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Draft genome sequences of Cylindrospermopsis raciborskii strains CS-508 and MVCC14, isolated from freshwater bloom events in Australia and Uruguay
Standards in Genomic Sciences volume 13, Article number: 26 (2018)
Members of the genus Cylindrospermopsis represent an important environmental and health concern. Strains CS-508 and MVCC14 of C. raciborskii were isolated from freshwater reservoirs located in Australia and Uruguay, respectively. While CS-508 has been reported as non-toxic, MVCC14 is a saxitoxin (STX) producer. We annotated the draft genomes of these C. raciborskii strains using the assembly of reads obtained from Illumina MiSeq sequencing. The final assemblies resulted in genome sizes close to 3.6 Mbp for both strains and included 3202 ORFs for CS-508 (in 163 contigs) and 3560 ORFs for MVCC14 (in 99 contigs). Finally, both the average nucleotide identity (ANI) and the similarity of gene content indicate that these two genomes should be considered as strains of the C. raciborskii species.
Cyanobacterial bloom-forming species are a persistent global problem [1, 2]. Cylindrospermopsis raciborskii, is a species responsible for algal blooms that cause serious problems because of the wide variety of toxic compounds that it produces [3, 4]. Animal consumption of contaminated water with toxic metabolites produces symptoms associated with dermal rash, neural disturbance, hepatic and digestive disorder, and in some cases causing death [4, 5]. C. raciborskii was first described in Java (Indonesia) in 1912 , and was morphologically characterized in 1972 by Seenayya and Subba-Raju  as a Gram-negative-like, cylindrical filament able to fix nitrogen. To date, this species has been characterized as a producer of saxitoxin, a neurotoxin able to block voltage dependent mammalian sodium channels . It also produces cylindrospermopsin, a toxin related with phosphatase metabolic inhibition in hepatocyte cells . Recently, an anti-fungal glycolipopeptide affecting the plasma membrane integrity of Candida albicans cells, classified as hassallidin, has also been identified [10,11,12].
In order to understand the mechanisms responsible for the synthesis of these toxins, representative strains of this species have been characterized both genetically and chromatographically . To date, Australian isolates have been characterized as CYL producers (CS-505 and CS-506), HAS producers (CS-505 and CS-509) and as non-toxin producers (CS-508) (unpublished data). In addition, the Uruguayan strain MVCC14 has been described as a STX producer . Moreover, a Brazilian isolate Raphidiopsis brookii D9, a species phylogenetically closely related to C. raciborskii (Fig. 1), has also been reported as a STX producer [15,16,17]. The complete genome of C. raciborskii CS-505 and draft genomes of strains CS-506, CS-509 and R. brookii D9 are currently available [16, 18].
To provide further data to better understand the genomics and physiology of C. raciborskii , including its high capacity for dispersal, we performed a genome sequence analysis of Australian strain CS-508 and Uruguayan strain MVCC14, including gene annotation using the Clusters of Orthologous Group (COG) database . Moreover, we also conducted a comparative genome analysis on five C. raciborskii strains: CS-505, CS-506, CS-508, CS-509 and MVCC14, in addition to R. brookii D9 to identify common genes.
Classification and features
C. raciborskii is a relevant environmental species causing harmful blooms in freshwater environments, with certain strains synthesizing toxins.
C. raciborskii species (Tables 1 and 2), were initially described as microorganisms growing in the tropics, however, they have been reported in temperate freshwaters . As previously described , the cells belonging to the genus Cylindrospermopsis could either be cylindrical filaments with terminal nitrogen fixation structures (heterocysts) (Fig. 1a-e) or resistant cells (akinetes). Both structures could be differentiated under nutrient-deficient culture media. In heterocyst-forming cyanobacteria, heterocysts are distributed in semi-regular intervals along the filament or only in the terminal position. The presence of intercalated heterocysts in C. raciborskii has been rarely observed, and has been thus described as a species with terminal heterocysts . However, we observed intercalated heterocysts in strain MVCC14 under nitrogen starvation and under different nitrogen conditions (Fig. 1c-e). The distribution of the heterocysts along the filament has been the subject of research by comparing genetic and physiological traits between Cylindrospermopsis and Anabaena , as models of differential patterns [23, 24]. Anabaena sp. PCC7120 differentiates heterocysts after every 8 to 12 vegetative cells under nitrogen deprivation [23, 24]. We were able to observe heterocysts more frequently in some filaments; regularity between heterocyst cells was approximately of 30 neighboring vegetative cells (SD ± 7, 4). This is the first report showing the transient presence of intercalary heterocyst in this C. raciborskii strain and further research should help to understand the genetic control that regulates this sporadic distribution of heterocysts in this C. raciborskii strain.
