De novo Transcriptome of the Non-saxitoxin Producing Alexandrium tamutum Reveals New Insights on Harmful Dinoflagellates
Abstract
:1. Introduction
2. Results and Discussion
2.1. Transcriptome Sequencing and De Novo Assembly
2.2. Functional Annotation
2.3. Differential Expression Analysis
2.3.1. DEGs Involved in Photosynthesis
2.3.2. DEGs Involved in Protein Synthesis
2.3.3. DEGs Related to Cellular Stress
2.3.4. DEGs Related to Cytoskeleton
2.4. Sequences Coding Enzymes Involved in Toxin Synthesis
2.5. Structure Prediction of Proteins Encoded by sxt Genes
2.6. Other Toxin-Related Transcripts
3. Materials and Methods
3.1. Cell Culturing and Harvesting
3.2. RNA Extraction
3.3. Library Preparation and Sequencing
3.4. Transcriptome Assembly and Annotation
3.5. Transcriptome Expression Quantification and Differential Expression Analysis
3.6. In Silico Protein Modelling
3.7. Phylogenetic Tree
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Number of Genes | 216,911 |
---|---|
Number of transcripts | 288,380 |
Percent GC content | 65.31 |
Contig N50 | 1204 |
Median contig length | 474 |
Average contig length | 778.28 |
Number of proteins | 179,258 |
Number of complete proteins | 26,230 |
Number of partial proteins | 153,028 |
Gene | Encoded Protein | Original Sequence Code in Hackett, 2013 | Sequence ID and Internal BLAST Results | NCBI BLAST Best Match and Accession Number |
---|---|---|---|---|
sxtA | Phosphopantetheine attachment site (ACP in PKS) | sxtA, N terminus Contig93306 | >TR16074|c0_g1_i1 Length = 3230 Score = 402 bits (203), Expect = e-110 Identities = 443/523 (84%) Strand = Plus/Minus | Alexandrium catenella strain CS319 sxtA-like (sxtA) gene, partial sequence; KM100452.1 |
sxtA | Aspartate aminotransferase | sxtA, C terminus Aspartate aminotransferase Contig106704 | >TR2168|c0_g2_i2 Length = 1724 Score = 371 bits (187), Expect = e-101 Identities = 352/407 (86%) Strand = Plus/Plus | Aminobacter sp. MSH1 chromosome, complete genome; CP026265.1 |
sxtG | Amidinotransferase | sxtG, Amidinotransferase Contig22175 | >TR24523|c0_g4_i1 Length = 3296 Score = 1292 bits (652), Expect = 0.0 Identities = 1483/1760 (84%) Strand = Plus/Plus | Ensifer adhaerens strain Casida A plasmid pCasidaAA, complete sequence; CP015881.1 |
sxtU | Short-chain alcohol dehydrogenase | sxtU, Short-chain alcohol dehydrogenase Contig1416 | >TR101104|c3_g5_i1 Length = 1221 Score = 712 bits (359), Expect = 0.0 Identities = 704/819 (85%) Strand = Plus/Minus | Polyangium brachysporum strain DSM 7029, complete genome; CP011371.1 |
sxtU | Short-chain alcohol dehydrogenase | sxtU, Short-chain alcohol dehydrogenase Contig22159 | >TR119378|c0_g1_i1 Length = 1982 Score = 696 bits (351), Expect = 0.0 Identities = 648/747 (86%) Strand = Plus/Minus | Sandaracinus amylolyticus strain DSM 53668, complete genome; CP011125.1 |
sxtU | Short-chain alcohol dehydrogenase | sxtU, Short-chain alcohol dehydrogenase Contig22852 | >TR140478|c0_g2_i1 Length = 1469 Score = 381 bits (192), Expect = e-104 Identities = 381/444 (85%) Strand = Plus/Minus | Emiliania huxleyi CCMP1516 hypothetical protein mRNA; XM_005787014.1 |
