Publications

Genetic and spatial organization of the unusual chromosomes of the dinoflagellate Symbiodinium microadriaticum

Journal Year: 2021 ISSN:1546-1718 DOI:10.1038/s41588-021-00841-y

Authors: Ankita Nand, Ye Zhan, Salazar Octavio, Manuel Aranda, Christian R. Voolstra, Job Dekker

Chromosome‐scale Assembly
Dinoflagellates
HiC

The evolution of calcification in reef-building corals

Journal Year: 2021 ISSN:0737-4038 DOI:https://doi.org/10.1093/molbev/msab103

Authors: Xin Wang, Zoccola Didier, Liew Yi Jin, Tambutté Eric, Cui Guoxin, Allemand Denis, Tambutte Sylvie, Manuel Aranda

Evolution
Coral Calcification
coral reef
Phylogenomics

The skeletome of the red coral Corallium rubrum indicates an independent evolution of biomineralization process in octocorals

Journal Year: 2021 ISSN:2730-7182 DOI:10.1186/s12862-020-01734-0

Authors: Nathalie Le Roy, Ganot Philippe, Manuel Aranda, Tambutté Sylvie, Allemand Denis

red coral
Biomineralization
octocorals
skeltome
mass spectrometry
Transcriptomics

Investing in Blue Natural Capital to Secure a Future for the Red Sea Ecosystems

Journal Year: 2021 ISSN:2296-7745 DOI:10.3389/fmars.2020.603722

Authors: Cziesielski Maha J., Carlos M. Duarte, Manuel Aranda, Schmidt-Roach S., Barreto Marcelle M.

reef
Red Sea
blue economy
ecotourism

Temperature transcends partner specificity in the symbiosis establishment of a cnidarian

Journal Year: 2020 ISSN:1751-7370 DOI:10.1038/s41396-020-00768-y

Authors: Herrera Marcela, Shannon G. Klein, Sara Campana, Jit Ern Chen, Arun Prasanna, Carlos M. Duarte, Manuel Aranda

coral reef
Temperature Stress
Coral-algal Symbiosis

Beyond Reef Restoration: Next-Generation Techniques for Coral Gardening, Landscaping, and Outreach

Journal Year: 2020 ISSN:2296-7745 DOI:10.3389/fmars.2020.00672

Authors: Sebastian Schmidt-Roach, Carlos M. Duarte, Charlotte A.E. Hauser, Aranda Manuel

coral restoration
blue economy
adaptive coral gardening
coral seeding hubs
ecotourism

Unfamiliar partnerships limit cnidarian holobiont acclimation to warming

Journal Year: 2020 ISSN:1354-1013 DOI:10.1111/gcb.15263

Authors: Marcela Herrera, Carlos M. Duarte, Sebastian Schmidt-Roach, Shannon G. Klein, Sara Campana, Maha J. Cziesielski, Jit Ern Chen, Aranda Manuel

Adaptation
SymPortal
Global Climate Change
coral reef
Heat Stress

Intergenerational epigenetic inheritance in reef-building corals

Year: 2020

Authors: Yi Jin Liew, Emily J. Howells, Xin Wang, Craig T. Michell, John A. Burt, Youssef Idaghdour, Manuel Aranda

Corals
DNA Methylation
CpG methylation
Climate Change

Characterization of a sponge microbiome using an integrative genome-centric approach

Year: 2020

Authors: J. Pamela Engelberts, Steven J. Robbins, Jasper M. De Goeij, Manuel Aranda, Sara C. Bell, Nicole S. Webster

Ircinia ramosa
symbiont community
MAGs

CATION-CHLORIDE CO-TRANSPORTER 1 (CCC1) Mediates Plant Resistance against Pseudomonas syringae

Year: 2019

Authors: Han Baoda, Yunhe Jiang, Guoxin Cui, Jianing Mi, M. Rob, G. Roelfsema, Grégory Mouille, Julien Sechet, Salim Al-Babili, Manuel Aranda, Heribert Hirt

Pseudomonas Syringae
Plant resistance
CCC1 ion transporter activity

A Genomic View of the Reef-Building Coral Porites Lutea and Its Microbial Symbionts

Year: 2019

Authors: S.J. Robbins, C.M. Singleton, C.X. Chan, L.F. Messer, A.U. Geers, H. Ying, A. Baker, S.C. Bell, K.M. Morrow, E. Ball, R. Beeden, M. Berumen, M. Aranda, T. Ravasi, P. Bongaerts, O. Hoegh-Guldberg, I. Cooke, B. Leggat, S. Sprungala Et Al

Porites Lutea
Genomes
coral holobiont

Anchorene Is a Carotenoid-Derived Regulatory Metabolite Required for Anchor Root Formation in Arabidopsis

Year: 2019

Authors: Jia, Kun-Peng, Alexandra J. Dickinson, Jianing Mi, Guoxin Cui, Ting Ting Xiao, Najeh M. Kharbatia, Xiujie Guo, Erli Sugiono, Manuel Aranda, Ikram Blilou, Magnus Rueping, Philip N. Benfey, Salim Al-Babili

Anchorene
Arabidopsis
Transcriptome
Nitrogen deficiency

With a Little Help From Friends—How Algae Help Corals Survive Temperature Stress

Year: 2019

Authors: Cziesielski Maha J., Aranda Manuel

Corals
Temperature Stress
Algae

The past, present, and future of coral heat stress studies

Year: 2019

Authors: Cziesielski Maha J., Sebastian Schmidt-Roach, Manuel Aranda

Coral Reefs
Transcriptomics
Heat Stress

Night-Time Temperature Reprieves Enhance the Thermal Tolerance of a Symbiotic Cnidarian

Year: 2019

Authors: Klein Shannon G., Kylie A. Pitt, Cathy H. Lucas, Shiou-Han Hung, Sebastian Schmidt-Roach, Manuel Aranda, Carlos M. Duarte

Cnidarian
Thermal Tolerance
Cassiopea

Genetic transformation of the dinoflagellate chloroplast

Year: 2019

Authors: Isabel C Nimmo, Adrian C Barbrook, Imen Lassadi, Jit Ern Chen, Katrin Geisler, Alison G Smith, Manuel Aranda, Saul Purton, Ross F Waller, R Ellen R Nisbet, Christopher J Howe

Dinoflagellate
Chloroplast Transformation

The Red Sea: Environmental Gradients Shape a Natural Laboratory in a Nascent Ocean

Year: 2019

Authors: Berumen Michael L., Christian R. Voolstra, Daniele Daffonchio, Susana Agusti, Manuel Aranda, Xabier Irigoien, Burton H. Jones, Xosé Anxelu G. Morán, Carlos M. Duarte

Red Sea
Environmental Gradients
Species Endemism

Host-dependent nitrogen recycling as a mechanism of symbiont control in Aiptasia

Year: 2019

Authors: Cui Guoxin, Yi Jin Liew, Yong Li, Najeh Kharbatia, Noura I. Zahran, Abdul-Hamid Emwas, Victor M. Eguiluz, Manuel Aranda

Nitrogen Recycling
Metabolomics
RNAseq
Host-symbiont Relationship

Long-Term Temperature Stress in the Coral Model Aiptasia Supports the “Anna Karenina Principle” for Bacterial Microbiomes

Year: 2019

Authors: Ahmed Hanin Ibrahim, Marcela Herrera, Yi Jin Liew, Manuel Aranda

Anna Karenina Principle
Host-microbial Partnerships
Environmental Stressors

The Genetic Intractability of Symbiodinium Microadriaticum to Standard Algal Transformation Methods

Year: 2019

Authors: Chen Jit Ern, Adrian C. Barbrook, Guoxin Cui, Christopher J. Howe, Manuel Aranda

Symbiodinium
Transformation Methods
CRISPR/cas9

Nutrient Stress Arrests Tentacle Growth in the Coral Model Aiptasia

Year: 2019

Authors: Rädecker Nils, Jit Ern Chen, Claudia Pogoreutz, Marcela Herrera, Manuel Aranda, Christian R. Voolstra

Nutrient Stress
Exaiptasia
Growth

Summarized Datasheet for Multi-Omics Response of Three Exaiptasia Strains to Heat Stress: A New Way to Process Omics Data

Year: 2018

Authors: Cziesielski Maha J., Yi Jin Liew, Manuel Aranda

Summarized Datasheet
Aiptasia
Omics Data

Finding Nemo’s Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula

Year: 2018 ISSN:1755-098X

Authors: Lehmann, Robert, Damien J. Lightfoot, Celia Schunter, Craig T. Michell, Hajime Ohyanagi, Katsuhiko Mineta, Sylvain Foret, michael l, Michael L. Berumen, David J. Miller, Manuel Aranda, Takashi Gojobori, Philip L. Munday, Timothy Ravasi

Amphiprion Percula
Chromosome‐scale Assembly
Coral Reef Fish
Fish Genomics
Functionalgenomics
Nemo
Orange Clownfish

DNA methylation regulates transcriptional homeostasis of algal endosymbiosis in the coral model Aiptasia

