Genomic insights into the sessile life and biofouling of barnacles (Crustacea: Cirripedia)

Comparative genomics reveals the dynamic evolutionary history of cement protein genes of barnacles from intertidal to deep-sea hydrothermal vents

Thoracican barnacles are a diverse group of marine organisms for which the availability of genome assemblies is currently limited. In this study, we sequenced the genomes of two neolepadoid species (Ashinkailepas kermadecensis, Imbricaverruca yamaguchii) from hydrothermal vents, in addition to two intertidal species. Genome sizes ranged from 481 to 1054 Mb, with repetitive sequence contents of 21.2% to 50.7%. Concordance rates of orthologs and heterozygosity rates were between 82.4% and 91.7% and between 1.0% and 2.1%, respectively, indicating high genetic diversity and heterozygosity. Based on phylogenomic analyses, we revised the nomenclature of cement genes encoding cement proteins that are not homologous to any known proteins. The major cement gene, CP100A, was found in all thoracican species, including vent-associated neolepadoids, and was hypothesised to be essential for thoracican settlement. Duplicated genes, CP100B and CP100C, were found only in balanids, suggesting potential functional redundancy or acquisition of new functions associated with the calcareous base. An ancestor of CP52 genes was duplicated dynamically among lepadids, pollicipedids with multiple copies on a single scaffold, and balanids with multiple sequential repeats of the conserved regions, but no CP52 genes were found in neolepadoids, providing insights into cement gene evolution among thoracican lineages. This study enhances our understanding of the adhesion mechanisms of thoracicans in underwater environments. The newly sequenced genomes provide opportunities for studying their evolution and ecology, shedding light on their adaptation to diverse marine environments, and contributing to our knowledge of barnacle biology with valuable genomic resources for further studies in this field.

An ancient whole-genome duplication in barnacles contributes to their diversification and intertidal sessile life adaptation

INTRODUCTION

Whole-genome duplication (WGD) is one of the most sudden and dramatic events rarely reported in invertebrates, but its occurrence can lead to physiological, morphological, and behavioral diversification. WGD has also never been reported in barnacles, which is one of the most unique groups of crustaceans with extremely speciallized morphology (calcareous shells) and habits (intertidal sessile lifestyle).

OBJECTIVES

To investigate whether WGD has occurred in barnacles and examine its potential role in driving the adaptive evolution and diversification of barnacles.

METHODS

Based on a newly sequenced and assembled chromosome-level barnacle genome, a novel WGD event has been identified in barnacles through a comprehensive analysis of interchromosomal synteny, the Hox gene cluster, and synonymous substitution distribution.

RESULTS

We provide ample evidences for WGD in the barnacle genomes. Comparative genomic analysis indicates that this WGD event predates the divergence of Thoracicalcarea, occurring more than 247 million years ago. The retained ohnologs from the WGD are primarily enriched in various pathways related to environmental information processing, shedding light on the adaptive evolution and diversification of intertidal sessile lifestyle. In addition, transcriptomic analyses show that most of these ohnologs were differentially expressed following the ebb of tide. And the cytochrome P450 ohnologs with differential expression patterns are subject to subfunctionalization and/or neofunctionalization for intertidal adaptation. Besides WGD, parallel evolution underlying intertidal adaptation has also occurred in barnacles.

CONCLUSION

This study revealed an ancient WGD event in the barnacle genomes, which is potentially associated with the origin and diversification of thoracican barnacles, and may have contributed to the adaptive evolution of their intertidal sessile lifestyle.

Thermal heterogeneity is an important factor for maintaining the genetic differentiation pattern of the pelagic barnacle Lepas anatifera in the northwest Pacific

Macrobenthic invertebrates are ubiquitously distributed in the epipelagic zone of the open ocean. Yet, our understanding of their genetic structure patterns remains poorly understood. Investigating the genetic differentiation patterns of pelagic Lepas anatifera and clarifying the potential roles of temperature maintaining this pattern are crucial for our understanding of the distribution and biodiversity of pelagic macrobenthos. In the present study, mitochondrial cytochrome oxidase subunit I (mtDNA COI) from three South China Sea (SCS) populations and six Kuroshio Extension (KE) region populations of L. anatifera sampled from fixed buoys and genome-wide SNPs from a subset of populations (two SCS populations and four KE region populations) were sequenced and analyzed for investigating the genetic pattern of the pelagic barnacle. Water temperature was different among sampling sites; in other words, the water temperature decreased with latitude increases, and the water temperature on the surface was higher than in the subsurface. Our result showed that three lineages with clear genetic differentiation were found in different geographical locations and depths based on mtDNA COI, all SNPs, neutral SNPs, and outlier SNPs. Lineage 1 and lineage 2 were dominant in the subsurface populations and surface populations from the KE region, respectively. Lineage 3 was dominant in the SCS populations. Historical events during the Pliocene epoch shaped the differentiation of the three lineages, while, nowadays, temperature heterogeneity maintains the current genetic pattern of L. anatifera in the northwest Pacific. The subsurface populations were genetically isolated from the surface populations in the Kuroshio Extension (KE) region, implying small-scale vertical thermal heterogeneity was also an important factor maintaining the genetic differentiation pattern of the pelagic species.

Identification of Hox genes and their expression profiles during embryonic development of the emerging model organism, Macrobrachium olfersii

Hox genes encode transcription factors that specify the body segment identity during development, including crustaceans, such as amphipods and decapods, that possess a remarkable diversity of segments and specialized appendages. In amphipods, alterations of specialized appendages have been obtained using knockout experiment of Hox genes, which suggests that these genes are involved in the evolution of morphology within crustaceans. However, studies of Hox genes in crustaceans have been limited to a few species. Here, we identified the homeodomain of nine Hox genes: labial (lab), proboscipedia (pb), Deformed (Dfd), Sex combs reduced (Scr), fushi tarazu (ftz), Antennapedia (Antp), Ultrabithorax (Ubx), abdominal-A (abdA), and Abdominal-B (AbdB), and evaluated their expression by RT-qPCR and RT-PCR in the ovary, during embryonic development, and at the first larval stage (Zoea I) of the decapod Macrobrachium olfersii. The transcript levels of lab, Dfd, and ftz decreased and transcripts of pb, Scr, Antp, Ubx, abdA, and AbdB increased during embryonic development. Hox genes were expressed in mature ovaries and Zoea I larval stages, except Scr and ftz, respectively. In addition, isoforms of Dfd, Scr, Ubx, and abdA, which have been scarcely reported in crustaceans, were described. New partial sequences of 87 Hox genes from other crustaceans were identified from the GenBank database. Our results are interesting for future studies to determine the specific function of Hox genes and their isoforms in the freshwater prawn M. olfersii and to contribute to the understanding of the diversity and evolution of body plans and appendages in Crustaceans.