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Coral life history and symbiosis: functional genomic resources for two reef building Caribbean corals, Acropora palmata and Montastraea faveolata.

Schwarz JA, Brokstein PB, Voolstra C, Terry AY, Manohar CF, Miller DJ, Szmant AM, Coffroth MA, Medina M - BMC Genomics (2008)

Bottom Line: Scleractinian corals are the foundation of reef ecosystems in tropical marine environments.To develop a foundation for studying coral biology and coral symbiosis, we have constructed a set of cDNA libraries and generated and annotated ESTs from two species of corals, Acropora palmata and Montastraea faveolata.Partial sequencing of 5 cDNA libraries each for A. palmata and M. faveolata has produced a rich set of candidate genes (4,980 genes from A. palmata, and 1,732 genes from M. faveolata) that we can use as a starting point for examining the life history and symbiosis of these two species, as well as to further expand the dataset of cnidarian genes for comparative genomics and evolutionary studies.

View Article: PubMed Central - HTML - PubMed

Affiliation: Biology Department, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA. joschwarz@vassar.edu

ABSTRACT

Background: Scleractinian corals are the foundation of reef ecosystems in tropical marine environments. Their great success is due to interactions with endosymbiotic dinoflagellates (Symbiodinium spp.), with which they are obligately symbiotic. To develop a foundation for studying coral biology and coral symbiosis, we have constructed a set of cDNA libraries and generated and annotated ESTs from two species of corals, Acropora palmata and Montastraea faveolata.

Results: We generated 14,588 (Ap) and 3,854 (Mf) high quality ESTs from five life history/symbiosis stages (spawned eggs, early-stage planula larvae, late-stage planula larvae either infected with symbionts or uninfected, and adult coral). The ESTs assembled into a set of primarily stage-specific clusters, producing 4,980 (Ap), and 1,732 (Mf) unigenes. The egg stage library, relative to the other developmental stages, was enriched in genes functioning in cell division and proliferation, transcription, signal transduction, and regulation of protein function. Fifteen unigenes were identified as candidate symbiosis-related genes as they were expressed in all libraries constructed from the symbiotic stages and were absent from all of the non symbiotic stages. These include several DNA interacting proteins, and one highly expressed unigene (containing 17 cDNAs) with no significant protein-coding region. A significant number of unigenes (25) encode potential pattern recognition receptors (lectins, scavenger receptors, and others), as well as genes that may function in signaling pathways involved in innate immune responses (toll-like signaling, NFkB p105, and MAP kinases). Comparison between the A. palmata and an A. millepora EST dataset identified ferritin as a highly expressed gene in both datasets that appears to be undergoing adaptive evolution. Five unigenes appear to be restricted to the Scleractinia, as they had no homology to any sequences in the nr databases nor to the non-scleractinian cnidarians Nematostella vectensis and Hydra magnipapillata.

Conclusion: Partial sequencing of 5 cDNA libraries each for A. palmata and M. faveolata has produced a rich set of candidate genes (4,980 genes from A. palmata, and 1,732 genes from M. faveolata) that we can use as a starting point for examining the life history and symbiosis of these two species, as well as to further expand the dataset of cnidarian genes for comparative genomics and evolutionary studies.

