Coral Reef Population Genomics in an Age of Global Change

Annual Review of Genetics, Journal Year: 2023, Volume and Issue: 57(1), P. 87 - 115

Published: June 29, 2023

Coral reefs are both exceptionally biodiverse and threatened by climate change other human activities. Here, we review population genomic processes in coral reef taxa their importance for understanding responses to global change. Many on characterized weak genetic drift, extensive gene flow, strong selection from complex biotic abiotic environments, which together present a fascinating test of microevolutionary theory. Selection, hybridization have played will continue play an important role the adaptation or extinction face rapid environmental change, but research remains limited compared urgent needs. Critical areas future investigation include evolutionary potential mechanisms local adaptation, developing historical baselines, building greater capacity countries where most diversity is concentrated.

Language: Английский

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Advances in coral immunity ‘omics in response to disease outbreaks

Frontiers in Marine Science, Journal Year: 2022, Volume and Issue: 9

Published: Oct. 7, 2022

Coral disease has progressively become one of the most pressing issues affecting coral reef survival. In last 50 years, several reefs throughout Caribbean have been severely impacted by increased frequency and intensity outbreaks leading to death. A recent example this is stony tissue loss which quickly spread Caribbean, devastating ecosystems. Emerging from these a coordinated research response that often integrates ‘omics techniques better understand immune system. ‘Omics encompass wide range technologies used identify large scale gene, DNA, metabolite, protein expression. review, we discuss what known about immunity an perspective. We reflect on development biomarkers ways in experiments test can be improved. Lastly, consider how existing data leveraged combat future outbreaks.

Language: Английский

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Living Coral Displays, Research Laboratories, and Biobanks as Important Reservoirs of Chemodiversity with Potential for Biodiscovery

Marine Drugs, Journal Year: 2025, Volume and Issue: 23(2), P. 89 - 89

Published: Feb. 19, 2025

Over the last decades, bioprospecting of tropical corals has revealed numerous bioactive compounds with potential for biotechnological applications. However, this search involves sampling in natural reefs, and is currently hampered by multiple ethical technological constraints. Living coral displays, research laboratories, biobanks offer an opportunity to continue unravel chemodiversity, acting as "Noah's Arks" that may support molecules interest. This issue even more relevant if one considers reefs face unprecedent threats irreversible losses impair biodiscovery new products, processes, services. displays provide controlled environments studying producing both known metabolites under varied conditions, they are not prone common bottlenecks associated such loss source replicability. Research laboratories focus on a particular species or compound using were cultured ex situ, although differ from wild conspecifics metabolite production quantitative qualitative terms. Biobanks collect preserve specimens, tissues, cells, and/or information (e.g., genes, microorganisms), which offers plethora data study compounds' mode action without having cope issues related access, standardization, regulatory compliance. Bioprospecting these settings faces several challenges opportunities. On hand, it difficult ensure complexity highly biodiverse ecosystems shape chemodiversity corals. other possible maximize biomass fine tune synthesis interest environments. Collaborative efforts needed overcome barriers foster opportunities fully harness before in-depth knowledge pool irreversibly lost due reefs' degradation.

Language: Английский

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Repeatome diversity in sea anemone genomics (Cnidaria: Actiniaria) based on the Actiniaria-REPlib library

BMC Genomics, Journal Year: 2025, Volume and Issue: 26(1)

Published: May 13, 2025

Genomic repetitive DNA sequences (Repeatomes, REPs) are widespread in eukaryotes, influencing biological form and function. In Cnidaria, an early-diverging animal lineage, these remain largely uncharacterized. This study investigates sea anemone REPs (Cnidaria: Actiniaria) a phylogenetic context. We sequenced assembled de novo the genome of Actinostella flosculifera analyzed total 38 nuclear genomes to create first ActiniariaREP library (Actiniaria-REPlib). compared Actiniaria-REPlib with Repbase RepeatModeler2 libraries, used dnaPipeTE annotate from genomic short-read datasets 36 species for divergence landscapes. Our annotated mitochondrial genomes, including 27 newly ones. re-annotated ~92% unknown initial library, finding that 6.4-30.6% were transposons, 2.1-11.6% retrotransposons, 1-28.4% tandem repeat sequences, 1.2-7% unclassifiable sequences. recovered 9.4x more REP actiniarian than Dfam 10.4x Repbase. It yielded 79,903 TE consensus (74,643 known, 5,260 unknown), 7,697 (3,742 3,944 unknown) Repbae (763 known). significantly enhances characterization DNA, assembling re-annotating identifying diverse elements. vastly outperforms existing databases, recovering providing comprehensive resource future evolutionary studies Actiniaria.