sxtU | Short-chain alcohol dehydrogenase | sxtU, Short-chain alcohol dehydrogenase Contig22852 | >TR140478|c0_g1_i1 Length = 1457 Score = 381 bits (192), Expect = e-104 Identities = 381/444 (85%) Strand = Plus/Minus | Emiliania huxleyi CCMP1516 hypothetical protein mRNA; XM_005787014.1 |
sxtU | Short-chain alcohol dehydrogenase | sxtU, Short-chain alcohol dehydrogenase Contig24779 | >TR3419|c0_g1_i1 Length = 1019 Score = 559 bits (282), Expect = e-158 Identities = 585/686 (85%) Strand = Plus/Minus | Emiliania huxleyi CCMP1516 hypothetical protein partial mRNA; XM_005768652.1 |
sxtU | Short-chain alcohol dehydrogenase | sxtU, Short-chain alcohol dehydrogenase Contig31067 | >TR32351|c0_g1_i1 Length = 691 Score = 394 bits (199), Expect = e-108 Identities = 415/487 (85%) Strand = Plus/Minus | Stigmatella aurantiaca DW4/3-1, complete genome; CP002271.1 |
sxtU | Short-chain alcohol dehydrogenase | sxtU, Short-chain alcohol dehydrogenase Contig34277 | >TR63446|c0_g4_i1 Length = 1023 Score = 533 bits (269), Expect = e-150 Identities = 551/645 (85%) Strand = Plus/Plus | Caulobacter mirabilis strain FWC 38 chromosome, complete genome; CP024201.1 |
sxtU | Short-chain alcohol dehydrogenase | sxtU, Short-chain alcohol dehydrogenase Contig34756 | >TR70482|c0_g1_i1 Length = 1181 Score = 486 bits (245), Expect = e-136 Identities = 587/701 (83%) Strand = Plus/Minus | Anopheles gambiae str. PEST AGAP008667-RA (AgaP_AGAP008667), partial mRNA; XM_314766.4 |
sxtU | Short-chain alcohol dehydrogenase | sxtU, Short-chain alcohol dehydrogenase Contig44170 | >TR142607|c0_g1_i1 Length = 1418 Score = 593 bits (299), Expect = e-168 Identities = 638/751 (84%) Strand = Plus/Minus | Chromobacterium vaccinii strain XC0014 chromosome, complete genome; CP022344.1 |
sxtU | Short-chain alcohol dehydrogenase | sxtU, Short-chain alcohol dehydrogenase Contig44865 | >TR84807|c0_g1_i1 Length = 1081 Score = 422 bits (213), Expect = e-117 Identities = 450/529 (85%) Strand = Plus/Minus | Phenylobacterium zucineum HLK1, complete genome; CP000747.1 |
sxtU | Short-chain alcohol dehydrogenase | sxtU, Short-chain alcohol dehydrogenase Contig64321 | >TR80533|c0_g3_i1 Length = 989 Score = 472 bits (238), Expect = e-131 Identities = 490/574 (85%) Strand = Plus/Plus | Bradyrhizobium diazoefficiens DNA, complete genome, strain: NK6; AP014685.1 |
sxtU | Short-chain alcohol dehydrogenase | sxtU, Short-chain alcohol dehydrogenase Contig64321 | >TR80533|c0_g2_i1 Length = 916 Score = 472 bits (238), Expect = e-131 Identities = 490/574 (85%) Strand = Plus/Plus | Bradyrhizobium diazoefficiens DNA, complete genome, strain: NK6; AP014685.1 |
sxtU | Short-chain alcohol dehydrogenase | sxtU, Short-chain alcohol dehydrogenase Contig86383 | >TR142098|c0_g1_i2 Length = 1193 Score = 448 bits (226), Expect = e-124 Identities = 427/494 (86%) Strand = Plus/Minus | PREDICTED: Aegilops tauschii subsp. tauschii momilactone A synthase-like (LOC109773470), mRNA; XM_020332162.1 |
