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De novo transcriptome assembly and gene annotation for the toxic dinoflagellate Dinophysis.

ABSTRACT: Species within the dinoflagellate genus Dinophysis can produce okadiac acid and dinophysistoxins leading to diarrhetic shellfish poisoning. Since the first report of D. ovum from the Gulf of Mexico in 2008, reports of other Dinophysis species across US have increased. Members of the D. cf. acuminata complex (D. acuminata, D. acuta, D. ovum, D. sacculus) are difficult to differentiate due to their morphological similarities. Dinophysis feeds on and steals the chloroplasts from the ciliate, Mesodinium rubrum, which in turn has fed on and captured the chloroplasts of its prey, the cryptophyte Teleaulax amphioxeia. The objective of this study was to generate de novo transcriptomes for new isolates of these mixotrophic organisms. The transcriptomes obtained will serve as a reference for future experiments to assess the effect of different abiotic and biotic conditions and will also provide a useful resource for screening potential marker genes to differentiate among the closely related species within the D. cf. acuminata-complex. The complete comprehensive detailed workflow and links to obtain the transcriptome data are provided.

SUBMITTER: Gaonkar CC

PROVIDER: S-EPMC10238436 | biostudies-literature | 2023 Jun

REPOSITORIES: biostudies-literature

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De novo transcriptome assembly and gene annotation for the toxic dinoflagellate Dinophysis.

Gaonkar Chetan C CC Campbell Lisa L

Scientific data 20230602 1

Species within the dinoflagellate genus Dinophysis can produce okadiac acid and dinophysistoxins leading to diarrhetic shellfish poisoning. Since the first report of D. ovum from the Gulf of Mexico in 2008, reports of other Dinophysis species across US have increased. Members of the D. cf. acuminata complex (D. acuminata, D. acuta, D. ovum, D. sacculus) are difficult to differentiate due to their morphological similarities. Dinophysis feeds on and steals the chloroplasts from the ciliate, Mesodi ...[more]

PMID: 37268695

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Project description:BackgroundKarenia brevis is a harmful algal species that blooms in the Gulf of Mexico and produces brevetoxins that cause neurotoxic shellfish poisoning. Elevated brevetoxin levels in K. brevis cells have been measured during laboratory hypo-osmotic stress treatments. To investigate mechanisms underlying K. brevis osmoacclimation and osmoregulation and establish a valuable resource for gene discovery, we assembled reference transcriptomes for three clones: Wilson-CCFWC268, SP3, and SP1 (a low-toxin producing variant). K. brevis transcriptomes were annotated with gene ontology terms and searched for putative transmembrane proteins that may elucidate cellular responses to hypo-osmotic stress. An analysis of single nucleotide polymorphisms among clones was used to characterize genetic divergence.ResultsK. brevis reference transcriptomes were assembled with 58.5 (Wilson), 78.0 (SP1), and 51.4 million (SP3) paired reads. Transcriptomes contained 86,580 (Wilson), 93,668 (SP1), and 84,309 (SP3) predicted transcripts. Approximately 40% of the transcripts were homologous to proteins in the BLAST nr database with an E value ≤ 1.00E-6. Greater than 80% of the highly conserved CEGMA core eukaryotic genes were identified in each transcriptome, which supports assembly completeness. Seven putative voltage-gated Na+ or Ca2+ channels, two aquaporin-like proteins, and twelve putative VATPase subunits were discovered in all clones using multiple bioinformatics approaches. Furthermore, 45% (Wilson) and 43% (SP1 and SP3) of the K. brevis putative peptides > 100 amino acids long produced significant hits to a sequence in the NCBI nr protein database. Of these, 77% (Wilson and SP1) and 73% (SP3) were successfully assigned gene ontology functional terms. The predicted single nucleotide polymorphism (SNP) frequencies between clones were 0.0028 (Wilson to SP1), 0.0030 (Wilson to SP3), and 0.0028 (SP1 to SP3).ConclusionsThe K. brevis transcriptomes assembled here provide a foundational resource for gene discovery and future RNA-seq experiments. The identification of ion channels, VATPases, and aquaporins in all three transcriptomes indicates that K. brevis regulates cellular ion and water concentrations via transmembrane proteins. Additionally, > 40,000 unannotated loci may include potentially novel K. brevis genes. Ultimately, the SNPs identified among the three ecologically diverse clones with different toxin profiles may help to elucidate variations in K. brevis brevetoxin production.

Project description:BackgroundSainfoin (Onobrychis viciifolia) is a highly nutritious tannin-containing forage legume. In the diet of ruminants sainfoin can have anti-parasitic effects and reduce methane emissions under in vitro conditions. Many of these benefits have been attributed to condensed tannins or proanthocyanidins in sainfoin. A combination of increased use of industrially produced nitrogen fertilizer, issues with establishment and productivity in the first year and more reliable alternatives, such as red clover led to a decline in the use of sainfoin since the middle of the last century. In recent years there has been a resurgence of interest in sainfoin due to its potential beneficial nutraceutical and environmental attributes. However, genomic resources are scarce, thus hampering progress in genetic analysis and improvement. To address this we have used next generation RNA sequencing technology to obtain the first transcriptome of sainfoin. We used the library to identify gene-based simple sequence repeats (SSRs) and potential single nucleotide polymorphisms (SNPs).ResultsOne genotype from each of five sainfoin accessions was sequenced. Paired-end (PE) sequences were generated from cDNA libraries of RNA extracted from 7 day old seedlings. A combined assembly of 92,772 transcripts was produced de novo using the Trinity programme. About 18,000 transcripts were annotated with at least one GO (gene ontology) term. A total of 63 transcripts were annotated as involved in the tannin biosynthesis pathway. We identified 3786 potential SSRs. SNPs were identified by mapping the reads of the individual assemblies against the combined assembly. After stringent filtering a total of 77,000 putative SNPs were identified. A phylogenetic analysis of single copy number genes showed that sainfoin was most closely related to red clover and Medicago truncatula, while Lotus japonicus, bean and soybean are more distant relatives.ConclusionsThis work describes the first transcriptome assembly in sainfoin. The 92 K transcripts provide a rich source of SNP and SSR polymorphisms for future use in genetic studies of this crop. Annotation of genes involved in the condensed tannin biosynthesis pathway has provided the basis for further studies of the genetic control of this important trait in sainfoin.

Dataset Information

De novo transcriptome assembly and gene annotation for the toxic dinoflagellate Dinophysis.

Publications

De novo transcriptome assembly and gene annotation for the toxic dinoflagellate Dinophysis.

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