Year: 2018

Authors: Li Yong, Yi Jin Liew, Guoxin Cui, Maha J. Cziesielski, Noura Zahran, Craig T. Michell, Christian R. Voolstra, Manuel Aranda

Cnidarians
Dinoflagellates
Symbiotic Relationship
DNA Methylation

Symbiodinium Genomes Reveal Adaptive Evolution of Functions Related to Coral-Dinoflagellate Symbiosis

Year: 2018

Authors: Liu Huanle, Stephens Timothy G., González-Pech Raúl A., Beltran Victor H., Lapeyre Bruno, Bongaerts Pim, Cooke Ira, Aranda Manuel, Bourne David G., Forêt Sylvain, Miller David J., Van Oppen Madeleine J. H., Voolstra Christian R., Ragan Mark A., Chan Cheon

Adaptive Evolution
Symbiodinium
Coral-algal Symbiosis
Light Stress

Using Aiptasia as a Model to Study Metabolic Interactions in Cnidarian-Symbiodinium Symbioses

Year: 2018

Authors: Rädecker Nils, Raina Jean-Baptiste, Pernice Mathieu, Perna Gabriela, Guagliardo Paul, Kilburn Matt R., Aranda Manuel, Voolstra Christian R.

Metaorganism
Holobiont
Carbon Translocation
Nitrogen Uptake
Symbiodinium
Selfish Symbiont

Multi-Omics Analysis of Thermal Stress Response in a Zooxanthellate Cnidarian Reveals the Importance of Associating with Thermotolerant Symbionts

Year: 2018

Authors: Cziesielski M. J., Liew Y. J., Cui G., Schmidt-Roach S., Campana S., Marondedze C., Aranda M.

Transcriptomics
Proteomics
Heat Stress
Thermotolerance
Aiptasia
Oxidative Stress

Epigenome-associated phenotypic acclimatization to ocean acidification in a reef-building coral

Year: 2018

Authors: Liew Yi Jin, Zoccola Didier, Li Yong, Tambutté Eric, Venn Alexander A, Michell Craig T., Cui Guoxin, Deutekom Eva S, Kaandorp Jaap A, Voolstra Christian R., Forêt Sylvain, Allemand Denis, Tambutté Sylvie, Aranda Manuel

Epigenome
Ocean Acidification
Acclimatization

Using a butterflyfish genome as a general tool for RAD-Seq studies in specialized reef fish

Year: 2017

Authors: DiBattista Joseph D., Saenz-Agudelo Pablo, Piatek Marek J., Wang Xin, Aranda Manuel, Berumen Michael L.

Adaptation
Chaetodontidae
ddRAD
Ecologicalgenomics
Next-generationsequencing
SNP

Condition-Specific Rna Editing in the Coral Symbiont Symbiodinium Microadriaticum

Year: 2017

Authors: Liew Yi Jin, Li Yong, Baumgarten Sebastian, Voolstra Christian R., Aranda Manuel

Symbiodinium
RNA Editing
Corals

Advancing Genomics through the Global Invertebrate Genomics Alliance (Giga)

Year: 2017

Authors: Voolstra Christian R., Giga Community Of Scientists, Wörheide Gert, Lopez Jose V.

Biodiversity
Evolution
Genetics
Metazoa

Laboratory-Cultured Strains of the Sea Anemone Exaiptasia Reveal Distinct Bacterial Communities

Year: 2017

Authors: Herrera Marcela, Ziegler Maren, Voolstra Christian R., Aranda Manuel

16S rRNA Gene
Coral
Core Microbiome
Host-specific
Model Organism

Draft Genomes of the Corallimorpharians Amplexidiscus Fenestrafer and Discosoma Sp.

Year: 2017

Authors: Wang Xin, Liew Yi Jin, Li Yong, Zoccola Didier, Tambutte Sylvie, Aranda Manuel

Amplexidiscus Fenestrafer
Corallimorpharia
Discosoma sp.
Naked Corals

Assessing the Effects of Iron Enrichment across Holobiont Compartments Reveals Reduced Microbial Nitrogen Fixation in the Red Sea Coral Pocillopora Verrucosa

Year: 2017

Authors: Rädecker Nils, Pogoreutz Claudia, Ziegler Maren, Ashok Ananya, Barreto Marcelle M., Chaidez Veronica, Grupstra Carsten G. B., Ng Yi Mei, Perna Gabriela, Aranda Manuel, Voolstra Christian R.

