Development of Gene Expression Markers of Acute Heat-Light Stress in Reef-Building Corals of the Genus Porites

Coral reefs are declining worldwide due to increased incidence of climate-induced coral bleaching, which will have widespread biodiversity and economic impacts. A simple method to measure the sub-bleaching level of heat-light stress experienced by corals would greatly inform reef management practices by making it possible to assess the distribution of bleaching risks among individual reef sites. Gene expression analysis based on quantitative PCR (qPCR) can be used as a diagnostic tool to determine coral condition in situ. We evaluated the expression of 13 candidate genes during heat-light stress in a common Caribbean coral Porites astreoides, and observed strong and consistent changes in gene expression in two independent experiments. Furthermore, we found that the apparent return to baseline expression levels during a recovery phase was rapid, despite visible signs of colony bleaching. We show that the response to acute heat-light stress in P. astreoides can be monitored by measuring the difference in expression of only two genes: Hsp16 and actin. We demonstrate that this assay discriminates between corals sampled from two field sites experiencing different temperatures. We also show that the assay is applicable to an Indo-Pacific congener, P. lobata, and therefore could potentially be used to diagnose acute heat-light stress on coral reefs worldwide

Extensive mitochondrial gene rearrangements in Ctenophora: insights from benthic Platyctenida

BACKGROUND: Complete mitochondrial (mt) genomes have been sequenced for thousands of animals and represent a molecule of choice for many evolutionary studies. Nevertheless, some animal groups have remained under-sampled. Ctenophora (comb jellies) is one such example, with only two complete mt sequences determined hitherto for this phylum, which encompasses ca. 150-200 described species. This lack of data derives from the extremely fast mt evolutionary rate in this lineage, complicating primer design and DNA amplification. Indeed, in the two ctenophore mt genomes sequenced to date, i.e. those of Mnemiopsis leidyi (order Lobata) and Pleurobrachia bachei (order Cydippida), both rRNA and protein coding genes exhibit an extraordinary size reduction and have highly derived sequences. Additionally, all tRNAs, and the atp6 and atp8 genes are absent. In order to determine whether these characteristics are shared by other ctenophores, we obtained the complete mt genomes of three benthic ctenophores belonging to the so far unsampled order of Platyctenida: Coeloplana loyai, Coeloplana yulianicorum and Vallicula multiformis. RESULTS: The mt genomes of benthic ctenophores reveal the same peculiarities found in Mnemiopsis and Pleurobrachia, demonstrating that the fast evolutionary rate is a general trait of the ctenophore mt genomes. Our results also indicate that this high evolutionary rate not only affects the nucleotide substitution but also gene rearrangements. Indeed, gene order was highly rearranged among representatives of the different taxonomic orders in which it was close to random, but also quite variable within Platyctenida, in which the genera Coeloplana and Vallicula share only four conserved synteny blocks. However, the two congeneric Coeloplana species display exactly the same gene order. Because of the extreme evolutionary rate, our phylogenetic analyses were unable to resolve the phylogenetic position of ctenophores within metazoans or the relationships among the different Ctenophora orders. Comparative sequence-analyses allowed us to correct the annotation of the Pleurobrachia mt genome, confirming the absence of tRNAs, the presence of both rRNA genes, and the existence of a reassignment of codon TGA from tryptophan to serine for this species. CONCLUSIONS: Since Platyctenida is an early diverging lineage among Ctenophora, our findings suggest that the mt traits described above are ancestral characteristics of this phylum

Additional file 5: of Extensive mitochondrial gene rearrangements in Ctenophora: insights from benthic Platyctenida

Alignment of the rnl sequences of ctenophores. (DOCX 937 kb

Additional file 1: of Extensive mitochondrial gene rearrangements in Ctenophora: insights from benthic Platyctenida

Comparison between annotation of the mt genome of Pleurobrachia bachei (accession JN392469) [18] and the re-annotation performed in the current work. (PPT 224 kb

Additional file 3: of Extensive mitochondrial gene rearrangements in Ctenophora: insights from benthic Platyctenida

Reannotation of the mt genome of Pleurobrachia bachei. Flatfile in Genbank format. (TXT 26 kb

Additional file 4: of Extensive mitochondrial gene rearrangements in Ctenophora: insights from benthic Platyctenida

Codon usage of Ctenophora species. (XLSX 29 kb

Additional file 7: of Extensive mitochondrial gene rearrangements in Ctenophora: insights from benthic Platyctenida

Sequence alignment file used in the phylogenetic analyses. DNA sequence alignment, in Nexus format, used to reconstruct the phylogenetic tree present in Fig. 3. (NEX 193 kb

Additional file 6: of Extensive mitochondrial gene rearrangements in Ctenophora: insights from benthic Platyctenida

Alignment of the rns sequences of ctenophores. (DOCX 584 kb

Development of gene expression markers of acute heat-light stress in reef-building corals of the genus porites

Coral reefs are declining worldwide due to increased incidence of climate-induced coral bleaching, which will have widespread biodiversity and economic impacts. A simple method to measure the sub-bleaching level of heat-light stress experienced by corals would greatly inform reef management practices by making it possible to assess the distribution of bleaching risks among individual reef sites. Gene expression analysis based on quantitative PCR (qPCR) can be used as a diagnostic tool to determine coral condition in situ. We evaluated the expression of 13 candidate genes during heat-light stress in a common Caribbean coral Porites astreoides, and observed strong and consistent changes in gene expression in two independent experiments. Furthermore, we found that the apparent return to baseline expression levels during a recovery phase was rapid, despite visible signs of colony bleaching. We show that the response to acute heat-light stress in P. astreoides can be monitored by measuring the difference in expression of only two genes: Hsp16 and actin. We demonstrate that this assay discriminates between corals sampled from two field sites experiencing different temperatures. We also show that the assay is applicable to an Indo-Pacific congener, P. lobata, and therefore could potentially be used to diagnose acute heat-light stress on coral reefs worldwide.National Science Foundation grant DEB-1054766 to MVM; Title V-Graduate programs/ELITE Graduate program: Event Travel Request program to LBS and JAH; Environmental Protection Agency Greater Research Opportunity Graduate Fellowship to KAK (MA-91697601); WIOMSA MARG III to PHM and RB; Aharon Katzir-Katchalsky Student Travel Fellowships and Anat Krauskopf Fund Travel Award to AA; NSF IOS-0747205 and funding from the University of Mississippi ORSP to TLG; Grants from both the National Science Council and Academia Sinica, Taiwan to KS; NSF GRF to RNS; Natural Environmental Research Council (NERC) studentship to CVP. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript