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Comparative genomics explains the evolutionary success of reef-forming corals

Published on May 24, 2016in eLife 7.55
· DOI :10.7554/eLife.13288
Debashish Bhattacharya64
Estimated H-index: 64
(RU: Rutgers University),
Shobhit Agrawal3
Estimated H-index: 3
(KAUST: King Abdullah University of Science and Technology)
+ 32 AuthorsPaul G. Falkowski107
Estimated H-index: 107
(RU: Rutgers University)
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Abstract
For millions of years, reef-building stony corals have created extensive habitats for numerous marine plants and animals in shallow tropical seas. Stony corals consist of many small, tentacled animals called polyps. These polyps secrete a mineral called aragonite to create the reef – an external ‘skeleton’ that supports and protects the corals. Photosynthesizing algae live inside the cells of stony corals, and each species depends on the other to survive. The algae produce the coral’s main source of food, although they also produce some waste products that can harm the coral if they build up inside cells. If the oceans become warmer and more acidic, the coral are more likely to become stressed and expel the algae from their cells in a process known as coral bleaching. This makes the coral more likely to die or become diseased. Corals have survived previous periods of ocean warming, although it is not known how they evolved to do so. The evolutionary history of an organism can be traced by studying its genome – its complete set of DNA – and the RNA molecules encoded by these genes. Bhattacharya et al. performed this analysis for twenty stony coral species, and compared the resulting genome and RNA sequences with the genomes of other related marine organisms, such as sea anemones and sponges. In particular, Bhattacharya et al. examined “ortholog” groups of genes, which are present in different species and evolved from a common ancestral gene. This analysis identified the genes in the corals that encode the proteins responsible for constructing the aragonite skeleton. The coral genome also encodes a network of environmental sensors that coordinate how the polyps respond to temperature, light and acidity. Bhattacharya et al. also uncovered a variety of stress-related pathways, including those that detoxify the polyps of the damaging molecules generated by algae, and the pathways that enable the polyps to adapt to environmental stress. Many of these genes were recruited from other species in a process known as horizontal gene transfer. The oceans are expected to become warmer and more acidic in the coming centuries. Provided that humans do not physically destroy the corals’ habitats, the evidence found by Bhattacharya et al. suggests that the genome of the corals contains the diversity that will allow them to adapt to these new conditions.
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  • Citations (63)
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References114
Newest
Published on Sep 1, 2015in Scientific Reports 4.01
Didier Zoccola30
Estimated H-index: 30
,
Philippe Ganot7
Estimated H-index: 7
+ 8 AuthorsJoseph R Casey1
Estimated H-index: 1
Bicarbonate transporters in corals point towards a key step in the evolution of cnidarian calcification
58 Citations Source Cite
Published on Aug 1, 2015in Journal of Phycology 2.83
Huan Qiu18
Estimated H-index: 18
(RU: Rutgers University),
Dana C. Price19
Estimated H-index: 19
(RU: Rutgers University)
+ 2 AuthorsDebashish Bhattacharya64
Estimated H-index: 64
(RU: Rutgers University)
Red algae (Rhodophyta) comprise a monophyletic eukaryotic lineage of ~6,500 species with a fossil record that extends back 1.2 billion years. A surprising aspect of red algal evolution is that sequenced genomes encode a relatively limited gene inventory (~5-10 thousand genes) when compared with other free-living algae or to other eukaryotes. This suggests that the common ancestor of red algae may have undergone extensive genome reduction, which can result from lineage specialization to a symbiot...
23 Citations Source Cite
Published on Jul 1, 2015in Neuropharmacology 4.37
O. A. Krishtal29
Estimated H-index: 29
Abstract The history of ASICs began in 1980 with unexpected observation. The concept of highly selective Na + current gated by specific receptors for protons was not easily accepted. It took 16 years to get these receptor/channels cloned and start a new stage in their investigation. “The receptor for protons” became ASIC comprising under this name a family of receptor/channels ubiquitous for mammalian nervous system, both peripheral and central. The role of ASICs as putative nociceptors was sugg...
19 Citations Source Cite
Published on Jan 2, 2015in Channels 2.29
Jaime S Horton4
Estimated H-index: 4
(U.H.: University of Hawaii at Manoa),
Clay Wakano3
Estimated H-index: 3
+ 1 AuthorsAlexander J. Stokes11
Estimated H-index: 11
(U.H.: University of Hawaii at Manoa)
Two-pore channels (TPC1, 2, and 3) are recently identified endolysosmal ion channels, but remain poorly characterized. In this study, we show for the first time a role for TPC1 in cytokinesis, the final step in cell division. HEK 293 T-REx cells inducibly overexpressing TPC1 demonstrated a lack of proliferation accompanied by multinucleation and an increase in G2/M cycling cells. Increased TPC1 was associated with a concomitant accumulation of active RhoGTP and a decrease in phosphorylated myosi...
