Genomics & Bioinformatics | del Campo Lab - Microbial Ecology and Evolution

A transcriptomic cell-atlas of reef coral bleaching

Sun, 30 Jun 2024 00:00:00 +0000

Coral reefs support hyperdiverse ecosystems and build natural offshore structures that protect our coastlines from storm surge and coastal inundation. The corals that build these structures are able to do so by forming intimate symbioses with dinoflagellates in the family Symbiodiniaceae that provide photosynthetically fixed carbon to the coral host as an energy source. However, when ocean temperatures increase (particularly during marine heatwaves that are becoming more intense due to climate change), this symbiosis breaks down, the algae are expelled, and corals lose their coloration — a phenomenon popularly known as bleaching. As a result of bleaching, corals can quickly suffer mass mortality, destabilising the entire reef ecosystem and threatening its survival.

After decades of research on bleaching, our understanding of the genomic basis for bleaching — for corals, their algal symbionts, and other partners (i.e., the coral holobiont) — remains very limited. What is missing is a granular understanding of the genomics of bleaching linked to the functional changes that occur during the process. To fill this knowledge gap, we need to comprehensively characterise the transcriptomic response of the coral holobiont at the single-cell level in order to capture the functional genomic response of the different members of the coral holobiont during bleaching events.

Our goal is to develop an approach that can be used to scrutinise the transcriptomic response of the coral holobiont at the single-cell level. Our central hypothesis is that not all coral and symbiont cell types have the same transcriptomic profile, and therefore they will not have the same response to bleaching. Having an integrated, granular understanding of the coral holobiont’s transcriptomic response across coral cell types and symbionts during a bleaching event will transform our understanding of coral bleaching and potentially help us identify better strategies for intervention.

Preprint

Bonacolta AM, et al., including Javier del Campo (2024). A Single-Cell Atlas of Coral Bleaching. Research Square.

The genome of Mediocremonas mediterraneus

Tue, 28 Sep 2021 00:00:00 +0000

There is a significant bias in eukaryotic genomics that impoverishes our understanding of eukaryotic diversity: most genomics research focuses on multicellular eukaryotes. Around 85% of sequenced eukaryotic genomes correspond to multicellular organisms — Metazoa, Fungi, or Land Plants — yet these lineages represent only ~23% of all operational taxonomic units (OTUs) in environmental surveys. This leaves the vast majority of eukaryotic diversity underrepresented in genomic databases, skewing our views of what a eukaryote is and what roles they play in the environment.

In this project, carried out as part of the Catalan Initiative for the Earth Biogenome Project, we are generating the reference genome of Mediocremonas mediterraneus, a heterotrophic nanoflagellate isolated from Blanes Bay (Catalonia). Mediocremonas mediterraneus belongs to the Developea within the supergroup Stramenopiles. Based on phylogenomics, the Developea are sister to all photosynthetic Stramenopiles (diatoms, kelps, etc.), making M. mediterraneus an ideal candidate to study the evolutionary origins of photosynthesis in Stramenopiles.

PR2 — A reference 18S rRNA sequence database

Wed, 27 Apr 2016 00:00:00 +0000

The PR2 database was initiated in 2010 in the frame of the BioMarks project, building on work developed over the previous decade in the Plankton Group at the Station Biologique de Roscoff. Its aim is to provide a reference database of carefully annotated 18S rRNA sequences using eight unique taxonomic fields (from kingdom to species). It currently contains over 184,000 sequences, with metadata fields including geo-localisation, culture or environmental origin, host type, and more.

Annotation of PR2 is performed by experts from each taxonomic group. An important partner in this effort is EukRef, which has merged its bioinformatics pipelines and workshop-based curation efforts with PR2. EukRef has built tools used during multiple workshops dedicated to specific taxonomic groups, including ciliates, choanoflagellates, and others.

Key publications

Laure Guillou et al. (2013). The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote small sub-unit rRNA sequences with curated taxonomy. Nucleic Acids Research.

Javier del Campo et al. (2018). EukRef: phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution. PLOS Biology.

Issues and contributions

Report issues or contribute on GitHub.

Genomics & Bioinformatics | del Campo Lab - Microbial Ecology and Evolution

A transcriptomic cell-atlas of reef coral bleaching

The genome of *Mediocremonas mediterraneus*

PR2 — A reference 18S rRNA sequence database

The genome of Mediocremonas mediterraneus