Comparative omics analysis of a deep-sea barnacle species (Cirripedia, Scalpellomorpha) and shallow-water barnacle species provides insights into deep-sea adaptation

Abstract

Barnacles have demonstrated adaptability to a range of habitats, spanning from shallow water to the deep sea. Given the harsh conditions present in hydrothermal vents, hydrothermal vent barnacles serve as the model organism for investigating the interplay between evolution and adaptability. In order to gain insights into barnacle adaptive characteristics, particularly within hydrothermal vents, we conducted a comprehensive analysis of the mitogenomes and transcriptome in a deep-sea barnacle (Vulcanolepas fijiensis), in comparison to its shallow-water related species. The mitogenomes with the same genetic skews and the non-synonymous/synonymous mutation ratios (Ka/Ks) of the mitogenomes indicate that the protein-coding genes (COIII, ND2, and ND6) of V. fijiensis are under positive selection. Meanwhile, the functional annotation shows that distinctly positive selected orthologs in V. fijiensis are predominately related to neural signal transduction, immunity, antiapoptotic, and energy metabolism. These results indicate that the mitogenomes and key genes found in transcriptomic analysis are under high-temperature and high-pressure conditions, and which may contribute V. fijiensis to have evolved to adapt to the extreme hydrothermal vent environments. The findings shed light on the mitogenome and transcriptome of V. fijiensis, which lays a foundation for the in-depth understanding of the adaptation mechanism of sessile invertebrates to the deep-sea environment.

Commentary: Comparative omics analysis of a new deep-sea barnacle species (Cirripedia, Scalpellomorpha) and shallow-water barnacle species provides insights into deep-sea adaptation

“…This sequence from Mao et al (2024) was identical to published sequences of N. marisindica from both Kairei (type locality; LC350008, LC350015) and Solitaire (LC350013) vent fields on the Central Indian Ridge (CIR). Searching on GenBank revealed another mitogenome listed as V. fijiensis (MW291947) linked to the Mao et al (2024) paper, but this too was nested within N. marisindica (Figure 1). Furthermore, a mitogenome of the real V. fijiensis from the North Fiji Basin had already been published (Lee et al, 2019; MN061491) using one of the original specimens sequenced in the description paper, and a BLAST comparison with the mitogenome (MZ772032) presented by Mao et al (2024) revealed a percentage identity of only 88.84% between these two mitogenomes.…”

“…Using the mitochondrial genome of V. fijiensis supplied by Mao et al (2024) in GenBank (MZ772032), we show in a phylogenetic tree that the mitochondrial COI (cytochrome c oxidase subunit I) barcode sequence of V. fijiensis in Mao et al (2023) is nested into a wellsupported clade with other available sequences of N. marisindica and not with V. fijiensis sequences from the original description by Chan et al (2019) that includes barcodes of the holotype (Figure 1). This sequence from Mao et al (2024) was identical to published sequences of N. marisindica from both Kairei (type locality; LC350008, LC350015) and Solitaire (LC350013) vent fields on the Central Indian Ridge (CIR). Searching on GenBank revealed another mitogenome listed as V. fijiensis (MW291947) linked to the Mao et al (2024) paper, but this too was nested within N. marisindica (Figure 1).…”

“…For simplicity, taxa other than Vulcanolepas fijiensis and Neolepas marisinidica have been collapsed. Accession numbers in bold refer to sequences referred to as V. fijiensis in Mao et al (2024). Node values indicate Bayesian posterior probability.…”

“…Searching on GenBank revealed another mitogenome listed as V. fijiensis (MW291947) linked to the Mao et al (2024) paper, but this too was nested within N. marisindica (Figure 1). Furthermore, a mitogenome of the real V. fijiensis from the North Fiji Basin had already been published (Lee et al, 2019; MN061491) using one of the original specimens sequenced in the description paper, and a BLAST comparison with the mitogenome (MZ772032) presented by Mao et al (2024) revealed a percentage identity of only 88.84% between these two mitogenomes. Altogether, these evidences show that the species identification in Mao et al (2024) was incorrect, and their hydrothermal vent barnacle was actually N. marisindica.…”

“…We also note that another layer of confusion came from an inset specimen photo used in Figure 1A of Mao et al (2024), which shows a photo of the real V. fijiensis directly taken from figure 3F of Chan et al (2019) (original authors were not consulted about this use prior to publication). This photograph is of the holotype of V. fijiensis housed in the collection of the Korea National Institute for Biological Resources (Incheon, Korea; NIBR-IV0000830370) where it still resides.…”