Coral Reefs
Diazotroph
Holobiont
Nutrient Limitation
Symbiodinium
Symbiosis

Association of coral algal symbionts with a diverse viral community responsive to heat shock

Year: 2017

Authors: Brüwer J. D., Agrawal S., Liew Y. J., Aranda M., Voolstra C. R.

RNA-Seq
Transcriptomics
Virus
Symbiodinium
coral reef
Heat Shock
Climate Change

Rapid adaptive responses to climate change in corals

Year: 2017

Authors: Torda Gergely, Donelson Jennifer M., Aranda Manuel, Barshis Daniel J., Bay Line, Berumen Michael L., Bourne David G., Cantin Neal, Foret Sylvain, Matz Mikhail, Miller David J., Moya Aurelie, Putnam Hollie M., Ravasi Timothy, Van Oppen Madeleine J. H., Thu

Adaptive Response
Corals
Climate Change
Transgenerational Plasticity

Genome-Based Analyses of Six Hexacorallian Species Reject the “Naked Coral” Hypothesis

Year: 2017

Authors: Wang Xin, Drillon Guénola, Ryu Taewoo, Voolstra Christian R., Aranda Manuel

Naked Corals
Scleractinia
Corallimorpharia
Phylogenomics
Evolution
Calcification

High Salinity Conveys Thermotolerance in the Coral Model Aiptasia

Year: 2017

Authors: Gegner Hagen M., Ziegler Maren, Rädecker Nils, Buitrago-López Carol, Aranda Manuel, Voolstra Christian R.

Coral Reefs
Climate Change
Symbiosis
Thermotolerance
Resilience
Symbiodinium
Bleaching
Heat Stress

Comparative Analysis of the Genomes of Stylophora Pistillata and Acropora Digitifera Provides Evidence for Extensive Differences between Species of Corals

Year: 2017

Authors: Voolstra Christian R., Li Yong, Liew Yi Jin, Baumgarten Sebastian, Zoccola Didier, Flot Jean-François, Tambutté Sylvie, Allemand Denis, Aranda Manuel

Stylophora
Acropora
Comparative Genomics

Evidence for Mirna-Mediated Modulation of the Host Transcriptome in Cnidarian–Dinoflagellate Symbiosis

Year: 2017 ISSN:0962-1083

Authors: Baumgarten Sebastian, Cziesielski Maha J., Thomas Ludivine, Michell Craig T., Esherick Lisl Y., Pringle John R., Aranda Manuel, Voolstra Christian R.

Aiptasia Anemone Argonaute Coral Cross-linking Immunoprecipitation

Recent Expansion of Heat-Activated Retrotransposons in the Coral Symbiont Symbiodinium Microadriaticum

Year: 2017

Authors: Chen Jit Ern, Cui Guoxin, Wang Xin, Liew Yi Jin, Aranda Manuel

Retrotransposon
Symbiodinium
Expansion Events

Hologenome analysis of two marine sponges with different microbiomes

Year: 2016

Authors: Ryu Taewoo, Seridi Loqmane, Moitinho-Silva Lucas, Oates Matthew, Liew Yi Jin, Mavromatis Charalampos, Wang Xiaolei, Haywood Annika, Lafi Feras F., Kupresanin Marija, Sougrat Rachid, Alzahrani Majed A., Giles Emily, Ghosheh Yanal, Schunter Celia, Baumgarte

Sponge
Stylissa Carteri
Xestospongia Testudinaria
Innate Immune System
Host-Microbial Symbionts
Hologenome

miRNA Repertoires of Demosponges Stylissa carteri and Xestospongia testudinaria

Year: 2016

Authors: Liew Yi Jin, Ryu Taewoo, Aranda Manuel, Ravasi Timothy

miRNA
Sponges
Biogenesis

Comparative genomics explains the evolutionary success of reef-forming corals

Year: 2016

Authors: Bhattacharya Debashish, Agrawal Shobhit, Aranda Manuel, Baumgarten Sebastian, Belcaid Mahdi, Drake Jeana L., Erwin Douglas, Foret Sylvian, Gates Ruth D., Gruber David F., Kamel Bishoy, Lesser Michael P., Levy Oren, Liew Yi Jin, MacManes Matthew, Mass Tali

Corals
Biomineralization
Stress Response
Symbiotsis
Horizontal Gene Transfer

Draft genome of an iconic Red Sea reef fish, the blacktail butterflyfish (Chaetodon austriacus): current status and its characteristics

Year: 2016

Authors: DiBattista Joseph D., Wang Xin, Saenz-Agudelo Pablo, Piatek Marek J., Aranda Manuel, Berumen Michael L.

