Computational characterization of the mtORF of Pocilloporid Corals: Insights into protein structure and function in Stylophora lineages from contrasting Environments

Eulalia Banguera-Hinestroza, Evandro Ferrada, Yvonne Sawall, Jean-François Flot

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5 Scopus citations


More than a decade ago, a new mitochondrial Open Reading Frame (mtORF) was discovered in corals of the family Pocilloporidae and has been used since then as an effective barcode for these corals. Recently, mtORF sequencing revealed the existence of two differentiated Stylophora lineages occurring in sympatry along the environmental gradient of the Red Sea (18.5°C to 33.9°C). In the endemic Red Sea lineage RS_LinB, the mtORF and the heat shock protein gene hsp70 uncovered similar phylogeographic patterns strongly correlated with environmental variations. This suggests that the mtORF too might be involved in thermal adaptation. Here, we used computational analyses to explore the features and putative function of this mtORF. In particular, we tested the likelihood that this gene encodes a functional protein and whether it may play a role in adaptation. Analyses of full mitogenomes showed that the mtORF originated in the common ancestor of Madracis and other pocilloporids, and that it encodes a transmembrane protein differing in length and domain architecture among genera. Homology-based annotation and the relative conservation of metal-binding sites revealed traces of an ancient hydrolase catalytic activity. Furthermore, signals of pervasive purifying selection, lack of stop codons in 1830 sequences analyzed, and a codon-usage bias similar to that of other mitochondrial genes indicate that the protein is functional, i.e., not a pseudogene. Other features, such as intrinsically disordered regions, tandem repeats, and signals of positive selection particularly in Stylophora RS_LinB populations, are consistent with a role of the mtORF in adaptive responses to environmental changes.
Original languageEnglish (US)
Pages (from-to)324
Issue number5
StatePublished - Apr 27 2019
Externally publishedYes

Bibliographical note

KAUST Repository Item: Exported on 2022-06-10
Acknowledgements: EBH’s postdoctoral position in Belgium was funded by an Action de Recherche Concertée (ARC) grant of the Fédération Wallonie-Bruxelles to JFF. The study was further supported by the King Abdullah University of Science and Technology (KAUST) and the bilateral project “The Jeddah Transect” of the King Abdulaziz University (KAU) in Saudi Arabia, and the Helmholtz Center for Ocean Research (GEOMAR) in Germany (YS). We thank Christian Voolstra and the Bioscience Core Lab at KAUST for sharing their facilities, Abdulmohsin Al-Sofyani at KAU for supporting coral sampling, and Patricia Warner for giving access to the chromatograms of Seriatopora species. Thanks also to Sandra Cervantes Arango, Dario Ojeda Alayon, Patrick Mardulyn, and Javier Fuertes Aguilar for useful discussions and advice. We are also grateful to the reviewers for their detailed checks of the manuscript and their useful comments and suggestions.
This publication acknowledges KAUST support, but has no KAUST affiliated authors.

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)


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