Language: Английский

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Deciphering omics atlases to aid stony corals in response to global change

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: March 11, 2024

Abstract Coral reefs are rapidly declining due to global climate change 1 . Alongside environmental protection, gene engineering technologies essential in protecting reef-building (stony) corals 2-7 Precise multi-omics backgrounds crucial for technique application 8-13 and understanding stony coral biology 2-5 However, high heterozygosity 4,14 exogenous sequence contamination 15-17 impede high-quality genome assembly. To address this, we developed a workflow assembly, achieving four chromosome-level genomes ( Acropora muricata , Montipora foliosa M. capricornis Pocillopora verrucosa ). A synteny analysis of chromosomes homeobox genes highlighted the highly conserved features Scleractinia genomes, even after an evolutionary divergence 250 million years ago (mya). Single-cell RNA sequencing (scRNA-seq), combined with pan-genomic analysis, aided our symbiosis calcification, both issues conservation concern. dynamics simulation mechanism systemic interference defective protein transmembrane family member (SIDT1) tetramer offered potential approach observe impacts on corals. This work enhances evolutionary, molecular, cellular aspects provides detailed dataset applying response challenges.

Language: Английский

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Contaminant or goldmine? In silico assessment of Symbiodiniaceae community using coral hologenomes

Frontiers in Protistology, Journal Year: 2024, Volume and Issue: 2

Published: April 2, 2024

Endosymbiotic dinoflagellates of the family Symbiodiniaceae are symbionts essential to corals and other marine organisms. A coral holobiont consists host, Symbiodiniaceae, microbes that together sustain overall productivity health. Coral hologenome data, generated from all interacting components a holobiont, key for elucidating molecular mechanisms underpin resilience changing environments. Although data often dominated by host genomic sequences, they provide an avenue recovering sequences in hospite . Here, we review recent advances approaches assessing community diversity data. Using case study based on existing datasets Acropora kenti coral, highlight how large numbers can useful analysis platform their function holobionts.

Language: Английский

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Peeling back the layers of coral holobiont multi-omics data

iScience, Journal Year: 2023, Volume and Issue: 26(9), P. 107623 - 107623

Published: Aug. 14, 2023

The integration of multiple 'omics' datasets is a promising avenue for answering many important and challenging questions in biology, particularly those relating to complex ecological systems. Although multi-omics was developed using data from model organisms with significant prior knowledge resources, its application non-model organisms, such as coral holobionts, less clear-cut. We explore, the emerging rice Montipora capitata, intersection holobiont transcriptomic, proteomic, metabolomic, microbiome amplicon investigate how well they correlate under high temperature treatment. Using typical thermal stress regime, we show that transcriptomic proteomic broadly capture response coral, whereas metabolome patterns likely reflect stochastic homeostatic processes associated each sample. These results provide framework interpreting generated systems, biotic interactions among microbial partners.

Language: Английский

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OMICS Approaches to Assess Dinoflagellate Responses to Chemical Stressors

Biology, Journal Year: 2023, Volume and Issue: 12(9), P. 1234 - 1234

Published: Sept. 13, 2023

Dinoflagellates are important primary producers known to form Harmful Algae Blooms (HABs). In water, nutrient availability, pH, salinity and anthropogenic contamination constitute chemical stressors for them. The emergence of OMICs approaches propelled our understanding dinoflagellates’ responses stressors. However, in dinoflagellates, these still biased, as transcriptomic largely conducted compared proteomic metabolomic approaches. Furthermore, integrated just emerging. Here, we report recent contributions the different investigation discuss current challenges need face push studies further despite lack genomic resources available dinoflagellates.

Language: Английский

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Decoding the Functional Interactome of Non-Model Organisms with PHILHARMONIC

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 29, 2024

Protein-protein interaction (PPI) networks are a fundamental resource for modeling cellular and molecular function, large sophisticated toolbox has been developed to leverage their structure topological organization predict the functional roles of under-studied genes, proteins, pathways. However, overwhelming majority experimentally-determined interactions from which such constructed come small number well-studied model organisms. Indeed, most species lack even single in these databases, much less network enable analysis methods computational PPI prediction too noisy apply directly. We introduce PHILHARMONIC, novel approach that couples deep learning

Language: Английский

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Identifying Rapidly Evolving Genes in Coral Species to Better Understand Coral Bleaching

2021 IEEE International Conference on Big Data (Big Data), Journal Year: 2024, Volume and Issue: unknown, P. 7407 - 7411

Published: Dec. 15, 2024

Language: Английский

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