea

View full text Add to dashboard Cite

show abstract

“…nivalis veils multiple species and extended molecular phylogenetic investigations could considerably reshape its taxonomic status and biogeography (Matsuzaki et al. , ). In addition, here we suggest that the genus Chloromonas would be understood just as a part of clade 1 (= core Chloromonas ; Fig.…”

Section: Discussionmentioning

confidence: 99%

Chloromonas svalbardensis n. sp. with Insights into the Phylogroup Chloromonadinia (Chlorophyceae)

Barcytė

Hodač

Nedbalová

et al. 2018

J Eukaryotic Microbiology

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The traditional green algal genus Chloromonas accommodates mesophilic, cold-tolerant and cold-adapted microorganisms. In this paper, we studied a new strain isolated from a wet hummock meadow in the High Arctic. We used morphological, ultrastructural and molecular data to assess the taxonomic position and phylogenetic relationships of the new isolate. The observed morphological features generally corresponded to the cold-tolerant Chloromonas characteristics. However, ellipsoidal or wide ellipsoidal vegetative cells, a massive parietal cup-shaped chloroplast with a number of continuously connected lobes, a thick cell wall, a prominent hemispherical papilla and the anterior position of an oblong or round eyespot distinguished the alga from all previously described Chloromonas species. Analyses of rbcL and 18S rRNA genes showed that the new strain formed an independent lineage within a clade containing mesophilic and psychrotolerant Chloromonas species. Comparisons of secondary structure models of a highly variable ITS2 rDNA marker supported a separate species identity of the new isolate. Considering the morphological and molecular differences from its relatives, a new psychrotolerant species, Chloromonas svalbardensis, is proposed. Further, our results demonstrated the paraphyletic origin of Chloromonas within Chloromonadinia with genetically, morphologically and ecologically well-defined clades. We discuss a scenario of a possible Chloromonas split and revision.

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Chilling out: the evolution and diversification of psychrophilic algae with a focus on Chlamydomonadales

2016

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Revisiting the taxonomic significance of aplanozygote morphologies of two cosmopolitan snow species of the genusChloromonas(Volvocales, Chlorophyceae)

Cited by 40 publications

References 48 publications

Evaluating amplicon high-throughput sequencing data of microalgae living in melting snow: improvements and limitations

Evaluating amplicon high-throughput sequencing data of microalgae living in melting snow: improvements and limitations

Chloromonas svalbardensis n. sp. with Insights into the Phylogroup Chloromonadinia (Chlorophyceae)

Chilling out: the evolution and diversification of psychrophilic algae with a focus on Chlamydomonadales

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