Abstract
The relatively conserved 18S is often used in the phylogenetic analysis of microalgae. However, whether it can really help in barcoding microalgae needs to be evaluated. In this study the multiple approaches of coalescent, distance and character-based barcoding are first employed in Chlorella and Scenedesmus to test the efficiency of 18S sequences for barcoding green microalgae. We show that most Chlorella and Scenedesmus species, including the cryptic species, can be distinguished by 18S sequences with all coalescent General Mixed Yule-coalescent (GMYC), poisson tree process (PTP), and P ID, distance (ABGD) and character-based approaches. Both GMYC and PTP analyses produce more genetic groups. The P ID and ABGD analyses only cluster some species. All species (apart from a few of lineages) can be separated in character-based barcoding analysis with more than three character attributes. In comparison with previous barcoding results with rbcL, tufA, ITS and 16S, 18S produces good resolution in identifying Chlorella and Scenedesmus. Our results reveal that 18S is highly efficient in identifying taxa of green microalgae at species level, based on a combination of multiple barcoding approaches. Combining 18S with other gene markers may be useful in barcoding microalgae.
Similar content being viewed by others
References
Bergmann T, Hadrys H, Breves G, Schierwater B. 2009. Character-based DNA barcoding: a superior tool for species classification. Berl. Munch. Tierarztl. Wochenschr., 122(11–12): 446–450.
Bock C, Pröschold T, Krienitz L. 2011. Updating the genus Dictyosphaerium and description of Mucidosphaerium gen. Nov.(Trebouxiophyceae) based on morphological and molecular data. J. Phycol., 47(3): 638–652.
CBOL Plant Working Group. 2009. A DNA barcode for land plants. Proc. Natl. Acad. Sci. U. S. A., 106(31): 12 794–12 797.
China Plant BOL Group, Li D Z, Gao L M, Li H T, Wang H, Ge X J, Liu J Q, Chen Z D, Zhou S L, Chen S L, Yang J B, Fu C X, Zeng C X, Yan H F, Zhu Y J, Sun Y S, Chen S Y, Zhao L, Wang K, Yang T, Duan G W. 2011. Comparative analysis of a large dataset indicates that internal transcribed spacer(ITS) should be incorporated into the core barcode for seed plants. Proc. Natl. Acad. Sci. U. S. A., 108(49): 19 641–19 646.
Damm S, Schierwater B, Hadrys H. 2010. An integrative approach to species discovery in odonates: from characterbased DNA barcoding to ecology. Mol. Ecol., 19(18): 3 881–3 893.
DeSalle R, Egan M G, Siddall M. 2005. The unholy trinity: taxonomy, species delimitation and DNA barcoding. Philos. Trans. Roy. Soc. B: Biol. Sci., 360(1462): 1 905–1 916.
Drummond A J, Rambaut A. 2007. BEAST: bayesian evolutionary analysis by sampling trees. BMC Evol. Biol., 7: 214.
Fujisawa T, Barraclough T G. 2013. Delimiting species using single-locus data and the generalized mixed Yule coalescent approach: a revised method and evaluation on simulated data sets. Syst. Biol., 62(5): 707–724.
Hebert P D N, Cywinska A C, Ball S L, de Waard J R. 2003. Biological identifications through DNA barcodes. Philos. Trans. Roy. Soc. B: Biol. Sci., 270(1512): 313–321.
Heeg J S, Wolf M. 2015. ITS2 and 18S rDNA sequencestructure phylogeny of Chlorella and allies(Chlorophyta, Trebouxiophyceae, Chlorellaceae). Plant Gene, 4: 20–28.
Kekkonen M, Hebert P D N. 2014. DNA barcode-based delineation of putative species: efficient start for taxonomic workflows. Mol. Ecol. Res., 14(4): 706–715.
Krawczyk K, Szczecińska M, Sawicki J. 2014. Evaluation of 11 single-locus and seven multilocus DNA barcodes in Lamium L.(Lamiaceae). Mol. Ecol. Res., 14(2): 272–285.