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Amino acid alignments ferritin type I and type II from A. palmata, A. millepora, and N. vectensis with mouse H ferritin. Residues associated with the metal-binding site are written in uppercase bold. Tyr30, Tyr 33 and Tyr 35 that make up the ferroxidase center and Glu63 and His66 that play a role in polynuclear Fe-complex formation are uppercase bold and underlined. Tyr30 is specific for H ferritin in vertebrates [34,35]. Positively selected sites by a BEB procedure are lowercase bold, respectively lowercase bold and underlined if posterior probability of being in positively selected class > 0.5. Numbering is that of the mouse H chain sequence. Apal_Fer1: A. palmata ferritin type I, Amil_Fer1: A. millepora ferritin type I, Nv_Fer1: N. vectensis ferritin type I, Apal_Fer2: A. palmata ferritin type II, Amil_Fer2: A. millepora ferritin type II, Nv_Fer2: N. vectensis ferritin type II, MusFth1: mouse ferritin H chain.
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Figure 5: Amino acid alignments ferritin type I and type II from A. palmata, A. millepora, and N. vectensis with mouse H ferritin. Residues associated with the metal-binding site are written in uppercase bold. Tyr30, Tyr 33 and Tyr 35 that make up the ferroxidase center and Glu63 and His66 that play a role in polynuclear Fe-complex formation are uppercase bold and underlined. Tyr30 is specific for H ferritin in vertebrates [34,35]. Positively selected sites by a BEB procedure are lowercase bold, respectively lowercase bold and underlined if posterior probability of being in positively selected class > 0.5. Numbering is that of the mouse H chain sequence. Apal_Fer1: A. palmata ferritin type I, Amil_Fer1: A. millepora ferritin type I, Nv_Fer1: N. vectensis ferritin type I, Apal_Fer2: A. palmata ferritin type II, Amil_Fer2: A. millepora ferritin type II, Nv_Fer2: N. vectensis ferritin type II, MusFth1: mouse ferritin H chain.

Mentions: We compared some of the most highly expressed genes in the A. palmata dataset with an EST dataset from Acropora millepora. Two different types of ferritins (referred to as ferritin type I and type II) were identified and that are highly expressed in both species. To differentiate the amino acids that are under positive selection, we identified homologues for both types of ferritin in the Nematostella vectensis database and carried out a site-specific analysis. Figure 5 illustrates alignments of the cnidarian ferritins to mouse ferritin, showing the amino acids predicted to be undergoing positive selection. The overall dN/dS value for the A. palmata and A. millepora EST sequence is ω = 1.0360 (dN= 0.0853, dS= 0.0823) for ferritin type I, and ω = 0.0799 (dN= 0.0093, dS= 0.1167) for ferritin type II. The dN/dS value for ferritin type I is unusually high and indicative of adaptive evolution. To differentiate the amino acids that are under positive selection, we identified homologues for both types of ferritin in the Nematostella vectensis database and carried out a site-specific analysis (Figure 5).


Coral life history and symbiosis: functional genomic resources for two reef building Caribbean corals, Acropora palmata and Montastraea faveolata.

Schwarz JA, Brokstein PB, Voolstra C, Terry AY, Manohar CF, Miller DJ, Szmant AM, Coffroth MA, Medina M - BMC Genomics (2008)

Amino acid alignments ferritin type I and type II from A. palmata, A. millepora, and N. vectensis with mouse H ferritin. Residues associated with the metal-binding site are written in uppercase bold. Tyr30, Tyr 33 and Tyr 35 that make up the ferroxidase center and Glu63 and His66 that play a role in polynuclear Fe-complex formation are uppercase bold and underlined. Tyr30 is specific for H ferritin in vertebrates [34,35]. Positively selected sites by a BEB procedure are lowercase bold, respectively lowercase bold and underlined if posterior probability of being in positively selected class > 0.5. Numbering is that of the mouse H chain sequence. Apal_Fer1: A. palmata ferritin type I, Amil_Fer1: A. millepora ferritin type I, Nv_Fer1: N. vectensis ferritin type I, Apal_Fer2: A. palmata ferritin type II, Amil_Fer2: A. millepora ferritin type II, Nv_Fer2: N. vectensis ferritin type II, MusFth1: mouse ferritin H chain.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC2291459&req=5