sxtU | Short-chain alcohol dehydrogenase | sxtU, Short-chain alcohol dehydrogenase Contig86383 | >TR142098|c0_g1_i3 Length = 936 Score = 424 bits (214), Expect = e-117 Identities = 424/494 (85%) Strand = Plus/Minus | PREDICTED: Aegilops tauschii subsp. tauschii momilactone A synthase-like (LOC109773470), mRNA; XM_020332162.1 |
sxtU | Short-chain alcohol dehydrogenase | sxtU, Short-chain alcohol dehydrogenase Contig97277 | >TR33997|c0_g1_i3 Length = 1012 Score = 555 bits (280), Expect = e-157 Identities = 616/728 (84%) Strand = Plus/Plus | Stenotrophomonas maltophilia strain AA1, complete genome; CP018756.1 |
A. tamutum sxt Putative Protein | Template (PDB Code) | Confidence | % id | CDD Search Output |
---|---|---|---|---|
sxtA N-Terminus; TR16074|c0_g1_i1 | Methyltransferase (6B3A) | 100% | 24% | Phosphopantetheine attachment site |
sxtG Amidinotransferase; TR24523|c0_g4_i1 | Arginine deaminase (1RXX) | 100% | 32% | Aminotransferase superfamily; Arginine deiminase |
sxtU Short-chain alcohol dehydrogenase; TR101104|c3_g5_i1 | Glucose dehydrogenase (1GEE) | 100% | 46% | Rossmann-fold NAD(P)(+)-binding proteins |
Transcript Automatic Annotation | Transcript ID | CDD Search Output | Potential Function |
---|---|---|---|
aflatoxin b1 aldehyde reductase member 2 | TR29768|c0_g1_i1 | Aldo-keto reductase (AKR) | Metabolites detoxification; carbon metabolism |
aflatoxin b1 aldehyde reductase member 4-like | TR93512|c0_g1_i1 | Aldo-keto reductase (AKR) | Metabolites detoxification; carbon metabolism |
gliotoxin biosynthesis protein | TR57386|c0_g1_i1 | GGCT-like domain | Metabolites biosynthesis; glutathione homeostasis |
“toxicos en levadura” | TR119771|c0_g1_i1 | HRD ubiquitin ligase complex | Ubiquitination; triggered immunity |
“toxicos en levadura” | TR119771|c0_g2_i1 | HRD ubiquitin ligase complex | Ubiquitination; triggered immunity |
toxin biosynthesis protein | TR47414|c1_g1_i2 | 2OG-Fe(II) oxygenase superfamily | Toxins/Metabolites production |
toxin biosynthesis protein | TR120505|c0_g1_i1 | 2OG-Fe(II) oxygenase superfamily | Toxins/Metabolites production |
toxin biosynthesis protein | TR120505|c0_g1_i2 | 2OG-Fe(II) oxygenase superfamily | Toxins/Metabolites production |
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Vingiani, G.M.; Štālberga, D.; De Luca, P.; Ianora, A.; De Luca, D.; Lauritano, C. De novo Transcriptome of the Non-saxitoxin Producing Alexandrium tamutum Reveals New Insights on Harmful Dinoflagellates. Mar. Drugs 2020, 18, 386. https://doi.org/10.3390/md18080386
Vingiani GM, Štālberga D, De Luca P, Ianora A, De Luca D, Lauritano C. De novo Transcriptome of the Non-saxitoxin Producing Alexandrium tamutum Reveals New Insights on Harmful Dinoflagellates. Marine Drugs. 2020; 18(8):386. https://doi.org/10.3390/md18080386
Chicago/Turabian StyleVingiani, Giorgio Maria, Dārta Štālberga, Pasquale De Luca, Adrianna Ianora, Daniele De Luca, and Chiara Lauritano. 2020. "De novo Transcriptome of the Non-saxitoxin Producing Alexandrium tamutum Reveals New Insights on Harmful Dinoflagellates" Marine Drugs 18, no. 8: 386. https://doi.org/10.3390/md18080386