Genomic and Genotypic Characterization of Cylindrospermopsis raciborskii: Toward an Intraspecific Phylogenetic Evaluation by Comparative Genomics

Abstract

Cylindrospermopsis raciborskii is a freshwater cyanobacterial species with increasing bloom reports worldwide that are likely due to factors related to climate change. In addition to the deleterious effects of blooms on aquatic ecosystems, the majority of ecotypes can synthesize toxic secondary metabolites causing public health issues. To overcome the harmful effects of C. raciborskii blooms, it is important to advance knowledge of diversity, genetic variation, and evolutionary processes within populations. An efficient approach to exploring this diversity and understanding the evolution of C. raciborskii is to use comparative genomics. Here, we report two new draft genomes of C. raciborskii (strains CENA302 and CENA303) from Brazilian isolates of different origins and explore their molecular diversity, phylogeny, and evolutionary diversification by comparing their genomes with sequences from other strains available in public databases. The results obtained by comparing seven C. raciborskii and the Raphidiopsis brookii D9 genomes revealed a set of conserved core genes and a variable set of accessory genes, such as those involved in the biosynthesis of natural products, heterocyte glycolipid formation, and nitrogen fixation. Gene cluster arrangements related to the biosynthesis of the antifungal cyclic glycosylated lipopeptide hassallidin were identified in four C. raciborskii genomes, including the non-nitrogen fixing strain CENA303. Shifts in gene clusters involved in toxin production according to geographic origins were observed, as well as a lack of nitrogen fixation (nif) and heterocyte glycolipid (hgl) gene clusters in some strains. Single gene phylogeny (16S rRNA sequences) was congruent with phylogeny based on 31 concatenated housekeeping protein sequences, and both analyses have shown, with high support values, that the species C. raciborskii is monophyletic. This comparative genomics study allowed a species-wide view of the biological diversity of C. raciborskii and in some cases linked genome differences to phenotype.

Keywords: bioinformatics; cyanobacteria; cyanotoxins; genome assembly; natural products; nitrogen fixation; pan-genome.

FIGURE 1

Pan- and core-genome plot of eight cyanobacterial strains (CS-505, CS-508, CR12, CENA303, CENA302, ITEP-A1, D9, and MVCC14). (A) Shows the progression of the pan-genome: the y axis indicates the number of non-redundant genes and the x axis indicates the number of genomes. (B) Shows the progression of core genome: the y axis indicates the number of genes presents in all strains and the x axis indicates the number of genomes.

FIGURE 2

(A) Pan-genome tree and matrix of similarity among strains. (B) Comparison of presence (filled circles) or absence (empty circles) of the genotypes evaluated in this study (hassallidin, cylindrospermopsin, saxitoxin, heterocyte glycolipids, and nitrogen fixation gene clusters). (C) Dendrogram based on the results of OrthoMCL clustering.

FIGURE 3

(A) Bayesian inference tree based on the 16S rRNA nucleotide sequences from 36 cyanobacterial strains. (B) Representation of the clades containing the strains involved in this study. (C) ML phylogenetic tree based on 31 conserved proteins from 39 cyanobacterial strains. The strains evaluated in this study are represented in bold.

FIGURE 4

CENA 302 growth in (A) ASM-1, scale bar = 5 μm; (B) ASM-1 without combined nitrogen, scale bar = 10 μm; (C) Jaworski, scale bar = 10 μm; (D) Jaworski without combined nitrogen, scale bar = 5 μm; (E) Z8, scale bar = 10 μm; and (F) Z8 without combined nitrogen, scale bar = 5 μm. CENA303 growth in (G) ASM-1, scale bar = 20 μm; and (H) Z8 medium, scale bar = 10 μm. “a”: akinete; “h”: heterocyte.

FIGURE 5

BLAST atlas analysis of seven Cylindrospermopsis strains (CS-505, CS-508, CR12, CENA303, CENA302, ITEP-A1, and MVCC14) and Raphidiopsis brookii D9, using the strains CS-505 as reference. The hassallidin (hass), cylindrospermopsin (cyr), saxitoxin (sxt), heterocyte glycolipid (hgl), and nitrogen fixation (nif; fdxN; hesA and B; feoaA) gene clusters are shown inside the boxes and their location in the genomes are indicated. The Cylindrospermopsis raciborskii ITEP-A1 genome showed an incomplete sxt gene cluster. The length in base pairs (bp) of the gene cluster and the function of the gene are also shown. ORF, open reading frame; PKS, polyketide synthase; NRPS,non-ribossomal peptide synthase.