Reefgenomics.Org - a Repository for Marine Genomics Data

Year: 2016

Authors: LiewYi Jin, Aranda Manuel, Voolstra Christian R.

Repository
Database
Website

Genomes of coral dinoflagellate symbionts highlight evolutionary adaptations conducive to a symbiotic lifestyle

Year: 2016

Authors: Aranda M., Li Y., Liew Y. J., Baumgarten S., Simakov O., Wilson M. C., Piel J., Ashoor H., Bougouffa S., Bajic V. B., Ryu T., Ravasi T., Bayer T., Micklem G., Kim H., Bhak J., LaJeunesse T. C., Voolstra C. R.

Dinoflagellate Symbionts
Adaptation
Comparative Genomics

Distinct Bacterial Communities Associated with the Coral Model Aiptasia in Aposymbiotic and Symbiotic States with Symbiodinium

Year: 2016

Authors: Röthig Till, Costa Rúben M., Simona Fabia, Baumgarten Sebastian, Torres Ana F., Radhakrishnan Anand, Aranda Manuel, Voolstra Christian R.

coral reef
Cnidarian-dinoflagellate Symbiosis
Microbial Community Profiling
16S rRNA Gene
Functional Profiling

Structural Molecular Components of Septate Junctions in Cnidarians Point to the Origin of Epithelial Junctions in Eukaryotes

Year: 2015

Authors: Ganot Philippe, Zoccola Didier, Tambutté Eric, Voolstra Christian R., Aranda Manuel, Allemand Denis, Tambutté Sylvie

Epitheliozoa
Claudin
Neurexin
Contactin
Neuroglian
Coracle
MAGUK
Na+/K+ ATPase Transporter
DSCAM
Nbl4
Para-cellular Pathway
Permselectivity
Corals
Ctenophores
Poriferans
Monosiga
Capsaspora

Bicarbonate transporters in corals point towards a key step in the evolution of cnidarian calcification

Year: 2015

Authors: Zoccola Didier, Ganot Philippe, Bertucci Anthony, Caminiti-Segonds Natacha, Techer Nathalie, Voolstra Christian R., Aranda Manuel, Tambutté Eric, Allemand Denis, Casey Joseph R., Tambutté Sylvie

Biocarbonate Transporters
Calcification
Stylophora

Microbiome structure of the fungid coral Ctenactis echinata aligns with environmental differences

Year: 2015

Authors: Roder Cornelia, Bayer Till, Aranda Manuel, Kruse Maren, Voolstra Christian R.

Coral Reefs
Ecological Niche
Holobiont
Metaorganism
Microbiome
Symbiosis

The Genome of Aiptasia, a Sea Anemone Model for Coral Symbiosis

Year: 2015

Authors: Baumgarten S., Simakov O., Esherick L. Y., Liew Y. J., Lehnert E. M., Michell C. T., Li Y., Hambleton E. A., Guse A., Oates M. E., Gough J., Weis V. M., Aranda M., Pringle J. R., Voolstra C. R., Knowlton N.

Coral Reefs
Endosymbiosis
Horizontal Gene Transfer
Dinoflagellate
Pattern-recognition Receptors

Identification of MicroRNAs in the Coral Stylophora pistillata

Year: 2014

Authors: Liew Yi Jin, Aranda Manuel, Carr Adrian, Baumgarten Sebastian, Zoccola Didier, Tambutté Sylvie, Allemand Denis, Micklem Gos, Voolstra Christian R.

miRNA
Coral Calcification
Symbiosis

Bacteria of the genus Endozoicomonas dominate the microbiome of the Mediterranean gorgonian coral Eunicella cavolini

Year: 2013

Authors: Bayer T., Arif C., Ferrier-Pagès C., Zoccola D., Aranda M., Voolstra C. R.

Microbial Communities
Gorgonian
Eunicella Cavolini
16S Tag Sequencing

In-situ Effects of Eutrophication and Overfishing on Physiology and Bacterial Diversity of the Red Sea Coral Acropora hemprichii

Year: 2013

Authors: Jessen Christian, Villa Lizcano Javier Felipe, Bayer Till, Roder Cornelia, Aranda Manuel, Wild Christian, Voolstra Christian R.

16S Based
Bacterial Community
Eutrophication

The microbiome of the Red Sea coral Stylophora pistillata is dominated by tissue-associated Endozoicomonas bacteria

Year: 2013

Authors: Bayer Till, Neave Matthew J., Alsheikh-Hussain Areej, Aranda Manuel, Yum Lauren K., Mincer Tracy, Hughen Konrad, Apprill Amy, Voolstra Christian R.