Figure 5: Amino acid alignments ferritin type I and type II from A. palmata, A. millepora, and N. vectensis with mouse H ferritin. Residues associated with the metal-binding site are written in uppercase bold. Tyr30, Tyr 33 and Tyr 35 that make up the ferroxidase center and Glu63 and His66 that play a role in polynuclear Fe-complex formation are uppercase bold and underlined. Tyr30 is specific for H ferritin in vertebrates [34,35]. Positively selected sites by a BEB procedure are lowercase bold, respectively lowercase bold and underlined if posterior probability of being in positively selected class > 0.5. Numbering is that of the mouse H chain sequence. Apal_Fer1: A. palmata ferritin type I, Amil_Fer1: A. millepora ferritin type I, Nv_Fer1: N. vectensis ferritin type I, Apal_Fer2: A. palmata ferritin type II, Amil_Fer2: A. millepora ferritin type II, Nv_Fer2: N. vectensis ferritin type II, MusFth1: mouse ferritin H chain.
Mentions: We compared some of the most highly expressed genes in the A. palmata dataset with an EST dataset from Acropora millepora. Two different types of ferritins (referred to as ferritin type I and type II) were identified and that are highly expressed in both species. To differentiate the amino acids that are under positive selection, we identified homologues for both types of ferritin in the Nematostella vectensis database and carried out a site-specific analysis. Figure 5 illustrates alignments of the cnidarian ferritins to mouse ferritin, showing the amino acids predicted to be undergoing positive selection. The overall dN/dS value for the A. palmata and A. millepora EST sequence is ω = 1.0360 (dN= 0.0853, dS= 0.0823) for ferritin type I, and ω = 0.0799 (dN= 0.0093, dS= 0.1167) for ferritin type II. The dN/dS value for ferritin type I is unusually high and indicative of adaptive evolution. To differentiate the amino acids that are under positive selection, we identified homologues for both types of ferritin in the Nematostella vectensis database and carried out a site-specific analysis (Figure 5).

Bottom Line: Scleractinian corals are the foundation of reef ecosystems in tropical marine environments.To develop a foundation for studying coral biology and coral symbiosis, we have constructed a set of cDNA libraries and generated and annotated ESTs from two species of corals, Acropora palmata and Montastraea faveolata.Partial sequencing of 5 cDNA libraries each for A. palmata and M. faveolata has produced a rich set of candidate genes (4,980 genes from A. palmata, and 1,732 genes from M. faveolata) that we can use as a starting point for examining the life history and symbiosis of these two species, as well as to further expand the dataset of cnidarian genes for comparative genomics and evolutionary studies.

View Article: PubMed Central - HTML - PubMed

Affiliation: Biology Department, Vassar College, 124 Raymond Avenue, Poughkeepsie, NY 12604, USA. joschwarz@vassar.edu

ABSTRACT

Background: Scleractinian corals are the foundation of reef ecosystems in tropical marine environments. Their great success is due to interactions with endosymbiotic dinoflagellates (Symbiodinium spp.), with which they are obligately symbiotic. To develop a foundation for studying coral biology and coral symbiosis, we have constructed a set of cDNA libraries and generated and annotated ESTs from two species of corals, Acropora palmata and Montastraea faveolata.

Results: We generated 14,588 (Ap) and 3,854 (Mf) high quality ESTs from five life history/symbiosis stages (spawned eggs, early-stage planula larvae, late-stage planula larvae either infected with symbionts or uninfected, and adult coral). The ESTs assembled into a set of primarily stage-specific clusters, producing 4,980 (Ap), and 1,732 (Mf) unigenes. The egg stage library, relative to the other developmental stages, was enriched in genes functioning in cell division and proliferation, transcription, signal transduction, and regulation of protein function. Fifteen unigenes were identified as candidate symbiosis-related genes as they were expressed in all libraries constructed from the symbiotic stages and were absent from all of the non symbiotic stages. These include several DNA interacting proteins, and one highly expressed unigene (containing 17 cDNAs) with no significant protein-coding region. A significant number of unigenes (25) encode potential pattern recognition receptors (lectins, scavenger receptors, and others), as well as genes that may function in signaling pathways involved in innate immune responses (toll-like signaling, NFkB p105, and MAP kinases). Comparison between the A. palmata and an A. millepora EST dataset identified ferritin as a highly expressed gene in both datasets that appears to be undergoing adaptive evolution. Five unigenes appear to be restricted to the Scleractinia, as they had no homology to any sequences in the nr databases nor to the non-scleractinian cnidarians Nematostella vectensis and Hydra magnipapillata.

Conclusion: Partial sequencing of 5 cDNA libraries each for A. palmata and M. faveolata has produced a rich set of candidate genes (4,980 genes from A. palmata, and 1,732 genes from M. faveolata) that we can use as a starting point for examining the life history and symbiosis of these two species, as well as to further expand the dataset of cnidarian genes for comparative genomics and evolutionary studies.

Show MeSH
Related in: MedlinePlus