Despite their very similar morphology, C. raciborskii and R. brookii have been classified as different species because the latter is unable of fix nitrogen and does not develop heterocysts (e.g. ). Here, the maximum likelihood phylogenetic tree of 16S-rRNA gene sequences shows that R. brookii and C. raciborskii strains constitute a statistically well-supported monophyletic clade (Fig. 2 and Additional file 1: Figure S1). This clade comprises sequences sharing ≥98% of similarity and show low evolutionary rate within the clade. Despite this, it is possible to identify some sub-clusters with a certain coherent phylo-geographical distribution as was previously described [26, 27]. For example, the sub-cluster comprising strains exclusively from South America (R. brookii D9, C. raciborskii MVCC14 and T3) is segregated with a well-supported statistical value (Fig. 2, Additional file 1: Figures. S2 and S4). Phylogenetic analyses from other phylogenetic markers also displayed the monophyletic nature among R. brookii and C. raciborskii strains (Additional file 1: Figures. S2, S3, S4 and S5). This is congruent with a previous study of phylogenetic relationships inferred from several conserved genes, which postulate that Cylindrospermopsis and Raphidiopsis representatives should be congeners . However, to assess the taxonomic classification of these microorganisms further phylogenetic analyses (e.g., global genome comparisons) or more complete physiological descriptions are required.
Genome sequencing information
Genome project history
Strains CS-508 and MVCC14 were selected for sequencing based on their phylogenetic relationship between strains from South America and Australia. Sequenced draft genomes were annotated using RAST  The CS-508 Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession MBQX00000000. The version described here is MBQX01000000. MVCC14 Whole Genome Shotgun Project has been deposited under the accession ID MBQY00000000. The version described in this paper is version MBQY01000000. A summary of the project information is shown in Table 3.
Growth conditions and genomic DNA preparation
C. raciborskii cultures were grown in MLA medium , under 12:12 light:dark cycles at 25 °C. Total DNA extractions were carried out using 100 mL of exponential growth culture, obtaining approximately 1 g of wet cell pellet. DNA purification was conducted by standard CTAB protocol . Total cell pellets were mechanically disrupted and resuspended in 500 μL of CTAB buffer, and incubated at 55 °C for 1 h under constant mixing. The DNA was purified using 500 μL phenol/chloroform/isoamyl alcohol (25:24:1) and centrifuged at 8000 x g for 7 min. DNA was precipitated using isopropanol/ammonium acetate (0.54 vol cold isopropanol, 0.08 vol ammonium acetate 7.5 M). Finally, DNA was washed with 70% and then with 90% ethanol and resuspended in 50 μL of pure water. DNA extraction was visualized using red gel staining in a 1% agarose gel under UV light.
Genome sequencing and assembly
Both genomes were obtained by a shotgun strategy using Illumina MiSeq sequencing technology. A total of 8,308,910 paired-end reads were obtained for CS-508 strain and 28,711,437 paired-end reads for MVCC14 strain. Quality control checks were performed on the raw FASTQ data using FastQC (version 0.10.1) . Sequencing reads were trimmed for sequencing adaptors using Trimmomatic (version 0.32)  and the quality filtering and trimming was done by Prinseq-lite (version 0.20.4) . Briefly, reads were trimmed for ‘N’ characters and low quality nucleotides (Phred score cutoff of 24) and then any read with an average Phred score below 29 and shorter than 80 nt was discarded. A de novo assembly strategy involving multiple algorithms and merging of the individual assemblies was performed. Assemblies by IDBA , SPADes , VELVET  and ABYSS  algorithms were generated by using the platform MIX software  to improve draft assembly by reducing contig fragmentation. Contigs shorter than 1000 bp were discarded. The final assembly resulted in 163 contigs for CS-508 and 99 contigs for MVCC14, accounting for 3,558,956 bp and 3,594,524 bp, respectively. CheckM analysis  indicated a genome completeness of 97.57% for CS-508 and 96.29% for MVCC14.
The gene annotation process was conducted using the RAST Server 2.0 . Predicted coding sequences were extracted from RAST platform and homology was evaluated by BLASTp scan, with each predicted ORF as a query against the complete bacterial database.
