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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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ESTs from A. palmata and M. faveolata form stage-specific clusters (unigenes). From the total set of ESTs from each species, over 92% (Ap) and 97% (Mf) of clusters contain ESTs from a single life history stage.
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Figure 2: ESTs from A. palmata and M. faveolata form stage-specific clusters (unigenes). From the total set of ESTs from each species, over 92% (Ap) and 97% (Mf) of clusters contain ESTs from a single life history stage.

Mentions: Only a small number of unigenes are found in more than one library (i.e. they are stage specific) (Figure 2). We annotated the unigene set by assigning putative identities based on blastx hits to nr, swissprot and GO databases (Table 1). A significant portion of the library had no putative identities. Of the unigenes with no blast hits, we searched for open reading frames encoding at least 100 amino acids beginning with an ATG start codon. From 3,654 unigenes in A. palmata, we found 665 ORFs. From 1,732 unigenes identified from M. faveolata, we identified 160 ORFs. Since secreted proteins are likely targets in setting the stage for the initial host-symbiont cell contact, we searched for potential secretory signals of these unigenes using SignalP [30]. For A. palmata we identified 97 and 111 predicted signal peptides for M. faveolata we identified 22 and 28 predicted signal peptides based on 2 different methods (Hidden Markov Model and Neural Network algorithm), thus providing a starting set of genes of the "secretome" of the symbiosis.


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)

ESTs from A. palmata and M. faveolata form stage-specific clusters (unigenes). From the total set of ESTs from each species, over 92% (Ap) and 97% (Mf) of clusters contain ESTs from a single life history stage.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: ESTs from A. palmata and M. faveolata form stage-specific clusters (unigenes). From the total set of ESTs from each species, over 92% (Ap) and 97% (Mf) of clusters contain ESTs from a single life history stage.
Mentions: Only a small number of unigenes are found in more than one library (i.e. they are stage specific) (Figure 2). We annotated the unigene set by assigning putative identities based on blastx hits to nr, swissprot and GO databases (Table 1). A significant portion of the library had no putative identities. Of the unigenes with no blast hits, we searched for open reading frames encoding at least 100 amino acids beginning with an ATG start codon. From 3,654 unigenes in A. palmata, we found 665 ORFs. From 1,732 unigenes identified from M. faveolata, we identified 160 ORFs. Since secreted proteins are likely targets in setting the stage for the initial host-symbiont cell contact, we searched for potential secretory signals of these unigenes using SignalP [30]. For A. palmata we identified 97 and 111 predicted signal peptides for M. faveolata we identified 22 and 28 predicted signal peptides based on 2 different methods (Hidden Markov Model and Neural Network algorithm), thus providing a starting set of genes of the "secretome" of the symbiosis.

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