Molecular diversity of the genus Cryptomonas (Cryptophyceae) in Russia

ABSTRACT

Molecular data were used to revise the diversity of the genus Cryptomonas in Russia, using samples collected across nine geographic regions within Russia from 2015–2019. Several molecular markers were used: nuclear SSU, LSU and ITS2 rDNA, and plastid psbA. In total, 24 species of the genus Cryptomonas were identified in the country’s fresh waters based on 122 different strains. Six new species were identified and are described here (Cryptomonas matvienkoae sp. nov., C. furtiva sp. nov., C. paludosa sp. nov., C. ursina sp. nov., C. kisselevii sp. nov. and C. meshchorana sp. nov.), and three taxa are emended (Cryptomonas skujae, C. platyuris and C. obovata). These new and emended species group in clades with the previously described species or represent new lineages on the phylogenetic tree. Seven morphospecies, previously reported in Russia, are confirmed by molecular methods, and two unidentified taxa are also reported.

HIGHLIGHTS

• Molecular investigations of the genus Cryptomonas in Russia revealed 24 species.

• Descriptions of three species were emended.

• Six species new to science were described.

KEYWORDS:

• Cryptomonas
• diversity
• ITS rDNA and psbA markers
• molecular methods
• morphology
• new species
• Russia
• SSU rDNA
• taxonomy

Acknowledgements

The authors are grateful to I. Sterlyagova and D. Kapustin for their help in sampling in some areas of Russia and two anonymous reviewers for helpful comments resulting in a considerable improvement of the manuscript.

Disclosure statement

No potential conflict of interest was reported by the authors.

Supplementary Information

The following supplementary material is accessible via the Supplementary Content tab on the article’s online page at https://doi.org/10.1080/09670262.2022.2031304

Supplementary table S1. List of studied strains with information about localities in Russia, environmental parameters and data on isolators.

Supplementary table S2. GenBank accession numbers of analyzed strains.

Supplementary table S3. Estimates of nucleotide sequence differences between the 31 Cryptomonas species, based on the divergence of the V4 region of the nuclear SSU rDNA (lengths 216–225 bp). The number of different nucleotides is shown in the lower-left matrix, p-distances (not corrected) are in the upper-right matrix. The analysis includes only the reference strains of species.

Supplementary table S4. Estimates of nucleotide sequence differences between the 31 Cryptomonas species, based on the divergence of the C1 region of the nuclear LSU rDNA (lengths 295–309). The number of different nucleotides is shown in the lower-left matrix, p-distances (not corrected) are in the upper-right matrix. The analysis includes only the reference strains of species.

Supplementary table S5. Estimates of nucleotide sequence differences between the 31 Cryptomonas species, based on the divergence of the nuclear ITS2 rDNA (lengths 335–613). The number of different nucleotides is shown in the lower-left matrix, p-distances (not corrected) are in the upper-right matrix. The analysis includes only the reference strains of species.

Supplementary figure S1. Bayesian tree of the partial nuclear small subunit rDNA (SSU rDNA) data set. The Bayesian posterior probability and maximum likelihood bootstrap value are shown left and right of the fraction line respectively. Scale bar represents substitutions per site. New species, described in this research, are marked with solid lines, emended taxa with dotted lines, and strains from Russia with asterisks.

Supplementary figure S2. Bayesian tree of the partial nuclear large subunit ribosomal rDNA (LSU rDNA) data set. The Bayesian posterior probability and maximum likelihood bootstrap value are shown left and right of the fraction line respectively. Scale bar represents substitutions per site. New species, described in this research, are marked with solid lines, emended taxa with dotted lines, and strains from Russia with asterisks.

Supplementary figure S3. Bayesian tree of the partial chloroplast psb A data set. The Bayesian posterior probability and maximum likelihood bootstrap value are shown left and right of the fraction line respectively. Scale bar represents: substitutions per site. New species, described in this research, are marked with solid lines, emended taxa with dotted lines, and strains from Russia with asterisks.

Supplementary figure S4. Predicted secondary structures of the nuclear internal transcribed spacer 2 (from 5’ to 3’ terminus in clockwise direction) of: A) Cryptomonas skujae (strain NN31), B) C. ursina (strain NN 11), C) C. platyuris (strain R244), D) C. kisselevii (strain NN21), E) C. obovata (strain NN17), F) C. paludosa (strain R 186), G) C. matvienkoae (strain R 246), H) C. furtiva (strain R 207), I) C. meshchyorana (strain R 171). In the figure F, differences between strains of C. paludosa, strains R 186 and Okgeum121809C, are outlined in grey ovals. Black boxes indicate the positions of Compensatory Base Changes (CBCs) between selected species.

Author contributions

E. Gusev: original concept, writing and drafting the manuscript, isolating strains, molecular investigation of strains, LM observations; N. Martynenko: isolating strains, molecular investigation of strains, creating the phylogenetic tree, editing the manuscript; P. Kulizin: isolating strains, LM observations, editing the manuscript, creation of figures; M. Kulikovskiy: critical reading and editing of the manuscript.

Additional information

Funding

Financial support was provided by the Russia Foundation for Basic Research (grants no. 18-04-01280_а and no. 20-34-90144) for sampling, culture isolation and morphological studies. Molecular studies were performed within the state assignment of Ministry of Science and Higher Education of the Russian Federation (theme No. 121041200194-7).