C. raciborskii CS-508 and MVCC14 draft genomes have a GC% content of 43 and 44 respectively (Table 4), containing 3202 and 3560 ORFs each. Table 5 shows the COG distribution of the corresponding genes. A high number of these encode metabolic proteins (COG codes R, S, M, C, E, P, O, H and T). Interestingly, no genes for the “RNA processing and modification” category were found in any genome. This has been observed in another cyanobacterial genome  and could be explained by genetic divergence of these cyanobacteria. Approximately 22% (CS-508) and 26% (MVCC14) of the total coding genes were not classified in any COG category.
Insights from the genome sequence
Photoautotrophic metabolic pathways were reconstructed in CS-508 and MVCC14 draft genomes, based on the predicted metabolic pathways in previous sequenced genomes of C. raciborskii [16, 18]. Nitrogen metabolic systems related to ammonium, nitrate and nitrite acquisition genes, as well as heterocyst differentiation and nitrogen fixation, were identified in both genome drafts.
Sequenced genomes were compared to previously published C. raciborskii and R. brookii genomes. We determined the average nucleotide identity in these genomes by a two-way comparison analysis (Table 6), using the inference tool ANI calculator . The percentage of shared genes between strains ranged from 93.23 to 99.77%. According to the ANI value, the complete group, C. raciborskii and R. brookii could be considered as members of the same species, considering a threshold value of 95% .
We identified four genes encoding a non-ribosomal peptide synthetase complex in the CS-508 genome related to the hassallidin biosynthesis. We found in CS-508 the same gene cluster as in the hassallidin producers CS-509, CS-505 and Anabaena SYKE748A [10, 16, 18], with no evidence of mutations in the hassallidin cluster. Surprisingly, we were not able to detect the presence of hassallidin in CS-508 cultures, according to LC-MS/MS analysis (unpublished results). In the MVCC14 draft genome, we identified a group of genes related to STX biosynthesis. STX is a paralytic biotoxin produced by marine dinoflagellates and freshwater cyanobacteria . The sxt gene cluster found in MVCC14 has a similar distribution and toxin profile to R. brookii D9 . We did not find NRPS sequences in the MVCC14 genome.
In order to understand the genomics of the toxin producing, bloom forming C. raciborskii , this work presents two drafts of sequenced genomes from the non-toxic Australian strain CS-508 and the Uruguayan neurotoxin-producer strain MVCC14. An NRPS gene cluster related with hassallidin production was identified in CS-508 and PKS-like set of genes related with STX production was identified in the genome of the MVCC14 strain. Considering the 16S rRNA gene phylogenetic analysis and genome level comparison, we identified a phylogeographical segregation of the C. raciborskii and R. brokii strains retrieved from South America. Disregarding nitrogen fixation ability, these results suggest R. brookii D9 and C. raciborskii mvcc14 are closely related at genome level, which could lead to new research to corroborate the Cylindrospermopsis /Raphidiopsis clade as one comprised by two genera or by a single genus with different species.
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This work was financed by the following grants: Fondecyt regular 1131037, 1161232, Fondecyt de Iniciación 11130518 and JJF PhD Conicyt Fellowship 21120837, CTM2016-80095-C2-1-R from the Spanish Ministry of Economy and Competitiveness; KSL was financed by postdoctoral Fondecyt N° 3130681, LB was funded by Postdoctoral Fondecyt N° 3140330. K. del Rio for strain cultivation and DNA extraction and Dr. Sylvia Bonilla for kindly providing the MVCC14 C. raciborskii strain.
The authors declare that they have no competing interests.
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Figure S1. Cyanobacterial ML phylogenetic tree based on 16S rRNA gene sequences. Figure S2. ML phylogenetic tree based on rbcL gene sequences from relatives cyanobacteria. Figure S3. ML phylogenetic tree based on ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (RbcL) proteins from relatives cyanobacteria. Figure S4. ML phylogenetic tree based on psbA gene sequences from relatives cyanobacteria. Figure S5. ML phylogenetic tree based on Photosystem II D1 (PsbA) proteins from relatives cyanobacteria. (DOCX 979 kb)
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Fuentes-Valdés, J.J., Soto-Liebe, K., Pérez-Pantoja, D. et al. Draft genome sequences of Cylindrospermopsis raciborskii strains CS-508 and MVCC14, isolated from freshwater bloom events in Australia and Uruguay. Stand in Genomic Sci 13, 26 (2018) doi:10.1186/s40793-018-0323-1
- Environmental toxicity
- Non-ribosomal peptide-synthetase
- Polyketide synthases