9 Citations Source Cite
Published on Jan 1, 2015in Molecular Biology and Evolution 14.80
Lam-Tung Nguyen2
Estimated H-index: 2
(Medical University of Vienna),
Heiko A. Schmidt15
Estimated H-index: 15
(Medical University of Vienna)
+ 1 AuthorsBui Quang Minh15
Estimated H-index: 15
(Medical University of Vienna)
Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbat...
1,485 Citations Source Cite
Published on Dec 1, 2014in Nature Communications 11.88
Nicola Allison22
Estimated H-index: 22
(St And: University of St Andrews),
Itay Cohen7
Estimated H-index: 7
+ 2 AuthorsAlexander W. Tudhope32
Estimated H-index: 32
Understanding how corals may react to ocean acidification is hampered due to a lack of insight into how corals source the inorganic carbon required to build their skeletons. Here, the authors show that corals are able to concentrate dissolved carbon and that bicarbonate contributes to the carbon pool used to build their skeletons.
50 Citations Source Cite
Published on Dec 1, 2014in Environmental Microbiology 5.15
Elizabeth A. C. Heath-Heckman11
Estimated H-index: 11
(UW: University of Wisconsin-Madison),
Amani A. Gillette6
Estimated H-index: 6
(UW: University of Wisconsin-Madison)
+ 3 AuthorsMargaret J. McFall-Ngai52
Estimated H-index: 52
(UW: University of Wisconsin-Madison)
Summary Most bacterial species make transitions between habitats, such as switching from free living to symbiotic niches. We provide evidence that a galaxin protein, EsGal1, of the squid Euprymna scolopes participates in both: (i) selection of the specific partner Vibrio fischeri from the bacterioplankton during symbiosis onset and, (ii) modulation of V. fischeri growth in symbiotic maintenance. We identified two galaxins in transcriptomic databases and showed by quantitative reverse-transcripta...
18 Citations Source Cite
Tali Mass12
Estimated H-index: 12
(RU: Rutgers University),
Jeana L. Drake9
Estimated H-index: 9
(RU: Rutgers University)
+ 2 AuthorsPaul G. Falkowski107
Estimated H-index: 107
(RU: Rutgers University)
The precipitation and assembly of calcium carbonate skeletons by stony corals is a precisely controlled process regulated by the secretion of an ECM. Recently, it has been reported that the proteome of the skeletal organic matrix (SOM) contains a group of coral acid-rich proteins as well as an assemblage of adhesion and structural proteins, which together, create a framework for the precipitation of aragonite. To date, we are aware of no report that has investigated the localization of individua...
37 Citations Source Cite
Published on Sep 1, 2014in Genome Biology and Evolution 3.73
Yehu Moran19
Estimated H-index: 19
(HUJI: Hebrew University of Jerusalem),
Harold H. Zakon36
Estimated H-index: 36
The alpha subunits of voltage-gated calcium channels (Cavs) are large transmembrane proteins responsible for crucial physiological processes in excitable cells. They are assisted by three auxiliary subunits that can modulate their electrical behavior. Little is known about the evolution and roles of the various subunits of Cavs in nonbilaterian animals and in nonanimal lineages. For this reason, we mapped the phyletic distribution of the four channel subunits and reconstructed their phylogeny. A...
18 Citations Source Cite
Steven D. Quistad5
Estimated H-index: 5
(SDSU: San Diego State University),
Aleksandr Stotland11
Estimated H-index: 11
(SDSU: San Diego State University)
+ 5 AuthorsForest Rohwer74
Estimated H-index: 74
(SDSU: San Diego State University)
The TNF receptor-ligand superfamily is a central mediator of apoptosis or programmed cell death. Here we show that TNF-induced apoptosis has been functionally maintained for more than half a billion years of evolution. In response to human TNFα, coral cells underwent the classical stages of apoptosis including cellular blebbing, caspase activation, and eventual cell death. Next, the reciprocal experiment showed that coral TNF kills human cells through direct interaction with the death receptor p...
47 Citations Source Cite
Cited By63
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Published on Feb 22, 2019in Scientific Reports 4.01
Alexander Shumaker1
Estimated H-index: 1
(RU: Rutgers University),
Hollie M. Putnam24
Estimated H-index: 24
(URI: University of Rhode Island)
+ 7 AuthorsDebashish Bhattacharya64
Estimated H-index: 64
(RU: Rutgers University)
Corals comprise a biomineralizing cnidarian, dinoflagellate algal symbionts, and associated microbiome of prokaryotes and viruses. Ongoing efforts to conserve coral reefs by identifying the major stress response pathways and thereby laying the foundation to select resistant genotypes rely on a robust genomic foundation. Here we generated and analyzed a high quality long-read based ~886 Mbp nuclear genome assembly and transcriptome data from the dominant rice coral, Montipora capitata from Hawai’...
