Insights into the innate immunome of actiniarians using a comparative genomic approach

Burg, Chloé A. van der; Prentis, Peter J.; Surm, Joachim M.; Pavasovic, Ana

doi:10.1186/s12864-016-3204-2

Cited by 49 publications

(43 citation statements)

References 68 publications

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“…Furthermore, these genes involved in the synthesis of omega‐3 LC‐PUFAs were investigated in six candidate actiniarian species with sequenced transcriptomes. These species include A. tenebrosa (four ecotypes: blue, brown, green, and red), Anthopleura buddemeieri , Aulactinia veratra , Calliactis polypus , Telmatactis sp., and Nemanthus annamensis from the NCBI Bioproject: PRJNA313244 (van der Burg, Prentis, Surm, & Pavasovic, 2016). All transcriptomic data were generated from either whole organism or multiple tissue types.…”

Section: Methodsmentioning

confidence: 99%

Insights into the phylogenetic and molecular evolutionary histories of Fad and Elovl gene families in Actiniaria

Surm

Toledo

Prentis

et al. 2018

Ecology and Evolution

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The biosynthesis of long‐chain polyunsaturated fatty acids (LC‐PUFAs, ≥ C20) is reliant on the action of desaturase and elongase enzymes, which are encoded by the fatty acyl desaturase (Fad) and elongation of very long‐chain fatty acid (Elovl) gene families, respectively. In Metazoa, research investigating the distribution and evolution of these gene families has been restricted largely to Bilateria. Here, we provide insights into the phylogenetic and molecular evolutionary histories of the Fad and Elovl gene families in Cnidaria, the sister phylum to Bilateria. Four model cnidarian genomes and six actiniarian transcriptomes were interrogated. Analysis of the fatty acid composition of a candidate cnidarian species, Actinia tenebrosa, was performed to determine the baseline profile of this species. Phylogenetic analysis revealed lineage‐specific gene duplication in actiniarians for both the Fad and Elovl gene families. Two distinct cnidarian Fad clades clustered with functionally characterized Δ5 and Δ6 proteins from fungal and plant species, respectively. Alternatively, only a single cnidarian Elovl clade clustered with functionally characterized Elovl proteins (Elovl4), while two additional clades were identified, one actiniarian‐specific (Novel ElovlA) and the another cnidarian‐specific (Novel ElovlB). In actiniarians, selection analyses revealed pervasive purifying selection acting on both gene families. However, codons in the Elovl gene family show patterns of nucleotide variation consistent with the action of episodic diversifying selection following gene duplication events. Significantly, these codons may encode amino acid residues that are functionally important for Elovl proteins to target and elongate different precursor fatty acids. In A. tenebrosa, the fatty acid analysis revealed an absence of LC‐PUFAs > C20 molecules and implies that the Elovl enzymes are not actively contributing to the elongation of these LC‐PUFAs. Overall, this study has revealed that actiniarians possess Fad and Elovl genes required for the biosynthesis of some LC‐PUFAs, and that these genes appear to be distinct from bilaterians.

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Section: Methodsmentioning

confidence: 99%

Insights into the phylogenetic and molecular evolutionary histories of Fad and Elovl gene families in Actiniaria

Surm

Toledo

Prentis

et al. 2018

Ecology and Evolution

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“…The ab initio gene model prediction identified 31,556 protein-coding genes in A. tenebrosa. All gene models were validated, receiving significant BLAST hits against multiple A. tenebrosa transcriptomes (van der Burg et al, 2016). Our ab initio gene model prediction was highly complete compared with other cnidarian genomes, increasing the previous BUSCO score to 94.6% (Table 1).…”

Section: Functional Annotation Of Predicted Gene Modelsmentioning

confidence: 92%

“…These reads included the Red and Brown ecotypes obtained from NCBI (Bioproject PRJNA313244; van der Burg, Prentis, Surm, & Pavasovic, 2016). These reads included the Red and Brown ecotypes obtained from NCBI (Bioproject PRJNA313244; van der Burg, Prentis, Surm, & Pavasovic, 2016).…”

Section: Gene Model Prediction and Annotationmentioning

confidence: 99%

“…Following the masking of repeat regions, gene models were predicted using ab initio methods guided by transcriptional expression. These reads included the Red and Brown ecotypes obtained from NCBI (Bioproject PRJNA313244; van der Burg, Prentis, Surm, & Pavasovic, 2016). Raw reads were quality trimmed using Trimmomatic (Bolger, Lohse, & Usadel, 2014) with parameters used by the Trinity de novo assembler (Haas et al, 2013;MacManes, 2014).…”