Krienitz L, Hegewald E H, Hepperle D, Huss V A R, Rohrs T, Wolf M. 2004. Phylogenetic relationship of Chlorella and Parachlorella gen. nov.(Chlorophyta, Trebouxiophyceae). Phycologia, 43: 529–542.
Kumar S, Stecher G, Tamura K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol. Biol. Evol., 33(7): 1870–4.
Luo W, Pflugmacher S, Pröeschold T, Walz N, Krienitz L. 2006. Genotype versus phenotype variability in Chlorella and Micractinium(Chlorophyta, Trebouxiophyceae). Protist, 157(3): 315–333.
Luo W, Pröeschold T, Bock C, Krienitz L. 2010. Generic concept in Chlorella-related coccoid green algae (Chlorophyta, Trebouxiophyceae). Plant Biol., 12(3): 545–553.
Maddison D R, Maddison W P. 2001. MacClade: Analysis of Phylogeny and Character Evolution, Version 4.03. Sinauer Associates, Sunderland, MA.
Posada D. 2008. jModelTest: phylogenetic model averaging. Mol. Biol. Evol., 25(7): 1 253–1 256.
R Core Team. 2014. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project. org/.
Rach J, DeSalle R, Sarkar I N, Schierwater B, Hadrys H. 2008. Character-based DNA barcoding allows discrimination of genera, species and populations in Odonata. Philos. Trans. Roy. Soc. B: Biol. Sci., 275(1632): 237–247.
Saunders G W, Kucera H. 2010. An evaluation of rbcL, tufA, UPA, LSU and ITS as DNA barcode markers for the marine green macroalgae. Cryptogamie Algol., 31(4): 487–528.
Škaloud P, Němcová Y, Pytela J, Bogdanov N I, Bock C, Pickinpaugh S H. 2014. Planktochlorella nurekis gen. et sp. nov.(Trebouxiophyceae, Chlorophyta), a novel coccoid green alga carrying significant biotechnological potential. Fottea, 14(1): 53–62.
Talavera G, Dincă V, Vila R. 2013. Factors affecting species delimitations with the GMYC model: insights from a butterfly survey. Methods Ecol. Evol., 4(12): 1 101–1 110.
Yassin A, Markow T A, Narechania A, O’Grady P M, DeSalle R. 2010. The genus Drosophila as a model for testing tree-and character-based methods of species identification using DNA barcoding. Mol. Phylogenet. Evol., 57(2): 509–517.
Zou S M, Fei C, Song J M, Bao Y C, He M L, Wang C H. 2016a. Combining and comparing coalescent, distance and character-based approaches for barcoding microalgaes: a test with Chlorella-like species (Chlorophyta). PLoS One, 11(4): e015383.
Zou S M, Fei C, Wang C, Gao Z, Bao Y C, He M L, Wang C H. 2016b. How DNA barcoding can be more effective in microalgae identification: a case of cryptic diversity revelation in Scenedesmus(Chlorophyceae). Sci. Rep., 6: 36 822.
Zou S M, Li Q, Kong L F, Yu H, Zheng X D. 2011. Comparing the usefulness of distance, monophyly and characterbased DNA barcoding methods in species identification: a case study of Neogastropoda. PLoS One, 6(10): e26619.
Acknowledgement
We acknowledge the collection of samples referred to in Zou et al. (2016a, b).
Author information
Authors and Affiliations
Corresponding author
Additional information
Supported by the China Post-doctoral Science Foundation (Nos. 2014M561661, 2015T80558), the Natural Science Foundation of Jiangsu Province (No. BK20150680), the National Natural Science Foundation of China (No. 31600294), and the Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization and Fundamental Research Funds for the Central Universities of Ministry of Education of China (No. Y0201600141)
Electronic supplementary material
Rights and permissions
About this article
Cite this article
Zou, S., Fei, C., Yang, W. et al. High-efficiency 18S microalgae barcoding by coalescent, distance and character-based approaches: a test in Chlorella and Scenedesmus. J. Ocean. Limnol. 36, 1771–1777 (2018). https://doi.org/10.1007/s00343-018-7201-y
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00343-018-7201-y