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Published on Feb 18, 2019in Scientific Reports 4.01
Alexander Venn10
Estimated H-index: 10
(CNRS: Centre national de la recherche scientifique),
Éric Tambutté8
Estimated H-index: 8
(CNRS: Centre national de la recherche scientifique)
+ 3 AuthorsSylvie Tambutté32
Estimated H-index: 32
(CNRS: Centre national de la recherche scientifique)
The resilience of corals to ocean acidification has been proposed to rely on regulation of extracellular calcifying medium pH (pHECM), but few studies have compared the capacity of coral species to control this parameter at elevated pCO2. Furthermore, exposure to light and darkness influences both pH regulation and calcification in corals, but little is known about its effect under conditions of seawater acidification. Here we investigated the effect of acidification in light and darkness on pHE...
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Published on May 24, 2019in bioRxiv
Chloé A. van der Burg1
Estimated H-index: 1
(QUT: Queensland University of Technology),
Ana Pavasovic14
Estimated H-index: 14
(QUT: Queensland University of Technology)
+ 4 AuthorsPeter J. Prentis19
Estimated H-index: 19
(QUT: Queensland University of Technology)
Regeneration of a limb or tissue can be achieved through multiple different pathways and mechanisms. The sea anemone Exaiptasia pallida has been observed to have excellent regenerative proficiency but this has not yet been described transcriptionally. In this study we examined the genetic expression changes during a regenerative timecourse and report key genes involved in regeneration and wound healing. We found that the major response was an early (within the first 8 hours) upregulation of gene...
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Published on May 10, 2019
M.J.C. Crabbe11
Estimated H-index: 11
(University of Oxford)
Reef-building corals throughout the world have an annual value of tens of billions of dollars, yet they are being degraded at an increasing rate by many anthropogenic and environmental factors. Despite this, some reefs show resilience to such extreme environmental changes. This review shows how techniques in computational modelling, genetics, and transcriptomics are being used to unravel the complexity of coral reef ecosystems, to try and understand if they can adapt to new and extreme environme...
1 Citations Source Cite
Published on May 1, 2019in G3: Genes, Genomes, Genetics 2.63
Sheila. A. Kitchen (PSU: Pennsylvania State University), Aakrosh Ratan20
Estimated H-index: 20
(UVA: University of Virginia)
+ 4 AuthorsIliana B. Baums29
Estimated H-index: 29
(PSU: Pennsylvania State University)
Genomic sequence data for non-model organisms are increasingly available requiring the development of efficient and reproducible workflows. Here, we develop the first genomic resources and reproducible workflows for two threatened members of the reef-building coral genus Acropora . We generated genomic sequence data from multiple samples of the Caribbean A. cervicornis (staghorn coral) and A. palmata (elkhorn coral), and predicted millions of nucleotide variants among these two species and the P...
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Published on May 1, 2019in Molecular Phylogenetics and Evolution 3.99
Zheng Bin Randolph Quek (NUS: National University of Singapore), Danwei Huang16
Estimated H-index: 16
(NUS: National University of Singapore)
Abstract Across the tree of life, phylogenetic analysis is increasingly being performed using transcriptome data. As a result of heterogeneous gene expression within individual organisms and unequal sequencing depth between samples, coverage of homologous loci in such datasets is typically inhomogeneous. Consequently, missing data are a common feature of phylotranscriptomic inference, but their impact on phylogenetic analysis remains poorly characterised empirically. Considering the complexity o...
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Published on Apr 9, 2019in Journal of Imaging
Andreas Jechow12
Estimated H-index: 12
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Christopher C. M. Kyba25
Estimated H-index: 25
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Franz Hölker32
Estimated H-index: 32
Artificial light at night is a novel anthropogenic stressor. The resulting ecological light pollution affects a wide breadth of biological systems on many spatio-temporal scales, from individual organisms to communities and ecosystems. However, a widely-applicable measurement method for nocturnal light providing spatially resolved full-spectrum radiance over the full solid angle is still missing. Here, we explain the first step to fill this gap, by using a commercial digital camera with a fishey...
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Published on Mar 31, 2019in bioRxiv
Nicola Conci1
Estimated H-index: 1
(LMU: Ludwig Maximilian University of Munich),
Gert Woerheide1
Estimated H-index: 1
(LMU: Ludwig Maximilian University of Munich),
Sergio Vargas9
Estimated H-index: 9
(LMU: Ludwig Maximilian University of Munich)
Abstract A general feature of animal skeletomes is the co-presence of taxonomically widespread and lineage-specific proteins that actively regulate the biomineralization process. Among cnidarians, the skeletomes of scleractinian corals have been shown to follow this trend, however in this group distribution and phylogenetic analyses of biomineralization-related genes have been often based on limited numbers of species, with other anthozoan calcifiers such as octocorals, being overlooked. We de-n...
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