Section: Gene Model Prediction and Annotationmentioning

confidence: 99%

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The draft genome of Actinia tenebrosa reveals insights into toxin evolution

Surm

Stewart

Papanicolaou

et al. 2019

Ecology and Evolution

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Sea anemones have a wide array of toxic compounds (peptide toxins found in their venom) which have potential uses as therapeutics. To date, the majority of studies characterizing toxins in sea anemones have been restricted to species from the superfamily, Actinioidea. No highly complete draft genomes are currently available for this superfamily, however, highlighting our limited understanding of the genes encoding toxins in this important group. Here we have sequenced, assembled, and annotated a draft genome for Actinia tenebrosa. The genome is estimated to be approximately 255 megabases, with 31,556 protein‐coding genes. Quality metrics revealed that this draft genome matches the quality and completeness of other model cnidarian genomes, including Nematostella, Hydra, and Acropora. Phylogenomic analyses revealed strong conservation of the Cnidaria and Hexacorallia core‐gene set. However, we found that lineage‐specific gene families have undergone significant expansion events compared with shared gene families. Enrichment analysis performed for both gene ontologies, and protein domains revealed that genes encoding toxins contribute to a significant proportion of the lineage‐specific genes and gene families. The results make clear that the draft genome of A. tenebrosa will provide insight into the evolution of toxins and lineage‐specific genes, and provide an important resource for the discovery of novel biological compounds.

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“…All results were uploaded to the SQLite database and an annotation report was generated. Adapted from van der Burg et al (2016) …”

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confidence: 99%

Characterisation of Duplicated Haemoglobin Genes in Bivalves

Klein¹

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Haemoglobins (Hbs) are found in virtually all phyla and are some of the most investigated proteins in biomedical sciences. These proteins exhibit an extraordinary diversity of form and function in invertebrate lineages. This provides a unique opportunity to explore the origin and evolution of Hbs yet little is known about their distribution, function and evolution in invertebrate lineages. To explore further the functions and evolution of those Hbs, recent transcriptome data for the Arcid bivalve Anadara trapezia is investigated here. This species shows the presence of duplicated Hb encoding genes suggesting that gene duplication may have been more extensive than previously thought in bivalves. This study tests the hypothesis that these duplicated genes show patterns of tissue specific expression and evidence of neofunctionalisation. This is shown here for at least three Hb encoding genes present in A. trapezia with strong tissue specific expression in haemolymph compared to other tissues. Furthermore, the expression of these genes remains unaffected by prolonged air exposure suggesting that neofunctionalisation may confer an evolutionary advantage to this bivalve. As well as the unique Hbs found in the bivalve order Arcoida, Hbs are also found in three other bivalve orders: Carditoida, Solemyoida and Veneroida. These four orders that possess Hbs provide compelling evidence for the independent evolution of these proteins in multiple bivalve lineages.To expand data on the distribution of Hbs in bivalves, a transcriptome sequence for Ctenoides ales in the order Limoida was generated in this project. Interrogation of the transcriptome shows the presence of at least three globin-like encoding genes including two Hb-like encoding genes providing preliminary evidence for another independent origin of Hb in a bivalve lineage. Overall, this study provides novel insights into the function, evolution and distribution of Hbs in bivalves by investigating two distantly related species. Results of this study are consistent with current theories that Hb diversity in bivalves is a result of repeated rounds of gene duplication providing the raw material for evolution. Investigation of hypoxic resistance also reinforces that greater expression of Hbs in haemolymph confers a physiological advantage suggesting that Hb would evolve more often in some lineages during adaptation to unfavourable environment conditions, particularlyAbstract ii hypoxia and prolonged air exposure.The finding of Hb-like encoding genes in another bivalve lineage also supports the evolution of this gene family through independent evolution and gene duplication, and gives insight into the distribution of globin genes in bivalves which is still poorly understood. The investigation of Hb genes in these bivalves also contributes to further understand the role of Hbs and provides potential novel insights for resistance in hypoxic environments, disease control and resistance to pollution in aquaculture.Abstract iii

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Insights into the innate immunome of actiniarians using a comparative genomic approach

Cited by 49 publications

References 68 publications

Insights into the phylogenetic and molecular evolutionary histories of Fad and Elovl gene families in Actiniaria

Insights into the phylogenetic and molecular evolutionary histories of Fad and Elovl gene families in Actiniaria

The draft genome of Actinia tenebrosa reveals insights into toxin evolution

Characterisation of Duplicated Haemoglobin Genes in Bivalves

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