The genome of the reef-building coral Porites harrisoni from the southern Persian/Arabian Gulf

Abstract

We present a genome assembly from the coral species Porites harrisoni from the southern Persian/Arabian Gulf, the hottest ocean basin where corals live. The assembly is 626.7 Mb in size, spanning 1,883 contigs with a contig N50 of 807.4 kb, including a single-contig mitochondrial genome. The assembly has a BUSCO completeness of 86.3% (single = 72.5%, duplicated = 13.7%, fragmented = 1.2%, missing = 12.5%). Within the nuclear genome, 59.23% are repeats (15.89% retroelements, 10.00% DNA transposons, and 31.71% unclassified repeats). Gene annotation of the nuclear genome assembly identified 27,823 protein-coding genes. The mitogenome is 18,639 bp long, with 13 protein-coding genes, 2 tRNAs, and 2 rRNAs. The P. harrisoni genome is a valuable resource of a coral from an extreme environment, enhancing understanding of the genomic architecture underlying thermal resilience. Comparative analyses will help elucidate the evolutionary basis of heat tolerance and the adaptive capacity of coral to rapid climate change.

Editors Assessment:

This data paper is a genome note presenting the assembly of Porites harrisoni, a stony coral species endemic to the thermally extreme southern Persian Gulf. Using ONT PromethION long nanopore reads the final genome size encompassed 626.7 Mb across 1,883 contigs, achieving a BUSCO completeness of 86.3%. This revealed significant repeat content, comprising 59.23% of the nuclear genome and highlighting a diploid structure with predominant homozygosity. A total of 27,823 protein-coding genes were annotated from this assembly, facilitating discussions on thermal resilience under climate change. The research underscores the genomic framework supporting adaptive capacities in corals, with implications for evolutionary biology and conservation science, especially in context to ongoing ocean warming.

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AbstractWe present a genome assembly from the coral species Porites harrisoni from the southern Persian/Arabian Gulf, the hottest ocean basin where corals live. The assembly is 626.7 Mb in size, spanning 1,883 contigs with a contig N50 of 807.4 kb, including a single-contig mitochondrial genome. The assembly has a BUSCO completeness of 86.3% (single = 72.5%, duplicated = 13.7%, fragmented = 1.2%, missing = 12.5%) using the eukaryota_odb10 reference set (n = 255). A total of 59.23% of the nuclear genome consists of repeats, comprising 15.89% retroelements, 10.00% DNA transposons, and 31.71% unclassified repeats. Gene annotation of this nuclear genome assembly identified 27,823 protein-coding genes. The mitogenome has an assembly size of 18,639 bp with 13 protein-coding genes as well as 2 tRNAs and 2 rRNAs. The genome of P. harrisoni provides a valuable genomic resource of a coral from an extreme environment, which will enable comparative analyses, enhancing our understanding of the genomic architecture underlying thermal resilience. Such comparisons will contribute to elucidating the evolutionary basis of heat tolerance and adaptive capacity of corals in the context of rapid climate change.

This work has now been published in GigaByte under a CC-BY 4.0 license: https://doi.org/10.46471/gigabyte.174

Reviewer 1. Oleg Simakov

Overall, a very useful resource, the manuscript is clearly written and the data is consistently described. The genome assembly and annotation is well executed given the available data. Two minor suggestions: - include a sentence or two on potential genome assembly improvements (and if any pitfalls can be encountered), for example using HiC data and/or long-read (re)sequencing. - specify explicitly which "shorter reads" (Nanopore?) were used for ONT polishing in the assembly section and their amount.

Reviewer 2. Yue Song

Is there sufficient detail in the methods and data-processing steps to allow reproduction? Yes. The authors provide a standard and well-documented methodology: assembly, transposable-element annotation, and gene structural annotation all rely on widely used software and established pipelines. The parameter settings and post-assembly processing steps have been described. Is there sufficient data validation and statistical analyses of data quality? No. With respect to data quality, the authors note that the number of annotated protein-coding genes in Porites harrisoni is lower than that reported for other congeneric species, yet they offer no further discussion. This discrepancy is striking and warrants clarification: is it a biological reality reflecting gene loss or genome compaction in this species, or is it an artefact arising from differences in annotation pipelines, gene-model thresholds, or assembly completeness among studies? A concise comparative analysis—and explicit acknowledgment of methodological variables—would help readers properly interpret this genomic feature. Is there sufficient information for others to reuse this dataset or integrate it with other data? No. Although the authors present a valuable and rare coral genome assembly, the manuscript appears to offer only basic genomic data. There is limited elaboration on the declared aim of illuminating the molecular basis of thermal tolerance. In particular, after the structural annotation of protein-coding genes, no systematic functional characterization (e.g., GO/KEGG enrichment, comparative analyses of heat-stress-related gene families, or symbiosis-related pathways) is provided. This section seems to have been undertaken but is neither described nor discussed in the current version. Additional Comments: (1) The quality of the figures could be further improved. Specifically, in Figure 1, the phylogenetic tree appears to be hand-drawn and lacks the polish typically seen in published phylogenetic analyses. It is recommended that the authors refer to examples from other studies for guidance on improving visual quality. Additionally, the tree currently lacks common indicators of phylogenetic robustness, such as bootstrap values or other support metrics. (2) In panel A (Figure 1), species highlighted in brown are presumably those included in this study. It would be helpful to add a legend clarifying the meaning of the different font colors to improve readability. Furthermore, the labeling format for sub-figures is inconsistent across the manuscript—for example, “Figure 1A, B” in one instance and “Figure 2A, B” in another. Standardizing the labeling format throughout would enhance clarity and professionalism. (3) Line 273: There appears to be an error in the unit used for “average protein length.” If this value refers to the length of the encoded proteins, it should not be expressed in base pairs (bp). Please clarify the meaning and use the appropriate unit (e.g., amino acids).

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The genome of the reef-building coral Porites harrisoni from the southern Persian/Arabian Gulf

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